Libre Pathology - User contributions [en]

Cytogenetics Review Questions

2015-08-05T15:55:14Z

Yuanny: /* Miscellaneous */

==Lecture 1==
{{hidden| List the three broad categories of clinical indications for chromosomal analysis.|Prenatal, Constitutional, Cancer/Acquired}}
{{hidden|Which family members should have chromosomal analysis?|
*1. Both parents of a child with structural chromosome rearrangement, deletion, duplication, and
*2. all family members at risk of having a chromosome rearrangement.}}
{{hidden|List 5 prenatal indications for cytogenetics analysis.|
*1. Advanced maternal age (Greater than 35 years old)
*2. Previous pregnancy with chromosomal disorder
*3. One parent is a known carrier (or other relative*)
*4. Couples at risk of x-linked disorders for which a molecular test is not available
*5. Fetal defects on ultrasound,
*6. Prenatal screen high risk pregnancies
*7. couples with 2+ spontaneous abortions
*8. infertility. }}
{{hidden|What are the indications for chromosomal analysis of products of conception?|
*1)Abortuses (missed abortions) of unknown reason,
*2)Malformed stillbirths,
*3)Stillbirth of undetermined etiology}}
{{hidden|Compare amniocentesis and chorionic villus sampling with regards to gestational age, complication rate, turn around time, and false results|}}
{{hidden|What are the clinical indications for tissue sampling instead of blood for cytogenetic analysis?|
*1)Suspicion of chromosomal mosaicism,
*2) blood is not available (e.g. POC),
*3) surgical or post-mortem tissue.}}
{{hidden|List 8 standard techniques for cytogenetics analysis.|
*1) Geimsa / G-Banding,
*2) Quinacrin / Q-banding
*3) Reverse / R-banding,
*4)Centromere / C-banding,
*5)NOR staining (nucleolus organizer regions),
*6)DAPI staining,
*7) Chromosomal breakage,
*8) Sister chromatid Exchange (SCE)}}
{{hidden|List 5 Molecular cytogenetics techniques.|
*1)FISH (flourescence in situ hybridization),
*2) Multi-colour FISH,
*3) SKY (spectral karyotyping),
*4) CGH (comparative genomic hybridization),
*5) CGH array}}
{{hidden|What is g-banding?|Chromosomes are treated with trypsine and then stained with Geimsa (or wrights) which darkly stains the AT rich regions (heterochromatin), and lightly stains the GC rich regions of the chromosome.}}
{{hidden|Outline the general procedure for cytogenetics study.|
*1) cell culture at 37C 5%CO2 in medium (dividing and stimulation),
*2) Chromosome elongation Thymidine BrdU,
*3) Metaphase arrest with Colcemide,
*4) Cell swelling with hypotonic KCl,* Hardening with acetic acid*
*5) Fixation with Cournay's (Methanol: Acetic acid, 3:1),
*6) Slide making (chromosome spread with ideal temperature and humidity),
*7) Slide aging (air dry slide warmer), 8)Staining (G, Q, C, R-banding),
*8) Molecular cytogenetic technique (FISH, multi-FISH, CGH, SKY, array CGH).}}
{{hidden|Broadly what at the three main morphological groups of chromosomes?|Metacentric, acrocentric, submetacentric.}}
{{hidden|What are the 4 minimum items included in a standard banding nomenclature?|
*1. Chromosome number,
*2) short or long arm,
*3) region on that arm,
*4) band number within that region}}
{{hidden|What are the clinical indications for an individual to have chromosomal analysis?|
*1)suspected classic chromosome syndrome,
*2) Mental retardation of undetermined etiology,
*3) dysmophic features,
*4) multiple congenital abnormalities,
*5) abnormalities of sexual development,
*6) ambiguous genitalia,
*7)pubertal failure,
*8)abnormalities of growth,
*9) certain types of malignancies.}}
{{hidden|What is q-banding?|Chromosomes are prepared with quinacrine which produces flourescent bands in the AT rich regions, particularly useful in identifying polymorphisms on the acrocentric chromosomes ( ) and the Y chromosome.}}
{{hidden|What is R-banding?|Darkly stains the GC rich regions of the chromosome (Euchromatin), aka Reverse-banding, and is used to detect subtle deletions or rearrangements that may not be detected by Q or G banding.}}
{{hidden|What is C-banding?|C-Banding stains the constitutive heterochromatin that is localized to the pericentromeric regions of all chromosomes and on the distal long arm of Y. Used to identify pericentric inversions and polymorphisms in centromeric regions of 1,9,16, and Yq, as well as confirming translocations of Y}}
{{hidden|What is NOR?|NOR is a silver staining procedure which stains the nucleolus organizer regions of satellited chromosomes (used to study the size of stalks and satellites in the acrocentric chromosomes)}}
{{hidden|List the metacentric chromosomes.|}}
{{hidden|List the submetacentric chromosomes.|}}
{{hidden|List the acrocentric chromosomes.|}}
{{hidden|What is Bloom syndrome?|Bloom syndrome is a rare AR genetic disorder with a defect in the BLM gene with a phenotype of short stature, tendency to sunburn, increased risk of malignancy, reduced or absent fertility, and prone to sister chromatid exchange [[http://ghr.nlm.nih.gov/condition/bloom-syndrome]] }}
{{hidden|What is SCE (Sister chromatid exchange?|SCE (sister chromatid exchange) is the interchange of homologous segments between two chromatids of one chromosome, grow the cells under special conditions to produce a differential staining of sister chromatids.}}
{{hidden|What is DAPI staining?|DAPI staining produces bright fluorescence of the heterochromatin regions of 1,9,16, and Y, as well as the centromere of 15, and is used to id marker chromosomes or translocations of Y.}}
{{hidden|Explain how chromosomal breakage studies are used to diagnose Fanconi's anemia.|Cultured cells are treated with Diepoxybutane, or mitomycin C to induce breakage, those cells with chromosomes prone to breakage are especially susceptible and this can be seen as gaps, breaks, deletions, triradial, quadriradial, dicentric, and complex figure in the metaphase.}}

==Lecture 2==
{{hidden|Describe the 4 steps of mitosis.|Prophase, metaphase, anaphase, telophase}}
{{hidden|List the 8 steps of meiosis.|
*Meiosis 1(Prophase 1, Metaphase 1, Anaphase 1, Telophase 1),
*Meiosis 2( Prophase 2, Metaphase 2, Anaphase 2, Telophase 2).}}
{{hidden|What is the main difference between constitutional and acquired chromosome anomalies.|Constitutional affects the whole patient, acquired usually limited to 1 organ.}}
{{hidden|What at the three main categories of patient features associated with unbalanced constitutional chromosomal anomalies?|
*1) dysmophy
*2) Visceral malformations,
*3) developmental/psychomotor delay.}}
{{hidden|What is meant by a homogeneous chromosomal anomaly?|Homogeneous chromosomal anomalies mean that all the cells STUDIED carry the anomaly, may be constitutional or acquired.}}
{{hidden|What is meant by a mosaic chromosomal anomaly?|Mosaic chromosomal anomalies mean that only some of the cells STUDIED carry the anomaly, may be constitutional or acquired.}}
{{hidden|What are chromosomal polymorphisms?|Chromosomal polymorphisms are variants of chromosomes that are widespread in a particular population which to date are not known to have any effect on the phenotype, they vary in size, position, and staining properties but must occur in heterochromatin regions usually near the centromere.}}
{{hidden|List 3 known chromosomal polymorphisms, according to ISCN 2013.|[[Chromosomal polymorphisms]]}}
{{hidden|Classify numerical abnormalities of chromosomes.|
*1) polyploidy (multiple complete sets of chromosomes, e.g. 3N),
*2) Aneuploidy (monosomy (e.g. Turner's syndrome), trisomy (e.g. trisomy 18, 13, or 21), tetrasomy))}}
{{hidden|What are the four main types of abnormalities in chromosome structure?|
*1) Deletion,
*2) Duplication,
*3) Rearrangement (inversion or insertion),
*4) Translocation}}
{{hidden|What is the key difference between a balanced and an unbalanced chromosomal rearrangement?|Balanced translocations imply that there is no missing or excess genetic material, while unbalanced translocations have either missing or excess genetic material from that of a normal genotype.}}
{{hidden|List three types of balanced chromosomal rearrangements.|Translocation, inversion, insertion.}}
{{hidden|List three unbalanced numerical chromosomal rearrangements.|trisomy, monosomy, multiploidy}}
{{hidden|List 5 structural unbalanced chromosomal rearrangements.|
*deletion
*duplication
*derivative chromsome
*recombination chromosome
*marker chromosome
*ring chromosome
*Dm & HSR}}
{{hidden|What is the karyotype for a female infant with cri-du-chat?|46,XX,del(5)(p15.1)}}

==Lecture 3==
{{hidden|What is FISH?|FISH is a molecular cytogenetic technique in which flourescently labelled DNA probes are hybridized to metaphase spreads or interphase nuclei.}}
{{hidden|When is interphase FISH more helpful than metaphase?|Interphase FISH is particularly useful in samples where there is poor culture growth such as bone marrow or cancer tissue.}}
{{hidden|What is the approximate resolution of cytogenetic FISH?|3-5Mb}}
{{hidden|What are the three types of FISH probes?|
*1)Probes for repetitive sequences (Centromeres, telomeric sequences),
*2) Unique sequence probes hybridized to a single copy of DNA sequences in a specific gene or chromosome,
*3) Whole chromosome paints (or arms) which are cocktails of probes that are chromosome specific and cover the entire length.}}
{{hidden|List 7 applications of FISH technology?|
*1) Microdeletion syndromes,
*2) Characterization of chromosomal structural abnormalities,
*3) identification of marker chromosomes,
*4) Aneuploidy detection,
*5) Cancer cytogenetics,
*6) Gene mapping,
*7)Rapid detection of sex chromosomes and the SRY gene}}
{{hidden|List 5 microdeletion syndromes.|[[List of Microdeletion Syndromes]]}}
{{hidden|Briefly describe Cri-du Chat Syndrome|}}
{{hidden|Describe 3 mechanisms by which uniparental disomy occurs.|
*1) Trisomic rescue (loss of a chromosome from a trisomic zygote),
*2) monosomic rescue (duplication of a chromosome from a monosomic zygote),
*3)Gamete complementation (fertilization of a gamete with two copies of a chromosome with no copies from other parent)}}
{{hidden|What is imprinting?|Normally we inherit one copy of each gene from each parent, some genes are only expressed when they are inherited paternally, some only when maternally, this differential expression based on inheritance is called imprinting, and changes generation to generation.}}
{{hidden|Which chromosomes are known to have imprinted genes?|Chromosomes 6,7,11,14,and 15.}}
{{hidden|Describe Prader-Willi Syndrome.|Features: hypotonia, obesity, developmental delay, hypogonadism, short stature, 70%: del(15q11-13), 25% uniparental disomy, 2%:other, diagnoses by FISH for microdeletion, or DNA methylation; due to absence of paternally derived PWS/AS gene }}
{{hidden|Briefly describe Williams Syndrome.|Deletion of one elastin allele (7q11.23 = 96% of cases), multi-system d/o characterized by: Growth & developmental delay, characteristic facies & personality, supra valvular stenosis, idiopathic infantile hypercalcemia (connective tissue / vascular)}}
{{hidden|Describe DeGeorge Syndrome.|
*95% 22q11.2 deletion, 5% FISH negative; AD inherit;
*1) Conotruncal heart defects,
*2)uropathy,
*3)polyhydramnios,
*4)increased nuchal translucency,
*5) IUGR,
*6)thymic hypoplasia,
*7) characteristic facies,
*8) hypoparathyroidism,
*9)MR/DD}}
{{hidden|What is SKY?|A chromosomal analysis technique that has the ability to paint each pair of chromosomes and the sex chromosomes a different flourescing colour.}}
{{hidden|What kinds of chromosomal transformations is SKY used for?|
*1) translocations,
*2) insertions,
*3)marker chromosome identification,
*4) cancer tumour genetics}}
{{hidden|What are thelimitations of SKY?|1) cannot detect del,dup,inv, 2) interpretation difficult if colours too similar}}
{{hidden|Explain the basic principle of Comparative Genomic Hybridization.|References genomes and the index genome are mixed, if the index genome substantially differs from the reference genome then there will be a neg signal loss or gain for that probe's flourescence, this can be used to determine if there is one allele in the index case that is missing or in excess compared to the reference genome.}}
{{hidden|How do CGH arrays work?|CGH arrays allow hundreds-thousands of probes to be used to compare the index and the reference genome, giving a complete chromosomal analysis that depends on the resolution of the probe.}}

==Lecture 4==
{{hidden|List 3 solid tumours for which cancer cytogenetics are currently used in prognosis and treatment.|
*1. Lymphoma
*2. Breast cancer
*3. Bladder carcinoma}}
{{hidden|What is a chromosomal instability syndrome?|There are several rare single gene syndromes in which there is a characteristic cytogenetic abnormality; affected individuals exhibit elevated rates of chromosome instability, leading to chromosomal rearrangements.}}
{{hidden|What are the features of ataxia telangiectasia?|
*1) AR inhertiance 1/40,000, ATM:11q22.3-q23.1
*2) Cerebellar ataxia
*3) Telangiectasia
*4) Growth retardation
*5) Immunodeficiency
*6) Radiosensitivity *tx with conventional radiation doses, could be fatal
*7) Cytogenetics: Chromosomal breakages, telomere instability, radiation sensitivity t(7;14)}}
{{hidden|What is Nijmegen Breakage Syndrome?|
*1. microcephaly
*2. Bird like face
*3. Radiosensitivity
*4. rearrangements between 7 and 14, AR, rare NBS1(8q21.3)
*5. sensitive to x-rays and bleomycin
*6. Growth and mental retardation
*7. Ovarian failure
*8. Prone to b-cell lymphomas}}
{{hidden|What is Bloom syndrome?|
*AR inheritance, rare (1/160,000, BLM:15q26.1, SCE and quadrils
* growth retartdation/ short stature
* sun sensitivity / facial lesions
*Ashkenazi jews}}
{{hidden|What is Xeroderma pigmentosum?|}}
{{hidden|What is Fanconi Anemia?|}}
{{hidden|What is ICF Syndrome?|}}
{{hidden|What is Roberts Syndrome?|}}
{{hidden|What karytype is most at risk of gonadoblastoma?|}}
{{hidden|What cancer are Kleinfelters patients at increased risk of?|}}
{{hidden|What lymphoproliferative disorders are associated with Down's Syndrome?|}}
{{hidden|

== Lecture 5 ==

==Miscellaneous==
{{hidden|What are the steps in preparing a cytogenetics tissue specimen?|
*1. Specimen received in flow medium and accessioned asap.
*2. Specimen cut-up (+/- treated with collagenase), filtered /18G needle
*3. Seeded into flask
*4. Cultured at 37C 5% CO2 x 48hours
*5. Flask flooded with 2ml of media
*6. Cultured at 37C 5% CO@ x 2-10days
*7. Trypsinize to coverslip when flask growth is confluent
*8. Colcemid added to the coverslip x 30min (1/12 dilution)
*9. Aspirate off colcemid
*10. Add hypo (1/2 0.54 KCl, 1/2 0.75 NaCitrate) x 30 min
*11. Add 2mL of fix (1/3 Methanol, 1/3 }}

{{hidden|What is Allerdice or Sandy Point Syndrome?|It is a chromosomal disorder discovered in Sandy Point, NL by Dr. Penny Allderdice, inv(3)(p25q21) characterized by affected offspring with multiple congenital anomalies with surviving children exhibiting severe growth and developmental delays.}}
{{hidden|What is the most common robertsonian translocation?|Translocation between the long arms of 13 and 14.}}
{{hidden|What is the most common non-robertsonian translocation?|t(11;22)(q23;q11)}}
{{hidden|What is a marker chromosome?|A structurally abnormal chromosome in which no part can be identified cytogenetically.}}
{{hidden|What is the most common chromosomal abnormality in humans?|Aneuploidy - about 5% of pregnancies.}}
{{hidden|What is the most common cause of triploidy?|Dispermy in 60%}}
{{hidden|What is the recurrence risk for parents of Down's syndrome child with a "free chromosome"?|1%}}

{{hidden|List 5 features of Trisomy 8.|
*1. Prominent cup-shaped ears
*2. Prominent lips
*3. Somewhat prominent forehead
*4. IQ usually 45 to 75 but some have near normal intelligence
*5. Deep, longitudinal grooves on soles of feet
*6. Joint abnormalities
*7. Usually mosaic }}

{{hidden|List 5 features of Trisomy 9.|
*1. Growth deficiency (prenatal)
*2. Deep-set eyes
*3. Low-set, misshapen ears
*4. Small lower jaw causes upper lip to overlap lower lip
*5. Joint abnormalities
*6. Heart and kidney abnormalities
*7. Small genitalia (males)
*8. Most have severe mental retardation
*9. Usually mosaic}}
{{hidden|List 5 features of Trisomy 13.|
*1. Cleft lip and/or palate
*2. Low set, misshapen ears
*3. Small eyes
*4. Hemangioma(s) on the face/forehead
*5. Defective lateral differentiation of the brain (some have holoprosencephaly)
*6. Sixth finger on ulnar side of hand
*7. Heart and kidney abnormalities
*8. Cryptorchidism in male; bicornate uterus in females
*9. Severe mental retardation}}

{{hidden|List 5 features of Trisomy 14.|
*1. Normal weight but short length at birth
*2. Narrow deep-set eyes
*3. Short, bulbous nose
*4. Small lower jaw
*5. Low-set, misshapen ears
*6. Heart abnormalities
*7. Severe mental retardation
*8. Usually mosaic }}

{{hidden|List 5 features of Trisomy 18.|
*1. Growth deficiency (prenatal)
*2. Prominent occiput
*3. Small mouth and jaw
*4. Low-set, misshapen ears
*5. Short sternum
*6. Clenched hand
*7. Short big toe, often flexed upward
*8. Rocker-bottom" feet
*9. Small pelvis with limited hip movement
*10. Heart abnormalities
*11. Severe mental retardation}}
{{hidden|List 5 features of Trisomy 21.|
*1. Flat face
*2. Brushfield spots present when eyes are blue
*3. Upslanting eyes
*4. Small ears
*5. Small mouth (with tongue often protruding)
*6. short fingers (especially fifth
*7. Heart abnormalities in some cases
*8. IQ usually 25-50 but occasionally higher}}

{{hidden|What is the most common outcome of a pregnancy when the parent has a balanced translocation?|Misscarriage}}

==Peripheral Blood Culture and Harvest==

Cytogenetics Review Questions

2015-08-05T15:45:00Z

Yuanny: /* Miscellaneous */

==Lecture 1==
{{hidden| List the three broad categories of clinical indications for chromosomal analysis.|Prenatal, Constitutional, Cancer/Acquired}}
{{hidden|Which family members should have chromosomal analysis?|
*1. Both parents of a child with structural chromosome rearrangement, deletion, duplication, and
*2. all family members at risk of having a chromosome rearrangement.}}
{{hidden|List 5 prenatal indications for cytogenetics analysis.|
*1. Advanced maternal age (Greater than 35 years old)
*2. Previous pregnancy with chromosomal disorder
*3. One parent is a known carrier (or other relative*)
*4. Couples at risk of x-linked disorders for which a molecular test is not available
*5. Fetal defects on ultrasound,
*6. Prenatal screen high risk pregnancies
*7. couples with 2+ spontaneous abortions
*8. infertility. }}
{{hidden|What are the indications for chromosomal analysis of products of conception?|
*1)Abortuses (missed abortions) of unknown reason,
*2)Malformed stillbirths,
*3)Stillbirth of undetermined etiology}}
{{hidden|Compare amniocentesis and chorionic villus sampling with regards to gestational age, complication rate, turn around time, and false results|}}
{{hidden|What are the clinical indications for tissue sampling instead of blood for cytogenetic analysis?|
*1)Suspicion of chromosomal mosaicism,
*2) blood is not available (e.g. POC),
*3) surgical or post-mortem tissue.}}
{{hidden|List 8 standard techniques for cytogenetics analysis.|
*1) Geimsa / G-Banding,
*2) Quinacrin / Q-banding
*3) Reverse / R-banding,
*4)Centromere / C-banding,
*5)NOR staining (nucleolus organizer regions),
*6)DAPI staining,
*7) Chromosomal breakage,
*8) Sister chromatid Exchange (SCE)}}
{{hidden|List 5 Molecular cytogenetics techniques.|
*1)FISH (flourescence in situ hybridization),
*2) Multi-colour FISH,
*3) SKY (spectral karyotyping),
*4) CGH (comparative genomic hybridization),
*5) CGH array}}
{{hidden|What is g-banding?|Chromosomes are treated with trypsine and then stained with Geimsa (or wrights) which darkly stains the AT rich regions (heterochromatin), and lightly stains the GC rich regions of the chromosome.}}
{{hidden|Outline the general procedure for cytogenetics study.|
*1) cell culture at 37C 5%CO2 in medium (dividing and stimulation),
*2) Chromosome elongation Thymidine BrdU,
*3) Metaphase arrest with Colcemide,
*4) Cell swelling with hypotonic KCl,* Hardening with acetic acid*
*5) Fixation with Cournay's (Methanol: Acetic acid, 3:1),
*6) Slide making (chromosome spread with ideal temperature and humidity),
*7) Slide aging (air dry slide warmer), 8)Staining (G, Q, C, R-banding),
*8) Molecular cytogenetic technique (FISH, multi-FISH, CGH, SKY, array CGH).}}
{{hidden|Broadly what at the three main morphological groups of chromosomes?|Metacentric, acrocentric, submetacentric.}}
{{hidden|What are the 4 minimum items included in a standard banding nomenclature?|
*1. Chromosome number,
*2) short or long arm,
*3) region on that arm,
*4) band number within that region}}
{{hidden|What are the clinical indications for an individual to have chromosomal analysis?|
*1)suspected classic chromosome syndrome,
*2) Mental retardation of undetermined etiology,
*3) dysmophic features,
*4) multiple congenital abnormalities,
*5) abnormalities of sexual development,
*6) ambiguous genitalia,
*7)pubertal failure,
*8)abnormalities of growth,
*9) certain types of malignancies.}}
{{hidden|What is q-banding?|Chromosomes are prepared with quinacrine which produces flourescent bands in the AT rich regions, particularly useful in identifying polymorphisms on the acrocentric chromosomes ( ) and the Y chromosome.}}
{{hidden|What is R-banding?|Darkly stains the GC rich regions of the chromosome (Euchromatin), aka Reverse-banding, and is used to detect subtle deletions or rearrangements that may not be detected by Q or G banding.}}
{{hidden|What is C-banding?|C-Banding stains the constitutive heterochromatin that is localized to the pericentromeric regions of all chromosomes and on the distal long arm of Y. Used to identify pericentric inversions and polymorphisms in centromeric regions of 1,9,16, and Yq, as well as confirming translocations of Y}}
{{hidden|What is NOR?|NOR is a silver staining procedure which stains the nucleolus organizer regions of satellited chromosomes (used to study the size of stalks and satellites in the acrocentric chromosomes)}}
{{hidden|List the metacentric chromosomes.|}}
{{hidden|List the submetacentric chromosomes.|}}
{{hidden|List the acrocentric chromosomes.|}}
{{hidden|What is Bloom syndrome?|Bloom syndrome is a rare AR genetic disorder with a defect in the BLM gene with a phenotype of short stature, tendency to sunburn, increased risk of malignancy, reduced or absent fertility, and prone to sister chromatid exchange [[http://ghr.nlm.nih.gov/condition/bloom-syndrome]] }}
{{hidden|What is SCE (Sister chromatid exchange?|SCE (sister chromatid exchange) is the interchange of homologous segments between two chromatids of one chromosome, grow the cells under special conditions to produce a differential staining of sister chromatids.}}
{{hidden|What is DAPI staining?|DAPI staining produces bright fluorescence of the heterochromatin regions of 1,9,16, and Y, as well as the centromere of 15, and is used to id marker chromosomes or translocations of Y.}}
{{hidden|Explain how chromosomal breakage studies are used to diagnose Fanconi's anemia.|Cultured cells are treated with Diepoxybutane, or mitomycin C to induce breakage, those cells with chromosomes prone to breakage are especially susceptible and this can be seen as gaps, breaks, deletions, triradial, quadriradial, dicentric, and complex figure in the metaphase.}}

==Lecture 2==
{{hidden|Describe the 4 steps of mitosis.|Prophase, metaphase, anaphase, telophase}}
{{hidden|List the 8 steps of meiosis.|
*Meiosis 1(Prophase 1, Metaphase 1, Anaphase 1, Telophase 1),
*Meiosis 2( Prophase 2, Metaphase 2, Anaphase 2, Telophase 2).}}
{{hidden|What is the main difference between constitutional and acquired chromosome anomalies.|Constitutional affects the whole patient, acquired usually limited to 1 organ.}}
{{hidden|What at the three main categories of patient features associated with unbalanced constitutional chromosomal anomalies?|
*1) dysmophy
*2) Visceral malformations,
*3) developmental/psychomotor delay.}}
{{hidden|What is meant by a homogeneous chromosomal anomaly?|Homogeneous chromosomal anomalies mean that all the cells STUDIED carry the anomaly, may be constitutional or acquired.}}
{{hidden|What is meant by a mosaic chromosomal anomaly?|Mosaic chromosomal anomalies mean that only some of the cells STUDIED carry the anomaly, may be constitutional or acquired.}}
{{hidden|What are chromosomal polymorphisms?|Chromosomal polymorphisms are variants of chromosomes that are widespread in a particular population which to date are not known to have any effect on the phenotype, they vary in size, position, and staining properties but must occur in heterochromatin regions usually near the centromere.}}
{{hidden|List 3 known chromosomal polymorphisms, according to ISCN 2013.|[[Chromosomal polymorphisms]]}}
{{hidden|Classify numerical abnormalities of chromosomes.|
*1) polyploidy (multiple complete sets of chromosomes, e.g. 3N),
*2) Aneuploidy (monosomy (e.g. Turner's syndrome), trisomy (e.g. trisomy 18, 13, or 21), tetrasomy))}}
{{hidden|What are the four main types of abnormalities in chromosome structure?|
*1) Deletion,
*2) Duplication,
*3) Rearrangement (inversion or insertion),
*4) Translocation}}
{{hidden|What is the key difference between a balanced and an unbalanced chromosomal rearrangement?|Balanced translocations imply that there is no missing or excess genetic material, while unbalanced translocations have either missing or excess genetic material from that of a normal genotype.}}
{{hidden|List three types of balanced chromosomal rearrangements.|Translocation, inversion, insertion.}}
{{hidden|List three unbalanced numerical chromosomal rearrangements.|trisomy, monosomy, multiploidy}}
{{hidden|List 5 structural unbalanced chromosomal rearrangements.|
*deletion
*duplication
*derivative chromsome
*recombination chromosome
*marker chromosome
*ring chromosome
*Dm & HSR}}
{{hidden|What is the karyotype for a female infant with cri-du-chat?|46,XX,del(5)(p15.1)}}

==Lecture 3==
{{hidden|What is FISH?|FISH is a molecular cytogenetic technique in which flourescently labelled DNA probes are hybridized to metaphase spreads or interphase nuclei.}}
{{hidden|When is interphase FISH more helpful than metaphase?|Interphase FISH is particularly useful in samples where there is poor culture growth such as bone marrow or cancer tissue.}}
{{hidden|What is the approximate resolution of cytogenetic FISH?|3-5Mb}}
{{hidden|What are the three types of FISH probes?|
*1)Probes for repetitive sequences (Centromeres, telomeric sequences),
*2) Unique sequence probes hybridized to a single copy of DNA sequences in a specific gene or chromosome,
*3) Whole chromosome paints (or arms) which are cocktails of probes that are chromosome specific and cover the entire length.}}
{{hidden|List 7 applications of FISH technology?|
*1) Microdeletion syndromes,
*2) Characterization of chromosomal structural abnormalities,
*3) identification of marker chromosomes,
*4) Aneuploidy detection,
*5) Cancer cytogenetics,
*6) Gene mapping,
*7)Rapid detection of sex chromosomes and the SRY gene}}
{{hidden|List 5 microdeletion syndromes.|[[List of Microdeletion Syndromes]]}}
{{hidden|Briefly describe Cri-du Chat Syndrome|}}
{{hidden|Describe 3 mechanisms by which uniparental disomy occurs.|
*1) Trisomic rescue (loss of a chromosome from a trisomic zygote),
*2) monosomic rescue (duplication of a chromosome from a monosomic zygote),
*3)Gamete complementation (fertilization of a gamete with two copies of a chromosome with no copies from other parent)}}
{{hidden|What is imprinting?|Normally we inherit one copy of each gene from each parent, some genes are only expressed when they are inherited paternally, some only when maternally, this differential expression based on inheritance is called imprinting, and changes generation to generation.}}
{{hidden|Which chromosomes are known to have imprinted genes?|Chromosomes 6,7,11,14,and 15.}}
{{hidden|Describe Prader-Willi Syndrome.|Features: hypotonia, obesity, developmental delay, hypogonadism, short stature, 70%: del(15q11-13), 25% uniparental disomy, 2%:other, diagnoses by FISH for microdeletion, or DNA methylation; due to absence of paternally derived PWS/AS gene }}
{{hidden|Briefly describe Williams Syndrome.|Deletion of one elastin allele (7q11.23 = 96% of cases), multi-system d/o characterized by: Growth & developmental delay, characteristic facies & personality, supra valvular stenosis, idiopathic infantile hypercalcemia (connective tissue / vascular)}}
{{hidden|Describe DeGeorge Syndrome.|
*95% 22q11.2 deletion, 5% FISH negative; AD inherit;
*1) Conotruncal heart defects,
*2)uropathy,
*3)polyhydramnios,
*4)increased nuchal translucency,
*5) IUGR,
*6)thymic hypoplasia,
*7) characteristic facies,
*8) hypoparathyroidism,
*9)MR/DD}}
{{hidden|What is SKY?|A chromosomal analysis technique that has the ability to paint each pair of chromosomes and the sex chromosomes a different flourescing colour.}}
{{hidden|What kinds of chromosomal transformations is SKY used for?|
*1) translocations,
*2) insertions,
*3)marker chromosome identification,
*4) cancer tumour genetics}}
{{hidden|What are thelimitations of SKY?|1) cannot detect del,dup,inv, 2) interpretation difficult if colours too similar}}
{{hidden|Explain the basic principle of Comparative Genomic Hybridization.|References genomes and the index genome are mixed, if the index genome substantially differs from the reference genome then there will be a neg signal loss or gain for that probe's flourescence, this can be used to determine if there is one allele in the index case that is missing or in excess compared to the reference genome.}}
{{hidden|How do CGH arrays work?|CGH arrays allow hundreds-thousands of probes to be used to compare the index and the reference genome, giving a complete chromosomal analysis that depends on the resolution of the probe.}}

==Lecture 4==
{{hidden|List 3 solid tumours for which cancer cytogenetics are currently used in prognosis and treatment.|
*1. Lymphoma
*2. Breast cancer
*3. Bladder carcinoma}}
{{hidden|What is a chromosomal instability syndrome?|There are several rare single gene syndromes in which there is a characteristic cytogenetic abnormality; affected individuals exhibit elevated rates of chromosome instability, leading to chromosomal rearrangements.}}
{{hidden|What are the features of ataxia telangiectasia?|
*1) AR inhertiance 1/40,000, ATM:11q22.3-q23.1
*2) Cerebellar ataxia
*3) Telangiectasia
*4) Growth retardation
*5) Immunodeficiency
*6) Radiosensitivity *tx with conventional radiation doses, could be fatal
*7) Cytogenetics: Chromosomal breakages, telomere instability, radiation sensitivity t(7;14)}}
{{hidden|What is Nijmegen Breakage Syndrome?|
*1. microcephaly
*2. Bird like face
*3. Radiosensitivity
*4. rearrangements between 7 and 14, AR, rare NBS1(8q21.3)
*5. sensitive to x-rays and bleomycin
*6. Growth and mental retardation
*7. Ovarian failure
*8. Prone to b-cell lymphomas}}
{{hidden|What is Bloom syndrome?|
*AR inheritance, rare (1/160,000, BLM:15q26.1, SCE and quadrils
* growth retartdation/ short stature
* sun sensitivity / facial lesions
*Ashkenazi jews}}
{{hidden|What is Xeroderma pigmentosum?|}}
{{hidden|What is Fanconi Anemia?|}}
{{hidden|What is ICF Syndrome?|}}
{{hidden|What is Roberts Syndrome?|}}
{{hidden|What karytype is most at risk of gonadoblastoma?|}}
{{hidden|What cancer are Kleinfelters patients at increased risk of?|}}
{{hidden|What lymphoproliferative disorders are associated with Down's Syndrome?|}}
{{hidden|

== Lecture 5 ==

==Miscellaneous==
{{hidden|What are the steps in preparing a cytogenetics tissue specimen?|
*1. Specimen received in flow medium and accessioned asap.
*2. Specimen cut-up (+/- treated with collagenase), filtered /18G needle
*3. Seeded into flask
*4. Cultured at 37C 5% CO2 x 48hours
*5. Flask flooded with 2ml of media
*6. Cultured at 37C 5% CO@ x 2-10days
*7. Trypsinize to coverslip when flask growth is confluent
*8. Colcemid added to the coverslip x 30min (1/12 dilution)
*9. Aspirate off colcemid
*10. Add hypo (1/2 0.54 KCl, 1/2 0.75 NaCitrate) x 30 min
*11. Add 2mL of fix (1/3 Methanol, 1/3 }}

{{hidden|What is Allerdice or Sandy Point Syndrome?|It is a chromosomal disorder discovered in Sandy Point, NL by Dr. Penny Allderdice, inv(3)(p25q21) characterized by affected offspring with multiple congenital anomalies with surviving children exhibiting severe growth and developmental delays.}}
{{hidden|What is the most common robertsonian translocation?|Translocation between the long arms of 13 and 14.}}
{{hidden|What is the most common non-robertsonian translocation?|t(11;22)(q23;q11)}}
{{hidden|What is a marker chromosome?|A structurally abnormal chromosome in which no part can be identified cytogenetically.}}
{{hidden|What is the most common chromosomal abnormality in humans?|Aneuploidy - about 5% of pregnancies.}}
{{hidden|What is the most common cause of triploidy?|Dispermy in 60%}}
{{hidden|What is the recurrence risk for parents of Down's syndrome child with a "free chromosome"?|1%}}
{{hidden|List 5 features of Trisomy 8.|
*1. Prominent cup-shaped ears
*2. Prominent lips
*3. Somewhat prominent forehead
*4. IQ usually 45 to 75 but some have near normal intelligence
*5. Deep, longitudinal grooves on soles of feet
*6. Joint abnormalities
*7. Usually mosaic }}
{{hidden|List 5 features of Trisomy 9.|}}
{{hidden|List 5 features of Trisomy 13.|}}
{{hidden|List 5 features of Trisomy 14.|}}
{{hidden|List 5 features of Trisomy 18.|}}
{{hidden|List 5 features of Trisomy 21.|}}
{{hidden|What is the most common outcome of a pregnancy when the parent has a balanced translocation?|Misscarriage}}

==Peripheral Blood Culture and Harvest==

Robbins and Cotran 9th Edition Questions

2015-05-27T17:52:11Z

Yuanny: /* Chapter 2: Cellular Responses to Stress and Toxic Insults: Adaptation, Injury and Death */

== Chapter 1: The Cell as a Unit of Health and Disease==

{{hidden| Short Answer Questions |
{{hidden|How much of the human genome is coding and what does it code?|Of the 3.2b basepairs, there are 20,000 genes that comprise about 1.5% of the genome that code for proteins (enzymes, structural components, and signaling molecules used to assemble and maintain all the cells in the body}}

{{hidden|What do we think that the rest of the genome does?|80% of the genome binds proteins, implying that it is involved in regulating gene expression, related to the regulation of gene expression, often in a cell-type specific fashion.}}

{{hidden|List the major classes of functional non-protein-coding sequences found in the human genome.|
*1. Promoter & enhancer
*2. Chromatin binding site structures
*3. non-coding regulatory RNAs
*4. Mobile genetic elements (transposons)
*5. telomeres
*6. centromers. }}

{{hidden|What are the two most common forms of DNA variation in the human genome?|
*1) Single nucleotide polymorphisms (SNPs)
*2) copy number variations (CNVs)}}

{{hidden|What are the possible implications of SNPs.|
*1) regulatory = alters gene expression
*2) Correlation with disease states when in close proximity with altered genes
*3) association used to define linkage disequilibrium,?}}

{{hidden|Define epigenetics.|Heritable changes in gene expression which are not caused by alterations in DNA sequence.}}

{{hidden|List the 6 types of epigenetic changes.|
*1) Histone & histone modifying factors (Histones organize chromatin into heterochromatin and euchromatin
*2) histone methylation
*3) histone acteylation
*4)histone phosphorylation
*5) DNA methylation
*6) Chromatin organizing factors.}}

{{hidden|What is the function of micro-RNA (mi-RNA)?|It does not encode protein, instead they function primarily to modulate the translation of target mRNAs into their corresponding proteins, and are responsible for post-transcriptional silencing of gene expression.}}

{{hidden|What is knockdown technology?|The use of synthetic si-RNA (short RNA sequences) introduced into cells that serve as substrates for Dicer and interact with the RISC complex in a manner analogous to endogenous miRNAs, and are used to study gene function, and are being developed as therapeutic agents to silence pathogenic genes, e.g. oncogenic in neoplasms.}}

{{hidden|What is long non coding RNA?|Lnc-RNA modulate gene expression by binding to regions of chromatin, restricting RNA polymerase access to coding genes within the region, and may exceed the number of mRNA's by 10-20 fold.}}

{{hidden|What is XIST?|XIST is a lnc-RNA which is transcribed from the X-chromosome and plays an essential role in physiologic X chromosome inactivation, though not inactivated itself, it forms a repressive cloak on the X chromosome from which it is transcribed resulting in gene silencing.}}

{{hidden|What are the cellular housekeeping functions?|1) protection from the environment, 2) nutrient acquisition, 3) communication, 4) movement, 5) renewal of senescent molecules, 6) molecular catabolism, 7) energy generation.}}

{{hidden|List the cellular compartments and the role in the cell.|1) cytosol = metabolism, transport, protein translation, 2) Mitochondria = energy generation, apoptosis, 3) Rough ER = synthesis of membrane and secreted proteins, 4) Smooth ER / Golgi = protein modification, sorting, catabolism, 5)Nucleus = cell regulation, proliferation, DNA transcription, 6) Endosomes = intracellular transport and export, ingestion of extracellular substances, 7) Lysosomes = cellular catabolism, 8) peroxisomes = very long-chain fatty acid metabolism}}

{{hidden|Describe the basic structure and functions of the cell membrane.| The plasma membrane is composed of a lipid bilayer of phospholipids studded with a variety of proteins and glycoproteins involved in ion and metabolite transport, fluid phase and receptor-mediated uptake of macromolecules, cell-ligand/cell matrix/cell-cell interactions.}}

{{hidden|How are the large complexes in the plasma membrane formed?|They aggregate under the control of chaperone molecules in the RER or by lateral diffusion in the plasma membrane followed by complex formation in situ.}}

{{hidden|What are aquaporins?|Special integral membrane proteins which augment passive water transport in tissues where water is transported in large volumes.}}

{{hidden|How are channel and carrier proteins different?|Channel proteins created hydrophilic pores, permit rapid movement of solutes, restricted by size and charge, where Carrier proteins bind to their specific solutes and undergo a series of conformational changes to transfer the ligand across the membrane, relatively slow transport.}}

{{hidden|What is the "multidrug resistance (MDR) protein"?|A type of transporter ATPases which pumps polar compounds (e.g. chemo drugs) out of cells which may render cancer cells resistant to treatment.}}

{{hidden|What are the two fundamental mechanisms of fluid or macromolecules by the cell (endocytosis)?|1)Caveolae -invaginations of the plasma membrane, 2) Pinocytosis/receptor mediated endocytosis - macromolecules bind to receptor and membranes invaginate around it.}}

{{hidden|What is exocytosis?|It is the opposite process of pinocytosis, where the receptor bound macromolecule is move to the cell surface and released.}}

{{hidden|Describe the difference between phagocytosis and transcytosis.|In phagocytosis microbes are ingested forming phagosomes, which fuse with lysosomes and become phagylosomes, releasing undigested residual material when fusing again with the external membrane, in contrast transcytosis the materials are carried across the cell membrane unaltered.}}

{{hidden|List the three major classes of 3 cytoskeleton proteins.|1) Actin, 2)Intermediate filaments, 3)Microtubules}}

{{hidden|Describe actin.|Actin - 5 to 9nm diam fibrils, G-actin polymerized into F-actin, the form double strands helices, which interact with myosin (filamentous protein).}}

{{hidden|List the various intermediate filaments, which are 10nm in diameter.|1) Lamin A, B, and C (nuclear lamins of all cells, 2) Vimentin (mesenchymal), 3)Desmin (scaffold for actin/myosin), 4) Neurofilaments (axons of neurons), 5) Glial filament protein (glial cells), 6)Cytokeratins (acid and basic and vary based on cell type). }}

{{hidden|Describe microtubules.|Microtubules are 25nm diam fibrils of dimers of a and b tubulin, with a negative end embedded in the centrosome near the nucleus, the + end grows or shrinks as needed. There are kinesins and dyneins motors that move stuff around the cell, also found in cilia and flagella.}}

{{hidden|What is clatharin?|A molecule found in the cell membrane that when the cell membrane invaginates forming a basket like structure.}}

{{hidden|List and describe the 3 main classifications of cell junctions.|1) Tight /occluding junctions - form a high resistance barrier to solute movement, and allows the cell to maintain polarity, 2) anchoring junctions / desmosomes - mechanically attach the cell and their cytoskeleton to other cells and the ECM (hemidesmosome), 3)communicating/gap junctions - mediate the passage of chemical or electrical signals from one cell to another.}}

{{hidden|What is the "unfolded protein response"?| Excess accumulation of misfolded protiens, which exceed the capacity of the ER to edit and degrade them, leads to the the ER stress response (UPR) that triggers cell death through apoptosis.}}

{{hidden|What cell organelle has a reactive hyperplasia with repeated exposure to phenobarbitol catabolism in the cytocrhome p450 system?|Smooth endoplasmic reticulum.}}

{{hidden|List three main functions of mitochondria.|1) Energy generation, 2) intermediate metabolism (instead of ATP make intemediate that can be used to make lipids, nucleic acids, and proteins), 3) Cell death ( necrosis & apoptosis)}}

{{hidden|List and describe the four extracellular cell-cell signaling pathways based on the distance the signal travels.|1)Paracrine (immediate vicinity), 2) Autocrine (cell affecting itself), 3) Synaptic (neurons sending neurotransmitters at synapse), 4) endocrine (signals released elsewhere into bloodstream).}}

{{hidden|What are the two characterizing features of stem cells?|Self renewal and asymmetric division (one daughter cell stays a stem cell)}}

{{hidden|What are the two types of stem cells?|embryonic stem cells (inner cell mass of the blastocyst, totipotent), and tissue/adult stem cells (found in stem cell niches associated with specialized tissues, limited repetoire of differentiation = multipotent)}}

{{hidden|What is the Warburg effect?|Increased cellular uptake of glucose and glutamine, increased glycolysis, and decreased oxidative phosphorylation by the cell.}}

{{hidden|Which CDKI's have selective effects on CDK4 and CDK6?|p15,p16,p17,and p19}}

{{hidden|List some examples of signal transduction pathways.|1) Receptor tyrosine kinases (RTKs), 2) Nonreceptor tyrosine kinase, 3) G-protein coupled receptors, 4) nuclear receptors, 5)Notch family receptors, 6) Wnt protein ligands (Frizzled family receptors).}}

{{hidden|Why does nuclear beta catenin occur in some neoplasms?|When Wnt ligand bins to frizzled it recruits Disheveled, this leads to the disruption of the wnt-ubiquitin complex, this stabilized pool of b-catening is then translocated to the nucleus forming a transcriptional complex}}

{{hidden|On Page 19 there is a table of growth factors involved in regeneration and repair, please review.|}}

{{hidden|Describe the function of cadherin.|}}

{{hidden|What are the functions of the extracellular matrix?|Mechanical support, control of cell proliferation, scaffolding for tissue renewal, establishment of tissue microenvironments}}

{{hidden|What are the two basic forms of the ECM?|interstitial matrix (fibrillar and non fibrillar collagen, fibronectin, elastin, proteoglycans, hyloronate, and other stuff), basement membrane (type IV collagen and laminin) }}

{{hidden|What are the three proteins groups in the ECM?|1) fibrous structural proteins (collagen, elastins), 2) water hydrated gels (proteoglycans and hyaluronan), 3) adhesive glycoproteins (connect ECM to each other and other cells)}}

{{hidden|Describe the structure of a protein that is dependent on vitamin C.|Collagen is composed of 3 seprate polypeptide chains braided into a rope like triple helix, lateral cross linking of the triple helices by lysyl oxidase (requires vitamin C) give it it's tensile strength. }}

{{hidden|List three non-fibrillar collagens.|Type IV -basement membrane, Type IX - Fibrillar associated collagen with interrupted triple helices (FACIT), Type VII (provides anchoring fibrils to basement membrane beneath skin)}}

{{hidden|Which structural protein is associated with Marfan syndrom?|Fibrillin synthetic defects, which wrap the elastin core. }}}}

== Chapter 2: Cellular Responses to Stress and Toxic Insults: Adaptation, Injury and Death ==
Experimenting, please ignore
{{hidden
| headerstyle = text-align: left;
| header = What are the four aspects of a disease?
| content = *1. Etiology
**Genetic - Inherited mutations and disease-associated gene variants, or polymorphisms.
**Acquired - Infectious, nutritional, chemical and physical.
*2. Pathogenesis - The sequence of cellular, biochemical, and molecular events that follow the exposure of cells or tissues to an injurious agent.
*3. Morphological changes - The structural alterations in cells or tissues that are either characteristic of a disease or diagnostic of an etiologic process.
*4. Clinical Manifestations - Symptoms and signs of disease, as well as its clinical course and outcome.}}

== Chapter 3 ==
== Chapter 4 ==
== Chapter 5 ==
{{hidden|MC cause of spontaneous abortion is ?|<center>[[ A demonstrable chromosomal abnormality.]]</center>}}

{{hidden|1% of all newborn infants possess a gross chromosomal abnormality and 5% of people <25y present with |<center>[[a genetic disease. ]]</center>}}

{{hidden|Mutation|<center>[[permanent change in the DNA, if affect germ cells are transmitted to the progeny ]]</center>}}

{{hidden|List and describe 4 broad categories of human genetic disorders:|<center>[[Disorders related to mutation sin single genes with large effects i. Usually follow classic Mendelian pattern of inheritance
ii. Often highly penetrant (large proportion of pop with gene has disease)
b. Chromosomal disorders
i. Structural or numerical alterations in autosomes and sex chromosomes
ii. Uncommon, high penetrance
c. Complex multigenic disorders
i. Interactions between multiple variant forms of genes and environmental factors (polymorphisms), poly genic means disease when many polymorphism present
d. Single gene disorders with nonclassic patterns of inheritance (not mendelian)
i. Disorders resulting from triplet repeat mutations
ii. Mutations in mitochondrial DNA
iii. Those influenced by genomic imprinting
iv. Those influenced by gonadal mosaicism]]</center>}}

{{hidden|List and describe the possible outcomes of a point mutation in a coding region?|[[a. Missense mutation – pt mutation changes amino acid code, conservative when the amino acid is preserved, non conservative when replaced with another amino acid, b. Nonsense mutation – makes a stop codon ]]</center>}}

{{hidden|List and describe the possible outcomes of point mutation or deletion in a non-coding region.|<center>[[a. Promoters/enhancers – interfere with binding of transcription factors, marker reduction or total lack of transcription, b. Introns – defective splicing > failure to make mature RNA > no translation]]</center>}}

{{hidden|List and describe the possible outcomes of deletions and insertions.|<center>[[a.Small coding: not multiple of three = frameshift, if multiple of 3 than add or del amino acids accordingly, often premature stop codon
i. Tay Sachs disease: 4 base pair insertion in Hexosaminidase A gene ]]}}

{{hidden|List and describe the possible outcomes of trinucleotide repeat mutations.|[[a. Usually G&C, dynamic and increase during gametogenesis, “RNA stutters”,b. Fragile X – CGG 250-4000, Huntinton’s Disease ]]}}

{{hidden|List and describe three examples of inheritance of single gene mutations|[[a. AD – manifested in the heterologous state, one parent of index case is usually affected, males and females affected and both can transmit conditioni. De novo cases may not have affected parentii. Penetrance = fraction of people with gene who have the traitiii. Variable expressivity = those with mutant gene have variety of phenotypesiv. Often age of onset is delayed so can reproduce before die from diseasev. Biochem mechanisms1. Reduced production of a protein or dysfunctional/inactive protein2. Involved in regulation of complex metabolic pathyway subject to feedback inhibition3. Key structural proteins (collagen and cytoskeleton of RBC)a. May be a dominant negative , e.g. osteogenesis imperfecta4. Gain of function are rare, 2 formsa. Increased in proteins normal function (excess enzyme activity)b. Huntinton’s diseas (abn protein accumulates, toxic to neurons)b. ARi. Largest category – both alleles at a locus are mutated1. Expression is uniform, complete penetrance common, early onset, unaffected carrier family members, mostly enzymesc. X Linkedi. All sex linked, and almost all are recessive , if Y Chromosome affected usually infertile males > no progenyii. Male expression b/c hemizygous, daughter carriers with variable phenotype because of lionization of 2nd X e.g G6DPiii. Dominant . vitamin D resistant rickets]]</center>}}

Stopped at P142

== Chapter 6 ==
== Chapter 7 ==
== Chapter 8 ==
== Chapter 9 ==
== Chapter 10 ==
== Chapter 11 ==
== Chapter 12 ==
== Chapter 13 ==
== Chapter 14 ==
== Chapter 15 ==
== Chapter 16 ==
== Chapter 17 ==
== Chapter 18 ==
== Chapter 19 ==
== Chapter 20 ==
== Chapter 21 ==
== Chapter 22 ==
== Chapter 23 ==
== Chapter 24 ==
== Chapter 25 ==
== Chapter 26 ==
== Chapter 27 ==
== Chapter 28 ==
== Chapter 29 ==

Robbins and Cotran 9th Edition Questions

2015-05-27T17:37:46Z

Yuanny: /* Chapter 2: Cellular Responses to Stress and Toxic Insults: Adaptation, Injury and Death */

== Chapter 1: The Cell as a Unit of Health and Disease==

{{hidden| Short Answer Questions |
{{hidden|How much of the human genome is coding and what does it code?|Of the 3.2b basepairs, there are 20,000 genes that comprise about 1.5% of the genome that code for proteins (enzymes, structural components, and signaling molecules used to assemble and maintain all the cells in the body}}

{{hidden|What do we think that the rest of the genome does?|80% of the genome binds proteins, implying that it is involved in regulating gene expression, related to the regulation of gene expression, often in a cell-type specific fashion.}}

{{hidden|List the major classes of functional non-protein-coding sequences found in the human genome.|
*1. Promoter & enhancer
*2. Chromatin binding site structures
*3. non-coding regulatory RNAs
*4. Mobile genetic elements (transposons)
*5. telomeres
*6. centromers. }}

{{hidden|What are the two most common forms of DNA variation in the human genome?|
*1) Single nucleotide polymorphisms (SNPs)
*2) copy number variations (CNVs)}}

{{hidden|What are the possible implications of SNPs.|
*1) regulatory = alters gene expression
*2) Correlation with disease states when in close proximity with altered genes
*3) association used to define linkage disequilibrium,?}}

{{hidden|Define epigenetics.|Heritable changes in gene expression which are not caused by alterations in DNA sequence.}}

{{hidden|List the 6 types of epigenetic changes.|
*1) Histone & histone modifying factors (Histones organize chromatin into heterochromatin and euchromatin
*2) histone methylation
*3) histone acteylation
*4)histone phosphorylation
*5) DNA methylation
*6) Chromatin organizing factors.}}

{{hidden|What is the function of micro-RNA (mi-RNA)?|It does not encode protein, instead they function primarily to modulate the translation of target mRNAs into their corresponding proteins, and are responsible for post-transcriptional silencing of gene expression.}}

{{hidden|What is knockdown technology?|The use of synthetic si-RNA (short RNA sequences) introduced into cells that serve as substrates for Dicer and interact with the RISC complex in a manner analogous to endogenous miRNAs, and are used to study gene function, and are being developed as therapeutic agents to silence pathogenic genes, e.g. oncogenic in neoplasms.}}

{{hidden|What is long non coding RNA?|Lnc-RNA modulate gene expression by binding to regions of chromatin, restricting RNA polymerase access to coding genes within the region, and may exceed the number of mRNA's by 10-20 fold.}}

{{hidden|What is XIST?|XIST is a lnc-RNA which is transcribed from the X-chromosome and plays an essential role in physiologic X chromosome inactivation, though not inactivated itself, it forms a repressive cloak on the X chromosome from which it is transcribed resulting in gene silencing.}}

{{hidden|What are the cellular housekeeping functions?|1) protection from the environment, 2) nutrient acquisition, 3) communication, 4) movement, 5) renewal of senescent molecules, 6) molecular catabolism, 7) energy generation.}}

{{hidden|List the cellular compartments and the role in the cell.|1) cytosol = metabolism, transport, protein translation, 2) Mitochondria = energy generation, apoptosis, 3) Rough ER = synthesis of membrane and secreted proteins, 4) Smooth ER / Golgi = protein modification, sorting, catabolism, 5)Nucleus = cell regulation, proliferation, DNA transcription, 6) Endosomes = intracellular transport and export, ingestion of extracellular substances, 7) Lysosomes = cellular catabolism, 8) peroxisomes = very long-chain fatty acid metabolism}}

{{hidden|Describe the basic structure and functions of the cell membrane.| The plasma membrane is composed of a lipid bilayer of phospholipids studded with a variety of proteins and glycoproteins involved in ion and metabolite transport, fluid phase and receptor-mediated uptake of macromolecules, cell-ligand/cell matrix/cell-cell interactions.}}

{{hidden|How are the large complexes in the plasma membrane formed?|They aggregate under the control of chaperone molecules in the RER or by lateral diffusion in the plasma membrane followed by complex formation in situ.}}

{{hidden|What are aquaporins?|Special integral membrane proteins which augment passive water transport in tissues where water is transported in large volumes.}}

{{hidden|How are channel and carrier proteins different?|Channel proteins created hydrophilic pores, permit rapid movement of solutes, restricted by size and charge, where Carrier proteins bind to their specific solutes and undergo a series of conformational changes to transfer the ligand across the membrane, relatively slow transport.}}

{{hidden|What is the "multidrug resistance (MDR) protein"?|A type of transporter ATPases which pumps polar compounds (e.g. chemo drugs) out of cells which may render cancer cells resistant to treatment.}}

{{hidden|What are the two fundamental mechanisms of fluid or macromolecules by the cell (endocytosis)?|1)Caveolae -invaginations of the plasma membrane, 2) Pinocytosis/receptor mediated endocytosis - macromolecules bind to receptor and membranes invaginate around it.}}

{{hidden|What is exocytosis?|It is the opposite process of pinocytosis, where the receptor bound macromolecule is move to the cell surface and released.}}

{{hidden|Describe the difference between phagocytosis and transcytosis.|In phagocytosis microbes are ingested forming phagosomes, which fuse with lysosomes and become phagylosomes, releasing undigested residual material when fusing again with the external membrane, in contrast transcytosis the materials are carried across the cell membrane unaltered.}}

{{hidden|List the three major classes of 3 cytoskeleton proteins.|1) Actin, 2)Intermediate filaments, 3)Microtubules}}

{{hidden|Describe actin.|Actin - 5 to 9nm diam fibrils, G-actin polymerized into F-actin, the form double strands helices, which interact with myosin (filamentous protein).}}

{{hidden|List the various intermediate filaments, which are 10nm in diameter.|1) Lamin A, B, and C (nuclear lamins of all cells, 2) Vimentin (mesenchymal), 3)Desmin (scaffold for actin/myosin), 4) Neurofilaments (axons of neurons), 5) Glial filament protein (glial cells), 6)Cytokeratins (acid and basic and vary based on cell type). }}

{{hidden|Describe microtubules.|Microtubules are 25nm diam fibrils of dimers of a and b tubulin, with a negative end embedded in the centrosome near the nucleus, the + end grows or shrinks as needed. There are kinesins and dyneins motors that move stuff around the cell, also found in cilia and flagella.}}

{{hidden|What is clatharin?|A molecule found in the cell membrane that when the cell membrane invaginates forming a basket like structure.}}

{{hidden|List and describe the 3 main classifications of cell junctions.|1) Tight /occluding junctions - form a high resistance barrier to solute movement, and allows the cell to maintain polarity, 2) anchoring junctions / desmosomes - mechanically attach the cell and their cytoskeleton to other cells and the ECM (hemidesmosome), 3)communicating/gap junctions - mediate the passage of chemical or electrical signals from one cell to another.}}

{{hidden|What is the "unfolded protein response"?| Excess accumulation of misfolded protiens, which exceed the capacity of the ER to edit and degrade them, leads to the the ER stress response (UPR) that triggers cell death through apoptosis.}}

{{hidden|What cell organelle has a reactive hyperplasia with repeated exposure to phenobarbitol catabolism in the cytocrhome p450 system?|Smooth endoplasmic reticulum.}}

{{hidden|List three main functions of mitochondria.|1) Energy generation, 2) intermediate metabolism (instead of ATP make intemediate that can be used to make lipids, nucleic acids, and proteins), 3) Cell death ( necrosis & apoptosis)}}

{{hidden|List and describe the four extracellular cell-cell signaling pathways based on the distance the signal travels.|1)Paracrine (immediate vicinity), 2) Autocrine (cell affecting itself), 3) Synaptic (neurons sending neurotransmitters at synapse), 4) endocrine (signals released elsewhere into bloodstream).}}

{{hidden|What are the two characterizing features of stem cells?|Self renewal and asymmetric division (one daughter cell stays a stem cell)}}

{{hidden|What are the two types of stem cells?|embryonic stem cells (inner cell mass of the blastocyst, totipotent), and tissue/adult stem cells (found in stem cell niches associated with specialized tissues, limited repetoire of differentiation = multipotent)}}

{{hidden|What is the Warburg effect?|Increased cellular uptake of glucose and glutamine, increased glycolysis, and decreased oxidative phosphorylation by the cell.}}

{{hidden|Which CDKI's have selective effects on CDK4 and CDK6?|p15,p16,p17,and p19}}

{{hidden|List some examples of signal transduction pathways.|1) Receptor tyrosine kinases (RTKs), 2) Nonreceptor tyrosine kinase, 3) G-protein coupled receptors, 4) nuclear receptors, 5)Notch family receptors, 6) Wnt protein ligands (Frizzled family receptors).}}

{{hidden|Why does nuclear beta catenin occur in some neoplasms?|When Wnt ligand bins to frizzled it recruits Disheveled, this leads to the disruption of the wnt-ubiquitin complex, this stabilized pool of b-catening is then translocated to the nucleus forming a transcriptional complex}}

{{hidden|On Page 19 there is a table of growth factors involved in regeneration and repair, please review.|}}

{{hidden|Describe the function of cadherin.|}}

{{hidden|What are the functions of the extracellular matrix?|Mechanical support, control of cell proliferation, scaffolding for tissue renewal, establishment of tissue microenvironments}}

{{hidden|What are the two basic forms of the ECM?|interstitial matrix (fibrillar and non fibrillar collagen, fibronectin, elastin, proteoglycans, hyloronate, and other stuff), basement membrane (type IV collagen and laminin) }}

{{hidden|What are the three proteins groups in the ECM?|1) fibrous structural proteins (collagen, elastins), 2) water hydrated gels (proteoglycans and hyaluronan), 3) adhesive glycoproteins (connect ECM to each other and other cells)}}

{{hidden|Describe the structure of a protein that is dependent on vitamin C.|Collagen is composed of 3 seprate polypeptide chains braided into a rope like triple helix, lateral cross linking of the triple helices by lysyl oxidase (requires vitamin C) give it it's tensile strength. }}

{{hidden|List three non-fibrillar collagens.|Type IV -basement membrane, Type IX - Fibrillar associated collagen with interrupted triple helices (FACIT), Type VII (provides anchoring fibrils to basement membrane beneath skin)}}

{{hidden|Which structural protein is associated with Marfan syndrom?|Fibrillin synthetic defects, which wrap the elastin core. }}}}

== Chapter 2: Cellular Responses to Stress and Toxic Insults: Adaptation, Injury and Death ==
Experimenting, please ignore
{{Hidden begin |title=What are the four aspects of a disease?}}
*1. Etiology
**Genetic - Inherited mutations and disease-associated gene variants, or polymorphisms
**Acquired - Infectious, nutritional, chemical and physical.
*2. Pathogenesis - The sequence of cellular, biochemical, and molecular events that follow the exposure of cells or tissues to an injurious agent.
*3. Morphological changes - The structural alterations in cells or tissues that are either characteristic of a disease or diagnostic of an etiologic process.
*4. Clinical Manifestations - Symptoms and signs of disease, as well as its clinical course and outcome

{{hidden end}}

== Chapter 3 ==
== Chapter 4 ==
== Chapter 5 ==
{{hidden|MC cause of spontaneous abortion is ?|<center>[[ A demonstrable chromosomal abnormality.]]</center>}}

{{hidden|1% of all newborn infants possess a gross chromosomal abnormality and 5% of people <25y present with |<center>[[a genetic disease. ]]</center>}}

{{hidden|Mutation|<center>[[permanent change in the DNA, if affect germ cells are transmitted to the progeny ]]</center>}}

{{hidden|List and describe 4 broad categories of human genetic disorders:|<center>[[Disorders related to mutation sin single genes with large effects i. Usually follow classic Mendelian pattern of inheritance
ii. Often highly penetrant (large proportion of pop with gene has disease)
b. Chromosomal disorders
i. Structural or numerical alterations in autosomes and sex chromosomes
ii. Uncommon, high penetrance
c. Complex multigenic disorders
i. Interactions between multiple variant forms of genes and environmental factors (polymorphisms), poly genic means disease when many polymorphism present
d. Single gene disorders with nonclassic patterns of inheritance (not mendelian)
i. Disorders resulting from triplet repeat mutations
ii. Mutations in mitochondrial DNA
iii. Those influenced by genomic imprinting
iv. Those influenced by gonadal mosaicism]]</center>}}

{{hidden|List and describe the possible outcomes of a point mutation in a coding region?|[[a. Missense mutation – pt mutation changes amino acid code, conservative when the amino acid is preserved, non conservative when replaced with another amino acid, b. Nonsense mutation – makes a stop codon ]]</center>}}

{{hidden|List and describe the possible outcomes of point mutation or deletion in a non-coding region.|<center>[[a. Promoters/enhancers – interfere with binding of transcription factors, marker reduction or total lack of transcription, b. Introns – defective splicing > failure to make mature RNA > no translation]]</center>}}

{{hidden|List and describe the possible outcomes of deletions and insertions.|<center>[[a.Small coding: not multiple of three = frameshift, if multiple of 3 than add or del amino acids accordingly, often premature stop codon
i. Tay Sachs disease: 4 base pair insertion in Hexosaminidase A gene ]]}}

{{hidden|List and describe the possible outcomes of trinucleotide repeat mutations.|[[a. Usually G&C, dynamic and increase during gametogenesis, “RNA stutters”,b. Fragile X – CGG 250-4000, Huntinton’s Disease ]]}}

{{hidden|List and describe three examples of inheritance of single gene mutations|[[a. AD – manifested in the heterologous state, one parent of index case is usually affected, males and females affected and both can transmit conditioni. De novo cases may not have affected parentii. Penetrance = fraction of people with gene who have the traitiii. Variable expressivity = those with mutant gene have variety of phenotypesiv. Often age of onset is delayed so can reproduce before die from diseasev. Biochem mechanisms1. Reduced production of a protein or dysfunctional/inactive protein2. Involved in regulation of complex metabolic pathyway subject to feedback inhibition3. Key structural proteins (collagen and cytoskeleton of RBC)a. May be a dominant negative , e.g. osteogenesis imperfecta4. Gain of function are rare, 2 formsa. Increased in proteins normal function (excess enzyme activity)b. Huntinton’s diseas (abn protein accumulates, toxic to neurons)b. ARi. Largest category – both alleles at a locus are mutated1. Expression is uniform, complete penetrance common, early onset, unaffected carrier family members, mostly enzymesc. X Linkedi. All sex linked, and almost all are recessive , if Y Chromosome affected usually infertile males > no progenyii. Male expression b/c hemizygous, daughter carriers with variable phenotype because of lionization of 2nd X e.g G6DPiii. Dominant . vitamin D resistant rickets]]</center>}}

Stopped at P142

== Chapter 6 ==
== Chapter 7 ==
== Chapter 8 ==
== Chapter 9 ==
== Chapter 10 ==
== Chapter 11 ==
== Chapter 12 ==
== Chapter 13 ==
== Chapter 14 ==
== Chapter 15 ==
== Chapter 16 ==
== Chapter 17 ==
== Chapter 18 ==
== Chapter 19 ==
== Chapter 20 ==
== Chapter 21 ==
== Chapter 22 ==
== Chapter 23 ==
== Chapter 24 ==
== Chapter 25 ==
== Chapter 26 ==
== Chapter 27 ==
== Chapter 28 ==
== Chapter 29 ==

Robbins and Cotran 9th Edition Questions

2015-05-27T17:33:19Z

Yuanny: /* Chapter 2: Cellular Responses to Stress and Toxic Insults: Adaptation, Injury and Death */

== Chapter 1: The Cell as a Unit of Health and Disease==

{{hidden| Short Answer Questions |
{{hidden|How much of the human genome is coding and what does it code?|Of the 3.2b basepairs, there are 20,000 genes that comprise about 1.5% of the genome that code for proteins (enzymes, structural components, and signaling molecules used to assemble and maintain all the cells in the body}}

{{hidden|What do we think that the rest of the genome does?|80% of the genome binds proteins, implying that it is involved in regulating gene expression, related to the regulation of gene expression, often in a cell-type specific fashion.}}

{{hidden|List the major classes of functional non-protein-coding sequences found in the human genome.|
*1. Promoter & enhancer
*2. Chromatin binding site structures
*3. non-coding regulatory RNAs
*4. Mobile genetic elements (transposons)
*5. telomeres
*6. centromers. }}

{{hidden|What are the two most common forms of DNA variation in the human genome?|
*1) Single nucleotide polymorphisms (SNPs)
*2) copy number variations (CNVs)}}

{{hidden|What are the possible implications of SNPs.|
*1) regulatory = alters gene expression
*2) Correlation with disease states when in close proximity with altered genes
*3) association used to define linkage disequilibrium,?}}

{{hidden|Define epigenetics.|Heritable changes in gene expression which are not caused by alterations in DNA sequence.}}

{{hidden|List the 6 types of epigenetic changes.|
*1) Histone & histone modifying factors (Histones organize chromatin into heterochromatin and euchromatin
*2) histone methylation
*3) histone acteylation
*4)histone phosphorylation
*5) DNA methylation
*6) Chromatin organizing factors.}}

{{hidden|What is the function of micro-RNA (mi-RNA)?|It does not encode protein, instead they function primarily to modulate the translation of target mRNAs into their corresponding proteins, and are responsible for post-transcriptional silencing of gene expression.}}

{{hidden|What is knockdown technology?|The use of synthetic si-RNA (short RNA sequences) introduced into cells that serve as substrates for Dicer and interact with the RISC complex in a manner analogous to endogenous miRNAs, and are used to study gene function, and are being developed as therapeutic agents to silence pathogenic genes, e.g. oncogenic in neoplasms.}}

{{hidden|What is long non coding RNA?|Lnc-RNA modulate gene expression by binding to regions of chromatin, restricting RNA polymerase access to coding genes within the region, and may exceed the number of mRNA's by 10-20 fold.}}

{{hidden|What is XIST?|XIST is a lnc-RNA which is transcribed from the X-chromosome and plays an essential role in physiologic X chromosome inactivation, though not inactivated itself, it forms a repressive cloak on the X chromosome from which it is transcribed resulting in gene silencing.}}

{{hidden|What are the cellular housekeeping functions?|1) protection from the environment, 2) nutrient acquisition, 3) communication, 4) movement, 5) renewal of senescent molecules, 6) molecular catabolism, 7) energy generation.}}

{{hidden|List the cellular compartments and the role in the cell.|1) cytosol = metabolism, transport, protein translation, 2) Mitochondria = energy generation, apoptosis, 3) Rough ER = synthesis of membrane and secreted proteins, 4) Smooth ER / Golgi = protein modification, sorting, catabolism, 5)Nucleus = cell regulation, proliferation, DNA transcription, 6) Endosomes = intracellular transport and export, ingestion of extracellular substances, 7) Lysosomes = cellular catabolism, 8) peroxisomes = very long-chain fatty acid metabolism}}

{{hidden|Describe the basic structure and functions of the cell membrane.| The plasma membrane is composed of a lipid bilayer of phospholipids studded with a variety of proteins and glycoproteins involved in ion and metabolite transport, fluid phase and receptor-mediated uptake of macromolecules, cell-ligand/cell matrix/cell-cell interactions.}}

{{hidden|How are the large complexes in the plasma membrane formed?|They aggregate under the control of chaperone molecules in the RER or by lateral diffusion in the plasma membrane followed by complex formation in situ.}}

{{hidden|What are aquaporins?|Special integral membrane proteins which augment passive water transport in tissues where water is transported in large volumes.}}

{{hidden|How are channel and carrier proteins different?|Channel proteins created hydrophilic pores, permit rapid movement of solutes, restricted by size and charge, where Carrier proteins bind to their specific solutes and undergo a series of conformational changes to transfer the ligand across the membrane, relatively slow transport.}}

{{hidden|What is the "multidrug resistance (MDR) protein"?|A type of transporter ATPases which pumps polar compounds (e.g. chemo drugs) out of cells which may render cancer cells resistant to treatment.}}

{{hidden|What are the two fundamental mechanisms of fluid or macromolecules by the cell (endocytosis)?|1)Caveolae -invaginations of the plasma membrane, 2) Pinocytosis/receptor mediated endocytosis - macromolecules bind to receptor and membranes invaginate around it.}}

{{hidden|What is exocytosis?|It is the opposite process of pinocytosis, where the receptor bound macromolecule is move to the cell surface and released.}}

{{hidden|Describe the difference between phagocytosis and transcytosis.|In phagocytosis microbes are ingested forming phagosomes, which fuse with lysosomes and become phagylosomes, releasing undigested residual material when fusing again with the external membrane, in contrast transcytosis the materials are carried across the cell membrane unaltered.}}

{{hidden|List the three major classes of 3 cytoskeleton proteins.|1) Actin, 2)Intermediate filaments, 3)Microtubules}}

{{hidden|Describe actin.|Actin - 5 to 9nm diam fibrils, G-actin polymerized into F-actin, the form double strands helices, which interact with myosin (filamentous protein).}}

{{hidden|List the various intermediate filaments, which are 10nm in diameter.|1) Lamin A, B, and C (nuclear lamins of all cells, 2) Vimentin (mesenchymal), 3)Desmin (scaffold for actin/myosin), 4) Neurofilaments (axons of neurons), 5) Glial filament protein (glial cells), 6)Cytokeratins (acid and basic and vary based on cell type). }}

{{hidden|Describe microtubules.|Microtubules are 25nm diam fibrils of dimers of a and b tubulin, with a negative end embedded in the centrosome near the nucleus, the + end grows or shrinks as needed. There are kinesins and dyneins motors that move stuff around the cell, also found in cilia and flagella.}}

{{hidden|What is clatharin?|A molecule found in the cell membrane that when the cell membrane invaginates forming a basket like structure.}}

{{hidden|List and describe the 3 main classifications of cell junctions.|1) Tight /occluding junctions - form a high resistance barrier to solute movement, and allows the cell to maintain polarity, 2) anchoring junctions / desmosomes - mechanically attach the cell and their cytoskeleton to other cells and the ECM (hemidesmosome), 3)communicating/gap junctions - mediate the passage of chemical or electrical signals from one cell to another.}}

{{hidden|What is the "unfolded protein response"?| Excess accumulation of misfolded protiens, which exceed the capacity of the ER to edit and degrade them, leads to the the ER stress response (UPR) that triggers cell death through apoptosis.}}

{{hidden|What cell organelle has a reactive hyperplasia with repeated exposure to phenobarbitol catabolism in the cytocrhome p450 system?|Smooth endoplasmic reticulum.}}

{{hidden|List three main functions of mitochondria.|1) Energy generation, 2) intermediate metabolism (instead of ATP make intemediate that can be used to make lipids, nucleic acids, and proteins), 3) Cell death ( necrosis & apoptosis)}}

{{hidden|List and describe the four extracellular cell-cell signaling pathways based on the distance the signal travels.|1)Paracrine (immediate vicinity), 2) Autocrine (cell affecting itself), 3) Synaptic (neurons sending neurotransmitters at synapse), 4) endocrine (signals released elsewhere into bloodstream).}}

{{hidden|What are the two characterizing features of stem cells?|Self renewal and asymmetric division (one daughter cell stays a stem cell)}}

{{hidden|What are the two types of stem cells?|embryonic stem cells (inner cell mass of the blastocyst, totipotent), and tissue/adult stem cells (found in stem cell niches associated with specialized tissues, limited repetoire of differentiation = multipotent)}}

{{hidden|What is the Warburg effect?|Increased cellular uptake of glucose and glutamine, increased glycolysis, and decreased oxidative phosphorylation by the cell.}}

{{hidden|Which CDKI's have selective effects on CDK4 and CDK6?|p15,p16,p17,and p19}}

{{hidden|List some examples of signal transduction pathways.|1) Receptor tyrosine kinases (RTKs), 2) Nonreceptor tyrosine kinase, 3) G-protein coupled receptors, 4) nuclear receptors, 5)Notch family receptors, 6) Wnt protein ligands (Frizzled family receptors).}}

{{hidden|Why does nuclear beta catenin occur in some neoplasms?|When Wnt ligand bins to frizzled it recruits Disheveled, this leads to the disruption of the wnt-ubiquitin complex, this stabilized pool of b-catening is then translocated to the nucleus forming a transcriptional complex}}

{{hidden|On Page 19 there is a table of growth factors involved in regeneration and repair, please review.|}}

{{hidden|Describe the function of cadherin.|}}

{{hidden|What are the functions of the extracellular matrix?|Mechanical support, control of cell proliferation, scaffolding for tissue renewal, establishment of tissue microenvironments}}

{{hidden|What are the two basic forms of the ECM?|interstitial matrix (fibrillar and non fibrillar collagen, fibronectin, elastin, proteoglycans, hyloronate, and other stuff), basement membrane (type IV collagen and laminin) }}

{{hidden|What are the three proteins groups in the ECM?|1) fibrous structural proteins (collagen, elastins), 2) water hydrated gels (proteoglycans and hyaluronan), 3) adhesive glycoproteins (connect ECM to each other and other cells)}}

{{hidden|Describe the structure of a protein that is dependent on vitamin C.|Collagen is composed of 3 seprate polypeptide chains braided into a rope like triple helix, lateral cross linking of the triple helices by lysyl oxidase (requires vitamin C) give it it's tensile strength. }}

{{hidden|List three non-fibrillar collagens.|Type IV -basement membrane, Type IX - Fibrillar associated collagen with interrupted triple helices (FACIT), Type VII (provides anchoring fibrils to basement membrane beneath skin)}}

{{hidden|Which structural protein is associated with Marfan syndrom?|Fibrillin synthetic defects, which wrap the elastin core. }}}}

== Chapter 2: Cellular Responses to Stress and Toxic Insults: Adaptation, Injury and Death ==
Experimenting, please ignore
{{Hidden begin |Title=What are the four aspects of a disease?}}
*1. Etiology
**Genetic - Inherited mutations and disease-associated gene variants, or polymorphisms
**Acquired - Infectious, nutritional, chemical and physical.
*2. Pathogenesis - The sequence of cellular, biochemical, and molecular events that follow the exposure of cells or tissues to an injurious agent.
*3. Morphological changes - The structural alterations in cells or tissues that are either characteristic of a disease or diagnostic of an etiologic process.
*4. Clinical Manifestations - Symptoms and signs of disease, as well as its clinical course and outcome

{{hidden end}}

== Chapter 3 ==
== Chapter 4 ==
== Chapter 5 ==
{{hidden|MC cause of spontaneous abortion is ?|<center>[[ A demonstrable chromosomal abnormality.]]</center>}}

{{hidden|1% of all newborn infants possess a gross chromosomal abnormality and 5% of people <25y present with |<center>[[a genetic disease. ]]</center>}}

{{hidden|Mutation|<center>[[permanent change in the DNA, if affect germ cells are transmitted to the progeny ]]</center>}}

{{hidden|List and describe 4 broad categories of human genetic disorders:|<center>[[Disorders related to mutation sin single genes with large effects i. Usually follow classic Mendelian pattern of inheritance
ii. Often highly penetrant (large proportion of pop with gene has disease)
b. Chromosomal disorders
i. Structural or numerical alterations in autosomes and sex chromosomes
ii. Uncommon, high penetrance
c. Complex multigenic disorders
i. Interactions between multiple variant forms of genes and environmental factors (polymorphisms), poly genic means disease when many polymorphism present
d. Single gene disorders with nonclassic patterns of inheritance (not mendelian)
i. Disorders resulting from triplet repeat mutations
ii. Mutations in mitochondrial DNA
iii. Those influenced by genomic imprinting
iv. Those influenced by gonadal mosaicism]]</center>}}

{{hidden|List and describe the possible outcomes of a point mutation in a coding region?|[[a. Missense mutation – pt mutation changes amino acid code, conservative when the amino acid is preserved, non conservative when replaced with another amino acid, b. Nonsense mutation – makes a stop codon ]]</center>}}

{{hidden|List and describe the possible outcomes of point mutation or deletion in a non-coding region.|<center>[[a. Promoters/enhancers – interfere with binding of transcription factors, marker reduction or total lack of transcription, b. Introns – defective splicing > failure to make mature RNA > no translation]]</center>}}

{{hidden|List and describe the possible outcomes of deletions and insertions.|<center>[[a.Small coding: not multiple of three = frameshift, if multiple of 3 than add or del amino acids accordingly, often premature stop codon
i. Tay Sachs disease: 4 base pair insertion in Hexosaminidase A gene ]]}}

{{hidden|List and describe the possible outcomes of trinucleotide repeat mutations.|[[a. Usually G&C, dynamic and increase during gametogenesis, “RNA stutters”,b. Fragile X – CGG 250-4000, Huntinton’s Disease ]]}}

{{hidden|List and describe three examples of inheritance of single gene mutations|[[a. AD – manifested in the heterologous state, one parent of index case is usually affected, males and females affected and both can transmit conditioni. De novo cases may not have affected parentii. Penetrance = fraction of people with gene who have the traitiii. Variable expressivity = those with mutant gene have variety of phenotypesiv. Often age of onset is delayed so can reproduce before die from diseasev. Biochem mechanisms1. Reduced production of a protein or dysfunctional/inactive protein2. Involved in regulation of complex metabolic pathyway subject to feedback inhibition3. Key structural proteins (collagen and cytoskeleton of RBC)a. May be a dominant negative , e.g. osteogenesis imperfecta4. Gain of function are rare, 2 formsa. Increased in proteins normal function (excess enzyme activity)b. Huntinton’s diseas (abn protein accumulates, toxic to neurons)b. ARi. Largest category – both alleles at a locus are mutated1. Expression is uniform, complete penetrance common, early onset, unaffected carrier family members, mostly enzymesc. X Linkedi. All sex linked, and almost all are recessive , if Y Chromosome affected usually infertile males > no progenyii. Male expression b/c hemizygous, daughter carriers with variable phenotype because of lionization of 2nd X e.g G6DPiii. Dominant . vitamin D resistant rickets]]</center>}}

Stopped at P142

== Chapter 6 ==
== Chapter 7 ==
== Chapter 8 ==
== Chapter 9 ==
== Chapter 10 ==
== Chapter 11 ==
== Chapter 12 ==
== Chapter 13 ==
== Chapter 14 ==
== Chapter 15 ==
== Chapter 16 ==
== Chapter 17 ==
== Chapter 18 ==
== Chapter 19 ==
== Chapter 20 ==
== Chapter 21 ==
== Chapter 22 ==
== Chapter 23 ==
== Chapter 24 ==
== Chapter 25 ==
== Chapter 26 ==
== Chapter 27 ==
== Chapter 28 ==
== Chapter 29 ==

Robbins and Cotran 9th Edition Questions

2015-05-27T17:32:30Z

Yuanny: /* Chapter 2: Cellular Responses to Stress and Toxic Insults: Adaptation, Injury and Death */

== Chapter 1: The Cell as a Unit of Health and Disease==

{{hidden| Short Answer Questions |
{{hidden|How much of the human genome is coding and what does it code?|Of the 3.2b basepairs, there are 20,000 genes that comprise about 1.5% of the genome that code for proteins (enzymes, structural components, and signaling molecules used to assemble and maintain all the cells in the body}}

{{hidden|What do we think that the rest of the genome does?|80% of the genome binds proteins, implying that it is involved in regulating gene expression, related to the regulation of gene expression, often in a cell-type specific fashion.}}

{{hidden|List the major classes of functional non-protein-coding sequences found in the human genome.|
*1. Promoter & enhancer
*2. Chromatin binding site structures
*3. non-coding regulatory RNAs
*4. Mobile genetic elements (transposons)
*5. telomeres
*6. centromers. }}

{{hidden|What are the two most common forms of DNA variation in the human genome?|
*1) Single nucleotide polymorphisms (SNPs)
*2) copy number variations (CNVs)}}

{{hidden|What are the possible implications of SNPs.|
*1) regulatory = alters gene expression
*2) Correlation with disease states when in close proximity with altered genes
*3) association used to define linkage disequilibrium,?}}

{{hidden|Define epigenetics.|Heritable changes in gene expression which are not caused by alterations in DNA sequence.}}

{{hidden|List the 6 types of epigenetic changes.|
*1) Histone & histone modifying factors (Histones organize chromatin into heterochromatin and euchromatin
*2) histone methylation
*3) histone acteylation
*4)histone phosphorylation
*5) DNA methylation
*6) Chromatin organizing factors.}}

{{hidden|What is the function of micro-RNA (mi-RNA)?|It does not encode protein, instead they function primarily to modulate the translation of target mRNAs into their corresponding proteins, and are responsible for post-transcriptional silencing of gene expression.}}

{{hidden|What is knockdown technology?|The use of synthetic si-RNA (short RNA sequences) introduced into cells that serve as substrates for Dicer and interact with the RISC complex in a manner analogous to endogenous miRNAs, and are used to study gene function, and are being developed as therapeutic agents to silence pathogenic genes, e.g. oncogenic in neoplasms.}}

{{hidden|What is long non coding RNA?|Lnc-RNA modulate gene expression by binding to regions of chromatin, restricting RNA polymerase access to coding genes within the region, and may exceed the number of mRNA's by 10-20 fold.}}

{{hidden|What is XIST?|XIST is a lnc-RNA which is transcribed from the X-chromosome and plays an essential role in physiologic X chromosome inactivation, though not inactivated itself, it forms a repressive cloak on the X chromosome from which it is transcribed resulting in gene silencing.}}

{{hidden|What are the cellular housekeeping functions?|1) protection from the environment, 2) nutrient acquisition, 3) communication, 4) movement, 5) renewal of senescent molecules, 6) molecular catabolism, 7) energy generation.}}

{{hidden|List the cellular compartments and the role in the cell.|1) cytosol = metabolism, transport, protein translation, 2) Mitochondria = energy generation, apoptosis, 3) Rough ER = synthesis of membrane and secreted proteins, 4) Smooth ER / Golgi = protein modification, sorting, catabolism, 5)Nucleus = cell regulation, proliferation, DNA transcription, 6) Endosomes = intracellular transport and export, ingestion of extracellular substances, 7) Lysosomes = cellular catabolism, 8) peroxisomes = very long-chain fatty acid metabolism}}

{{hidden|Describe the basic structure and functions of the cell membrane.| The plasma membrane is composed of a lipid bilayer of phospholipids studded with a variety of proteins and glycoproteins involved in ion and metabolite transport, fluid phase and receptor-mediated uptake of macromolecules, cell-ligand/cell matrix/cell-cell interactions.}}

{{hidden|How are the large complexes in the plasma membrane formed?|They aggregate under the control of chaperone molecules in the RER or by lateral diffusion in the plasma membrane followed by complex formation in situ.}}

{{hidden|What are aquaporins?|Special integral membrane proteins which augment passive water transport in tissues where water is transported in large volumes.}}

{{hidden|How are channel and carrier proteins different?|Channel proteins created hydrophilic pores, permit rapid movement of solutes, restricted by size and charge, where Carrier proteins bind to their specific solutes and undergo a series of conformational changes to transfer the ligand across the membrane, relatively slow transport.}}

{{hidden|What is the "multidrug resistance (MDR) protein"?|A type of transporter ATPases which pumps polar compounds (e.g. chemo drugs) out of cells which may render cancer cells resistant to treatment.}}

{{hidden|What are the two fundamental mechanisms of fluid or macromolecules by the cell (endocytosis)?|1)Caveolae -invaginations of the plasma membrane, 2) Pinocytosis/receptor mediated endocytosis - macromolecules bind to receptor and membranes invaginate around it.}}

{{hidden|What is exocytosis?|It is the opposite process of pinocytosis, where the receptor bound macromolecule is move to the cell surface and released.}}

{{hidden|Describe the difference between phagocytosis and transcytosis.|In phagocytosis microbes are ingested forming phagosomes, which fuse with lysosomes and become phagylosomes, releasing undigested residual material when fusing again with the external membrane, in contrast transcytosis the materials are carried across the cell membrane unaltered.}}

{{hidden|List the three major classes of 3 cytoskeleton proteins.|1) Actin, 2)Intermediate filaments, 3)Microtubules}}

{{hidden|Describe actin.|Actin - 5 to 9nm diam fibrils, G-actin polymerized into F-actin, the form double strands helices, which interact with myosin (filamentous protein).}}

{{hidden|List the various intermediate filaments, which are 10nm in diameter.|1) Lamin A, B, and C (nuclear lamins of all cells, 2) Vimentin (mesenchymal), 3)Desmin (scaffold for actin/myosin), 4) Neurofilaments (axons of neurons), 5) Glial filament protein (glial cells), 6)Cytokeratins (acid and basic and vary based on cell type). }}

{{hidden|Describe microtubules.|Microtubules are 25nm diam fibrils of dimers of a and b tubulin, with a negative end embedded in the centrosome near the nucleus, the + end grows or shrinks as needed. There are kinesins and dyneins motors that move stuff around the cell, also found in cilia and flagella.}}

{{hidden|What is clatharin?|A molecule found in the cell membrane that when the cell membrane invaginates forming a basket like structure.}}

{{hidden|List and describe the 3 main classifications of cell junctions.|1) Tight /occluding junctions - form a high resistance barrier to solute movement, and allows the cell to maintain polarity, 2) anchoring junctions / desmosomes - mechanically attach the cell and their cytoskeleton to other cells and the ECM (hemidesmosome), 3)communicating/gap junctions - mediate the passage of chemical or electrical signals from one cell to another.}}

{{hidden|What is the "unfolded protein response"?| Excess accumulation of misfolded protiens, which exceed the capacity of the ER to edit and degrade them, leads to the the ER stress response (UPR) that triggers cell death through apoptosis.}}

{{hidden|What cell organelle has a reactive hyperplasia with repeated exposure to phenobarbitol catabolism in the cytocrhome p450 system?|Smooth endoplasmic reticulum.}}

{{hidden|List three main functions of mitochondria.|1) Energy generation, 2) intermediate metabolism (instead of ATP make intemediate that can be used to make lipids, nucleic acids, and proteins), 3) Cell death ( necrosis & apoptosis)}}

{{hidden|List and describe the four extracellular cell-cell signaling pathways based on the distance the signal travels.|1)Paracrine (immediate vicinity), 2) Autocrine (cell affecting itself), 3) Synaptic (neurons sending neurotransmitters at synapse), 4) endocrine (signals released elsewhere into bloodstream).}}

{{hidden|What are the two characterizing features of stem cells?|Self renewal and asymmetric division (one daughter cell stays a stem cell)}}

{{hidden|What are the two types of stem cells?|embryonic stem cells (inner cell mass of the blastocyst, totipotent), and tissue/adult stem cells (found in stem cell niches associated with specialized tissues, limited repetoire of differentiation = multipotent)}}

{{hidden|What is the Warburg effect?|Increased cellular uptake of glucose and glutamine, increased glycolysis, and decreased oxidative phosphorylation by the cell.}}

{{hidden|Which CDKI's have selective effects on CDK4 and CDK6?|p15,p16,p17,and p19}}

{{hidden|List some examples of signal transduction pathways.|1) Receptor tyrosine kinases (RTKs), 2) Nonreceptor tyrosine kinase, 3) G-protein coupled receptors, 4) nuclear receptors, 5)Notch family receptors, 6) Wnt protein ligands (Frizzled family receptors).}}

{{hidden|Why does nuclear beta catenin occur in some neoplasms?|When Wnt ligand bins to frizzled it recruits Disheveled, this leads to the disruption of the wnt-ubiquitin complex, this stabilized pool of b-catening is then translocated to the nucleus forming a transcriptional complex}}

{{hidden|On Page 19 there is a table of growth factors involved in regeneration and repair, please review.|}}

{{hidden|Describe the function of cadherin.|}}

{{hidden|What are the functions of the extracellular matrix?|Mechanical support, control of cell proliferation, scaffolding for tissue renewal, establishment of tissue microenvironments}}

{{hidden|What are the two basic forms of the ECM?|interstitial matrix (fibrillar and non fibrillar collagen, fibronectin, elastin, proteoglycans, hyloronate, and other stuff), basement membrane (type IV collagen and laminin) }}

{{hidden|What are the three proteins groups in the ECM?|1) fibrous structural proteins (collagen, elastins), 2) water hydrated gels (proteoglycans and hyaluronan), 3) adhesive glycoproteins (connect ECM to each other and other cells)}}

{{hidden|Describe the structure of a protein that is dependent on vitamin C.|Collagen is composed of 3 seprate polypeptide chains braided into a rope like triple helix, lateral cross linking of the triple helices by lysyl oxidase (requires vitamin C) give it it's tensile strength. }}

{{hidden|List three non-fibrillar collagens.|Type IV -basement membrane, Type IX - Fibrillar associated collagen with interrupted triple helices (FACIT), Type VII (provides anchoring fibrils to basement membrane beneath skin)}}

{{hidden|Which structural protein is associated with Marfan syndrom?|Fibrillin synthetic defects, which wrap the elastin core. }}}}

== Chapter 2: Cellular Responses to Stress and Toxic Insults: Adaptation, Injury and Death ==
Experimenting, please ignore
{{hidden begin |Title=What are the four aspects of a disease?}}
*1. Etiology
**Genetic - Inherited mutations and disease-associated gene variants, or polymorphisms
**Acquired - Infectious, nutritional, chemical and physical.
*2. Pathogenesis - The sequence of cellular, biochemical, and molecular events that follow the exposure of cells or tissues to an injurious agent.
*3. Morphological changes - The structural alterations in cells or tissues that are either characteristic of a disease or diagnostic of an etiologic process.
*4. Clinical Manifestations - Symptoms and signs of disease, as well as its clinical course and outcome{{hidden end}}

== Chapter 3 ==
== Chapter 4 ==
== Chapter 5 ==
{{hidden|MC cause of spontaneous abortion is ?|<center>[[ A demonstrable chromosomal abnormality.]]</center>}}

{{hidden|1% of all newborn infants possess a gross chromosomal abnormality and 5% of people <25y present with |<center>[[a genetic disease. ]]</center>}}

{{hidden|Mutation|<center>[[permanent change in the DNA, if affect germ cells are transmitted to the progeny ]]</center>}}

{{hidden|List and describe 4 broad categories of human genetic disorders:|<center>[[Disorders related to mutation sin single genes with large effects i. Usually follow classic Mendelian pattern of inheritance
ii. Often highly penetrant (large proportion of pop with gene has disease)
b. Chromosomal disorders
i. Structural or numerical alterations in autosomes and sex chromosomes
ii. Uncommon, high penetrance
c. Complex multigenic disorders
i. Interactions between multiple variant forms of genes and environmental factors (polymorphisms), poly genic means disease when many polymorphism present
d. Single gene disorders with nonclassic patterns of inheritance (not mendelian)
i. Disorders resulting from triplet repeat mutations
ii. Mutations in mitochondrial DNA
iii. Those influenced by genomic imprinting
iv. Those influenced by gonadal mosaicism]]</center>}}

{{hidden|List and describe the possible outcomes of a point mutation in a coding region?|[[a. Missense mutation – pt mutation changes amino acid code, conservative when the amino acid is preserved, non conservative when replaced with another amino acid, b. Nonsense mutation – makes a stop codon ]]</center>}}

{{hidden|List and describe the possible outcomes of point mutation or deletion in a non-coding region.|<center>[[a. Promoters/enhancers – interfere with binding of transcription factors, marker reduction or total lack of transcription, b. Introns – defective splicing > failure to make mature RNA > no translation]]</center>}}

{{hidden|List and describe the possible outcomes of deletions and insertions.|<center>[[a.Small coding: not multiple of three = frameshift, if multiple of 3 than add or del amino acids accordingly, often premature stop codon
i. Tay Sachs disease: 4 base pair insertion in Hexosaminidase A gene ]]}}

{{hidden|List and describe the possible outcomes of trinucleotide repeat mutations.|[[a. Usually G&C, dynamic and increase during gametogenesis, “RNA stutters”,b. Fragile X – CGG 250-4000, Huntinton’s Disease ]]}}

{{hidden|List and describe three examples of inheritance of single gene mutations|[[a. AD – manifested in the heterologous state, one parent of index case is usually affected, males and females affected and both can transmit conditioni. De novo cases may not have affected parentii. Penetrance = fraction of people with gene who have the traitiii. Variable expressivity = those with mutant gene have variety of phenotypesiv. Often age of onset is delayed so can reproduce before die from diseasev. Biochem mechanisms1. Reduced production of a protein or dysfunctional/inactive protein2. Involved in regulation of complex metabolic pathyway subject to feedback inhibition3. Key structural proteins (collagen and cytoskeleton of RBC)a. May be a dominant negative , e.g. osteogenesis imperfecta4. Gain of function are rare, 2 formsa. Increased in proteins normal function (excess enzyme activity)b. Huntinton’s diseas (abn protein accumulates, toxic to neurons)b. ARi. Largest category – both alleles at a locus are mutated1. Expression is uniform, complete penetrance common, early onset, unaffected carrier family members, mostly enzymesc. X Linkedi. All sex linked, and almost all are recessive , if Y Chromosome affected usually infertile males > no progenyii. Male expression b/c hemizygous, daughter carriers with variable phenotype because of lionization of 2nd X e.g G6DPiii. Dominant . vitamin D resistant rickets]]</center>}}

Stopped at P142

== Chapter 6 ==
== Chapter 7 ==
== Chapter 8 ==
== Chapter 9 ==
== Chapter 10 ==
== Chapter 11 ==
== Chapter 12 ==
== Chapter 13 ==
== Chapter 14 ==
== Chapter 15 ==
== Chapter 16 ==
== Chapter 17 ==
== Chapter 18 ==
== Chapter 19 ==
== Chapter 20 ==
== Chapter 21 ==
== Chapter 22 ==
== Chapter 23 ==
== Chapter 24 ==
== Chapter 25 ==
== Chapter 26 ==
== Chapter 27 ==
== Chapter 28 ==
== Chapter 29 ==

Robbins and Cotran 9th Edition Questions

2015-05-27T17:32:04Z

Yuanny: /* Chapter 2: Cellular Responses to Stress and Toxic Insults: Adaptation, Injury and Death */

== Chapter 1: The Cell as a Unit of Health and Disease==

{{hidden| Short Answer Questions |
{{hidden|How much of the human genome is coding and what does it code?|Of the 3.2b basepairs, there are 20,000 genes that comprise about 1.5% of the genome that code for proteins (enzymes, structural components, and signaling molecules used to assemble and maintain all the cells in the body}}

{{hidden|What do we think that the rest of the genome does?|80% of the genome binds proteins, implying that it is involved in regulating gene expression, related to the regulation of gene expression, often in a cell-type specific fashion.}}

{{hidden|List the major classes of functional non-protein-coding sequences found in the human genome.|
*1. Promoter & enhancer
*2. Chromatin binding site structures
*3. non-coding regulatory RNAs
*4. Mobile genetic elements (transposons)
*5. telomeres
*6. centromers. }}

{{hidden|What are the two most common forms of DNA variation in the human genome?|
*1) Single nucleotide polymorphisms (SNPs)
*2) copy number variations (CNVs)}}

{{hidden|What are the possible implications of SNPs.|
*1) regulatory = alters gene expression
*2) Correlation with disease states when in close proximity with altered genes
*3) association used to define linkage disequilibrium,?}}

{{hidden|Define epigenetics.|Heritable changes in gene expression which are not caused by alterations in DNA sequence.}}

{{hidden|List the 6 types of epigenetic changes.|
*1) Histone & histone modifying factors (Histones organize chromatin into heterochromatin and euchromatin
*2) histone methylation
*3) histone acteylation
*4)histone phosphorylation
*5) DNA methylation
*6) Chromatin organizing factors.}}

{{hidden|What is the function of micro-RNA (mi-RNA)?|It does not encode protein, instead they function primarily to modulate the translation of target mRNAs into their corresponding proteins, and are responsible for post-transcriptional silencing of gene expression.}}

{{hidden|What is knockdown technology?|The use of synthetic si-RNA (short RNA sequences) introduced into cells that serve as substrates for Dicer and interact with the RISC complex in a manner analogous to endogenous miRNAs, and are used to study gene function, and are being developed as therapeutic agents to silence pathogenic genes, e.g. oncogenic in neoplasms.}}

{{hidden|What is long non coding RNA?|Lnc-RNA modulate gene expression by binding to regions of chromatin, restricting RNA polymerase access to coding genes within the region, and may exceed the number of mRNA's by 10-20 fold.}}

{{hidden|What is XIST?|XIST is a lnc-RNA which is transcribed from the X-chromosome and plays an essential role in physiologic X chromosome inactivation, though not inactivated itself, it forms a repressive cloak on the X chromosome from which it is transcribed resulting in gene silencing.}}

{{hidden|What are the cellular housekeeping functions?|1) protection from the environment, 2) nutrient acquisition, 3) communication, 4) movement, 5) renewal of senescent molecules, 6) molecular catabolism, 7) energy generation.}}

{{hidden|List the cellular compartments and the role in the cell.|1) cytosol = metabolism, transport, protein translation, 2) Mitochondria = energy generation, apoptosis, 3) Rough ER = synthesis of membrane and secreted proteins, 4) Smooth ER / Golgi = protein modification, sorting, catabolism, 5)Nucleus = cell regulation, proliferation, DNA transcription, 6) Endosomes = intracellular transport and export, ingestion of extracellular substances, 7) Lysosomes = cellular catabolism, 8) peroxisomes = very long-chain fatty acid metabolism}}

{{hidden|Describe the basic structure and functions of the cell membrane.| The plasma membrane is composed of a lipid bilayer of phospholipids studded with a variety of proteins and glycoproteins involved in ion and metabolite transport, fluid phase and receptor-mediated uptake of macromolecules, cell-ligand/cell matrix/cell-cell interactions.}}

{{hidden|How are the large complexes in the plasma membrane formed?|They aggregate under the control of chaperone molecules in the RER or by lateral diffusion in the plasma membrane followed by complex formation in situ.}}

{{hidden|What are aquaporins?|Special integral membrane proteins which augment passive water transport in tissues where water is transported in large volumes.}}

{{hidden|How are channel and carrier proteins different?|Channel proteins created hydrophilic pores, permit rapid movement of solutes, restricted by size and charge, where Carrier proteins bind to their specific solutes and undergo a series of conformational changes to transfer the ligand across the membrane, relatively slow transport.}}

{{hidden|What is the "multidrug resistance (MDR) protein"?|A type of transporter ATPases which pumps polar compounds (e.g. chemo drugs) out of cells which may render cancer cells resistant to treatment.}}

{{hidden|What are the two fundamental mechanisms of fluid or macromolecules by the cell (endocytosis)?|1)Caveolae -invaginations of the plasma membrane, 2) Pinocytosis/receptor mediated endocytosis - macromolecules bind to receptor and membranes invaginate around it.}}

{{hidden|What is exocytosis?|It is the opposite process of pinocytosis, where the receptor bound macromolecule is move to the cell surface and released.}}

{{hidden|Describe the difference between phagocytosis and transcytosis.|In phagocytosis microbes are ingested forming phagosomes, which fuse with lysosomes and become phagylosomes, releasing undigested residual material when fusing again with the external membrane, in contrast transcytosis the materials are carried across the cell membrane unaltered.}}

{{hidden|List the three major classes of 3 cytoskeleton proteins.|1) Actin, 2)Intermediate filaments, 3)Microtubules}}

{{hidden|Describe actin.|Actin - 5 to 9nm diam fibrils, G-actin polymerized into F-actin, the form double strands helices, which interact with myosin (filamentous protein).}}

{{hidden|List the various intermediate filaments, which are 10nm in diameter.|1) Lamin A, B, and C (nuclear lamins of all cells, 2) Vimentin (mesenchymal), 3)Desmin (scaffold for actin/myosin), 4) Neurofilaments (axons of neurons), 5) Glial filament protein (glial cells), 6)Cytokeratins (acid and basic and vary based on cell type). }}

{{hidden|Describe microtubules.|Microtubules are 25nm diam fibrils of dimers of a and b tubulin, with a negative end embedded in the centrosome near the nucleus, the + end grows or shrinks as needed. There are kinesins and dyneins motors that move stuff around the cell, also found in cilia and flagella.}}

{{hidden|What is clatharin?|A molecule found in the cell membrane that when the cell membrane invaginates forming a basket like structure.}}

{{hidden|List and describe the 3 main classifications of cell junctions.|1) Tight /occluding junctions - form a high resistance barrier to solute movement, and allows the cell to maintain polarity, 2) anchoring junctions / desmosomes - mechanically attach the cell and their cytoskeleton to other cells and the ECM (hemidesmosome), 3)communicating/gap junctions - mediate the passage of chemical or electrical signals from one cell to another.}}

{{hidden|What is the "unfolded protein response"?| Excess accumulation of misfolded protiens, which exceed the capacity of the ER to edit and degrade them, leads to the the ER stress response (UPR) that triggers cell death through apoptosis.}}

{{hidden|What cell organelle has a reactive hyperplasia with repeated exposure to phenobarbitol catabolism in the cytocrhome p450 system?|Smooth endoplasmic reticulum.}}

{{hidden|List three main functions of mitochondria.|1) Energy generation, 2) intermediate metabolism (instead of ATP make intemediate that can be used to make lipids, nucleic acids, and proteins), 3) Cell death ( necrosis & apoptosis)}}

{{hidden|List and describe the four extracellular cell-cell signaling pathways based on the distance the signal travels.|1)Paracrine (immediate vicinity), 2) Autocrine (cell affecting itself), 3) Synaptic (neurons sending neurotransmitters at synapse), 4) endocrine (signals released elsewhere into bloodstream).}}

{{hidden|What are the two characterizing features of stem cells?|Self renewal and asymmetric division (one daughter cell stays a stem cell)}}

{{hidden|What are the two types of stem cells?|embryonic stem cells (inner cell mass of the blastocyst, totipotent), and tissue/adult stem cells (found in stem cell niches associated with specialized tissues, limited repetoire of differentiation = multipotent)}}

{{hidden|What is the Warburg effect?|Increased cellular uptake of glucose and glutamine, increased glycolysis, and decreased oxidative phosphorylation by the cell.}}

{{hidden|Which CDKI's have selective effects on CDK4 and CDK6?|p15,p16,p17,and p19}}

{{hidden|List some examples of signal transduction pathways.|1) Receptor tyrosine kinases (RTKs), 2) Nonreceptor tyrosine kinase, 3) G-protein coupled receptors, 4) nuclear receptors, 5)Notch family receptors, 6) Wnt protein ligands (Frizzled family receptors).}}

{{hidden|Why does nuclear beta catenin occur in some neoplasms?|When Wnt ligand bins to frizzled it recruits Disheveled, this leads to the disruption of the wnt-ubiquitin complex, this stabilized pool of b-catening is then translocated to the nucleus forming a transcriptional complex}}

{{hidden|On Page 19 there is a table of growth factors involved in regeneration and repair, please review.|}}

{{hidden|Describe the function of cadherin.|}}

{{hidden|What are the functions of the extracellular matrix?|Mechanical support, control of cell proliferation, scaffolding for tissue renewal, establishment of tissue microenvironments}}

{{hidden|What are the two basic forms of the ECM?|interstitial matrix (fibrillar and non fibrillar collagen, fibronectin, elastin, proteoglycans, hyloronate, and other stuff), basement membrane (type IV collagen and laminin) }}

{{hidden|What are the three proteins groups in the ECM?|1) fibrous structural proteins (collagen, elastins), 2) water hydrated gels (proteoglycans and hyaluronan), 3) adhesive glycoproteins (connect ECM to each other and other cells)}}

{{hidden|Describe the structure of a protein that is dependent on vitamin C.|Collagen is composed of 3 seprate polypeptide chains braided into a rope like triple helix, lateral cross linking of the triple helices by lysyl oxidase (requires vitamin C) give it it's tensile strength. }}

{{hidden|List three non-fibrillar collagens.|Type IV -basement membrane, Type IX - Fibrillar associated collagen with interrupted triple helices (FACIT), Type VII (provides anchoring fibrils to basement membrane beneath skin)}}

{{hidden|Which structural protein is associated with Marfan syndrom?|Fibrillin synthetic defects, which wrap the elastin core. }}}}

== Chapter 2: Cellular Responses to Stress and Toxic Insults: Adaptation, Injury and Death ==
Experimenting, please ignore
{{hidden begin|Title=What are the four aspects of a disease?}}
*1. Etiology
**Genetic - Inherited mutations and disease-associated gene variants, or polymorphisms
**Acquired - Infectious, nutritional, chemical and physical.
*2. Pathogenesis - The sequence of cellular, biochemical, and molecular events that follow the exposure of cells or tissues to an injurious agent.
*3. Morphological changes - The structural alterations in cells or tissues that are either characteristic of a disease or diagnostic of an etiologic process.
*4. Clinical Manifestations - Symptoms and signs of disease, as well as its clinical course and outcome{{hidden end}}

== Chapter 3 ==
== Chapter 4 ==
== Chapter 5 ==
{{hidden|MC cause of spontaneous abortion is ?|<center>[[ A demonstrable chromosomal abnormality.]]</center>}}

{{hidden|1% of all newborn infants possess a gross chromosomal abnormality and 5% of people <25y present with |<center>[[a genetic disease. ]]</center>}}

{{hidden|Mutation|<center>[[permanent change in the DNA, if affect germ cells are transmitted to the progeny ]]</center>}}

{{hidden|List and describe 4 broad categories of human genetic disorders:|<center>[[Disorders related to mutation sin single genes with large effects i. Usually follow classic Mendelian pattern of inheritance
ii. Often highly penetrant (large proportion of pop with gene has disease)
b. Chromosomal disorders
i. Structural or numerical alterations in autosomes and sex chromosomes
ii. Uncommon, high penetrance
c. Complex multigenic disorders
i. Interactions between multiple variant forms of genes and environmental factors (polymorphisms), poly genic means disease when many polymorphism present
d. Single gene disorders with nonclassic patterns of inheritance (not mendelian)
i. Disorders resulting from triplet repeat mutations
ii. Mutations in mitochondrial DNA
iii. Those influenced by genomic imprinting
iv. Those influenced by gonadal mosaicism]]</center>}}

{{hidden|List and describe the possible outcomes of a point mutation in a coding region?|[[a. Missense mutation – pt mutation changes amino acid code, conservative when the amino acid is preserved, non conservative when replaced with another amino acid, b. Nonsense mutation – makes a stop codon ]]</center>}}

{{hidden|List and describe the possible outcomes of point mutation or deletion in a non-coding region.|<center>[[a. Promoters/enhancers – interfere with binding of transcription factors, marker reduction or total lack of transcription, b. Introns – defective splicing > failure to make mature RNA > no translation]]</center>}}

{{hidden|List and describe the possible outcomes of deletions and insertions.|<center>[[a.Small coding: not multiple of three = frameshift, if multiple of 3 than add or del amino acids accordingly, often premature stop codon
i. Tay Sachs disease: 4 base pair insertion in Hexosaminidase A gene ]]}}

{{hidden|List and describe the possible outcomes of trinucleotide repeat mutations.|[[a. Usually G&C, dynamic and increase during gametogenesis, “RNA stutters”,b. Fragile X – CGG 250-4000, Huntinton’s Disease ]]}}

{{hidden|List and describe three examples of inheritance of single gene mutations|[[a. AD – manifested in the heterologous state, one parent of index case is usually affected, males and females affected and both can transmit conditioni. De novo cases may not have affected parentii. Penetrance = fraction of people with gene who have the traitiii. Variable expressivity = those with mutant gene have variety of phenotypesiv. Often age of onset is delayed so can reproduce before die from diseasev. Biochem mechanisms1. Reduced production of a protein or dysfunctional/inactive protein2. Involved in regulation of complex metabolic pathyway subject to feedback inhibition3. Key structural proteins (collagen and cytoskeleton of RBC)a. May be a dominant negative , e.g. osteogenesis imperfecta4. Gain of function are rare, 2 formsa. Increased in proteins normal function (excess enzyme activity)b. Huntinton’s diseas (abn protein accumulates, toxic to neurons)b. ARi. Largest category – both alleles at a locus are mutated1. Expression is uniform, complete penetrance common, early onset, unaffected carrier family members, mostly enzymesc. X Linkedi. All sex linked, and almost all are recessive , if Y Chromosome affected usually infertile males > no progenyii. Male expression b/c hemizygous, daughter carriers with variable phenotype because of lionization of 2nd X e.g G6DPiii. Dominant . vitamin D resistant rickets]]</center>}}

Stopped at P142

== Chapter 6 ==
== Chapter 7 ==
== Chapter 8 ==
== Chapter 9 ==
== Chapter 10 ==
== Chapter 11 ==
== Chapter 12 ==
== Chapter 13 ==
== Chapter 14 ==
== Chapter 15 ==
== Chapter 16 ==
== Chapter 17 ==
== Chapter 18 ==
== Chapter 19 ==
== Chapter 20 ==
== Chapter 21 ==
== Chapter 22 ==
== Chapter 23 ==
== Chapter 24 ==
== Chapter 25 ==
== Chapter 26 ==
== Chapter 27 ==
== Chapter 28 ==
== Chapter 29 ==

Robbins and Cotran 9th Edition Questions

2015-05-27T17:31:20Z

Yuanny: /* Chapter 2: Cellular Responses to Stress and Toxic Insults: Adaptation, Injury and Death */

== Chapter 1: The Cell as a Unit of Health and Disease==

{{hidden| Short Answer Questions |
{{hidden|How much of the human genome is coding and what does it code?|Of the 3.2b basepairs, there are 20,000 genes that comprise about 1.5% of the genome that code for proteins (enzymes, structural components, and signaling molecules used to assemble and maintain all the cells in the body}}

{{hidden|What do we think that the rest of the genome does?|80% of the genome binds proteins, implying that it is involved in regulating gene expression, related to the regulation of gene expression, often in a cell-type specific fashion.}}

{{hidden|List the major classes of functional non-protein-coding sequences found in the human genome.|
*1. Promoter & enhancer
*2. Chromatin binding site structures
*3. non-coding regulatory RNAs
*4. Mobile genetic elements (transposons)
*5. telomeres
*6. centromers. }}

{{hidden|What are the two most common forms of DNA variation in the human genome?|
*1) Single nucleotide polymorphisms (SNPs)
*2) copy number variations (CNVs)}}

{{hidden|What are the possible implications of SNPs.|
*1) regulatory = alters gene expression
*2) Correlation with disease states when in close proximity with altered genes
*3) association used to define linkage disequilibrium,?}}

{{hidden|Define epigenetics.|Heritable changes in gene expression which are not caused by alterations in DNA sequence.}}

{{hidden|List the 6 types of epigenetic changes.|
*1) Histone & histone modifying factors (Histones organize chromatin into heterochromatin and euchromatin
*2) histone methylation
*3) histone acteylation
*4)histone phosphorylation
*5) DNA methylation
*6) Chromatin organizing factors.}}

{{hidden|What is the function of micro-RNA (mi-RNA)?|It does not encode protein, instead they function primarily to modulate the translation of target mRNAs into their corresponding proteins, and are responsible for post-transcriptional silencing of gene expression.}}

{{hidden|What is knockdown technology?|The use of synthetic si-RNA (short RNA sequences) introduced into cells that serve as substrates for Dicer and interact with the RISC complex in a manner analogous to endogenous miRNAs, and are used to study gene function, and are being developed as therapeutic agents to silence pathogenic genes, e.g. oncogenic in neoplasms.}}

{{hidden|What is long non coding RNA?|Lnc-RNA modulate gene expression by binding to regions of chromatin, restricting RNA polymerase access to coding genes within the region, and may exceed the number of mRNA's by 10-20 fold.}}

{{hidden|What is XIST?|XIST is a lnc-RNA which is transcribed from the X-chromosome and plays an essential role in physiologic X chromosome inactivation, though not inactivated itself, it forms a repressive cloak on the X chromosome from which it is transcribed resulting in gene silencing.}}

{{hidden|What are the cellular housekeeping functions?|1) protection from the environment, 2) nutrient acquisition, 3) communication, 4) movement, 5) renewal of senescent molecules, 6) molecular catabolism, 7) energy generation.}}

{{hidden|List the cellular compartments and the role in the cell.|1) cytosol = metabolism, transport, protein translation, 2) Mitochondria = energy generation, apoptosis, 3) Rough ER = synthesis of membrane and secreted proteins, 4) Smooth ER / Golgi = protein modification, sorting, catabolism, 5)Nucleus = cell regulation, proliferation, DNA transcription, 6) Endosomes = intracellular transport and export, ingestion of extracellular substances, 7) Lysosomes = cellular catabolism, 8) peroxisomes = very long-chain fatty acid metabolism}}

{{hidden|Describe the basic structure and functions of the cell membrane.| The plasma membrane is composed of a lipid bilayer of phospholipids studded with a variety of proteins and glycoproteins involved in ion and metabolite transport, fluid phase and receptor-mediated uptake of macromolecules, cell-ligand/cell matrix/cell-cell interactions.}}

{{hidden|How are the large complexes in the plasma membrane formed?|They aggregate under the control of chaperone molecules in the RER or by lateral diffusion in the plasma membrane followed by complex formation in situ.}}

{{hidden|What are aquaporins?|Special integral membrane proteins which augment passive water transport in tissues where water is transported in large volumes.}}

{{hidden|How are channel and carrier proteins different?|Channel proteins created hydrophilic pores, permit rapid movement of solutes, restricted by size and charge, where Carrier proteins bind to their specific solutes and undergo a series of conformational changes to transfer the ligand across the membrane, relatively slow transport.}}

{{hidden|What is the "multidrug resistance (MDR) protein"?|A type of transporter ATPases which pumps polar compounds (e.g. chemo drugs) out of cells which may render cancer cells resistant to treatment.}}

{{hidden|What are the two fundamental mechanisms of fluid or macromolecules by the cell (endocytosis)?|1)Caveolae -invaginations of the plasma membrane, 2) Pinocytosis/receptor mediated endocytosis - macromolecules bind to receptor and membranes invaginate around it.}}

{{hidden|What is exocytosis?|It is the opposite process of pinocytosis, where the receptor bound macromolecule is move to the cell surface and released.}}

{{hidden|Describe the difference between phagocytosis and transcytosis.|In phagocytosis microbes are ingested forming phagosomes, which fuse with lysosomes and become phagylosomes, releasing undigested residual material when fusing again with the external membrane, in contrast transcytosis the materials are carried across the cell membrane unaltered.}}

{{hidden|List the three major classes of 3 cytoskeleton proteins.|1) Actin, 2)Intermediate filaments, 3)Microtubules}}

{{hidden|Describe actin.|Actin - 5 to 9nm diam fibrils, G-actin polymerized into F-actin, the form double strands helices, which interact with myosin (filamentous protein).}}

{{hidden|List the various intermediate filaments, which are 10nm in diameter.|1) Lamin A, B, and C (nuclear lamins of all cells, 2) Vimentin (mesenchymal), 3)Desmin (scaffold for actin/myosin), 4) Neurofilaments (axons of neurons), 5) Glial filament protein (glial cells), 6)Cytokeratins (acid and basic and vary based on cell type). }}

{{hidden|Describe microtubules.|Microtubules are 25nm diam fibrils of dimers of a and b tubulin, with a negative end embedded in the centrosome near the nucleus, the + end grows or shrinks as needed. There are kinesins and dyneins motors that move stuff around the cell, also found in cilia and flagella.}}

{{hidden|What is clatharin?|A molecule found in the cell membrane that when the cell membrane invaginates forming a basket like structure.}}

{{hidden|List and describe the 3 main classifications of cell junctions.|1) Tight /occluding junctions - form a high resistance barrier to solute movement, and allows the cell to maintain polarity, 2) anchoring junctions / desmosomes - mechanically attach the cell and their cytoskeleton to other cells and the ECM (hemidesmosome), 3)communicating/gap junctions - mediate the passage of chemical or electrical signals from one cell to another.}}

{{hidden|What is the "unfolded protein response"?| Excess accumulation of misfolded protiens, which exceed the capacity of the ER to edit and degrade them, leads to the the ER stress response (UPR) that triggers cell death through apoptosis.}}

{{hidden|What cell organelle has a reactive hyperplasia with repeated exposure to phenobarbitol catabolism in the cytocrhome p450 system?|Smooth endoplasmic reticulum.}}

{{hidden|List three main functions of mitochondria.|1) Energy generation, 2) intermediate metabolism (instead of ATP make intemediate that can be used to make lipids, nucleic acids, and proteins), 3) Cell death ( necrosis & apoptosis)}}

{{hidden|List and describe the four extracellular cell-cell signaling pathways based on the distance the signal travels.|1)Paracrine (immediate vicinity), 2) Autocrine (cell affecting itself), 3) Synaptic (neurons sending neurotransmitters at synapse), 4) endocrine (signals released elsewhere into bloodstream).}}

{{hidden|What are the two characterizing features of stem cells?|Self renewal and asymmetric division (one daughter cell stays a stem cell)}}

{{hidden|What are the two types of stem cells?|embryonic stem cells (inner cell mass of the blastocyst, totipotent), and tissue/adult stem cells (found in stem cell niches associated with specialized tissues, limited repetoire of differentiation = multipotent)}}

{{hidden|What is the Warburg effect?|Increased cellular uptake of glucose and glutamine, increased glycolysis, and decreased oxidative phosphorylation by the cell.}}

{{hidden|Which CDKI's have selective effects on CDK4 and CDK6?|p15,p16,p17,and p19}}

{{hidden|List some examples of signal transduction pathways.|1) Receptor tyrosine kinases (RTKs), 2) Nonreceptor tyrosine kinase, 3) G-protein coupled receptors, 4) nuclear receptors, 5)Notch family receptors, 6) Wnt protein ligands (Frizzled family receptors).}}

{{hidden|Why does nuclear beta catenin occur in some neoplasms?|When Wnt ligand bins to frizzled it recruits Disheveled, this leads to the disruption of the wnt-ubiquitin complex, this stabilized pool of b-catening is then translocated to the nucleus forming a transcriptional complex}}

{{hidden|On Page 19 there is a table of growth factors involved in regeneration and repair, please review.|}}

{{hidden|Describe the function of cadherin.|}}

{{hidden|What are the functions of the extracellular matrix?|Mechanical support, control of cell proliferation, scaffolding for tissue renewal, establishment of tissue microenvironments}}

{{hidden|What are the two basic forms of the ECM?|interstitial matrix (fibrillar and non fibrillar collagen, fibronectin, elastin, proteoglycans, hyloronate, and other stuff), basement membrane (type IV collagen and laminin) }}

{{hidden|What are the three proteins groups in the ECM?|1) fibrous structural proteins (collagen, elastins), 2) water hydrated gels (proteoglycans and hyaluronan), 3) adhesive glycoproteins (connect ECM to each other and other cells)}}

{{hidden|Describe the structure of a protein that is dependent on vitamin C.|Collagen is composed of 3 seprate polypeptide chains braided into a rope like triple helix, lateral cross linking of the triple helices by lysyl oxidase (requires vitamin C) give it it's tensile strength. }}

{{hidden|List three non-fibrillar collagens.|Type IV -basement membrane, Type IX - Fibrillar associated collagen with interrupted triple helices (FACIT), Type VII (provides anchoring fibrils to basement membrane beneath skin)}}

{{hidden|Which structural protein is associated with Marfan syndrom?|Fibrillin synthetic defects, which wrap the elastin core. }}}}

== Chapter 2: Cellular Responses to Stress and Toxic Insults: Adaptation, Injury and Death ==
{{hidden begin|Title=What are the four aspects of a disease?}}
*1. Etiology
**Genetic - Inherited mutations and disease-associated gene variants, or polymorphisms
**Acquired - Infectious, nutritional, chemical and physical.
*2. Pathogenesis - The sequence of cellular, biochemical, and molecular events that follow the exposure of cells or tissues to an injurious agent.
*3. Morphological changes - The structural alterations in cells or tissues that are either characteristic of a disease or diagnostic of an etiologic process.
*4. Clinical Manifestations - Symptoms and signs of disease, as well as its clinical course and outcome{{hidden end}}

== Chapter 3 ==
== Chapter 4 ==
== Chapter 5 ==
{{hidden|MC cause of spontaneous abortion is ?|<center>[[ A demonstrable chromosomal abnormality.]]</center>}}

{{hidden|1% of all newborn infants possess a gross chromosomal abnormality and 5% of people <25y present with |<center>[[a genetic disease. ]]</center>}}

{{hidden|Mutation|<center>[[permanent change in the DNA, if affect germ cells are transmitted to the progeny ]]</center>}}

{{hidden|List and describe 4 broad categories of human genetic disorders:|<center>[[Disorders related to mutation sin single genes with large effects i. Usually follow classic Mendelian pattern of inheritance
ii. Often highly penetrant (large proportion of pop with gene has disease)
b. Chromosomal disorders
i. Structural or numerical alterations in autosomes and sex chromosomes
ii. Uncommon, high penetrance
c. Complex multigenic disorders
i. Interactions between multiple variant forms of genes and environmental factors (polymorphisms), poly genic means disease when many polymorphism present
d. Single gene disorders with nonclassic patterns of inheritance (not mendelian)
i. Disorders resulting from triplet repeat mutations
ii. Mutations in mitochondrial DNA
iii. Those influenced by genomic imprinting
iv. Those influenced by gonadal mosaicism]]</center>}}

{{hidden|List and describe the possible outcomes of a point mutation in a coding region?|[[a. Missense mutation – pt mutation changes amino acid code, conservative when the amino acid is preserved, non conservative when replaced with another amino acid, b. Nonsense mutation – makes a stop codon ]]</center>}}

{{hidden|List and describe the possible outcomes of point mutation or deletion in a non-coding region.|<center>[[a. Promoters/enhancers – interfere with binding of transcription factors, marker reduction or total lack of transcription, b. Introns – defective splicing > failure to make mature RNA > no translation]]</center>}}

{{hidden|List and describe the possible outcomes of deletions and insertions.|<center>[[a.Small coding: not multiple of three = frameshift, if multiple of 3 than add or del amino acids accordingly, often premature stop codon
i. Tay Sachs disease: 4 base pair insertion in Hexosaminidase A gene ]]}}

{{hidden|List and describe the possible outcomes of trinucleotide repeat mutations.|[[a. Usually G&C, dynamic and increase during gametogenesis, “RNA stutters”,b. Fragile X – CGG 250-4000, Huntinton’s Disease ]]}}

{{hidden|List and describe three examples of inheritance of single gene mutations|[[a. AD – manifested in the heterologous state, one parent of index case is usually affected, males and females affected and both can transmit conditioni. De novo cases may not have affected parentii. Penetrance = fraction of people with gene who have the traitiii. Variable expressivity = those with mutant gene have variety of phenotypesiv. Often age of onset is delayed so can reproduce before die from diseasev. Biochem mechanisms1. Reduced production of a protein or dysfunctional/inactive protein2. Involved in regulation of complex metabolic pathyway subject to feedback inhibition3. Key structural proteins (collagen and cytoskeleton of RBC)a. May be a dominant negative , e.g. osteogenesis imperfecta4. Gain of function are rare, 2 formsa. Increased in proteins normal function (excess enzyme activity)b. Huntinton’s diseas (abn protein accumulates, toxic to neurons)b. ARi. Largest category – both alleles at a locus are mutated1. Expression is uniform, complete penetrance common, early onset, unaffected carrier family members, mostly enzymesc. X Linkedi. All sex linked, and almost all are recessive , if Y Chromosome affected usually infertile males > no progenyii. Male expression b/c hemizygous, daughter carriers with variable phenotype because of lionization of 2nd X e.g G6DPiii. Dominant . vitamin D resistant rickets]]</center>}}

Stopped at P142

== Chapter 6 ==
== Chapter 7 ==
== Chapter 8 ==
== Chapter 9 ==
== Chapter 10 ==
== Chapter 11 ==
== Chapter 12 ==
== Chapter 13 ==
== Chapter 14 ==
== Chapter 15 ==
== Chapter 16 ==
== Chapter 17 ==
== Chapter 18 ==
== Chapter 19 ==
== Chapter 20 ==
== Chapter 21 ==
== Chapter 22 ==
== Chapter 23 ==
== Chapter 24 ==
== Chapter 25 ==
== Chapter 26 ==
== Chapter 27 ==
== Chapter 28 ==
== Chapter 29 ==

Robbins and Cotran 9th Edition Questions

2015-05-27T17:29:41Z

Yuanny: /* Chapter 2: Cellular Responses to Stress and Toxic Insults: Adaptation, Injury and Death */

== Chapter 1: The Cell as a Unit of Health and Disease==

{{hidden| Short Answer Questions |
{{hidden|How much of the human genome is coding and what does it code?|Of the 3.2b basepairs, there are 20,000 genes that comprise about 1.5% of the genome that code for proteins (enzymes, structural components, and signaling molecules used to assemble and maintain all the cells in the body}}

{{hidden|What do we think that the rest of the genome does?|80% of the genome binds proteins, implying that it is involved in regulating gene expression, related to the regulation of gene expression, often in a cell-type specific fashion.}}

{{hidden|List the major classes of functional non-protein-coding sequences found in the human genome.|
*1. Promoter & enhancer
*2. Chromatin binding site structures
*3. non-coding regulatory RNAs
*4. Mobile genetic elements (transposons)
*5. telomeres
*6. centromers. }}

{{hidden|What are the two most common forms of DNA variation in the human genome?|
*1) Single nucleotide polymorphisms (SNPs)
*2) copy number variations (CNVs)}}

{{hidden|What are the possible implications of SNPs.|
*1) regulatory = alters gene expression
*2) Correlation with disease states when in close proximity with altered genes
*3) association used to define linkage disequilibrium,?}}

{{hidden|Define epigenetics.|Heritable changes in gene expression which are not caused by alterations in DNA sequence.}}

{{hidden|List the 6 types of epigenetic changes.|
*1) Histone & histone modifying factors (Histones organize chromatin into heterochromatin and euchromatin
*2) histone methylation
*3) histone acteylation
*4)histone phosphorylation
*5) DNA methylation
*6) Chromatin organizing factors.}}

{{hidden|What is the function of micro-RNA (mi-RNA)?|It does not encode protein, instead they function primarily to modulate the translation of target mRNAs into their corresponding proteins, and are responsible for post-transcriptional silencing of gene expression.}}

{{hidden|What is knockdown technology?|The use of synthetic si-RNA (short RNA sequences) introduced into cells that serve as substrates for Dicer and interact with the RISC complex in a manner analogous to endogenous miRNAs, and are used to study gene function, and are being developed as therapeutic agents to silence pathogenic genes, e.g. oncogenic in neoplasms.}}

{{hidden|What is long non coding RNA?|Lnc-RNA modulate gene expression by binding to regions of chromatin, restricting RNA polymerase access to coding genes within the region, and may exceed the number of mRNA's by 10-20 fold.}}

{{hidden|What is XIST?|XIST is a lnc-RNA which is transcribed from the X-chromosome and plays an essential role in physiologic X chromosome inactivation, though not inactivated itself, it forms a repressive cloak on the X chromosome from which it is transcribed resulting in gene silencing.}}

{{hidden|What are the cellular housekeeping functions?|1) protection from the environment, 2) nutrient acquisition, 3) communication, 4) movement, 5) renewal of senescent molecules, 6) molecular catabolism, 7) energy generation.}}

{{hidden|List the cellular compartments and the role in the cell.|1) cytosol = metabolism, transport, protein translation, 2) Mitochondria = energy generation, apoptosis, 3) Rough ER = synthesis of membrane and secreted proteins, 4) Smooth ER / Golgi = protein modification, sorting, catabolism, 5)Nucleus = cell regulation, proliferation, DNA transcription, 6) Endosomes = intracellular transport and export, ingestion of extracellular substances, 7) Lysosomes = cellular catabolism, 8) peroxisomes = very long-chain fatty acid metabolism}}

{{hidden|Describe the basic structure and functions of the cell membrane.| The plasma membrane is composed of a lipid bilayer of phospholipids studded with a variety of proteins and glycoproteins involved in ion and metabolite transport, fluid phase and receptor-mediated uptake of macromolecules, cell-ligand/cell matrix/cell-cell interactions.}}

{{hidden|How are the large complexes in the plasma membrane formed?|They aggregate under the control of chaperone molecules in the RER or by lateral diffusion in the plasma membrane followed by complex formation in situ.}}

{{hidden|What are aquaporins?|Special integral membrane proteins which augment passive water transport in tissues where water is transported in large volumes.}}

{{hidden|How are channel and carrier proteins different?|Channel proteins created hydrophilic pores, permit rapid movement of solutes, restricted by size and charge, where Carrier proteins bind to their specific solutes and undergo a series of conformational changes to transfer the ligand across the membrane, relatively slow transport.}}

{{hidden|What is the "multidrug resistance (MDR) protein"?|A type of transporter ATPases which pumps polar compounds (e.g. chemo drugs) out of cells which may render cancer cells resistant to treatment.}}

{{hidden|What are the two fundamental mechanisms of fluid or macromolecules by the cell (endocytosis)?|1)Caveolae -invaginations of the plasma membrane, 2) Pinocytosis/receptor mediated endocytosis - macromolecules bind to receptor and membranes invaginate around it.}}

{{hidden|What is exocytosis?|It is the opposite process of pinocytosis, where the receptor bound macromolecule is move to the cell surface and released.}}

{{hidden|Describe the difference between phagocytosis and transcytosis.|In phagocytosis microbes are ingested forming phagosomes, which fuse with lysosomes and become phagylosomes, releasing undigested residual material when fusing again with the external membrane, in contrast transcytosis the materials are carried across the cell membrane unaltered.}}

{{hidden|List the three major classes of 3 cytoskeleton proteins.|1) Actin, 2)Intermediate filaments, 3)Microtubules}}

{{hidden|Describe actin.|Actin - 5 to 9nm diam fibrils, G-actin polymerized into F-actin, the form double strands helices, which interact with myosin (filamentous protein).}}

{{hidden|List the various intermediate filaments, which are 10nm in diameter.|1) Lamin A, B, and C (nuclear lamins of all cells, 2) Vimentin (mesenchymal), 3)Desmin (scaffold for actin/myosin), 4) Neurofilaments (axons of neurons), 5) Glial filament protein (glial cells), 6)Cytokeratins (acid and basic and vary based on cell type). }}

{{hidden|Describe microtubules.|Microtubules are 25nm diam fibrils of dimers of a and b tubulin, with a negative end embedded in the centrosome near the nucleus, the + end grows or shrinks as needed. There are kinesins and dyneins motors that move stuff around the cell, also found in cilia and flagella.}}

{{hidden|What is clatharin?|A molecule found in the cell membrane that when the cell membrane invaginates forming a basket like structure.}}

{{hidden|List and describe the 3 main classifications of cell junctions.|1) Tight /occluding junctions - form a high resistance barrier to solute movement, and allows the cell to maintain polarity, 2) anchoring junctions / desmosomes - mechanically attach the cell and their cytoskeleton to other cells and the ECM (hemidesmosome), 3)communicating/gap junctions - mediate the passage of chemical or electrical signals from one cell to another.}}

{{hidden|What is the "unfolded protein response"?| Excess accumulation of misfolded protiens, which exceed the capacity of the ER to edit and degrade them, leads to the the ER stress response (UPR) that triggers cell death through apoptosis.}}

{{hidden|What cell organelle has a reactive hyperplasia with repeated exposure to phenobarbitol catabolism in the cytocrhome p450 system?|Smooth endoplasmic reticulum.}}

{{hidden|List three main functions of mitochondria.|1) Energy generation, 2) intermediate metabolism (instead of ATP make intemediate that can be used to make lipids, nucleic acids, and proteins), 3) Cell death ( necrosis & apoptosis)}}

{{hidden|List and describe the four extracellular cell-cell signaling pathways based on the distance the signal travels.|1)Paracrine (immediate vicinity), 2) Autocrine (cell affecting itself), 3) Synaptic (neurons sending neurotransmitters at synapse), 4) endocrine (signals released elsewhere into bloodstream).}}

{{hidden|What are the two characterizing features of stem cells?|Self renewal and asymmetric division (one daughter cell stays a stem cell)}}

{{hidden|What are the two types of stem cells?|embryonic stem cells (inner cell mass of the blastocyst, totipotent), and tissue/adult stem cells (found in stem cell niches associated with specialized tissues, limited repetoire of differentiation = multipotent)}}

{{hidden|What is the Warburg effect?|Increased cellular uptake of glucose and glutamine, increased glycolysis, and decreased oxidative phosphorylation by the cell.}}

{{hidden|Which CDKI's have selective effects on CDK4 and CDK6?|p15,p16,p17,and p19}}

{{hidden|List some examples of signal transduction pathways.|1) Receptor tyrosine kinases (RTKs), 2) Nonreceptor tyrosine kinase, 3) G-protein coupled receptors, 4) nuclear receptors, 5)Notch family receptors, 6) Wnt protein ligands (Frizzled family receptors).}}

{{hidden|Why does nuclear beta catenin occur in some neoplasms?|When Wnt ligand bins to frizzled it recruits Disheveled, this leads to the disruption of the wnt-ubiquitin complex, this stabilized pool of b-catening is then translocated to the nucleus forming a transcriptional complex}}

{{hidden|On Page 19 there is a table of growth factors involved in regeneration and repair, please review.|}}

{{hidden|Describe the function of cadherin.|}}

{{hidden|What are the functions of the extracellular matrix?|Mechanical support, control of cell proliferation, scaffolding for tissue renewal, establishment of tissue microenvironments}}

{{hidden|What are the two basic forms of the ECM?|interstitial matrix (fibrillar and non fibrillar collagen, fibronectin, elastin, proteoglycans, hyloronate, and other stuff), basement membrane (type IV collagen and laminin) }}

{{hidden|What are the three proteins groups in the ECM?|1) fibrous structural proteins (collagen, elastins), 2) water hydrated gels (proteoglycans and hyaluronan), 3) adhesive glycoproteins (connect ECM to each other and other cells)}}

{{hidden|Describe the structure of a protein that is dependent on vitamin C.|Collagen is composed of 3 seprate polypeptide chains braided into a rope like triple helix, lateral cross linking of the triple helices by lysyl oxidase (requires vitamin C) give it it's tensile strength. }}

{{hidden|List three non-fibrillar collagens.|Type IV -basement membrane, Type IX - Fibrillar associated collagen with interrupted triple helices (FACIT), Type VII (provides anchoring fibrils to basement membrane beneath skin)}}

{{hidden|Which structural protein is associated with Marfan syndrom?|Fibrillin synthetic defects, which wrap the elastin core. }}}}

== Chapter 2: Cellular Responses to Stress and Toxic Insults: Adaptation, Injury and Death ==
{{hidden begin|Title=What are the four aspects of a disease?|
*1. Etiology
**Genetic - Inherited mutations and disease-associated gene variants, or polymorphisms
**Acquired - Infectious, nutritional, chemical and physical.
*2. Pathogenesis - The sequence of cellular, biochemical, and molecular events that follow the exposure of cells or tissues to an injurious agent.
*3. Morphological changes - The structural alterations in cells or tissues that are either characteristic of a disease or diagnostic of an etiologic process.
*4. Clinical Manifestations - Symptoms and signs of disease, as well as its clinical course and outcome{{hidden end}}

}}

== Chapter 3 ==
== Chapter 4 ==
== Chapter 5 ==
{{hidden|MC cause of spontaneous abortion is ?|<center>[[ A demonstrable chromosomal abnormality.]]</center>}}

{{hidden|1% of all newborn infants possess a gross chromosomal abnormality and 5% of people <25y present with |<center>[[a genetic disease. ]]</center>}}

{{hidden|Mutation|<center>[[permanent change in the DNA, if affect germ cells are transmitted to the progeny ]]</center>}}

{{hidden|List and describe 4 broad categories of human genetic disorders:|<center>[[Disorders related to mutation sin single genes with large effects i. Usually follow classic Mendelian pattern of inheritance
ii. Often highly penetrant (large proportion of pop with gene has disease)
b. Chromosomal disorders
i. Structural or numerical alterations in autosomes and sex chromosomes
ii. Uncommon, high penetrance
c. Complex multigenic disorders
i. Interactions between multiple variant forms of genes and environmental factors (polymorphisms), poly genic means disease when many polymorphism present
d. Single gene disorders with nonclassic patterns of inheritance (not mendelian)
i. Disorders resulting from triplet repeat mutations
ii. Mutations in mitochondrial DNA
iii. Those influenced by genomic imprinting
iv. Those influenced by gonadal mosaicism]]</center>}}

{{hidden|List and describe the possible outcomes of a point mutation in a coding region?|[[a. Missense mutation – pt mutation changes amino acid code, conservative when the amino acid is preserved, non conservative when replaced with another amino acid, b. Nonsense mutation – makes a stop codon ]]</center>}}

{{hidden|List and describe the possible outcomes of point mutation or deletion in a non-coding region.|<center>[[a. Promoters/enhancers – interfere with binding of transcription factors, marker reduction or total lack of transcription, b. Introns – defective splicing > failure to make mature RNA > no translation]]</center>}}

{{hidden|List and describe the possible outcomes of deletions and insertions.|<center>[[a.Small coding: not multiple of three = frameshift, if multiple of 3 than add or del amino acids accordingly, often premature stop codon
i. Tay Sachs disease: 4 base pair insertion in Hexosaminidase A gene ]]}}

{{hidden|List and describe the possible outcomes of trinucleotide repeat mutations.|[[a. Usually G&C, dynamic and increase during gametogenesis, “RNA stutters”,b. Fragile X – CGG 250-4000, Huntinton’s Disease ]]}}

{{hidden|List and describe three examples of inheritance of single gene mutations|[[a. AD – manifested in the heterologous state, one parent of index case is usually affected, males and females affected and both can transmit conditioni. De novo cases may not have affected parentii. Penetrance = fraction of people with gene who have the traitiii. Variable expressivity = those with mutant gene have variety of phenotypesiv. Often age of onset is delayed so can reproduce before die from diseasev. Biochem mechanisms1. Reduced production of a protein or dysfunctional/inactive protein2. Involved in regulation of complex metabolic pathyway subject to feedback inhibition3. Key structural proteins (collagen and cytoskeleton of RBC)a. May be a dominant negative , e.g. osteogenesis imperfecta4. Gain of function are rare, 2 formsa. Increased in proteins normal function (excess enzyme activity)b. Huntinton’s diseas (abn protein accumulates, toxic to neurons)b. ARi. Largest category – both alleles at a locus are mutated1. Expression is uniform, complete penetrance common, early onset, unaffected carrier family members, mostly enzymesc. X Linkedi. All sex linked, and almost all are recessive , if Y Chromosome affected usually infertile males > no progenyii. Male expression b/c hemizygous, daughter carriers with variable phenotype because of lionization of 2nd X e.g G6DPiii. Dominant . vitamin D resistant rickets]]</center>}}

Stopped at P142

== Chapter 6 ==
== Chapter 7 ==
== Chapter 8 ==
== Chapter 9 ==
== Chapter 10 ==
== Chapter 11 ==
== Chapter 12 ==
== Chapter 13 ==
== Chapter 14 ==
== Chapter 15 ==
== Chapter 16 ==
== Chapter 17 ==
== Chapter 18 ==
== Chapter 19 ==
== Chapter 20 ==
== Chapter 21 ==
== Chapter 22 ==
== Chapter 23 ==
== Chapter 24 ==
== Chapter 25 ==
== Chapter 26 ==
== Chapter 27 ==
== Chapter 28 ==
== Chapter 29 ==

Robbins and Cotran 9th Edition Questions

2015-05-27T17:29:03Z

Yuanny: /* Chapter 2: Cellular Responses to Stress and Toxic Insults: Adaptation, Injury and Death */

== Chapter 1: The Cell as a Unit of Health and Disease==

{{hidden| Short Answer Questions |
{{hidden|How much of the human genome is coding and what does it code?|Of the 3.2b basepairs, there are 20,000 genes that comprise about 1.5% of the genome that code for proteins (enzymes, structural components, and signaling molecules used to assemble and maintain all the cells in the body}}

{{hidden|What do we think that the rest of the genome does?|80% of the genome binds proteins, implying that it is involved in regulating gene expression, related to the regulation of gene expression, often in a cell-type specific fashion.}}

{{hidden|List the major classes of functional non-protein-coding sequences found in the human genome.|
*1. Promoter & enhancer
*2. Chromatin binding site structures
*3. non-coding regulatory RNAs
*4. Mobile genetic elements (transposons)
*5. telomeres
*6. centromers. }}

{{hidden|What are the two most common forms of DNA variation in the human genome?|
*1) Single nucleotide polymorphisms (SNPs)
*2) copy number variations (CNVs)}}

{{hidden|What are the possible implications of SNPs.|
*1) regulatory = alters gene expression
*2) Correlation with disease states when in close proximity with altered genes
*3) association used to define linkage disequilibrium,?}}

{{hidden|Define epigenetics.|Heritable changes in gene expression which are not caused by alterations in DNA sequence.}}

{{hidden|List the 6 types of epigenetic changes.|
*1) Histone & histone modifying factors (Histones organize chromatin into heterochromatin and euchromatin
*2) histone methylation
*3) histone acteylation
*4)histone phosphorylation
*5) DNA methylation
*6) Chromatin organizing factors.}}

{{hidden|What is the function of micro-RNA (mi-RNA)?|It does not encode protein, instead they function primarily to modulate the translation of target mRNAs into their corresponding proteins, and are responsible for post-transcriptional silencing of gene expression.}}

{{hidden|What is knockdown technology?|The use of synthetic si-RNA (short RNA sequences) introduced into cells that serve as substrates for Dicer and interact with the RISC complex in a manner analogous to endogenous miRNAs, and are used to study gene function, and are being developed as therapeutic agents to silence pathogenic genes, e.g. oncogenic in neoplasms.}}

{{hidden|What is long non coding RNA?|Lnc-RNA modulate gene expression by binding to regions of chromatin, restricting RNA polymerase access to coding genes within the region, and may exceed the number of mRNA's by 10-20 fold.}}

{{hidden|What is XIST?|XIST is a lnc-RNA which is transcribed from the X-chromosome and plays an essential role in physiologic X chromosome inactivation, though not inactivated itself, it forms a repressive cloak on the X chromosome from which it is transcribed resulting in gene silencing.}}

{{hidden|What are the cellular housekeeping functions?|1) protection from the environment, 2) nutrient acquisition, 3) communication, 4) movement, 5) renewal of senescent molecules, 6) molecular catabolism, 7) energy generation.}}

{{hidden|List the cellular compartments and the role in the cell.|1) cytosol = metabolism, transport, protein translation, 2) Mitochondria = energy generation, apoptosis, 3) Rough ER = synthesis of membrane and secreted proteins, 4) Smooth ER / Golgi = protein modification, sorting, catabolism, 5)Nucleus = cell regulation, proliferation, DNA transcription, 6) Endosomes = intracellular transport and export, ingestion of extracellular substances, 7) Lysosomes = cellular catabolism, 8) peroxisomes = very long-chain fatty acid metabolism}}

{{hidden|Describe the basic structure and functions of the cell membrane.| The plasma membrane is composed of a lipid bilayer of phospholipids studded with a variety of proteins and glycoproteins involved in ion and metabolite transport, fluid phase and receptor-mediated uptake of macromolecules, cell-ligand/cell matrix/cell-cell interactions.}}

{{hidden|How are the large complexes in the plasma membrane formed?|They aggregate under the control of chaperone molecules in the RER or by lateral diffusion in the plasma membrane followed by complex formation in situ.}}

{{hidden|What are aquaporins?|Special integral membrane proteins which augment passive water transport in tissues where water is transported in large volumes.}}

{{hidden|How are channel and carrier proteins different?|Channel proteins created hydrophilic pores, permit rapid movement of solutes, restricted by size and charge, where Carrier proteins bind to their specific solutes and undergo a series of conformational changes to transfer the ligand across the membrane, relatively slow transport.}}

{{hidden|What is the "multidrug resistance (MDR) protein"?|A type of transporter ATPases which pumps polar compounds (e.g. chemo drugs) out of cells which may render cancer cells resistant to treatment.}}

{{hidden|What are the two fundamental mechanisms of fluid or macromolecules by the cell (endocytosis)?|1)Caveolae -invaginations of the plasma membrane, 2) Pinocytosis/receptor mediated endocytosis - macromolecules bind to receptor and membranes invaginate around it.}}

{{hidden|What is exocytosis?|It is the opposite process of pinocytosis, where the receptor bound macromolecule is move to the cell surface and released.}}

{{hidden|Describe the difference between phagocytosis and transcytosis.|In phagocytosis microbes are ingested forming phagosomes, which fuse with lysosomes and become phagylosomes, releasing undigested residual material when fusing again with the external membrane, in contrast transcytosis the materials are carried across the cell membrane unaltered.}}

{{hidden|List the three major classes of 3 cytoskeleton proteins.|1) Actin, 2)Intermediate filaments, 3)Microtubules}}

{{hidden|Describe actin.|Actin - 5 to 9nm diam fibrils, G-actin polymerized into F-actin, the form double strands helices, which interact with myosin (filamentous protein).}}

{{hidden|List the various intermediate filaments, which are 10nm in diameter.|1) Lamin A, B, and C (nuclear lamins of all cells, 2) Vimentin (mesenchymal), 3)Desmin (scaffold for actin/myosin), 4) Neurofilaments (axons of neurons), 5) Glial filament protein (glial cells), 6)Cytokeratins (acid and basic and vary based on cell type). }}

{{hidden|Describe microtubules.|Microtubules are 25nm diam fibrils of dimers of a and b tubulin, with a negative end embedded in the centrosome near the nucleus, the + end grows or shrinks as needed. There are kinesins and dyneins motors that move stuff around the cell, also found in cilia and flagella.}}

{{hidden|What is clatharin?|A molecule found in the cell membrane that when the cell membrane invaginates forming a basket like structure.}}

{{hidden|List and describe the 3 main classifications of cell junctions.|1) Tight /occluding junctions - form a high resistance barrier to solute movement, and allows the cell to maintain polarity, 2) anchoring junctions / desmosomes - mechanically attach the cell and their cytoskeleton to other cells and the ECM (hemidesmosome), 3)communicating/gap junctions - mediate the passage of chemical or electrical signals from one cell to another.}}

{{hidden|What is the "unfolded protein response"?| Excess accumulation of misfolded protiens, which exceed the capacity of the ER to edit and degrade them, leads to the the ER stress response (UPR) that triggers cell death through apoptosis.}}

{{hidden|What cell organelle has a reactive hyperplasia with repeated exposure to phenobarbitol catabolism in the cytocrhome p450 system?|Smooth endoplasmic reticulum.}}

{{hidden|List three main functions of mitochondria.|1) Energy generation, 2) intermediate metabolism (instead of ATP make intemediate that can be used to make lipids, nucleic acids, and proteins), 3) Cell death ( necrosis & apoptosis)}}

{{hidden|List and describe the four extracellular cell-cell signaling pathways based on the distance the signal travels.|1)Paracrine (immediate vicinity), 2) Autocrine (cell affecting itself), 3) Synaptic (neurons sending neurotransmitters at synapse), 4) endocrine (signals released elsewhere into bloodstream).}}

{{hidden|What are the two characterizing features of stem cells?|Self renewal and asymmetric division (one daughter cell stays a stem cell)}}

{{hidden|What are the two types of stem cells?|embryonic stem cells (inner cell mass of the blastocyst, totipotent), and tissue/adult stem cells (found in stem cell niches associated with specialized tissues, limited repetoire of differentiation = multipotent)}}

{{hidden|What is the Warburg effect?|Increased cellular uptake of glucose and glutamine, increased glycolysis, and decreased oxidative phosphorylation by the cell.}}

{{hidden|Which CDKI's have selective effects on CDK4 and CDK6?|p15,p16,p17,and p19}}

{{hidden|List some examples of signal transduction pathways.|1) Receptor tyrosine kinases (RTKs), 2) Nonreceptor tyrosine kinase, 3) G-protein coupled receptors, 4) nuclear receptors, 5)Notch family receptors, 6) Wnt protein ligands (Frizzled family receptors).}}

{{hidden|Why does nuclear beta catenin occur in some neoplasms?|When Wnt ligand bins to frizzled it recruits Disheveled, this leads to the disruption of the wnt-ubiquitin complex, this stabilized pool of b-catening is then translocated to the nucleus forming a transcriptional complex}}

{{hidden|On Page 19 there is a table of growth factors involved in regeneration and repair, please review.|}}

{{hidden|Describe the function of cadherin.|}}

{{hidden|What are the functions of the extracellular matrix?|Mechanical support, control of cell proliferation, scaffolding for tissue renewal, establishment of tissue microenvironments}}

{{hidden|What are the two basic forms of the ECM?|interstitial matrix (fibrillar and non fibrillar collagen, fibronectin, elastin, proteoglycans, hyloronate, and other stuff), basement membrane (type IV collagen and laminin) }}

{{hidden|What are the three proteins groups in the ECM?|1) fibrous structural proteins (collagen, elastins), 2) water hydrated gels (proteoglycans and hyaluronan), 3) adhesive glycoproteins (connect ECM to each other and other cells)}}

{{hidden|Describe the structure of a protein that is dependent on vitamin C.|Collagen is composed of 3 seprate polypeptide chains braided into a rope like triple helix, lateral cross linking of the triple helices by lysyl oxidase (requires vitamin C) give it it's tensile strength. }}

{{hidden|List three non-fibrillar collagens.|Type IV -basement membrane, Type IX - Fibrillar associated collagen with interrupted triple helices (FACIT), Type VII (provides anchoring fibrils to basement membrane beneath skin)}}

{{hidden|Which structural protein is associated with Marfan syndrom?|Fibrillin synthetic defects, which wrap the elastin core. }}}}

== Chapter 2: Cellular Responses to Stress and Toxic Insults: Adaptation, Injury and Death ==
{{hidden begin|title=Short Answer Questions|}}
{{hidden|What are the four aspects of a disease?|
*1. Etiology
**Genetic - Inherited mutations and disease-associated gene variants, or polymorphisms
**Acquired - Infectious, nutritional, chemical and physical.
*2. Pathogenesis - The sequence of cellular, biochemical, and molecular events that follow the exposure of cells or tissues to an injurious agent.
*3. Morphological changes - The structural alterations in cells or tissues that are either characteristic of a disease or diagnostic of an etiologic process.
*4. Clinical Manifestations - Symptoms and signs of disease, as well as its clinical course and outcome}}{{hidden end}}

}}

== Chapter 3 ==
== Chapter 4 ==
== Chapter 5 ==
{{hidden|MC cause of spontaneous abortion is ?|<center>[[ A demonstrable chromosomal abnormality.]]</center>}}

{{hidden|1% of all newborn infants possess a gross chromosomal abnormality and 5% of people <25y present with |<center>[[a genetic disease. ]]</center>}}

{{hidden|Mutation|<center>[[permanent change in the DNA, if affect germ cells are transmitted to the progeny ]]</center>}}

{{hidden|List and describe 4 broad categories of human genetic disorders:|<center>[[Disorders related to mutation sin single genes with large effects i. Usually follow classic Mendelian pattern of inheritance
ii. Often highly penetrant (large proportion of pop with gene has disease)
b. Chromosomal disorders
i. Structural or numerical alterations in autosomes and sex chromosomes
ii. Uncommon, high penetrance
c. Complex multigenic disorders
i. Interactions between multiple variant forms of genes and environmental factors (polymorphisms), poly genic means disease when many polymorphism present
d. Single gene disorders with nonclassic patterns of inheritance (not mendelian)
i. Disorders resulting from triplet repeat mutations
ii. Mutations in mitochondrial DNA
iii. Those influenced by genomic imprinting
iv. Those influenced by gonadal mosaicism]]</center>}}

{{hidden|List and describe the possible outcomes of a point mutation in a coding region?|[[a. Missense mutation – pt mutation changes amino acid code, conservative when the amino acid is preserved, non conservative when replaced with another amino acid, b. Nonsense mutation – makes a stop codon ]]</center>}}

{{hidden|List and describe the possible outcomes of point mutation or deletion in a non-coding region.|<center>[[a. Promoters/enhancers – interfere with binding of transcription factors, marker reduction or total lack of transcription, b. Introns – defective splicing > failure to make mature RNA > no translation]]</center>}}

{{hidden|List and describe the possible outcomes of deletions and insertions.|<center>[[a.Small coding: not multiple of three = frameshift, if multiple of 3 than add or del amino acids accordingly, often premature stop codon
i. Tay Sachs disease: 4 base pair insertion in Hexosaminidase A gene ]]}}

{{hidden|List and describe the possible outcomes of trinucleotide repeat mutations.|[[a. Usually G&C, dynamic and increase during gametogenesis, “RNA stutters”,b. Fragile X – CGG 250-4000, Huntinton’s Disease ]]}}

{{hidden|List and describe three examples of inheritance of single gene mutations|[[a. AD – manifested in the heterologous state, one parent of index case is usually affected, males and females affected and both can transmit conditioni. De novo cases may not have affected parentii. Penetrance = fraction of people with gene who have the traitiii. Variable expressivity = those with mutant gene have variety of phenotypesiv. Often age of onset is delayed so can reproduce before die from diseasev. Biochem mechanisms1. Reduced production of a protein or dysfunctional/inactive protein2. Involved in regulation of complex metabolic pathyway subject to feedback inhibition3. Key structural proteins (collagen and cytoskeleton of RBC)a. May be a dominant negative , e.g. osteogenesis imperfecta4. Gain of function are rare, 2 formsa. Increased in proteins normal function (excess enzyme activity)b. Huntinton’s diseas (abn protein accumulates, toxic to neurons)b. ARi. Largest category – both alleles at a locus are mutated1. Expression is uniform, complete penetrance common, early onset, unaffected carrier family members, mostly enzymesc. X Linkedi. All sex linked, and almost all are recessive , if Y Chromosome affected usually infertile males > no progenyii. Male expression b/c hemizygous, daughter carriers with variable phenotype because of lionization of 2nd X e.g G6DPiii. Dominant . vitamin D resistant rickets]]</center>}}

Stopped at P142

== Chapter 6 ==
== Chapter 7 ==
== Chapter 8 ==
== Chapter 9 ==
== Chapter 10 ==
== Chapter 11 ==
== Chapter 12 ==
== Chapter 13 ==
== Chapter 14 ==
== Chapter 15 ==
== Chapter 16 ==
== Chapter 17 ==
== Chapter 18 ==
== Chapter 19 ==
== Chapter 20 ==
== Chapter 21 ==
== Chapter 22 ==
== Chapter 23 ==
== Chapter 24 ==
== Chapter 25 ==
== Chapter 26 ==
== Chapter 27 ==
== Chapter 28 ==
== Chapter 29 ==

Robbins and Cotran 9th Edition Questions

2015-05-27T17:27:15Z

Yuanny: /* Chapter 1: The Cell as a Unit of Health and Disease */

== Chapter 1: The Cell as a Unit of Health and Disease==

{{hidden| Short Answer Questions |
{{hidden|How much of the human genome is coding and what does it code?|Of the 3.2b basepairs, there are 20,000 genes that comprise about 1.5% of the genome that code for proteins (enzymes, structural components, and signaling molecules used to assemble and maintain all the cells in the body}}

{{hidden|What do we think that the rest of the genome does?|80% of the genome binds proteins, implying that it is involved in regulating gene expression, related to the regulation of gene expression, often in a cell-type specific fashion.}}

{{hidden|List the major classes of functional non-protein-coding sequences found in the human genome.|
*1. Promoter & enhancer
*2. Chromatin binding site structures
*3. non-coding regulatory RNAs
*4. Mobile genetic elements (transposons)
*5. telomeres
*6. centromers. }}

{{hidden|What are the two most common forms of DNA variation in the human genome?|
*1) Single nucleotide polymorphisms (SNPs)
*2) copy number variations (CNVs)}}

{{hidden|What are the possible implications of SNPs.|
*1) regulatory = alters gene expression
*2) Correlation with disease states when in close proximity with altered genes
*3) association used to define linkage disequilibrium,?}}

{{hidden|Define epigenetics.|Heritable changes in gene expression which are not caused by alterations in DNA sequence.}}

{{hidden|List the 6 types of epigenetic changes.|
*1) Histone & histone modifying factors (Histones organize chromatin into heterochromatin and euchromatin
*2) histone methylation
*3) histone acteylation
*4)histone phosphorylation
*5) DNA methylation
*6) Chromatin organizing factors.}}

{{hidden|What is the function of micro-RNA (mi-RNA)?|It does not encode protein, instead they function primarily to modulate the translation of target mRNAs into their corresponding proteins, and are responsible for post-transcriptional silencing of gene expression.}}

{{hidden|What is knockdown technology?|The use of synthetic si-RNA (short RNA sequences) introduced into cells that serve as substrates for Dicer and interact with the RISC complex in a manner analogous to endogenous miRNAs, and are used to study gene function, and are being developed as therapeutic agents to silence pathogenic genes, e.g. oncogenic in neoplasms.}}

{{hidden|What is long non coding RNA?|Lnc-RNA modulate gene expression by binding to regions of chromatin, restricting RNA polymerase access to coding genes within the region, and may exceed the number of mRNA's by 10-20 fold.}}

{{hidden|What is XIST?|XIST is a lnc-RNA which is transcribed from the X-chromosome and plays an essential role in physiologic X chromosome inactivation, though not inactivated itself, it forms a repressive cloak on the X chromosome from which it is transcribed resulting in gene silencing.}}

{{hidden|What are the cellular housekeeping functions?|1) protection from the environment, 2) nutrient acquisition, 3) communication, 4) movement, 5) renewal of senescent molecules, 6) molecular catabolism, 7) energy generation.}}

{{hidden|List the cellular compartments and the role in the cell.|1) cytosol = metabolism, transport, protein translation, 2) Mitochondria = energy generation, apoptosis, 3) Rough ER = synthesis of membrane and secreted proteins, 4) Smooth ER / Golgi = protein modification, sorting, catabolism, 5)Nucleus = cell regulation, proliferation, DNA transcription, 6) Endosomes = intracellular transport and export, ingestion of extracellular substances, 7) Lysosomes = cellular catabolism, 8) peroxisomes = very long-chain fatty acid metabolism}}

{{hidden|Describe the basic structure and functions of the cell membrane.| The plasma membrane is composed of a lipid bilayer of phospholipids studded with a variety of proteins and glycoproteins involved in ion and metabolite transport, fluid phase and receptor-mediated uptake of macromolecules, cell-ligand/cell matrix/cell-cell interactions.}}

{{hidden|How are the large complexes in the plasma membrane formed?|They aggregate under the control of chaperone molecules in the RER or by lateral diffusion in the plasma membrane followed by complex formation in situ.}}

{{hidden|What are aquaporins?|Special integral membrane proteins which augment passive water transport in tissues where water is transported in large volumes.}}

{{hidden|How are channel and carrier proteins different?|Channel proteins created hydrophilic pores, permit rapid movement of solutes, restricted by size and charge, where Carrier proteins bind to their specific solutes and undergo a series of conformational changes to transfer the ligand across the membrane, relatively slow transport.}}

{{hidden|What is the "multidrug resistance (MDR) protein"?|A type of transporter ATPases which pumps polar compounds (e.g. chemo drugs) out of cells which may render cancer cells resistant to treatment.}}

{{hidden|What are the two fundamental mechanisms of fluid or macromolecules by the cell (endocytosis)?|1)Caveolae -invaginations of the plasma membrane, 2) Pinocytosis/receptor mediated endocytosis - macromolecules bind to receptor and membranes invaginate around it.}}

{{hidden|What is exocytosis?|It is the opposite process of pinocytosis, where the receptor bound macromolecule is move to the cell surface and released.}}

{{hidden|Describe the difference between phagocytosis and transcytosis.|In phagocytosis microbes are ingested forming phagosomes, which fuse with lysosomes and become phagylosomes, releasing undigested residual material when fusing again with the external membrane, in contrast transcytosis the materials are carried across the cell membrane unaltered.}}

{{hidden|List the three major classes of 3 cytoskeleton proteins.|1) Actin, 2)Intermediate filaments, 3)Microtubules}}

{{hidden|Describe actin.|Actin - 5 to 9nm diam fibrils, G-actin polymerized into F-actin, the form double strands helices, which interact with myosin (filamentous protein).}}

{{hidden|List the various intermediate filaments, which are 10nm in diameter.|1) Lamin A, B, and C (nuclear lamins of all cells, 2) Vimentin (mesenchymal), 3)Desmin (scaffold for actin/myosin), 4) Neurofilaments (axons of neurons), 5) Glial filament protein (glial cells), 6)Cytokeratins (acid and basic and vary based on cell type). }}

{{hidden|Describe microtubules.|Microtubules are 25nm diam fibrils of dimers of a and b tubulin, with a negative end embedded in the centrosome near the nucleus, the + end grows or shrinks as needed. There are kinesins and dyneins motors that move stuff around the cell, also found in cilia and flagella.}}

{{hidden|What is clatharin?|A molecule found in the cell membrane that when the cell membrane invaginates forming a basket like structure.}}

{{hidden|List and describe the 3 main classifications of cell junctions.|1) Tight /occluding junctions - form a high resistance barrier to solute movement, and allows the cell to maintain polarity, 2) anchoring junctions / desmosomes - mechanically attach the cell and their cytoskeleton to other cells and the ECM (hemidesmosome), 3)communicating/gap junctions - mediate the passage of chemical or electrical signals from one cell to another.}}

{{hidden|What is the "unfolded protein response"?| Excess accumulation of misfolded protiens, which exceed the capacity of the ER to edit and degrade them, leads to the the ER stress response (UPR) that triggers cell death through apoptosis.}}

{{hidden|What cell organelle has a reactive hyperplasia with repeated exposure to phenobarbitol catabolism in the cytocrhome p450 system?|Smooth endoplasmic reticulum.}}

{{hidden|List three main functions of mitochondria.|1) Energy generation, 2) intermediate metabolism (instead of ATP make intemediate that can be used to make lipids, nucleic acids, and proteins), 3) Cell death ( necrosis & apoptosis)}}

{{hidden|List and describe the four extracellular cell-cell signaling pathways based on the distance the signal travels.|1)Paracrine (immediate vicinity), 2) Autocrine (cell affecting itself), 3) Synaptic (neurons sending neurotransmitters at synapse), 4) endocrine (signals released elsewhere into bloodstream).}}

{{hidden|What are the two characterizing features of stem cells?|Self renewal and asymmetric division (one daughter cell stays a stem cell)}}

{{hidden|What are the two types of stem cells?|embryonic stem cells (inner cell mass of the blastocyst, totipotent), and tissue/adult stem cells (found in stem cell niches associated with specialized tissues, limited repetoire of differentiation = multipotent)}}

{{hidden|What is the Warburg effect?|Increased cellular uptake of glucose and glutamine, increased glycolysis, and decreased oxidative phosphorylation by the cell.}}

{{hidden|Which CDKI's have selective effects on CDK4 and CDK6?|p15,p16,p17,and p19}}

{{hidden|List some examples of signal transduction pathways.|1) Receptor tyrosine kinases (RTKs), 2) Nonreceptor tyrosine kinase, 3) G-protein coupled receptors, 4) nuclear receptors, 5)Notch family receptors, 6) Wnt protein ligands (Frizzled family receptors).}}

{{hidden|Why does nuclear beta catenin occur in some neoplasms?|When Wnt ligand bins to frizzled it recruits Disheveled, this leads to the disruption of the wnt-ubiquitin complex, this stabilized pool of b-catening is then translocated to the nucleus forming a transcriptional complex}}

{{hidden|On Page 19 there is a table of growth factors involved in regeneration and repair, please review.|}}

{{hidden|Describe the function of cadherin.|}}

{{hidden|What are the functions of the extracellular matrix?|Mechanical support, control of cell proliferation, scaffolding for tissue renewal, establishment of tissue microenvironments}}

{{hidden|What are the two basic forms of the ECM?|interstitial matrix (fibrillar and non fibrillar collagen, fibronectin, elastin, proteoglycans, hyloronate, and other stuff), basement membrane (type IV collagen and laminin) }}

{{hidden|What are the three proteins groups in the ECM?|1) fibrous structural proteins (collagen, elastins), 2) water hydrated gels (proteoglycans and hyaluronan), 3) adhesive glycoproteins (connect ECM to each other and other cells)}}

{{hidden|Describe the structure of a protein that is dependent on vitamin C.|Collagen is composed of 3 seprate polypeptide chains braided into a rope like triple helix, lateral cross linking of the triple helices by lysyl oxidase (requires vitamin C) give it it's tensile strength. }}

{{hidden|List three non-fibrillar collagens.|Type IV -basement membrane, Type IX - Fibrillar associated collagen with interrupted triple helices (FACIT), Type VII (provides anchoring fibrils to basement membrane beneath skin)}}

{{hidden|Which structural protein is associated with Marfan syndrom?|Fibrillin synthetic defects, which wrap the elastin core. }}}}

== Chapter 2: Cellular Responses to Stress and Toxic Insults: Adaptation, Injury and Death ==
{{hidden|Short Answer Questions|
{{hidden|What are the four aspects of a disease?|
*1. Etiology
**Genetic - Inherited mutations and disease-associated gene variants, or polymorphisms
**Acquired - Infectious, nutritional, chemical and physical.
*2. Pathogenesis - The sequence of cellular, biochemical, and molecular events that follow the exposure of cells or tissues to an injurious agent.
*3. Morphological changes - The structural alterations in cells or tissues that are either characteristic of a disease or diagnostic of an etiologic process.
*4. Clinical Manifestations - Symptoms and signs of disease, as well as its clinical course and outcome}}

}}

== Chapter 3 ==
== Chapter 4 ==
== Chapter 5 ==
{{hidden|MC cause of spontaneous abortion is ?|<center>[[ A demonstrable chromosomal abnormality.]]</center>}}

{{hidden|1% of all newborn infants possess a gross chromosomal abnormality and 5% of people <25y present with |<center>[[a genetic disease. ]]</center>}}

{{hidden|Mutation|<center>[[permanent change in the DNA, if affect germ cells are transmitted to the progeny ]]</center>}}

{{hidden|List and describe 4 broad categories of human genetic disorders:|<center>[[Disorders related to mutation sin single genes with large effects i. Usually follow classic Mendelian pattern of inheritance
ii. Often highly penetrant (large proportion of pop with gene has disease)
b. Chromosomal disorders
i. Structural or numerical alterations in autosomes and sex chromosomes
ii. Uncommon, high penetrance
c. Complex multigenic disorders
i. Interactions between multiple variant forms of genes and environmental factors (polymorphisms), poly genic means disease when many polymorphism present
d. Single gene disorders with nonclassic patterns of inheritance (not mendelian)
i. Disorders resulting from triplet repeat mutations
ii. Mutations in mitochondrial DNA
iii. Those influenced by genomic imprinting
iv. Those influenced by gonadal mosaicism]]</center>}}

{{hidden|List and describe the possible outcomes of a point mutation in a coding region?|[[a. Missense mutation – pt mutation changes amino acid code, conservative when the amino acid is preserved, non conservative when replaced with another amino acid, b. Nonsense mutation – makes a stop codon ]]</center>}}

{{hidden|List and describe the possible outcomes of point mutation or deletion in a non-coding region.|<center>[[a. Promoters/enhancers – interfere with binding of transcription factors, marker reduction or total lack of transcription, b. Introns – defective splicing > failure to make mature RNA > no translation]]</center>}}

{{hidden|List and describe the possible outcomes of deletions and insertions.|<center>[[a.Small coding: not multiple of three = frameshift, if multiple of 3 than add or del amino acids accordingly, often premature stop codon
i. Tay Sachs disease: 4 base pair insertion in Hexosaminidase A gene ]]}}

{{hidden|List and describe the possible outcomes of trinucleotide repeat mutations.|[[a. Usually G&C, dynamic and increase during gametogenesis, “RNA stutters”,b. Fragile X – CGG 250-4000, Huntinton’s Disease ]]}}

{{hidden|List and describe three examples of inheritance of single gene mutations|[[a. AD – manifested in the heterologous state, one parent of index case is usually affected, males and females affected and both can transmit conditioni. De novo cases may not have affected parentii. Penetrance = fraction of people with gene who have the traitiii. Variable expressivity = those with mutant gene have variety of phenotypesiv. Often age of onset is delayed so can reproduce before die from diseasev. Biochem mechanisms1. Reduced production of a protein or dysfunctional/inactive protein2. Involved in regulation of complex metabolic pathyway subject to feedback inhibition3. Key structural proteins (collagen and cytoskeleton of RBC)a. May be a dominant negative , e.g. osteogenesis imperfecta4. Gain of function are rare, 2 formsa. Increased in proteins normal function (excess enzyme activity)b. Huntinton’s diseas (abn protein accumulates, toxic to neurons)b. ARi. Largest category – both alleles at a locus are mutated1. Expression is uniform, complete penetrance common, early onset, unaffected carrier family members, mostly enzymesc. X Linkedi. All sex linked, and almost all are recessive , if Y Chromosome affected usually infertile males > no progenyii. Male expression b/c hemizygous, daughter carriers with variable phenotype because of lionization of 2nd X e.g G6DPiii. Dominant . vitamin D resistant rickets]]</center>}}

Stopped at P142

== Chapter 6 ==
== Chapter 7 ==
== Chapter 8 ==
== Chapter 9 ==
== Chapter 10 ==
== Chapter 11 ==
== Chapter 12 ==
== Chapter 13 ==
== Chapter 14 ==
== Chapter 15 ==
== Chapter 16 ==
== Chapter 17 ==
== Chapter 18 ==
== Chapter 19 ==
== Chapter 20 ==
== Chapter 21 ==
== Chapter 22 ==
== Chapter 23 ==
== Chapter 24 ==
== Chapter 25 ==
== Chapter 26 ==
== Chapter 27 ==
== Chapter 28 ==
== Chapter 29 ==

Robbins and Cotran 9th Edition Questions

2015-05-27T17:26:14Z

Yuanny: /* Chapter 1: The Cell as a Unit of Health and Disease */

== Chapter 1: The Cell as a Unit of Health and Disease==

{{hidden begin| Short Answer Questions |
{{hidden|How much of the human genome is coding and what does it code?|Of the 3.2b basepairs, there are 20,000 genes that comprise about 1.5% of the genome that code for proteins (enzymes, structural components, and signaling molecules used to assemble and maintain all the cells in the body}}

{{hidden|What do we think that the rest of the genome does?|80% of the genome binds proteins, implying that it is involved in regulating gene expression, related to the regulation of gene expression, often in a cell-type specific fashion.}}

{{hidden|List the major classes of functional non-protein-coding sequences found in the human genome.|
*1. Promoter & enhancer
*2. Chromatin binding site structures
*3. non-coding regulatory RNAs
*4. Mobile genetic elements (transposons)
*5. telomeres
*6. centromers. }}

{{hidden|What are the two most common forms of DNA variation in the human genome?|
*1) Single nucleotide polymorphisms (SNPs)
*2) copy number variations (CNVs)}}

{{hidden|What are the possible implications of SNPs.|
*1) regulatory = alters gene expression
*2) Correlation with disease states when in close proximity with altered genes
*3) association used to define linkage disequilibrium,?}}

{{hidden|Define epigenetics.|Heritable changes in gene expression which are not caused by alterations in DNA sequence.}}

{{hidden|List the 6 types of epigenetic changes.|
*1) Histone & histone modifying factors (Histones organize chromatin into heterochromatin and euchromatin
*2) histone methylation
*3) histone acteylation
*4)histone phosphorylation
*5) DNA methylation
*6) Chromatin organizing factors.}}

{{hidden|What is the function of micro-RNA (mi-RNA)?|It does not encode protein, instead they function primarily to modulate the translation of target mRNAs into their corresponding proteins, and are responsible for post-transcriptional silencing of gene expression.}}

{{hidden|What is knockdown technology?|The use of synthetic si-RNA (short RNA sequences) introduced into cells that serve as substrates for Dicer and interact with the RISC complex in a manner analogous to endogenous miRNAs, and are used to study gene function, and are being developed as therapeutic agents to silence pathogenic genes, e.g. oncogenic in neoplasms.}}

{{hidden|What is long non coding RNA?|Lnc-RNA modulate gene expression by binding to regions of chromatin, restricting RNA polymerase access to coding genes within the region, and may exceed the number of mRNA's by 10-20 fold.}}

{{hidden|What is XIST?|XIST is a lnc-RNA which is transcribed from the X-chromosome and plays an essential role in physiologic X chromosome inactivation, though not inactivated itself, it forms a repressive cloak on the X chromosome from which it is transcribed resulting in gene silencing.}}

{{hidden|What are the cellular housekeeping functions?|1) protection from the environment, 2) nutrient acquisition, 3) communication, 4) movement, 5) renewal of senescent molecules, 6) molecular catabolism, 7) energy generation.}}

{{hidden|List the cellular compartments and the role in the cell.|1) cytosol = metabolism, transport, protein translation, 2) Mitochondria = energy generation, apoptosis, 3) Rough ER = synthesis of membrane and secreted proteins, 4) Smooth ER / Golgi = protein modification, sorting, catabolism, 5)Nucleus = cell regulation, proliferation, DNA transcription, 6) Endosomes = intracellular transport and export, ingestion of extracellular substances, 7) Lysosomes = cellular catabolism, 8) peroxisomes = very long-chain fatty acid metabolism}}

{{hidden|Describe the basic structure and functions of the cell membrane.| The plasma membrane is composed of a lipid bilayer of phospholipids studded with a variety of proteins and glycoproteins involved in ion and metabolite transport, fluid phase and receptor-mediated uptake of macromolecules, cell-ligand/cell matrix/cell-cell interactions.}}

{{hidden|How are the large complexes in the plasma membrane formed?|They aggregate under the control of chaperone molecules in the RER or by lateral diffusion in the plasma membrane followed by complex formation in situ.}}

{{hidden|What are aquaporins?|Special integral membrane proteins which augment passive water transport in tissues where water is transported in large volumes.}}

{{hidden|How are channel and carrier proteins different?|Channel proteins created hydrophilic pores, permit rapid movement of solutes, restricted by size and charge, where Carrier proteins bind to their specific solutes and undergo a series of conformational changes to transfer the ligand across the membrane, relatively slow transport.}}

{{hidden|What is the "multidrug resistance (MDR) protein"?|A type of transporter ATPases which pumps polar compounds (e.g. chemo drugs) out of cells which may render cancer cells resistant to treatment.}}

{{hidden|What are the two fundamental mechanisms of fluid or macromolecules by the cell (endocytosis)?|1)Caveolae -invaginations of the plasma membrane, 2) Pinocytosis/receptor mediated endocytosis - macromolecules bind to receptor and membranes invaginate around it.}}

{{hidden|What is exocytosis?|It is the opposite process of pinocytosis, where the receptor bound macromolecule is move to the cell surface and released.}}

{{hidden|Describe the difference between phagocytosis and transcytosis.|In phagocytosis microbes are ingested forming phagosomes, which fuse with lysosomes and become phagylosomes, releasing undigested residual material when fusing again with the external membrane, in contrast transcytosis the materials are carried across the cell membrane unaltered.}}

{{hidden|List the three major classes of 3 cytoskeleton proteins.|1) Actin, 2)Intermediate filaments, 3)Microtubules}}

{{hidden|Describe actin.|Actin - 5 to 9nm diam fibrils, G-actin polymerized into F-actin, the form double strands helices, which interact with myosin (filamentous protein).}}

{{hidden|List the various intermediate filaments, which are 10nm in diameter.|1) Lamin A, B, and C (nuclear lamins of all cells, 2) Vimentin (mesenchymal), 3)Desmin (scaffold for actin/myosin), 4) Neurofilaments (axons of neurons), 5) Glial filament protein (glial cells), 6)Cytokeratins (acid and basic and vary based on cell type). }}

{{hidden|Describe microtubules.|Microtubules are 25nm diam fibrils of dimers of a and b tubulin, with a negative end embedded in the centrosome near the nucleus, the + end grows or shrinks as needed. There are kinesins and dyneins motors that move stuff around the cell, also found in cilia and flagella.}}

{{hidden|What is clatharin?|A molecule found in the cell membrane that when the cell membrane invaginates forming a basket like structure.}}

{{hidden|List and describe the 3 main classifications of cell junctions.|1) Tight /occluding junctions - form a high resistance barrier to solute movement, and allows the cell to maintain polarity, 2) anchoring junctions / desmosomes - mechanically attach the cell and their cytoskeleton to other cells and the ECM (hemidesmosome), 3)communicating/gap junctions - mediate the passage of chemical or electrical signals from one cell to another.}}

{{hidden|What is the "unfolded protein response"?| Excess accumulation of misfolded protiens, which exceed the capacity of the ER to edit and degrade them, leads to the the ER stress response (UPR) that triggers cell death through apoptosis.}}

{{hidden|What cell organelle has a reactive hyperplasia with repeated exposure to phenobarbitol catabolism in the cytocrhome p450 system?|Smooth endoplasmic reticulum.}}

{{hidden|List three main functions of mitochondria.|1) Energy generation, 2) intermediate metabolism (instead of ATP make intemediate that can be used to make lipids, nucleic acids, and proteins), 3) Cell death ( necrosis & apoptosis)}}

{{hidden|List and describe the four extracellular cell-cell signaling pathways based on the distance the signal travels.|1)Paracrine (immediate vicinity), 2) Autocrine (cell affecting itself), 3) Synaptic (neurons sending neurotransmitters at synapse), 4) endocrine (signals released elsewhere into bloodstream).}}

{{hidden|What are the two characterizing features of stem cells?|Self renewal and asymmetric division (one daughter cell stays a stem cell)}}

{{hidden|What are the two types of stem cells?|embryonic stem cells (inner cell mass of the blastocyst, totipotent), and tissue/adult stem cells (found in stem cell niches associated with specialized tissues, limited repetoire of differentiation = multipotent)}}

{{hidden|What is the Warburg effect?|Increased cellular uptake of glucose and glutamine, increased glycolysis, and decreased oxidative phosphorylation by the cell.}}

{{hidden|Which CDKI's have selective effects on CDK4 and CDK6?|p15,p16,p17,and p19}}

{{hidden|List some examples of signal transduction pathways.|1) Receptor tyrosine kinases (RTKs), 2) Nonreceptor tyrosine kinase, 3) G-protein coupled receptors, 4) nuclear receptors, 5)Notch family receptors, 6) Wnt protein ligands (Frizzled family receptors).}}

{{hidden|Why does nuclear beta catenin occur in some neoplasms?|When Wnt ligand bins to frizzled it recruits Disheveled, this leads to the disruption of the wnt-ubiquitin complex, this stabilized pool of b-catening is then translocated to the nucleus forming a transcriptional complex}}

{{hidden|On Page 19 there is a table of growth factors involved in regeneration and repair, please review.|}}

{{hidden|Describe the function of cadherin.|}}

{{hidden|What are the functions of the extracellular matrix?|Mechanical support, control of cell proliferation, scaffolding for tissue renewal, establishment of tissue microenvironments}}

{{hidden|What are the two basic forms of the ECM?|interstitial matrix (fibrillar and non fibrillar collagen, fibronectin, elastin, proteoglycans, hyloronate, and other stuff), basement membrane (type IV collagen and laminin) }}

{{hidden|What are the three proteins groups in the ECM?|1) fibrous structural proteins (collagen, elastins), 2) water hydrated gels (proteoglycans and hyaluronan), 3) adhesive glycoproteins (connect ECM to each other and other cells)}}

{{hidden|Describe the structure of a protein that is dependent on vitamin C.|Collagen is composed of 3 seprate polypeptide chains braided into a rope like triple helix, lateral cross linking of the triple helices by lysyl oxidase (requires vitamin C) give it it's tensile strength. }}

{{hidden|List three non-fibrillar collagens.|Type IV -basement membrane, Type IX - Fibrillar associated collagen with interrupted triple helices (FACIT), Type VII (provides anchoring fibrils to basement membrane beneath skin)}}

{{hidden|Which structural protein is associated with Marfan syndrom?|Fibrillin synthetic defects, which wrap the elastin core. }}}}

== Chapter 2: Cellular Responses to Stress and Toxic Insults: Adaptation, Injury and Death ==
{{hidden|Short Answer Questions|
{{hidden|What are the four aspects of a disease?|
*1. Etiology
**Genetic - Inherited mutations and disease-associated gene variants, or polymorphisms
**Acquired - Infectious, nutritional, chemical and physical.
*2. Pathogenesis - The sequence of cellular, biochemical, and molecular events that follow the exposure of cells or tissues to an injurious agent.
*3. Morphological changes - The structural alterations in cells or tissues that are either characteristic of a disease or diagnostic of an etiologic process.
*4. Clinical Manifestations - Symptoms and signs of disease, as well as its clinical course and outcome}}

}}

== Chapter 3 ==
== Chapter 4 ==
== Chapter 5 ==
{{hidden|MC cause of spontaneous abortion is ?|<center>[[ A demonstrable chromosomal abnormality.]]</center>}}

{{hidden|1% of all newborn infants possess a gross chromosomal abnormality and 5% of people <25y present with |<center>[[a genetic disease. ]]</center>}}

{{hidden|Mutation|<center>[[permanent change in the DNA, if affect germ cells are transmitted to the progeny ]]</center>}}

{{hidden|List and describe 4 broad categories of human genetic disorders:|<center>[[Disorders related to mutation sin single genes with large effects i. Usually follow classic Mendelian pattern of inheritance
ii. Often highly penetrant (large proportion of pop with gene has disease)
b. Chromosomal disorders
i. Structural or numerical alterations in autosomes and sex chromosomes
ii. Uncommon, high penetrance
c. Complex multigenic disorders
i. Interactions between multiple variant forms of genes and environmental factors (polymorphisms), poly genic means disease when many polymorphism present
d. Single gene disorders with nonclassic patterns of inheritance (not mendelian)
i. Disorders resulting from triplet repeat mutations
ii. Mutations in mitochondrial DNA
iii. Those influenced by genomic imprinting
iv. Those influenced by gonadal mosaicism]]</center>}}

{{hidden|List and describe the possible outcomes of a point mutation in a coding region?|[[a. Missense mutation – pt mutation changes amino acid code, conservative when the amino acid is preserved, non conservative when replaced with another amino acid, b. Nonsense mutation – makes a stop codon ]]</center>}}

{{hidden|List and describe the possible outcomes of point mutation or deletion in a non-coding region.|<center>[[a. Promoters/enhancers – interfere with binding of transcription factors, marker reduction or total lack of transcription, b. Introns – defective splicing > failure to make mature RNA > no translation]]</center>}}

{{hidden|List and describe the possible outcomes of deletions and insertions.|<center>[[a.Small coding: not multiple of three = frameshift, if multiple of 3 than add or del amino acids accordingly, often premature stop codon
i. Tay Sachs disease: 4 base pair insertion in Hexosaminidase A gene ]]}}

{{hidden|List and describe the possible outcomes of trinucleotide repeat mutations.|[[a. Usually G&C, dynamic and increase during gametogenesis, “RNA stutters”,b. Fragile X – CGG 250-4000, Huntinton’s Disease ]]}}

{{hidden|List and describe three examples of inheritance of single gene mutations|[[a. AD – manifested in the heterologous state, one parent of index case is usually affected, males and females affected and both can transmit conditioni. De novo cases may not have affected parentii. Penetrance = fraction of people with gene who have the traitiii. Variable expressivity = those with mutant gene have variety of phenotypesiv. Often age of onset is delayed so can reproduce before die from diseasev. Biochem mechanisms1. Reduced production of a protein or dysfunctional/inactive protein2. Involved in regulation of complex metabolic pathyway subject to feedback inhibition3. Key structural proteins (collagen and cytoskeleton of RBC)a. May be a dominant negative , e.g. osteogenesis imperfecta4. Gain of function are rare, 2 formsa. Increased in proteins normal function (excess enzyme activity)b. Huntinton’s diseas (abn protein accumulates, toxic to neurons)b. ARi. Largest category – both alleles at a locus are mutated1. Expression is uniform, complete penetrance common, early onset, unaffected carrier family members, mostly enzymesc. X Linkedi. All sex linked, and almost all are recessive , if Y Chromosome affected usually infertile males > no progenyii. Male expression b/c hemizygous, daughter carriers with variable phenotype because of lionization of 2nd X e.g G6DPiii. Dominant . vitamin D resistant rickets]]</center>}}

Stopped at P142

== Chapter 6 ==
== Chapter 7 ==
== Chapter 8 ==
== Chapter 9 ==
== Chapter 10 ==
== Chapter 11 ==
== Chapter 12 ==
== Chapter 13 ==
== Chapter 14 ==
== Chapter 15 ==
== Chapter 16 ==
== Chapter 17 ==
== Chapter 18 ==
== Chapter 19 ==
== Chapter 20 ==
== Chapter 21 ==
== Chapter 22 ==
== Chapter 23 ==
== Chapter 24 ==
== Chapter 25 ==
== Chapter 26 ==
== Chapter 27 ==
== Chapter 28 ==
== Chapter 29 ==

Robbins and Cotran 9th Edition Questions

2015-05-27T17:21:56Z

Yuanny: /* Chapter 2: Cellular Responses to Stress and Toxic Insults: Adaptation, Injury and Death */

== Chapter 1: The Cell as a Unit of Health and Disease==

{{hidden| Short Answer Questions |
{{hidden|How much of the human genome is coding and what does it code?|Of the 3.2b basepairs, there are 20,000 genes that comprise about 1.5% of the genome that code for proteins (enzymes, structural components, and signaling molecules used to assemble and maintain all the cells in the body}}

{{hidden|What do we think that the rest of the genome does?|80% of the genome binds proteins, implying that it is involved in regulating gene expression, related to the regulation of gene expression, often in a cell-type specific fashion.}}

{{hidden|List the major classes of functional non-protein-coding sequences found in the human genome.|1. Promoter & enhancer, 2. Chromatin binding site structures, 3. non-coding regulatory RNAs, 4. Mobile genetic elements (transposons), 5. telomeres, 6. centromers. }}

{{hidden|What are the two most common forms of DNA variation in the human genome?|1) Single nucleotide polymorphisms (SNPs), 2) copy number variations (CNVs)}}

{{hidden|What are the possible implications of SNPs.|1) regulatory = alters gene expression, 2) Correlation with disease states when in close proximity with altered genes, 3) association used to define linkage disequilibrium,?}}

{{hidden|Define epigenetics.|Heritable changes in gene expression which are not caused by alterations in DNA sequence.}}

{{hidden|List the 6 types of epigenetic changes.|1) Histone & histone modifying factors (Histones organize chromatin into heterochromatin and euchromatin, 2) histone methylation, 3) histone acteylation, 4)histone phosphorylation, 5) DNA methylation, 6) Chromatin organizing factors.}}

{{hidden|What is the function of micro-RNA (mi-RNA)?|It does not encode protein, instead they function primarily to modulate the translation of target mRNAs into their corresponding proteins, and are responsible for post-transcriptional silencing of gene expression.}}

{{hidden|What is knockdown technology?|The use of synthetic si-RNA (short RNA sequences) introduced into cells that serve as substrates for Dicer and interact with the RISC complex in a manner analogous to endogenous miRNAs, and are used to study gene function, and are being developed as therapeutic agents to silence pathogenic genes, e.g. oncogenic in neoplasms.}}

{{hidden|What is long non coding RNA?|Lnc-RNA modulate gene expression by binding to regions of chromatin, restricting RNA polymerase access to coding genes within the region, and may exceed the number of mRNA's by 10-20 fold.}}

{{hidden|What is XIST?|XIST is a lnc-RNA which is transcribed from the X-chromosome and plays an essential role in physiologic X chromosome inactivation, though not inactivated itself, it forms a repressive cloak on the X chromosome from which it is transcribed resulting in gene silencing.}}

{{hidden|What are the cellular housekeeping functions?|1) protection from the environment, 2) nutrient acquisition, 3) communication, 4) movement, 5) renewal of senescent molecules, 6) molecular catabolism, 7) energy generation.}}

{{hidden|List the cellular compartments and the role in the cell.|1) cytosol = metabolism, transport, protein translation, 2) Mitochondria = energy generation, apoptosis, 3) Rough ER = synthesis of membrane and secreted proteins, 4) Smooth ER / Golgi = protein modification, sorting, catabolism, 5)Nucleus = cell regulation, proliferation, DNA transcription, 6) Endosomes = intracellular transport and export, ingestion of extracellular substances, 7) Lysosomes = cellular catabolism, 8) peroxisomes = very long-chain fatty acid metabolism}}

{{hidden|Describe the basic structure and functions of the cell membrane.| The plasma membrane is composed of a lipid bilayer of phospholipids studded with a variety of proteins and glycoproteins involved in ion and metabolite transport, fluid phase and receptor-mediated uptake of macromolecules, cell-ligand/cell matrix/cell-cell interactions.}}

{{hidden|How are the large complexes in the plasma membrane formed?|They aggregate under the control of chaperone molecules in the RER or by lateral diffusion in the plasma membrane followed by complex formation in situ.}}

{{hidden|What are aquaporins?|Special integral membrane proteins which augment passive water transport in tissues where water is transported in large volumes.}}

{{hidden|How are channel and carrier proteins different?|Channel proteins created hydrophilic pores, permit rapid movement of solutes, restricted by size and charge, where Carrier proteins bind to their specific solutes and undergo a series of conformational changes to transfer the ligand across the membrane, relatively slow transport.}}

{{hidden|What is the "multidrug resistance (MDR) protein"?|A type of transporter ATPases which pumps polar compounds (e.g. chemo drugs) out of cells which may render cancer cells resistant to treatment.}}

{{hidden|What are the two fundamental mechanisms of fluid or macromolecules by the cell (endocytosis)?|1)Caveolae -invaginations of the plasma membrane, 2) Pinocytosis/receptor mediated endocytosis - macromolecules bind to receptor and membranes invaginate around it.}}

{{hidden|What is exocytosis?|It is the opposite process of pinocytosis, where the receptor bound macromolecule is move to the cell surface and released.}}

{{hidden|Describe the difference between phagocytosis and transcytosis.|In phagocytosis microbes are ingested forming phagosomes, which fuse with lysosomes and become phagylosomes, releasing undigested residual material when fusing again with the external membrane, in contrast transcytosis the materials are carried across the cell membrane unaltered.}}

{{hidden|List the three major classes of 3 cytoskeleton proteins.|1) Actin, 2)Intermediate filaments, 3)Microtubules}}

{{hidden|Describe actin.|Actin - 5 to 9nm diam fibrils, G-actin polymerized into F-actin, the form double strands helices, which interact with myosin (filamentous protein).}}

{{hidden|List the various intermediate filaments, which are 10nm in diameter.|1) Lamin A, B, and C (nuclear lamins of all cells, 2) Vimentin (mesenchymal), 3)Desmin (scaffold for actin/myosin), 4) Neurofilaments (axons of neurons), 5) Glial filament protein (glial cells), 6)Cytokeratins (acid and basic and vary based on cell type). }}

{{hidden|Describe microtubules.|Microtubules are 25nm diam fibrils of dimers of a and b tubulin, with a negative end embedded in the centrosome near the nucleus, the + end grows or shrinks as needed. There are kinesins and dyneins motors that move stuff around the cell, also found in cilia and flagella.}}

{{hidden|What is clatharin?|A molecule found in the cell membrane that when the cell membrane invaginates forming a basket like structure.}}

{{hidden|List and describe the 3 main classifications of cell junctions.|1) Tight /occluding junctions - form a high resistance barrier to solute movement, and allows the cell to maintain polarity, 2) anchoring junctions / desmosomes - mechanically attach the cell and their cytoskeleton to other cells and the ECM (hemidesmosome), 3)communicating/gap junctions - mediate the passage of chemical or electrical signals from one cell to another.}}

{{hidden|What is the "unfolded protein response"?| Excess accumulation of misfolded protiens, which exceed the capacity of the ER to edit and degrade them, leads to the the ER stress response (UPR) that triggers cell death through apoptosis.}}

{{hidden|What cell organelle has a reactive hyperplasia with repeated exposure to phenobarbitol catabolism in the cytocrhome p450 system?|Smooth endoplasmic reticulum.}}

{{hidden|List three main functions of mitochondria.|1) Energy generation, 2) intermediate metabolism (instead of ATP make intemediate that can be used to make lipids, nucleic acids, and proteins), 3) Cell death ( necrosis & apoptosis)}}

{{hidden|List and describe the four extracellular cell-cell signaling pathways based on the distance the signal travels.|1)Paracrine (immediate vicinity), 2) Autocrine (cell affecting itself), 3) Synaptic (neurons sending neurotransmitters at synapse), 4) endocrine (signals released elsewhere into bloodstream).}}

{{hidden|What are the two characterizing features of stem cells?|Self renewal and asymmetric division (one daughter cell stays a stem cell)}}

{{hidden|What are the two types of stem cells?|embryonic stem cells (inner cell mass of the blastocyst, totipotent), and tissue/adult stem cells (found in stem cell niches associated with specialized tissues, limited repetoire of differentiation = multipotent)}}

{{hidden|What is the Warburg effect?|Increased cellular uptake of glucose and glutamine, increased glycolysis, and decreased oxidative phosphorylation by the cell.}}

{{hidden|Which CDKI's have selective effects on CDK4 and CDK6?|p15,p16,p17,and p19}}

{{hidden|List some examples of signal transduction pathways.|1) Receptor tyrosine kinases (RTKs), 2) Nonreceptor tyrosine kinase, 3) G-protein coupled receptors, 4) nuclear receptors, 5)Notch family receptors, 6) Wnt protein ligands (Frizzled family receptors).}}

{{hidden|Why does nuclear beta catenin occur in some neoplasms?|When Wnt ligand bins to frizzled it recruits Disheveled, this leads to the disruption of the wnt-ubiquitin complex, this stabilized pool of b-catening is then translocated to the nucleus forming a transcriptional complex}}

{{hidden|On Page 19 there is a table of growth factors involved in regeneration and repair, please review.|}}

{{hidden|Describe the function of cadherin.|}}

{{hidden|What are the functions of the extracellular matrix?|Mechanical support, control of cell proliferation, scaffolding for tissue renewal, establishment of tissue microenvironments}}

{{hidden|What are the two basic forms of the ECM?|interstitial matrix (fibrillar and non fibrillar collagen, fibronectin, elastin, proteoglycans, hyloronate, and other stuff), basement membrane (type IV collagen and laminin) }}

{{hidden|What are the three proteins groups in the ECM?|1) fibrous structural proteins (collagen, elastins), 2) water hydrated gels (proteoglycans and hyaluronan), 3) adhesive glycoproteins (connect ECM to each other and other cells)}}

{{hidden|Describe the structure of a protein that is dependent on vitamin C.|Collagen is composed of 3 seprate polypeptide chains braided into a rope like triple helix, lateral cross linking of the triple helices by lysyl oxidase (requires vitamin C) give it it's tensile strength. }}

{{hidden|List three non-fibrillar collagens.|Type IV -basement membrane, Type IX - Fibrillar associated collagen with interrupted triple helices (FACIT), Type VII (provides anchoring fibrils to basement membrane beneath skin)}}

{{hidden|Which structural protein is associated with Marfan syndrom?|Fibrillin synthetic defects, which wrap the elastin core. }}}}

== Chapter 2: Cellular Responses to Stress and Toxic Insults: Adaptation, Injury and Death ==
{{hidden|Short Answer Questions|
{{hidden|What are the four aspects of a disease?|
*1. Etiology
**Genetic - Inherited mutations and disease-associated gene variants, or polymorphisms
**Acquired - Infectious, nutritional, chemical and physical.
*2. Pathogenesis - The sequence of cellular, biochemical, and molecular events that follow the exposure of cells or tissues to an injurious agent.
*3. Morphological changes - The structural alterations in cells or tissues that are either characteristic of a disease or diagnostic of an etiologic process.
*4. Clinical Manifestations - Symptoms and signs of disease, as well as its clinical course and outcome}}

}}

== Chapter 3 ==
== Chapter 4 ==
== Chapter 5 ==
{{hidden|MC cause of spontaneous abortion is ?|<center>[[ A demonstrable chromosomal abnormality.]]</center>}}

{{hidden|1% of all newborn infants possess a gross chromosomal abnormality and 5% of people <25y present with |<center>[[a genetic disease. ]]</center>}}

{{hidden|Mutation|<center>[[permanent change in the DNA, if affect germ cells are transmitted to the progeny ]]</center>}}

{{hidden|List and describe 4 broad categories of human genetic disorders:|<center>[[Disorders related to mutation sin single genes with large effects i. Usually follow classic Mendelian pattern of inheritance
ii. Often highly penetrant (large proportion of pop with gene has disease)
b. Chromosomal disorders
i. Structural or numerical alterations in autosomes and sex chromosomes
ii. Uncommon, high penetrance
c. Complex multigenic disorders
i. Interactions between multiple variant forms of genes and environmental factors (polymorphisms), poly genic means disease when many polymorphism present
d. Single gene disorders with nonclassic patterns of inheritance (not mendelian)
i. Disorders resulting from triplet repeat mutations
ii. Mutations in mitochondrial DNA
iii. Those influenced by genomic imprinting
iv. Those influenced by gonadal mosaicism]]</center>}}

{{hidden|List and describe the possible outcomes of a point mutation in a coding region?|[[a. Missense mutation – pt mutation changes amino acid code, conservative when the amino acid is preserved, non conservative when replaced with another amino acid, b. Nonsense mutation – makes a stop codon ]]</center>}}

{{hidden|List and describe the possible outcomes of point mutation or deletion in a non-coding region.|<center>[[a. Promoters/enhancers – interfere with binding of transcription factors, marker reduction or total lack of transcription, b. Introns – defective splicing > failure to make mature RNA > no translation]]</center>}}

{{hidden|List and describe the possible outcomes of deletions and insertions.|<center>[[a.Small coding: not multiple of three = frameshift, if multiple of 3 than add or del amino acids accordingly, often premature stop codon
i. Tay Sachs disease: 4 base pair insertion in Hexosaminidase A gene ]]}}

{{hidden|List and describe the possible outcomes of trinucleotide repeat mutations.|[[a. Usually G&C, dynamic and increase during gametogenesis, “RNA stutters”,b. Fragile X – CGG 250-4000, Huntinton’s Disease ]]}}

{{hidden|List and describe three examples of inheritance of single gene mutations|[[a. AD – manifested in the heterologous state, one parent of index case is usually affected, males and females affected and both can transmit conditioni. De novo cases may not have affected parentii. Penetrance = fraction of people with gene who have the traitiii. Variable expressivity = those with mutant gene have variety of phenotypesiv. Often age of onset is delayed so can reproduce before die from diseasev. Biochem mechanisms1. Reduced production of a protein or dysfunctional/inactive protein2. Involved in regulation of complex metabolic pathyway subject to feedback inhibition3. Key structural proteins (collagen and cytoskeleton of RBC)a. May be a dominant negative , e.g. osteogenesis imperfecta4. Gain of function are rare, 2 formsa. Increased in proteins normal function (excess enzyme activity)b. Huntinton’s diseas (abn protein accumulates, toxic to neurons)b. ARi. Largest category – both alleles at a locus are mutated1. Expression is uniform, complete penetrance common, early onset, unaffected carrier family members, mostly enzymesc. X Linkedi. All sex linked, and almost all are recessive , if Y Chromosome affected usually infertile males > no progenyii. Male expression b/c hemizygous, daughter carriers with variable phenotype because of lionization of 2nd X e.g G6DPiii. Dominant . vitamin D resistant rickets]]</center>}}

Stopped at P142

== Chapter 6 ==
== Chapter 7 ==
== Chapter 8 ==
== Chapter 9 ==
== Chapter 10 ==
== Chapter 11 ==
== Chapter 12 ==
== Chapter 13 ==
== Chapter 14 ==
== Chapter 15 ==
== Chapter 16 ==
== Chapter 17 ==
== Chapter 18 ==
== Chapter 19 ==
== Chapter 20 ==
== Chapter 21 ==
== Chapter 22 ==
== Chapter 23 ==
== Chapter 24 ==
== Chapter 25 ==
== Chapter 26 ==
== Chapter 27 ==
== Chapter 28 ==
== Chapter 29 ==

Robbins and Cotran 9th Edition Questions

2015-05-27T17:21:21Z

Yuanny: /* Chapter 2: Cellular Responses to Stress and Toxic Insults: Adaptation, Injury and Death */

== Chapter 1: The Cell as a Unit of Health and Disease==

{{hidden| Short Answer Questions |
{{hidden|How much of the human genome is coding and what does it code?|Of the 3.2b basepairs, there are 20,000 genes that comprise about 1.5% of the genome that code for proteins (enzymes, structural components, and signaling molecules used to assemble and maintain all the cells in the body}}

{{hidden|What do we think that the rest of the genome does?|80% of the genome binds proteins, implying that it is involved in regulating gene expression, related to the regulation of gene expression, often in a cell-type specific fashion.}}

{{hidden|List the major classes of functional non-protein-coding sequences found in the human genome.|1. Promoter & enhancer, 2. Chromatin binding site structures, 3. non-coding regulatory RNAs, 4. Mobile genetic elements (transposons), 5. telomeres, 6. centromers. }}

{{hidden|What are the two most common forms of DNA variation in the human genome?|1) Single nucleotide polymorphisms (SNPs), 2) copy number variations (CNVs)}}

{{hidden|What are the possible implications of SNPs.|1) regulatory = alters gene expression, 2) Correlation with disease states when in close proximity with altered genes, 3) association used to define linkage disequilibrium,?}}

{{hidden|Define epigenetics.|Heritable changes in gene expression which are not caused by alterations in DNA sequence.}}

{{hidden|List the 6 types of epigenetic changes.|1) Histone & histone modifying factors (Histones organize chromatin into heterochromatin and euchromatin, 2) histone methylation, 3) histone acteylation, 4)histone phosphorylation, 5) DNA methylation, 6) Chromatin organizing factors.}}

{{hidden|What is the function of micro-RNA (mi-RNA)?|It does not encode protein, instead they function primarily to modulate the translation of target mRNAs into their corresponding proteins, and are responsible for post-transcriptional silencing of gene expression.}}

{{hidden|What is knockdown technology?|The use of synthetic si-RNA (short RNA sequences) introduced into cells that serve as substrates for Dicer and interact with the RISC complex in a manner analogous to endogenous miRNAs, and are used to study gene function, and are being developed as therapeutic agents to silence pathogenic genes, e.g. oncogenic in neoplasms.}}

{{hidden|What is long non coding RNA?|Lnc-RNA modulate gene expression by binding to regions of chromatin, restricting RNA polymerase access to coding genes within the region, and may exceed the number of mRNA's by 10-20 fold.}}

{{hidden|What is XIST?|XIST is a lnc-RNA which is transcribed from the X-chromosome and plays an essential role in physiologic X chromosome inactivation, though not inactivated itself, it forms a repressive cloak on the X chromosome from which it is transcribed resulting in gene silencing.}}

{{hidden|What are the cellular housekeeping functions?|1) protection from the environment, 2) nutrient acquisition, 3) communication, 4) movement, 5) renewal of senescent molecules, 6) molecular catabolism, 7) energy generation.}}

{{hidden|List the cellular compartments and the role in the cell.|1) cytosol = metabolism, transport, protein translation, 2) Mitochondria = energy generation, apoptosis, 3) Rough ER = synthesis of membrane and secreted proteins, 4) Smooth ER / Golgi = protein modification, sorting, catabolism, 5)Nucleus = cell regulation, proliferation, DNA transcription, 6) Endosomes = intracellular transport and export, ingestion of extracellular substances, 7) Lysosomes = cellular catabolism, 8) peroxisomes = very long-chain fatty acid metabolism}}

{{hidden|Describe the basic structure and functions of the cell membrane.| The plasma membrane is composed of a lipid bilayer of phospholipids studded with a variety of proteins and glycoproteins involved in ion and metabolite transport, fluid phase and receptor-mediated uptake of macromolecules, cell-ligand/cell matrix/cell-cell interactions.}}

{{hidden|How are the large complexes in the plasma membrane formed?|They aggregate under the control of chaperone molecules in the RER or by lateral diffusion in the plasma membrane followed by complex formation in situ.}}

{{hidden|What are aquaporins?|Special integral membrane proteins which augment passive water transport in tissues where water is transported in large volumes.}}

{{hidden|How are channel and carrier proteins different?|Channel proteins created hydrophilic pores, permit rapid movement of solutes, restricted by size and charge, where Carrier proteins bind to their specific solutes and undergo a series of conformational changes to transfer the ligand across the membrane, relatively slow transport.}}

{{hidden|What is the "multidrug resistance (MDR) protein"?|A type of transporter ATPases which pumps polar compounds (e.g. chemo drugs) out of cells which may render cancer cells resistant to treatment.}}

{{hidden|What are the two fundamental mechanisms of fluid or macromolecules by the cell (endocytosis)?|1)Caveolae -invaginations of the plasma membrane, 2) Pinocytosis/receptor mediated endocytosis - macromolecules bind to receptor and membranes invaginate around it.}}

{{hidden|What is exocytosis?|It is the opposite process of pinocytosis, where the receptor bound macromolecule is move to the cell surface and released.}}

{{hidden|Describe the difference between phagocytosis and transcytosis.|In phagocytosis microbes are ingested forming phagosomes, which fuse with lysosomes and become phagylosomes, releasing undigested residual material when fusing again with the external membrane, in contrast transcytosis the materials are carried across the cell membrane unaltered.}}

{{hidden|List the three major classes of 3 cytoskeleton proteins.|1) Actin, 2)Intermediate filaments, 3)Microtubules}}

{{hidden|Describe actin.|Actin - 5 to 9nm diam fibrils, G-actin polymerized into F-actin, the form double strands helices, which interact with myosin (filamentous protein).}}

{{hidden|List the various intermediate filaments, which are 10nm in diameter.|1) Lamin A, B, and C (nuclear lamins of all cells, 2) Vimentin (mesenchymal), 3)Desmin (scaffold for actin/myosin), 4) Neurofilaments (axons of neurons), 5) Glial filament protein (glial cells), 6)Cytokeratins (acid and basic and vary based on cell type). }}

{{hidden|Describe microtubules.|Microtubules are 25nm diam fibrils of dimers of a and b tubulin, with a negative end embedded in the centrosome near the nucleus, the + end grows or shrinks as needed. There are kinesins and dyneins motors that move stuff around the cell, also found in cilia and flagella.}}

{{hidden|What is clatharin?|A molecule found in the cell membrane that when the cell membrane invaginates forming a basket like structure.}}

{{hidden|List and describe the 3 main classifications of cell junctions.|1) Tight /occluding junctions - form a high resistance barrier to solute movement, and allows the cell to maintain polarity, 2) anchoring junctions / desmosomes - mechanically attach the cell and their cytoskeleton to other cells and the ECM (hemidesmosome), 3)communicating/gap junctions - mediate the passage of chemical or electrical signals from one cell to another.}}

{{hidden|What is the "unfolded protein response"?| Excess accumulation of misfolded protiens, which exceed the capacity of the ER to edit and degrade them, leads to the the ER stress response (UPR) that triggers cell death through apoptosis.}}

{{hidden|What cell organelle has a reactive hyperplasia with repeated exposure to phenobarbitol catabolism in the cytocrhome p450 system?|Smooth endoplasmic reticulum.}}

{{hidden|List three main functions of mitochondria.|1) Energy generation, 2) intermediate metabolism (instead of ATP make intemediate that can be used to make lipids, nucleic acids, and proteins), 3) Cell death ( necrosis & apoptosis)}}

{{hidden|List and describe the four extracellular cell-cell signaling pathways based on the distance the signal travels.|1)Paracrine (immediate vicinity), 2) Autocrine (cell affecting itself), 3) Synaptic (neurons sending neurotransmitters at synapse), 4) endocrine (signals released elsewhere into bloodstream).}}

{{hidden|What are the two characterizing features of stem cells?|Self renewal and asymmetric division (one daughter cell stays a stem cell)}}

{{hidden|What are the two types of stem cells?|embryonic stem cells (inner cell mass of the blastocyst, totipotent), and tissue/adult stem cells (found in stem cell niches associated with specialized tissues, limited repetoire of differentiation = multipotent)}}

{{hidden|What is the Warburg effect?|Increased cellular uptake of glucose and glutamine, increased glycolysis, and decreased oxidative phosphorylation by the cell.}}

{{hidden|Which CDKI's have selective effects on CDK4 and CDK6?|p15,p16,p17,and p19}}

{{hidden|List some examples of signal transduction pathways.|1) Receptor tyrosine kinases (RTKs), 2) Nonreceptor tyrosine kinase, 3) G-protein coupled receptors, 4) nuclear receptors, 5)Notch family receptors, 6) Wnt protein ligands (Frizzled family receptors).}}

{{hidden|Why does nuclear beta catenin occur in some neoplasms?|When Wnt ligand bins to frizzled it recruits Disheveled, this leads to the disruption of the wnt-ubiquitin complex, this stabilized pool of b-catening is then translocated to the nucleus forming a transcriptional complex}}

{{hidden|On Page 19 there is a table of growth factors involved in regeneration and repair, please review.|}}

{{hidden|Describe the function of cadherin.|}}

{{hidden|What are the functions of the extracellular matrix?|Mechanical support, control of cell proliferation, scaffolding for tissue renewal, establishment of tissue microenvironments}}

{{hidden|What are the two basic forms of the ECM?|interstitial matrix (fibrillar and non fibrillar collagen, fibronectin, elastin, proteoglycans, hyloronate, and other stuff), basement membrane (type IV collagen and laminin) }}

{{hidden|What are the three proteins groups in the ECM?|1) fibrous structural proteins (collagen, elastins), 2) water hydrated gels (proteoglycans and hyaluronan), 3) adhesive glycoproteins (connect ECM to each other and other cells)}}

{{hidden|Describe the structure of a protein that is dependent on vitamin C.|Collagen is composed of 3 seprate polypeptide chains braided into a rope like triple helix, lateral cross linking of the triple helices by lysyl oxidase (requires vitamin C) give it it's tensile strength. }}

{{hidden|List three non-fibrillar collagens.|Type IV -basement membrane, Type IX - Fibrillar associated collagen with interrupted triple helices (FACIT), Type VII (provides anchoring fibrils to basement membrane beneath skin)}}

{{hidden|Which structural protein is associated with Marfan syndrom?|Fibrillin synthetic defects, which wrap the elastin core. }}}}

== Chapter 2: Cellular Responses to Stress and Toxic Insults: Adaptation, Injury and Death ==
{{hidden|Short Answer Questions|
{{hidden|<div class="left" style="width: auto; margin-left: auto; margin-right: auto;">(What are the four aspects of a disease?)</div>|
*1. Etiology
**Genetic - Inherited mutations and disease-associated gene variants, or polymorphisms
**Acquired - Infectious, nutritional, chemical and physical.
*2. Pathogenesis - The sequence of cellular, biochemical, and molecular events that follow the exposure of cells or tissues to an injurious agent.
*3. Morphological changes - The structural alterations in cells or tissues that are either characteristic of a disease or diagnostic of an etiologic process.
*4. Clinical Manifestations - Symptoms and signs of disease, as well as its clinical course and outcome}}

}}

== Chapter 3 ==
== Chapter 4 ==
== Chapter 5 ==
{{hidden|MC cause of spontaneous abortion is ?|<center>[[ A demonstrable chromosomal abnormality.]]</center>}}

{{hidden|1% of all newborn infants possess a gross chromosomal abnormality and 5% of people <25y present with |<center>[[a genetic disease. ]]</center>}}

{{hidden|Mutation|<center>[[permanent change in the DNA, if affect germ cells are transmitted to the progeny ]]</center>}}

{{hidden|List and describe 4 broad categories of human genetic disorders:|<center>[[Disorders related to mutation sin single genes with large effects i. Usually follow classic Mendelian pattern of inheritance
ii. Often highly penetrant (large proportion of pop with gene has disease)
b. Chromosomal disorders
i. Structural or numerical alterations in autosomes and sex chromosomes
ii. Uncommon, high penetrance
c. Complex multigenic disorders
i. Interactions between multiple variant forms of genes and environmental factors (polymorphisms), poly genic means disease when many polymorphism present
d. Single gene disorders with nonclassic patterns of inheritance (not mendelian)
i. Disorders resulting from triplet repeat mutations
ii. Mutations in mitochondrial DNA
iii. Those influenced by genomic imprinting
iv. Those influenced by gonadal mosaicism]]</center>}}

{{hidden|List and describe the possible outcomes of a point mutation in a coding region?|[[a. Missense mutation – pt mutation changes amino acid code, conservative when the amino acid is preserved, non conservative when replaced with another amino acid, b. Nonsense mutation – makes a stop codon ]]</center>}}

{{hidden|List and describe the possible outcomes of point mutation or deletion in a non-coding region.|<center>[[a. Promoters/enhancers – interfere with binding of transcription factors, marker reduction or total lack of transcription, b. Introns – defective splicing > failure to make mature RNA > no translation]]</center>}}

{{hidden|List and describe the possible outcomes of deletions and insertions.|<center>[[a.Small coding: not multiple of three = frameshift, if multiple of 3 than add or del amino acids accordingly, often premature stop codon
i. Tay Sachs disease: 4 base pair insertion in Hexosaminidase A gene ]]}}

{{hidden|List and describe the possible outcomes of trinucleotide repeat mutations.|[[a. Usually G&C, dynamic and increase during gametogenesis, “RNA stutters”,b. Fragile X – CGG 250-4000, Huntinton’s Disease ]]}}

{{hidden|List and describe three examples of inheritance of single gene mutations|[[a. AD – manifested in the heterologous state, one parent of index case is usually affected, males and females affected and both can transmit conditioni. De novo cases may not have affected parentii. Penetrance = fraction of people with gene who have the traitiii. Variable expressivity = those with mutant gene have variety of phenotypesiv. Often age of onset is delayed so can reproduce before die from diseasev. Biochem mechanisms1. Reduced production of a protein or dysfunctional/inactive protein2. Involved in regulation of complex metabolic pathyway subject to feedback inhibition3. Key structural proteins (collagen and cytoskeleton of RBC)a. May be a dominant negative , e.g. osteogenesis imperfecta4. Gain of function are rare, 2 formsa. Increased in proteins normal function (excess enzyme activity)b. Huntinton’s diseas (abn protein accumulates, toxic to neurons)b. ARi. Largest category – both alleles at a locus are mutated1. Expression is uniform, complete penetrance common, early onset, unaffected carrier family members, mostly enzymesc. X Linkedi. All sex linked, and almost all are recessive , if Y Chromosome affected usually infertile males > no progenyii. Male expression b/c hemizygous, daughter carriers with variable phenotype because of lionization of 2nd X e.g G6DPiii. Dominant . vitamin D resistant rickets]]</center>}}

Stopped at P142

== Chapter 6 ==
== Chapter 7 ==
== Chapter 8 ==
== Chapter 9 ==
== Chapter 10 ==
== Chapter 11 ==
== Chapter 12 ==
== Chapter 13 ==
== Chapter 14 ==
== Chapter 15 ==
== Chapter 16 ==
== Chapter 17 ==
== Chapter 18 ==
== Chapter 19 ==
== Chapter 20 ==
== Chapter 21 ==
== Chapter 22 ==
== Chapter 23 ==
== Chapter 24 ==
== Chapter 25 ==
== Chapter 26 ==
== Chapter 27 ==
== Chapter 28 ==
== Chapter 29 ==

Robbins and Cotran 9th Edition Questions

2015-05-27T17:17:51Z

Yuanny: /* Chapter 2: Cellular Responses to Stress and Toxic Insults: Adaptation, Injury and Death */

== Chapter 1: The Cell as a Unit of Health and Disease==

{{hidden| Short Answer Questions |
{{hidden|How much of the human genome is coding and what does it code?|Of the 3.2b basepairs, there are 20,000 genes that comprise about 1.5% of the genome that code for proteins (enzymes, structural components, and signaling molecules used to assemble and maintain all the cells in the body}}

{{hidden|What do we think that the rest of the genome does?|80% of the genome binds proteins, implying that it is involved in regulating gene expression, related to the regulation of gene expression, often in a cell-type specific fashion.}}

{{hidden|List the major classes of functional non-protein-coding sequences found in the human genome.|1. Promoter & enhancer, 2. Chromatin binding site structures, 3. non-coding regulatory RNAs, 4. Mobile genetic elements (transposons), 5. telomeres, 6. centromers. }}

{{hidden|What are the two most common forms of DNA variation in the human genome?|1) Single nucleotide polymorphisms (SNPs), 2) copy number variations (CNVs)}}

{{hidden|What are the possible implications of SNPs.|1) regulatory = alters gene expression, 2) Correlation with disease states when in close proximity with altered genes, 3) association used to define linkage disequilibrium,?}}

{{hidden|Define epigenetics.|Heritable changes in gene expression which are not caused by alterations in DNA sequence.}}

{{hidden|List the 6 types of epigenetic changes.|1) Histone & histone modifying factors (Histones organize chromatin into heterochromatin and euchromatin, 2) histone methylation, 3) histone acteylation, 4)histone phosphorylation, 5) DNA methylation, 6) Chromatin organizing factors.}}

{{hidden|What is the function of micro-RNA (mi-RNA)?|It does not encode protein, instead they function primarily to modulate the translation of target mRNAs into their corresponding proteins, and are responsible for post-transcriptional silencing of gene expression.}}

{{hidden|What is knockdown technology?|The use of synthetic si-RNA (short RNA sequences) introduced into cells that serve as substrates for Dicer and interact with the RISC complex in a manner analogous to endogenous miRNAs, and are used to study gene function, and are being developed as therapeutic agents to silence pathogenic genes, e.g. oncogenic in neoplasms.}}

{{hidden|What is long non coding RNA?|Lnc-RNA modulate gene expression by binding to regions of chromatin, restricting RNA polymerase access to coding genes within the region, and may exceed the number of mRNA's by 10-20 fold.}}

{{hidden|What is XIST?|XIST is a lnc-RNA which is transcribed from the X-chromosome and plays an essential role in physiologic X chromosome inactivation, though not inactivated itself, it forms a repressive cloak on the X chromosome from which it is transcribed resulting in gene silencing.}}

{{hidden|What are the cellular housekeeping functions?|1) protection from the environment, 2) nutrient acquisition, 3) communication, 4) movement, 5) renewal of senescent molecules, 6) molecular catabolism, 7) energy generation.}}

{{hidden|List the cellular compartments and the role in the cell.|1) cytosol = metabolism, transport, protein translation, 2) Mitochondria = energy generation, apoptosis, 3) Rough ER = synthesis of membrane and secreted proteins, 4) Smooth ER / Golgi = protein modification, sorting, catabolism, 5)Nucleus = cell regulation, proliferation, DNA transcription, 6) Endosomes = intracellular transport and export, ingestion of extracellular substances, 7) Lysosomes = cellular catabolism, 8) peroxisomes = very long-chain fatty acid metabolism}}

{{hidden|Describe the basic structure and functions of the cell membrane.| The plasma membrane is composed of a lipid bilayer of phospholipids studded with a variety of proteins and glycoproteins involved in ion and metabolite transport, fluid phase and receptor-mediated uptake of macromolecules, cell-ligand/cell matrix/cell-cell interactions.}}

{{hidden|How are the large complexes in the plasma membrane formed?|They aggregate under the control of chaperone molecules in the RER or by lateral diffusion in the plasma membrane followed by complex formation in situ.}}

{{hidden|What are aquaporins?|Special integral membrane proteins which augment passive water transport in tissues where water is transported in large volumes.}}

{{hidden|How are channel and carrier proteins different?|Channel proteins created hydrophilic pores, permit rapid movement of solutes, restricted by size and charge, where Carrier proteins bind to their specific solutes and undergo a series of conformational changes to transfer the ligand across the membrane, relatively slow transport.}}

{{hidden|What is the "multidrug resistance (MDR) protein"?|A type of transporter ATPases which pumps polar compounds (e.g. chemo drugs) out of cells which may render cancer cells resistant to treatment.}}

{{hidden|What are the two fundamental mechanisms of fluid or macromolecules by the cell (endocytosis)?|1)Caveolae -invaginations of the plasma membrane, 2) Pinocytosis/receptor mediated endocytosis - macromolecules bind to receptor and membranes invaginate around it.}}

{{hidden|What is exocytosis?|It is the opposite process of pinocytosis, where the receptor bound macromolecule is move to the cell surface and released.}}

{{hidden|Describe the difference between phagocytosis and transcytosis.|In phagocytosis microbes are ingested forming phagosomes, which fuse with lysosomes and become phagylosomes, releasing undigested residual material when fusing again with the external membrane, in contrast transcytosis the materials are carried across the cell membrane unaltered.}}

{{hidden|List the three major classes of 3 cytoskeleton proteins.|1) Actin, 2)Intermediate filaments, 3)Microtubules}}

{{hidden|Describe actin.|Actin - 5 to 9nm diam fibrils, G-actin polymerized into F-actin, the form double strands helices, which interact with myosin (filamentous protein).}}

{{hidden|List the various intermediate filaments, which are 10nm in diameter.|1) Lamin A, B, and C (nuclear lamins of all cells, 2) Vimentin (mesenchymal), 3)Desmin (scaffold for actin/myosin), 4) Neurofilaments (axons of neurons), 5) Glial filament protein (glial cells), 6)Cytokeratins (acid and basic and vary based on cell type). }}

{{hidden|Describe microtubules.|Microtubules are 25nm diam fibrils of dimers of a and b tubulin, with a negative end embedded in the centrosome near the nucleus, the + end grows or shrinks as needed. There are kinesins and dyneins motors that move stuff around the cell, also found in cilia and flagella.}}

{{hidden|What is clatharin?|A molecule found in the cell membrane that when the cell membrane invaginates forming a basket like structure.}}

{{hidden|List and describe the 3 main classifications of cell junctions.|1) Tight /occluding junctions - form a high resistance barrier to solute movement, and allows the cell to maintain polarity, 2) anchoring junctions / desmosomes - mechanically attach the cell and their cytoskeleton to other cells and the ECM (hemidesmosome), 3)communicating/gap junctions - mediate the passage of chemical or electrical signals from one cell to another.}}

{{hidden|What is the "unfolded protein response"?| Excess accumulation of misfolded protiens, which exceed the capacity of the ER to edit and degrade them, leads to the the ER stress response (UPR) that triggers cell death through apoptosis.}}

{{hidden|What cell organelle has a reactive hyperplasia with repeated exposure to phenobarbitol catabolism in the cytocrhome p450 system?|Smooth endoplasmic reticulum.}}

{{hidden|List three main functions of mitochondria.|1) Energy generation, 2) intermediate metabolism (instead of ATP make intemediate that can be used to make lipids, nucleic acids, and proteins), 3) Cell death ( necrosis & apoptosis)}}

{{hidden|List and describe the four extracellular cell-cell signaling pathways based on the distance the signal travels.|1)Paracrine (immediate vicinity), 2) Autocrine (cell affecting itself), 3) Synaptic (neurons sending neurotransmitters at synapse), 4) endocrine (signals released elsewhere into bloodstream).}}

{{hidden|What are the two characterizing features of stem cells?|Self renewal and asymmetric division (one daughter cell stays a stem cell)}}

{{hidden|What are the two types of stem cells?|embryonic stem cells (inner cell mass of the blastocyst, totipotent), and tissue/adult stem cells (found in stem cell niches associated with specialized tissues, limited repetoire of differentiation = multipotent)}}

{{hidden|What is the Warburg effect?|Increased cellular uptake of glucose and glutamine, increased glycolysis, and decreased oxidative phosphorylation by the cell.}}

{{hidden|Which CDKI's have selective effects on CDK4 and CDK6?|p15,p16,p17,and p19}}

{{hidden|List some examples of signal transduction pathways.|1) Receptor tyrosine kinases (RTKs), 2) Nonreceptor tyrosine kinase, 3) G-protein coupled receptors, 4) nuclear receptors, 5)Notch family receptors, 6) Wnt protein ligands (Frizzled family receptors).}}

{{hidden|Why does nuclear beta catenin occur in some neoplasms?|When Wnt ligand bins to frizzled it recruits Disheveled, this leads to the disruption of the wnt-ubiquitin complex, this stabilized pool of b-catening is then translocated to the nucleus forming a transcriptional complex}}

{{hidden|On Page 19 there is a table of growth factors involved in regeneration and repair, please review.|}}

{{hidden|Describe the function of cadherin.|}}

{{hidden|What are the functions of the extracellular matrix?|Mechanical support, control of cell proliferation, scaffolding for tissue renewal, establishment of tissue microenvironments}}

{{hidden|What are the two basic forms of the ECM?|interstitial matrix (fibrillar and non fibrillar collagen, fibronectin, elastin, proteoglycans, hyloronate, and other stuff), basement membrane (type IV collagen and laminin) }}

{{hidden|What are the three proteins groups in the ECM?|1) fibrous structural proteins (collagen, elastins), 2) water hydrated gels (proteoglycans and hyaluronan), 3) adhesive glycoproteins (connect ECM to each other and other cells)}}

{{hidden|Describe the structure of a protein that is dependent on vitamin C.|Collagen is composed of 3 seprate polypeptide chains braided into a rope like triple helix, lateral cross linking of the triple helices by lysyl oxidase (requires vitamin C) give it it's tensile strength. }}

{{hidden|List three non-fibrillar collagens.|Type IV -basement membrane, Type IX - Fibrillar associated collagen with interrupted triple helices (FACIT), Type VII (provides anchoring fibrils to basement membrane beneath skin)}}

{{hidden|Which structural protein is associated with Marfan syndrom?|Fibrillin synthetic defects, which wrap the elastin core. }}}}

== Chapter 2: Cellular Responses to Stress and Toxic Insults: Adaptation, Injury and Death ==
{{hidden|Short Answer Questions|
{{hidden|<left>What are the four aspects of a disease?</left>|
*1. Etiology
**Genetic - Inherited mutations and disease-associated gene variants, or polymorphisms
**Acquired - Infectious, nutritional, chemical and physical.
*2. Pathogenesis - The sequence of cellular, biochemical, and molecular events that follow the exposure of cells or tissues to an injurious agent.
*3. Morphological changes - The structural alterations in cells or tissues that are either characteristic of a disease or diagnostic of an etiologic process.
*4. Clinical Manifestations - Symptoms and signs of disease, as well as its clinical course and outcome}}

}}

== Chapter 3 ==
== Chapter 4 ==
== Chapter 5 ==
{{hidden|MC cause of spontaneous abortion is ?|<center>[[ A demonstrable chromosomal abnormality.]]</center>}}

{{hidden|1% of all newborn infants possess a gross chromosomal abnormality and 5% of people <25y present with |<center>[[a genetic disease. ]]</center>}}

{{hidden|Mutation|<center>[[permanent change in the DNA, if affect germ cells are transmitted to the progeny ]]</center>}}

{{hidden|List and describe 4 broad categories of human genetic disorders:|<center>[[Disorders related to mutation sin single genes with large effects i. Usually follow classic Mendelian pattern of inheritance
ii. Often highly penetrant (large proportion of pop with gene has disease)
b. Chromosomal disorders
i. Structural or numerical alterations in autosomes and sex chromosomes
ii. Uncommon, high penetrance
c. Complex multigenic disorders
i. Interactions between multiple variant forms of genes and environmental factors (polymorphisms), poly genic means disease when many polymorphism present
d. Single gene disorders with nonclassic patterns of inheritance (not mendelian)
i. Disorders resulting from triplet repeat mutations
ii. Mutations in mitochondrial DNA
iii. Those influenced by genomic imprinting
iv. Those influenced by gonadal mosaicism]]</center>}}

{{hidden|List and describe the possible outcomes of a point mutation in a coding region?|[[a. Missense mutation – pt mutation changes amino acid code, conservative when the amino acid is preserved, non conservative when replaced with another amino acid, b. Nonsense mutation – makes a stop codon ]]</center>}}

{{hidden|List and describe the possible outcomes of point mutation or deletion in a non-coding region.|<center>[[a. Promoters/enhancers – interfere with binding of transcription factors, marker reduction or total lack of transcription, b. Introns – defective splicing > failure to make mature RNA > no translation]]</center>}}

{{hidden|List and describe the possible outcomes of deletions and insertions.|<center>[[a.Small coding: not multiple of three = frameshift, if multiple of 3 than add or del amino acids accordingly, often premature stop codon
i. Tay Sachs disease: 4 base pair insertion in Hexosaminidase A gene ]]}}

{{hidden|List and describe the possible outcomes of trinucleotide repeat mutations.|[[a. Usually G&C, dynamic and increase during gametogenesis, “RNA stutters”,b. Fragile X – CGG 250-4000, Huntinton’s Disease ]]}}

{{hidden|List and describe three examples of inheritance of single gene mutations|[[a. AD – manifested in the heterologous state, one parent of index case is usually affected, males and females affected and both can transmit conditioni. De novo cases may not have affected parentii. Penetrance = fraction of people with gene who have the traitiii. Variable expressivity = those with mutant gene have variety of phenotypesiv. Often age of onset is delayed so can reproduce before die from diseasev. Biochem mechanisms1. Reduced production of a protein or dysfunctional/inactive protein2. Involved in regulation of complex metabolic pathyway subject to feedback inhibition3. Key structural proteins (collagen and cytoskeleton of RBC)a. May be a dominant negative , e.g. osteogenesis imperfecta4. Gain of function are rare, 2 formsa. Increased in proteins normal function (excess enzyme activity)b. Huntinton’s diseas (abn protein accumulates, toxic to neurons)b. ARi. Largest category – both alleles at a locus are mutated1. Expression is uniform, complete penetrance common, early onset, unaffected carrier family members, mostly enzymesc. X Linkedi. All sex linked, and almost all are recessive , if Y Chromosome affected usually infertile males > no progenyii. Male expression b/c hemizygous, daughter carriers with variable phenotype because of lionization of 2nd X e.g G6DPiii. Dominant . vitamin D resistant rickets]]</center>}}

Stopped at P142

== Chapter 6 ==
== Chapter 7 ==
== Chapter 8 ==
== Chapter 9 ==
== Chapter 10 ==
== Chapter 11 ==
== Chapter 12 ==
== Chapter 13 ==
== Chapter 14 ==
== Chapter 15 ==
== Chapter 16 ==
== Chapter 17 ==
== Chapter 18 ==
== Chapter 19 ==
== Chapter 20 ==
== Chapter 21 ==
== Chapter 22 ==
== Chapter 23 ==
== Chapter 24 ==
== Chapter 25 ==
== Chapter 26 ==
== Chapter 27 ==
== Chapter 28 ==
== Chapter 29 ==

Robbins and Cotran 9th Edition Questions

2015-05-27T17:14:13Z

Yuanny: /* Chapter 2: Cellular Responses to Stress and Toxic Insults: Adaptation, Injury and Death */

== Chapter 1: The Cell as a Unit of Health and Disease==

{{hidden| Short Answer Questions |
{{hidden|How much of the human genome is coding and what does it code?|Of the 3.2b basepairs, there are 20,000 genes that comprise about 1.5% of the genome that code for proteins (enzymes, structural components, and signaling molecules used to assemble and maintain all the cells in the body}}

{{hidden|What do we think that the rest of the genome does?|80% of the genome binds proteins, implying that it is involved in regulating gene expression, related to the regulation of gene expression, often in a cell-type specific fashion.}}

{{hidden|List the major classes of functional non-protein-coding sequences found in the human genome.|1. Promoter & enhancer, 2. Chromatin binding site structures, 3. non-coding regulatory RNAs, 4. Mobile genetic elements (transposons), 5. telomeres, 6. centromers. }}

{{hidden|What are the two most common forms of DNA variation in the human genome?|1) Single nucleotide polymorphisms (SNPs), 2) copy number variations (CNVs)}}

{{hidden|What are the possible implications of SNPs.|1) regulatory = alters gene expression, 2) Correlation with disease states when in close proximity with altered genes, 3) association used to define linkage disequilibrium,?}}

{{hidden|Define epigenetics.|Heritable changes in gene expression which are not caused by alterations in DNA sequence.}}

{{hidden|List the 6 types of epigenetic changes.|1) Histone & histone modifying factors (Histones organize chromatin into heterochromatin and euchromatin, 2) histone methylation, 3) histone acteylation, 4)histone phosphorylation, 5) DNA methylation, 6) Chromatin organizing factors.}}

{{hidden|What is the function of micro-RNA (mi-RNA)?|It does not encode protein, instead they function primarily to modulate the translation of target mRNAs into their corresponding proteins, and are responsible for post-transcriptional silencing of gene expression.}}

{{hidden|What is knockdown technology?|The use of synthetic si-RNA (short RNA sequences) introduced into cells that serve as substrates for Dicer and interact with the RISC complex in a manner analogous to endogenous miRNAs, and are used to study gene function, and are being developed as therapeutic agents to silence pathogenic genes, e.g. oncogenic in neoplasms.}}

{{hidden|What is long non coding RNA?|Lnc-RNA modulate gene expression by binding to regions of chromatin, restricting RNA polymerase access to coding genes within the region, and may exceed the number of mRNA's by 10-20 fold.}}

{{hidden|What is XIST?|XIST is a lnc-RNA which is transcribed from the X-chromosome and plays an essential role in physiologic X chromosome inactivation, though not inactivated itself, it forms a repressive cloak on the X chromosome from which it is transcribed resulting in gene silencing.}}

{{hidden|What are the cellular housekeeping functions?|1) protection from the environment, 2) nutrient acquisition, 3) communication, 4) movement, 5) renewal of senescent molecules, 6) molecular catabolism, 7) energy generation.}}

{{hidden|List the cellular compartments and the role in the cell.|1) cytosol = metabolism, transport, protein translation, 2) Mitochondria = energy generation, apoptosis, 3) Rough ER = synthesis of membrane and secreted proteins, 4) Smooth ER / Golgi = protein modification, sorting, catabolism, 5)Nucleus = cell regulation, proliferation, DNA transcription, 6) Endosomes = intracellular transport and export, ingestion of extracellular substances, 7) Lysosomes = cellular catabolism, 8) peroxisomes = very long-chain fatty acid metabolism}}

{{hidden|Describe the basic structure and functions of the cell membrane.| The plasma membrane is composed of a lipid bilayer of phospholipids studded with a variety of proteins and glycoproteins involved in ion and metabolite transport, fluid phase and receptor-mediated uptake of macromolecules, cell-ligand/cell matrix/cell-cell interactions.}}

{{hidden|How are the large complexes in the plasma membrane formed?|They aggregate under the control of chaperone molecules in the RER or by lateral diffusion in the plasma membrane followed by complex formation in situ.}}

{{hidden|What are aquaporins?|Special integral membrane proteins which augment passive water transport in tissues where water is transported in large volumes.}}

{{hidden|How are channel and carrier proteins different?|Channel proteins created hydrophilic pores, permit rapid movement of solutes, restricted by size and charge, where Carrier proteins bind to their specific solutes and undergo a series of conformational changes to transfer the ligand across the membrane, relatively slow transport.}}

{{hidden|What is the "multidrug resistance (MDR) protein"?|A type of transporter ATPases which pumps polar compounds (e.g. chemo drugs) out of cells which may render cancer cells resistant to treatment.}}

{{hidden|What are the two fundamental mechanisms of fluid or macromolecules by the cell (endocytosis)?|1)Caveolae -invaginations of the plasma membrane, 2) Pinocytosis/receptor mediated endocytosis - macromolecules bind to receptor and membranes invaginate around it.}}

{{hidden|What is exocytosis?|It is the opposite process of pinocytosis, where the receptor bound macromolecule is move to the cell surface and released.}}

{{hidden|Describe the difference between phagocytosis and transcytosis.|In phagocytosis microbes are ingested forming phagosomes, which fuse with lysosomes and become phagylosomes, releasing undigested residual material when fusing again with the external membrane, in contrast transcytosis the materials are carried across the cell membrane unaltered.}}

{{hidden|List the three major classes of 3 cytoskeleton proteins.|1) Actin, 2)Intermediate filaments, 3)Microtubules}}

{{hidden|Describe actin.|Actin - 5 to 9nm diam fibrils, G-actin polymerized into F-actin, the form double strands helices, which interact with myosin (filamentous protein).}}

{{hidden|List the various intermediate filaments, which are 10nm in diameter.|1) Lamin A, B, and C (nuclear lamins of all cells, 2) Vimentin (mesenchymal), 3)Desmin (scaffold for actin/myosin), 4) Neurofilaments (axons of neurons), 5) Glial filament protein (glial cells), 6)Cytokeratins (acid and basic and vary based on cell type). }}

{{hidden|Describe microtubules.|Microtubules are 25nm diam fibrils of dimers of a and b tubulin, with a negative end embedded in the centrosome near the nucleus, the + end grows or shrinks as needed. There are kinesins and dyneins motors that move stuff around the cell, also found in cilia and flagella.}}

{{hidden|What is clatharin?|A molecule found in the cell membrane that when the cell membrane invaginates forming a basket like structure.}}

{{hidden|List and describe the 3 main classifications of cell junctions.|1) Tight /occluding junctions - form a high resistance barrier to solute movement, and allows the cell to maintain polarity, 2) anchoring junctions / desmosomes - mechanically attach the cell and their cytoskeleton to other cells and the ECM (hemidesmosome), 3)communicating/gap junctions - mediate the passage of chemical or electrical signals from one cell to another.}}

{{hidden|What is the "unfolded protein response"?| Excess accumulation of misfolded protiens, which exceed the capacity of the ER to edit and degrade them, leads to the the ER stress response (UPR) that triggers cell death through apoptosis.}}

{{hidden|What cell organelle has a reactive hyperplasia with repeated exposure to phenobarbitol catabolism in the cytocrhome p450 system?|Smooth endoplasmic reticulum.}}

{{hidden|List three main functions of mitochondria.|1) Energy generation, 2) intermediate metabolism (instead of ATP make intemediate that can be used to make lipids, nucleic acids, and proteins), 3) Cell death ( necrosis & apoptosis)}}

{{hidden|List and describe the four extracellular cell-cell signaling pathways based on the distance the signal travels.|1)Paracrine (immediate vicinity), 2) Autocrine (cell affecting itself), 3) Synaptic (neurons sending neurotransmitters at synapse), 4) endocrine (signals released elsewhere into bloodstream).}}

{{hidden|What are the two characterizing features of stem cells?|Self renewal and asymmetric division (one daughter cell stays a stem cell)}}

{{hidden|What are the two types of stem cells?|embryonic stem cells (inner cell mass of the blastocyst, totipotent), and tissue/adult stem cells (found in stem cell niches associated with specialized tissues, limited repetoire of differentiation = multipotent)}}

{{hidden|What is the Warburg effect?|Increased cellular uptake of glucose and glutamine, increased glycolysis, and decreased oxidative phosphorylation by the cell.}}

{{hidden|Which CDKI's have selective effects on CDK4 and CDK6?|p15,p16,p17,and p19}}

{{hidden|List some examples of signal transduction pathways.|1) Receptor tyrosine kinases (RTKs), 2) Nonreceptor tyrosine kinase, 3) G-protein coupled receptors, 4) nuclear receptors, 5)Notch family receptors, 6) Wnt protein ligands (Frizzled family receptors).}}

{{hidden|Why does nuclear beta catenin occur in some neoplasms?|When Wnt ligand bins to frizzled it recruits Disheveled, this leads to the disruption of the wnt-ubiquitin complex, this stabilized pool of b-catening is then translocated to the nucleus forming a transcriptional complex}}

{{hidden|On Page 19 there is a table of growth factors involved in regeneration and repair, please review.|}}

{{hidden|Describe the function of cadherin.|}}

{{hidden|What are the functions of the extracellular matrix?|Mechanical support, control of cell proliferation, scaffolding for tissue renewal, establishment of tissue microenvironments}}

{{hidden|What are the two basic forms of the ECM?|interstitial matrix (fibrillar and non fibrillar collagen, fibronectin, elastin, proteoglycans, hyloronate, and other stuff), basement membrane (type IV collagen and laminin) }}

{{hidden|What are the three proteins groups in the ECM?|1) fibrous structural proteins (collagen, elastins), 2) water hydrated gels (proteoglycans and hyaluronan), 3) adhesive glycoproteins (connect ECM to each other and other cells)}}

{{hidden|Describe the structure of a protein that is dependent on vitamin C.|Collagen is composed of 3 seprate polypeptide chains braided into a rope like triple helix, lateral cross linking of the triple helices by lysyl oxidase (requires vitamin C) give it it's tensile strength. }}

{{hidden|List three non-fibrillar collagens.|Type IV -basement membrane, Type IX - Fibrillar associated collagen with interrupted triple helices (FACIT), Type VII (provides anchoring fibrils to basement membrane beneath skin)}}

{{hidden|Which structural protein is associated with Marfan syndrom?|Fibrillin synthetic defects, which wrap the elastin core. }}}}

== Chapter 2: Cellular Responses to Stress and Toxic Insults: Adaptation, Injury and Death ==
{{hidden|Short Answer Questions|
{{hidden|What are the four aspects of a disease?|
*1. Etiology
**Genetic - Inherited mutations and disease-associated gene variants, or polymorphisms
**Acquired - Infectious, nutritional, chemical and physical.
*2. Pathogenesis - The sequence of cellular, biochemical, and molecular events that follow the exposure of cells or tissues to an injurious agent.
*3. Morphological changes - The structural alterations in cells or tissues that are either characteristic of a disease or diagnostic of an etiologic process.
*4. Clinical Manifestations - Symptoms and signs of disease, as well as its clinical course and outcome}}

}}

== Chapter 3 ==
== Chapter 4 ==
== Chapter 5 ==
{{hidden|MC cause of spontaneous abortion is ?|<center>[[ A demonstrable chromosomal abnormality.]]</center>}}

{{hidden|1% of all newborn infants possess a gross chromosomal abnormality and 5% of people <25y present with |<center>[[a genetic disease. ]]</center>}}

{{hidden|Mutation|<center>[[permanent change in the DNA, if affect germ cells are transmitted to the progeny ]]</center>}}

{{hidden|List and describe 4 broad categories of human genetic disorders:|<center>[[Disorders related to mutation sin single genes with large effects i. Usually follow classic Mendelian pattern of inheritance
ii. Often highly penetrant (large proportion of pop with gene has disease)
b. Chromosomal disorders
i. Structural or numerical alterations in autosomes and sex chromosomes
ii. Uncommon, high penetrance
c. Complex multigenic disorders
i. Interactions between multiple variant forms of genes and environmental factors (polymorphisms), poly genic means disease when many polymorphism present
d. Single gene disorders with nonclassic patterns of inheritance (not mendelian)
i. Disorders resulting from triplet repeat mutations
ii. Mutations in mitochondrial DNA
iii. Those influenced by genomic imprinting
iv. Those influenced by gonadal mosaicism]]</center>}}

{{hidden|List and describe the possible outcomes of a point mutation in a coding region?|[[a. Missense mutation – pt mutation changes amino acid code, conservative when the amino acid is preserved, non conservative when replaced with another amino acid, b. Nonsense mutation – makes a stop codon ]]</center>}}

{{hidden|List and describe the possible outcomes of point mutation or deletion in a non-coding region.|<center>[[a. Promoters/enhancers – interfere with binding of transcription factors, marker reduction or total lack of transcription, b. Introns – defective splicing > failure to make mature RNA > no translation]]</center>}}

{{hidden|List and describe the possible outcomes of deletions and insertions.|<center>[[a.Small coding: not multiple of three = frameshift, if multiple of 3 than add or del amino acids accordingly, often premature stop codon
i. Tay Sachs disease: 4 base pair insertion in Hexosaminidase A gene ]]}}

{{hidden|List and describe the possible outcomes of trinucleotide repeat mutations.|[[a. Usually G&C, dynamic and increase during gametogenesis, “RNA stutters”,b. Fragile X – CGG 250-4000, Huntinton’s Disease ]]}}

{{hidden|List and describe three examples of inheritance of single gene mutations|[[a. AD – manifested in the heterologous state, one parent of index case is usually affected, males and females affected and both can transmit conditioni. De novo cases may not have affected parentii. Penetrance = fraction of people with gene who have the traitiii. Variable expressivity = those with mutant gene have variety of phenotypesiv. Often age of onset is delayed so can reproduce before die from diseasev. Biochem mechanisms1. Reduced production of a protein or dysfunctional/inactive protein2. Involved in regulation of complex metabolic pathyway subject to feedback inhibition3. Key structural proteins (collagen and cytoskeleton of RBC)a. May be a dominant negative , e.g. osteogenesis imperfecta4. Gain of function are rare, 2 formsa. Increased in proteins normal function (excess enzyme activity)b. Huntinton’s diseas (abn protein accumulates, toxic to neurons)b. ARi. Largest category – both alleles at a locus are mutated1. Expression is uniform, complete penetrance common, early onset, unaffected carrier family members, mostly enzymesc. X Linkedi. All sex linked, and almost all are recessive , if Y Chromosome affected usually infertile males > no progenyii. Male expression b/c hemizygous, daughter carriers with variable phenotype because of lionization of 2nd X e.g G6DPiii. Dominant . vitamin D resistant rickets]]</center>}}

Stopped at P142

== Chapter 6 ==
== Chapter 7 ==
== Chapter 8 ==
== Chapter 9 ==
== Chapter 10 ==
== Chapter 11 ==
== Chapter 12 ==
== Chapter 13 ==
== Chapter 14 ==
== Chapter 15 ==
== Chapter 16 ==
== Chapter 17 ==
== Chapter 18 ==
== Chapter 19 ==
== Chapter 20 ==
== Chapter 21 ==
== Chapter 22 ==
== Chapter 23 ==
== Chapter 24 ==
== Chapter 25 ==
== Chapter 26 ==
== Chapter 27 ==
== Chapter 28 ==
== Chapter 29 ==

Robbins and Cotran 9th Edition Questions

2015-05-27T17:10:51Z

Yuanny: /* Chapter 1: The Cell as a Unit of Health and Disease */

== Chapter 1: The Cell as a Unit of Health and Disease==

{{hidden| Short Answer Questions |
{{hidden|How much of the human genome is coding and what does it code?|Of the 3.2b basepairs, there are 20,000 genes that comprise about 1.5% of the genome that code for proteins (enzymes, structural components, and signaling molecules used to assemble and maintain all the cells in the body}}

{{hidden|What do we think that the rest of the genome does?|80% of the genome binds proteins, implying that it is involved in regulating gene expression, related to the regulation of gene expression, often in a cell-type specific fashion.}}

{{hidden|List the major classes of functional non-protein-coding sequences found in the human genome.|1. Promoter & enhancer, 2. Chromatin binding site structures, 3. non-coding regulatory RNAs, 4. Mobile genetic elements (transposons), 5. telomeres, 6. centromers. }}

{{hidden|What are the two most common forms of DNA variation in the human genome?|1) Single nucleotide polymorphisms (SNPs), 2) copy number variations (CNVs)}}

{{hidden|What are the possible implications of SNPs.|1) regulatory = alters gene expression, 2) Correlation with disease states when in close proximity with altered genes, 3) association used to define linkage disequilibrium,?}}

{{hidden|Define epigenetics.|Heritable changes in gene expression which are not caused by alterations in DNA sequence.}}

{{hidden|List the 6 types of epigenetic changes.|1) Histone & histone modifying factors (Histones organize chromatin into heterochromatin and euchromatin, 2) histone methylation, 3) histone acteylation, 4)histone phosphorylation, 5) DNA methylation, 6) Chromatin organizing factors.}}

{{hidden|What is the function of micro-RNA (mi-RNA)?|It does not encode protein, instead they function primarily to modulate the translation of target mRNAs into their corresponding proteins, and are responsible for post-transcriptional silencing of gene expression.}}

{{hidden|What is knockdown technology?|The use of synthetic si-RNA (short RNA sequences) introduced into cells that serve as substrates for Dicer and interact with the RISC complex in a manner analogous to endogenous miRNAs, and are used to study gene function, and are being developed as therapeutic agents to silence pathogenic genes, e.g. oncogenic in neoplasms.}}

{{hidden|What is long non coding RNA?|Lnc-RNA modulate gene expression by binding to regions of chromatin, restricting RNA polymerase access to coding genes within the region, and may exceed the number of mRNA's by 10-20 fold.}}

{{hidden|What is XIST?|XIST is a lnc-RNA which is transcribed from the X-chromosome and plays an essential role in physiologic X chromosome inactivation, though not inactivated itself, it forms a repressive cloak on the X chromosome from which it is transcribed resulting in gene silencing.}}

{{hidden|What are the cellular housekeeping functions?|1) protection from the environment, 2) nutrient acquisition, 3) communication, 4) movement, 5) renewal of senescent molecules, 6) molecular catabolism, 7) energy generation.}}

{{hidden|List the cellular compartments and the role in the cell.|1) cytosol = metabolism, transport, protein translation, 2) Mitochondria = energy generation, apoptosis, 3) Rough ER = synthesis of membrane and secreted proteins, 4) Smooth ER / Golgi = protein modification, sorting, catabolism, 5)Nucleus = cell regulation, proliferation, DNA transcription, 6) Endosomes = intracellular transport and export, ingestion of extracellular substances, 7) Lysosomes = cellular catabolism, 8) peroxisomes = very long-chain fatty acid metabolism}}

{{hidden|Describe the basic structure and functions of the cell membrane.| The plasma membrane is composed of a lipid bilayer of phospholipids studded with a variety of proteins and glycoproteins involved in ion and metabolite transport, fluid phase and receptor-mediated uptake of macromolecules, cell-ligand/cell matrix/cell-cell interactions.}}

{{hidden|How are the large complexes in the plasma membrane formed?|They aggregate under the control of chaperone molecules in the RER or by lateral diffusion in the plasma membrane followed by complex formation in situ.}}

{{hidden|What are aquaporins?|Special integral membrane proteins which augment passive water transport in tissues where water is transported in large volumes.}}

{{hidden|How are channel and carrier proteins different?|Channel proteins created hydrophilic pores, permit rapid movement of solutes, restricted by size and charge, where Carrier proteins bind to their specific solutes and undergo a series of conformational changes to transfer the ligand across the membrane, relatively slow transport.}}

{{hidden|What is the "multidrug resistance (MDR) protein"?|A type of transporter ATPases which pumps polar compounds (e.g. chemo drugs) out of cells which may render cancer cells resistant to treatment.}}

{{hidden|What are the two fundamental mechanisms of fluid or macromolecules by the cell (endocytosis)?|1)Caveolae -invaginations of the plasma membrane, 2) Pinocytosis/receptor mediated endocytosis - macromolecules bind to receptor and membranes invaginate around it.}}

{{hidden|What is exocytosis?|It is the opposite process of pinocytosis, where the receptor bound macromolecule is move to the cell surface and released.}}

{{hidden|Describe the difference between phagocytosis and transcytosis.|In phagocytosis microbes are ingested forming phagosomes, which fuse with lysosomes and become phagylosomes, releasing undigested residual material when fusing again with the external membrane, in contrast transcytosis the materials are carried across the cell membrane unaltered.}}

{{hidden|List the three major classes of 3 cytoskeleton proteins.|1) Actin, 2)Intermediate filaments, 3)Microtubules}}

{{hidden|Describe actin.|Actin - 5 to 9nm diam fibrils, G-actin polymerized into F-actin, the form double strands helices, which interact with myosin (filamentous protein).}}

{{hidden|List the various intermediate filaments, which are 10nm in diameter.|1) Lamin A, B, and C (nuclear lamins of all cells, 2) Vimentin (mesenchymal), 3)Desmin (scaffold for actin/myosin), 4) Neurofilaments (axons of neurons), 5) Glial filament protein (glial cells), 6)Cytokeratins (acid and basic and vary based on cell type). }}

{{hidden|Describe microtubules.|Microtubules are 25nm diam fibrils of dimers of a and b tubulin, with a negative end embedded in the centrosome near the nucleus, the + end grows or shrinks as needed. There are kinesins and dyneins motors that move stuff around the cell, also found in cilia and flagella.}}

{{hidden|What is clatharin?|A molecule found in the cell membrane that when the cell membrane invaginates forming a basket like structure.}}

{{hidden|List and describe the 3 main classifications of cell junctions.|1) Tight /occluding junctions - form a high resistance barrier to solute movement, and allows the cell to maintain polarity, 2) anchoring junctions / desmosomes - mechanically attach the cell and their cytoskeleton to other cells and the ECM (hemidesmosome), 3)communicating/gap junctions - mediate the passage of chemical or electrical signals from one cell to another.}}

{{hidden|What is the "unfolded protein response"?| Excess accumulation of misfolded protiens, which exceed the capacity of the ER to edit and degrade them, leads to the the ER stress response (UPR) that triggers cell death through apoptosis.}}

{{hidden|What cell organelle has a reactive hyperplasia with repeated exposure to phenobarbitol catabolism in the cytocrhome p450 system?|Smooth endoplasmic reticulum.}}

{{hidden|List three main functions of mitochondria.|1) Energy generation, 2) intermediate metabolism (instead of ATP make intemediate that can be used to make lipids, nucleic acids, and proteins), 3) Cell death ( necrosis & apoptosis)}}

{{hidden|List and describe the four extracellular cell-cell signaling pathways based on the distance the signal travels.|1)Paracrine (immediate vicinity), 2) Autocrine (cell affecting itself), 3) Synaptic (neurons sending neurotransmitters at synapse), 4) endocrine (signals released elsewhere into bloodstream).}}

{{hidden|What are the two characterizing features of stem cells?|Self renewal and asymmetric division (one daughter cell stays a stem cell)}}

{{hidden|What are the two types of stem cells?|embryonic stem cells (inner cell mass of the blastocyst, totipotent), and tissue/adult stem cells (found in stem cell niches associated with specialized tissues, limited repetoire of differentiation = multipotent)}}

{{hidden|What is the Warburg effect?|Increased cellular uptake of glucose and glutamine, increased glycolysis, and decreased oxidative phosphorylation by the cell.}}

{{hidden|Which CDKI's have selective effects on CDK4 and CDK6?|p15,p16,p17,and p19}}

{{hidden|List some examples of signal transduction pathways.|1) Receptor tyrosine kinases (RTKs), 2) Nonreceptor tyrosine kinase, 3) G-protein coupled receptors, 4) nuclear receptors, 5)Notch family receptors, 6) Wnt protein ligands (Frizzled family receptors).}}

{{hidden|Why does nuclear beta catenin occur in some neoplasms?|When Wnt ligand bins to frizzled it recruits Disheveled, this leads to the disruption of the wnt-ubiquitin complex, this stabilized pool of b-catening is then translocated to the nucleus forming a transcriptional complex}}

{{hidden|On Page 19 there is a table of growth factors involved in regeneration and repair, please review.|}}

{{hidden|Describe the function of cadherin.|}}

{{hidden|What are the functions of the extracellular matrix?|Mechanical support, control of cell proliferation, scaffolding for tissue renewal, establishment of tissue microenvironments}}

{{hidden|What are the two basic forms of the ECM?|interstitial matrix (fibrillar and non fibrillar collagen, fibronectin, elastin, proteoglycans, hyloronate, and other stuff), basement membrane (type IV collagen and laminin) }}

{{hidden|What are the three proteins groups in the ECM?|1) fibrous structural proteins (collagen, elastins), 2) water hydrated gels (proteoglycans and hyaluronan), 3) adhesive glycoproteins (connect ECM to each other and other cells)}}

{{hidden|Describe the structure of a protein that is dependent on vitamin C.|Collagen is composed of 3 seprate polypeptide chains braided into a rope like triple helix, lateral cross linking of the triple helices by lysyl oxidase (requires vitamin C) give it it's tensile strength. }}

{{hidden|List three non-fibrillar collagens.|Type IV -basement membrane, Type IX - Fibrillar associated collagen with interrupted triple helices (FACIT), Type VII (provides anchoring fibrils to basement membrane beneath skin)}}

{{hidden|Which structural protein is associated with Marfan syndrom?|Fibrillin synthetic defects, which wrap the elastin core. }}}}

== Chapter 2: Cellular Responses to Stress and Toxic Insults: Adaptation, Injury and Death ==

{{hidden|What are the four aspects of a disease?|
*1. Etiology
**Genetic - Inherited mutations and disease-associated gene variants, or polymorphisms
**Acquired - Infectious, nutritional, chemical and physical.
*2. Pathogenesis - The sequence of cellular, biochemical, and molecular events that follow the exposure of cells or tissues to an injurious agent.
*3. Morphological changes - The structural alterations in cells or tissues that are either characteristic of a disease or diagnostic of an etiologic process.
*4. Clinical Manifestations - Symptoms and signs of disease, as well as its clinical course and outcome}}

== Chapter 3 ==
== Chapter 4 ==
== Chapter 5 ==
{{hidden|MC cause of spontaneous abortion is ?|<center>[[ A demonstrable chromosomal abnormality.]]</center>}}

{{hidden|1% of all newborn infants possess a gross chromosomal abnormality and 5% of people <25y present with |<center>[[a genetic disease. ]]</center>}}

{{hidden|Mutation|<center>[[permanent change in the DNA, if affect germ cells are transmitted to the progeny ]]</center>}}

{{hidden|List and describe 4 broad categories of human genetic disorders:|<center>[[Disorders related to mutation sin single genes with large effects i. Usually follow classic Mendelian pattern of inheritance
ii. Often highly penetrant (large proportion of pop with gene has disease)
b. Chromosomal disorders
i. Structural or numerical alterations in autosomes and sex chromosomes
ii. Uncommon, high penetrance
c. Complex multigenic disorders
i. Interactions between multiple variant forms of genes and environmental factors (polymorphisms), poly genic means disease when many polymorphism present
d. Single gene disorders with nonclassic patterns of inheritance (not mendelian)
i. Disorders resulting from triplet repeat mutations
ii. Mutations in mitochondrial DNA
iii. Those influenced by genomic imprinting
iv. Those influenced by gonadal mosaicism]]</center>}}

{{hidden|List and describe the possible outcomes of a point mutation in a coding region?|[[a. Missense mutation – pt mutation changes amino acid code, conservative when the amino acid is preserved, non conservative when replaced with another amino acid, b. Nonsense mutation – makes a stop codon ]]</center>}}

{{hidden|List and describe the possible outcomes of point mutation or deletion in a non-coding region.|<center>[[a. Promoters/enhancers – interfere with binding of transcription factors, marker reduction or total lack of transcription, b. Introns – defective splicing > failure to make mature RNA > no translation]]</center>}}

{{hidden|List and describe the possible outcomes of deletions and insertions.|<center>[[a.Small coding: not multiple of three = frameshift, if multiple of 3 than add or del amino acids accordingly, often premature stop codon
i. Tay Sachs disease: 4 base pair insertion in Hexosaminidase A gene ]]}}

{{hidden|List and describe the possible outcomes of trinucleotide repeat mutations.|[[a. Usually G&C, dynamic and increase during gametogenesis, “RNA stutters”,b. Fragile X – CGG 250-4000, Huntinton’s Disease ]]}}

{{hidden|List and describe three examples of inheritance of single gene mutations|[[a. AD – manifested in the heterologous state, one parent of index case is usually affected, males and females affected and both can transmit conditioni. De novo cases may not have affected parentii. Penetrance = fraction of people with gene who have the traitiii. Variable expressivity = those with mutant gene have variety of phenotypesiv. Often age of onset is delayed so can reproduce before die from diseasev. Biochem mechanisms1. Reduced production of a protein or dysfunctional/inactive protein2. Involved in regulation of complex metabolic pathyway subject to feedback inhibition3. Key structural proteins (collagen and cytoskeleton of RBC)a. May be a dominant negative , e.g. osteogenesis imperfecta4. Gain of function are rare, 2 formsa. Increased in proteins normal function (excess enzyme activity)b. Huntinton’s diseas (abn protein accumulates, toxic to neurons)b. ARi. Largest category – both alleles at a locus are mutated1. Expression is uniform, complete penetrance common, early onset, unaffected carrier family members, mostly enzymesc. X Linkedi. All sex linked, and almost all are recessive , if Y Chromosome affected usually infertile males > no progenyii. Male expression b/c hemizygous, daughter carriers with variable phenotype because of lionization of 2nd X e.g G6DPiii. Dominant . vitamin D resistant rickets]]</center>}}

Stopped at P142

== Chapter 6 ==
== Chapter 7 ==
== Chapter 8 ==
== Chapter 9 ==
== Chapter 10 ==
== Chapter 11 ==
== Chapter 12 ==
== Chapter 13 ==
== Chapter 14 ==
== Chapter 15 ==
== Chapter 16 ==
== Chapter 17 ==
== Chapter 18 ==
== Chapter 19 ==
== Chapter 20 ==
== Chapter 21 ==
== Chapter 22 ==
== Chapter 23 ==
== Chapter 24 ==
== Chapter 25 ==
== Chapter 26 ==
== Chapter 27 ==
== Chapter 28 ==
== Chapter 29 ==

Robbins and Cotran 9th Edition Questions

2015-05-27T17:09:46Z

Yuanny: /* Chapter 1: The Cell as a Unit of Health and Disease */

== Chapter 1: The Cell as a Unit of Health and Disease==

{{hidden| == Chapter 1: The Cell as a Unit of Health and Disease== |
{{hidden|How much of the human genome is coding and what does it code?|Of the 3.2b basepairs, there are 20,000 genes that comprise about 1.5% of the genome that code for proteins (enzymes, structural components, and signaling molecules used to assemble and maintain all the cells in the body}}

{{hidden|What do we think that the rest of the genome does?|80% of the genome binds proteins, implying that it is involved in regulating gene expression, related to the regulation of gene expression, often in a cell-type specific fashion.}}

{{hidden|List the major classes of functional non-protein-coding sequences found in the human genome.|1. Promoter & enhancer, 2. Chromatin binding site structures, 3. non-coding regulatory RNAs, 4. Mobile genetic elements (transposons), 5. telomeres, 6. centromers. }}

{{hidden|What are the two most common forms of DNA variation in the human genome?|1) Single nucleotide polymorphisms (SNPs), 2) copy number variations (CNVs)}}

{{hidden|What are the possible implications of SNPs.|1) regulatory = alters gene expression, 2) Correlation with disease states when in close proximity with altered genes, 3) association used to define linkage disequilibrium,?}}

{{hidden|Define epigenetics.|Heritable changes in gene expression which are not caused by alterations in DNA sequence.}}

{{hidden|List the 6 types of epigenetic changes.|1) Histone & histone modifying factors (Histones organize chromatin into heterochromatin and euchromatin, 2) histone methylation, 3) histone acteylation, 4)histone phosphorylation, 5) DNA methylation, 6) Chromatin organizing factors.}}

{{hidden|What is the function of micro-RNA (mi-RNA)?|It does not encode protein, instead they function primarily to modulate the translation of target mRNAs into their corresponding proteins, and are responsible for post-transcriptional silencing of gene expression.}}

{{hidden|What is knockdown technology?|The use of synthetic si-RNA (short RNA sequences) introduced into cells that serve as substrates for Dicer and interact with the RISC complex in a manner analogous to endogenous miRNAs, and are used to study gene function, and are being developed as therapeutic agents to silence pathogenic genes, e.g. oncogenic in neoplasms.}}

{{hidden|What is long non coding RNA?|Lnc-RNA modulate gene expression by binding to regions of chromatin, restricting RNA polymerase access to coding genes within the region, and may exceed the number of mRNA's by 10-20 fold.}}

{{hidden|What is XIST?|XIST is a lnc-RNA which is transcribed from the X-chromosome and plays an essential role in physiologic X chromosome inactivation, though not inactivated itself, it forms a repressive cloak on the X chromosome from which it is transcribed resulting in gene silencing.}}

{{hidden|What are the cellular housekeeping functions?|1) protection from the environment, 2) nutrient acquisition, 3) communication, 4) movement, 5) renewal of senescent molecules, 6) molecular catabolism, 7) energy generation.}}

{{hidden|List the cellular compartments and the role in the cell.|1) cytosol = metabolism, transport, protein translation, 2) Mitochondria = energy generation, apoptosis, 3) Rough ER = synthesis of membrane and secreted proteins, 4) Smooth ER / Golgi = protein modification, sorting, catabolism, 5)Nucleus = cell regulation, proliferation, DNA transcription, 6) Endosomes = intracellular transport and export, ingestion of extracellular substances, 7) Lysosomes = cellular catabolism, 8) peroxisomes = very long-chain fatty acid metabolism}}

{{hidden|Describe the basic structure and functions of the cell membrane.| The plasma membrane is composed of a lipid bilayer of phospholipids studded with a variety of proteins and glycoproteins involved in ion and metabolite transport, fluid phase and receptor-mediated uptake of macromolecules, cell-ligand/cell matrix/cell-cell interactions.}}

{{hidden|How are the large complexes in the plasma membrane formed?|They aggregate under the control of chaperone molecules in the RER or by lateral diffusion in the plasma membrane followed by complex formation in situ.}}

{{hidden|What are aquaporins?|Special integral membrane proteins which augment passive water transport in tissues where water is transported in large volumes.}}

{{hidden|How are channel and carrier proteins different?|Channel proteins created hydrophilic pores, permit rapid movement of solutes, restricted by size and charge, where Carrier proteins bind to their specific solutes and undergo a series of conformational changes to transfer the ligand across the membrane, relatively slow transport.}}

{{hidden|What is the "multidrug resistance (MDR) protein"?|A type of transporter ATPases which pumps polar compounds (e.g. chemo drugs) out of cells which may render cancer cells resistant to treatment.}}

{{hidden|What are the two fundamental mechanisms of fluid or macromolecules by the cell (endocytosis)?|1)Caveolae -invaginations of the plasma membrane, 2) Pinocytosis/receptor mediated endocytosis - macromolecules bind to receptor and membranes invaginate around it.}}

{{hidden|What is exocytosis?|It is the opposite process of pinocytosis, where the receptor bound macromolecule is move to the cell surface and released.}}

{{hidden|Describe the difference between phagocytosis and transcytosis.|In phagocytosis microbes are ingested forming phagosomes, which fuse with lysosomes and become phagylosomes, releasing undigested residual material when fusing again with the external membrane, in contrast transcytosis the materials are carried across the cell membrane unaltered.}}

{{hidden|List the three major classes of 3 cytoskeleton proteins.|1) Actin, 2)Intermediate filaments, 3)Microtubules}}

{{hidden|Describe actin.|Actin - 5 to 9nm diam fibrils, G-actin polymerized into F-actin, the form double strands helices, which interact with myosin (filamentous protein).}}

{{hidden|List the various intermediate filaments, which are 10nm in diameter.|1) Lamin A, B, and C (nuclear lamins of all cells, 2) Vimentin (mesenchymal), 3)Desmin (scaffold for actin/myosin), 4) Neurofilaments (axons of neurons), 5) Glial filament protein (glial cells), 6)Cytokeratins (acid and basic and vary based on cell type). }}

{{hidden|Describe microtubules.|Microtubules are 25nm diam fibrils of dimers of a and b tubulin, with a negative end embedded in the centrosome near the nucleus, the + end grows or shrinks as needed. There are kinesins and dyneins motors that move stuff around the cell, also found in cilia and flagella.}}

{{hidden|What is clatharin?|A molecule found in the cell membrane that when the cell membrane invaginates forming a basket like structure.}}

{{hidden|List and describe the 3 main classifications of cell junctions.|1) Tight /occluding junctions - form a high resistance barrier to solute movement, and allows the cell to maintain polarity, 2) anchoring junctions / desmosomes - mechanically attach the cell and their cytoskeleton to other cells and the ECM (hemidesmosome), 3)communicating/gap junctions - mediate the passage of chemical or electrical signals from one cell to another.}}

{{hidden|What is the "unfolded protein response"?| Excess accumulation of misfolded protiens, which exceed the capacity of the ER to edit and degrade them, leads to the the ER stress response (UPR) that triggers cell death through apoptosis.}}

{{hidden|What cell organelle has a reactive hyperplasia with repeated exposure to phenobarbitol catabolism in the cytocrhome p450 system?|Smooth endoplasmic reticulum.}}

{{hidden|List three main functions of mitochondria.|1) Energy generation, 2) intermediate metabolism (instead of ATP make intemediate that can be used to make lipids, nucleic acids, and proteins), 3) Cell death ( necrosis & apoptosis)}}

{{hidden|List and describe the four extracellular cell-cell signaling pathways based on the distance the signal travels.|1)Paracrine (immediate vicinity), 2) Autocrine (cell affecting itself), 3) Synaptic (neurons sending neurotransmitters at synapse), 4) endocrine (signals released elsewhere into bloodstream).}}

{{hidden|What are the two characterizing features of stem cells?|Self renewal and asymmetric division (one daughter cell stays a stem cell)}}

{{hidden|What are the two types of stem cells?|embryonic stem cells (inner cell mass of the blastocyst, totipotent), and tissue/adult stem cells (found in stem cell niches associated with specialized tissues, limited repetoire of differentiation = multipotent)}}

{{hidden|What is the Warburg effect?|Increased cellular uptake of glucose and glutamine, increased glycolysis, and decreased oxidative phosphorylation by the cell.}}

{{hidden|Which CDKI's have selective effects on CDK4 and CDK6?|p15,p16,p17,and p19}}

{{hidden|List some examples of signal transduction pathways.|1) Receptor tyrosine kinases (RTKs), 2) Nonreceptor tyrosine kinase, 3) G-protein coupled receptors, 4) nuclear receptors, 5)Notch family receptors, 6) Wnt protein ligands (Frizzled family receptors).}}

{{hidden|Why does nuclear beta catenin occur in some neoplasms?|When Wnt ligand bins to frizzled it recruits Disheveled, this leads to the disruption of the wnt-ubiquitin complex, this stabilized pool of b-catening is then translocated to the nucleus forming a transcriptional complex}}

{{hidden|On Page 19 there is a table of growth factors involved in regeneration and repair, please review.|}}

{{hidden|Describe the function of cadherin.|}}

{{hidden|What are the functions of the extracellular matrix?|Mechanical support, control of cell proliferation, scaffolding for tissue renewal, establishment of tissue microenvironments}}

{{hidden|What are the two basic forms of the ECM?|interstitial matrix (fibrillar and non fibrillar collagen, fibronectin, elastin, proteoglycans, hyloronate, and other stuff), basement membrane (type IV collagen and laminin) }}

{{hidden|What are the three proteins groups in the ECM?|1) fibrous structural proteins (collagen, elastins), 2) water hydrated gels (proteoglycans and hyaluronan), 3) adhesive glycoproteins (connect ECM to each other and other cells)}}

{{hidden|Describe the structure of a protein that is dependent on vitamin C.|Collagen is composed of 3 seprate polypeptide chains braided into a rope like triple helix, lateral cross linking of the triple helices by lysyl oxidase (requires vitamin C) give it it's tensile strength. }}

{{hidden|List three non-fibrillar collagens.|Type IV -basement membrane, Type IX - Fibrillar associated collagen with interrupted triple helices (FACIT), Type VII (provides anchoring fibrils to basement membrane beneath skin)}}

{{hidden|Which structural protein is associated with Marfan syndrom?|Fibrillin synthetic defects, which wrap the elastin core. }}}}

== Chapter 2: Cellular Responses to Stress and Toxic Insults: Adaptation, Injury and Death ==

{{hidden|What are the four aspects of a disease?|
*1. Etiology
**Genetic - Inherited mutations and disease-associated gene variants, or polymorphisms
**Acquired - Infectious, nutritional, chemical and physical.
*2. Pathogenesis - The sequence of cellular, biochemical, and molecular events that follow the exposure of cells or tissues to an injurious agent.
*3. Morphological changes - The structural alterations in cells or tissues that are either characteristic of a disease or diagnostic of an etiologic process.
*4. Clinical Manifestations - Symptoms and signs of disease, as well as its clinical course and outcome}}

== Chapter 3 ==
== Chapter 4 ==
== Chapter 5 ==
{{hidden|MC cause of spontaneous abortion is ?|<center>[[ A demonstrable chromosomal abnormality.]]</center>}}

{{hidden|1% of all newborn infants possess a gross chromosomal abnormality and 5% of people <25y present with |<center>[[a genetic disease. ]]</center>}}

{{hidden|Mutation|<center>[[permanent change in the DNA, if affect germ cells are transmitted to the progeny ]]</center>}}

{{hidden|List and describe 4 broad categories of human genetic disorders:|<center>[[Disorders related to mutation sin single genes with large effects i. Usually follow classic Mendelian pattern of inheritance
ii. Often highly penetrant (large proportion of pop with gene has disease)
b. Chromosomal disorders
i. Structural or numerical alterations in autosomes and sex chromosomes
ii. Uncommon, high penetrance
c. Complex multigenic disorders
i. Interactions between multiple variant forms of genes and environmental factors (polymorphisms), poly genic means disease when many polymorphism present
d. Single gene disorders with nonclassic patterns of inheritance (not mendelian)
i. Disorders resulting from triplet repeat mutations
ii. Mutations in mitochondrial DNA
iii. Those influenced by genomic imprinting
iv. Those influenced by gonadal mosaicism]]</center>}}

{{hidden|List and describe the possible outcomes of a point mutation in a coding region?|[[a. Missense mutation – pt mutation changes amino acid code, conservative when the amino acid is preserved, non conservative when replaced with another amino acid, b. Nonsense mutation – makes a stop codon ]]</center>}}

{{hidden|List and describe the possible outcomes of point mutation or deletion in a non-coding region.|<center>[[a. Promoters/enhancers – interfere with binding of transcription factors, marker reduction or total lack of transcription, b. Introns – defective splicing > failure to make mature RNA > no translation]]</center>}}

{{hidden|List and describe the possible outcomes of deletions and insertions.|<center>[[a.Small coding: not multiple of three = frameshift, if multiple of 3 than add or del amino acids accordingly, often premature stop codon
i. Tay Sachs disease: 4 base pair insertion in Hexosaminidase A gene ]]}}

{{hidden|List and describe the possible outcomes of trinucleotide repeat mutations.|[[a. Usually G&C, dynamic and increase during gametogenesis, “RNA stutters”,b. Fragile X – CGG 250-4000, Huntinton’s Disease ]]}}

{{hidden|List and describe three examples of inheritance of single gene mutations|[[a. AD – manifested in the heterologous state, one parent of index case is usually affected, males and females affected and both can transmit conditioni. De novo cases may not have affected parentii. Penetrance = fraction of people with gene who have the traitiii. Variable expressivity = those with mutant gene have variety of phenotypesiv. Often age of onset is delayed so can reproduce before die from diseasev. Biochem mechanisms1. Reduced production of a protein or dysfunctional/inactive protein2. Involved in regulation of complex metabolic pathyway subject to feedback inhibition3. Key structural proteins (collagen and cytoskeleton of RBC)a. May be a dominant negative , e.g. osteogenesis imperfecta4. Gain of function are rare, 2 formsa. Increased in proteins normal function (excess enzyme activity)b. Huntinton’s diseas (abn protein accumulates, toxic to neurons)b. ARi. Largest category – both alleles at a locus are mutated1. Expression is uniform, complete penetrance common, early onset, unaffected carrier family members, mostly enzymesc. X Linkedi. All sex linked, and almost all are recessive , if Y Chromosome affected usually infertile males > no progenyii. Male expression b/c hemizygous, daughter carriers with variable phenotype because of lionization of 2nd X e.g G6DPiii. Dominant . vitamin D resistant rickets]]</center>}}

Stopped at P142

== Chapter 6 ==
== Chapter 7 ==
== Chapter 8 ==
== Chapter 9 ==
== Chapter 10 ==
== Chapter 11 ==
== Chapter 12 ==
== Chapter 13 ==
== Chapter 14 ==
== Chapter 15 ==
== Chapter 16 ==
== Chapter 17 ==
== Chapter 18 ==
== Chapter 19 ==
== Chapter 20 ==
== Chapter 21 ==
== Chapter 22 ==
== Chapter 23 ==
== Chapter 24 ==
== Chapter 25 ==
== Chapter 26 ==
== Chapter 27 ==
== Chapter 28 ==
== Chapter 29 ==

Robbins and Cotran 9th Edition Questions

2015-05-27T17:06:16Z

Yuanny: /* Chapter 1: The Cell as a Unit of Health and Disease */

== Chapter 1: The Cell as a Unit of Health and Disease==

{{hidden|Short Answer Questions|
{{hidden|How much of the human genome is coding and what does it code?|Of the 3.2b basepairs, there are 20,000 genes that comprise about 1.5% of the genome that code for proteins (enzymes, structural components, and signaling molecules used to assemble and maintain all the cells in the body}}

{{hidden|What do we think that the rest of the genome does?|80% of the genome binds proteins, implying that it is involved in regulating gene expression, related to the regulation of gene expression, often in a cell-type specific fashion.}}

{{hidden|List the major classes of functional non-protein-coding sequences found in the human genome.|1. Promoter & enhancer, 2. Chromatin binding site structures, 3. non-coding regulatory RNAs, 4. Mobile genetic elements (transposons), 5. telomeres, 6. centromers. }}

{{hidden|What are the two most common forms of DNA variation in the human genome?|1) Single nucleotide polymorphisms (SNPs), 2) copy number variations (CNVs)}}

{{hidden|What are the possible implications of SNPs.|1) regulatory = alters gene expression, 2) Correlation with disease states when in close proximity with altered genes, 3) association used to define linkage disequilibrium,?}}

{{hidden|Define epigenetics.|Heritable changes in gene expression which are not caused by alterations in DNA sequence.}}

{{hidden|List the 6 types of epigenetic changes.|1) Histone & histone modifying factors (Histones organize chromatin into heterochromatin and euchromatin, 2) histone methylation, 3) histone acteylation, 4)histone phosphorylation, 5) DNA methylation, 6) Chromatin organizing factors.}}

{{hidden|What is the function of micro-RNA (mi-RNA)?|It does not encode protein, instead they function primarily to modulate the translation of target mRNAs into their corresponding proteins, and are responsible for post-transcriptional silencing of gene expression.}}

{{hidden|What is knockdown technology?|The use of synthetic si-RNA (short RNA sequences) introduced into cells that serve as substrates for Dicer and interact with the RISC complex in a manner analogous to endogenous miRNAs, and are used to study gene function, and are being developed as therapeutic agents to silence pathogenic genes, e.g. oncogenic in neoplasms.}}

{{hidden|What is long non coding RNA?|Lnc-RNA modulate gene expression by binding to regions of chromatin, restricting RNA polymerase access to coding genes within the region, and may exceed the number of mRNA's by 10-20 fold.}}

{{hidden|What is XIST?|XIST is a lnc-RNA which is transcribed from the X-chromosome and plays an essential role in physiologic X chromosome inactivation, though not inactivated itself, it forms a repressive cloak on the X chromosome from which it is transcribed resulting in gene silencing.}}

{{hidden|What are the cellular housekeeping functions?|1) protection from the environment, 2) nutrient acquisition, 3) communication, 4) movement, 5) renewal of senescent molecules, 6) molecular catabolism, 7) energy generation.}}

{{hidden|List the cellular compartments and the role in the cell.|1) cytosol = metabolism, transport, protein translation, 2) Mitochondria = energy generation, apoptosis, 3) Rough ER = synthesis of membrane and secreted proteins, 4) Smooth ER / Golgi = protein modification, sorting, catabolism, 5)Nucleus = cell regulation, proliferation, DNA transcription, 6) Endosomes = intracellular transport and export, ingestion of extracellular substances, 7) Lysosomes = cellular catabolism, 8) peroxisomes = very long-chain fatty acid metabolism}}

{{hidden|Describe the basic structure and functions of the cell membrane.| The plasma membrane is composed of a lipid bilayer of phospholipids studded with a variety of proteins and glycoproteins involved in ion and metabolite transport, fluid phase and receptor-mediated uptake of macromolecules, cell-ligand/cell matrix/cell-cell interactions.}}

{{hidden|How are the large complexes in the plasma membrane formed?|They aggregate under the control of chaperone molecules in the RER or by lateral diffusion in the plasma membrane followed by complex formation in situ.}}

{{hidden|What are aquaporins?|Special integral membrane proteins which augment passive water transport in tissues where water is transported in large volumes.}}

{{hidden|How are channel and carrier proteins different?|Channel proteins created hydrophilic pores, permit rapid movement of solutes, restricted by size and charge, where Carrier proteins bind to their specific solutes and undergo a series of conformational changes to transfer the ligand across the membrane, relatively slow transport.}}

{{hidden|What is the "multidrug resistance (MDR) protein"?|A type of transporter ATPases which pumps polar compounds (e.g. chemo drugs) out of cells which may render cancer cells resistant to treatment.}}

{{hidden|What are the two fundamental mechanisms of fluid or macromolecules by the cell (endocytosis)?|1)Caveolae -invaginations of the plasma membrane, 2) Pinocytosis/receptor mediated endocytosis - macromolecules bind to receptor and membranes invaginate around it.}}

{{hidden|What is exocytosis?|It is the opposite process of pinocytosis, where the receptor bound macromolecule is move to the cell surface and released.}}

{{hidden|Describe the difference between phagocytosis and transcytosis.|In phagocytosis microbes are ingested forming phagosomes, which fuse with lysosomes and become phagylosomes, releasing undigested residual material when fusing again with the external membrane, in contrast transcytosis the materials are carried across the cell membrane unaltered.}}

{{hidden|List the three major classes of 3 cytoskeleton proteins.|1) Actin, 2)Intermediate filaments, 3)Microtubules}}

{{hidden|Describe actin.|Actin - 5 to 9nm diam fibrils, G-actin polymerized into F-actin, the form double strands helices, which interact with myosin (filamentous protein).}}

{{hidden|List the various intermediate filaments, which are 10nm in diameter.|1) Lamin A, B, and C (nuclear lamins of all cells, 2) Vimentin (mesenchymal), 3)Desmin (scaffold for actin/myosin), 4) Neurofilaments (axons of neurons), 5) Glial filament protein (glial cells), 6)Cytokeratins (acid and basic and vary based on cell type). }}

{{hidden|Describe microtubules.|Microtubules are 25nm diam fibrils of dimers of a and b tubulin, with a negative end embedded in the centrosome near the nucleus, the + end grows or shrinks as needed. There are kinesins and dyneins motors that move stuff around the cell, also found in cilia and flagella.}}

{{hidden|What is clatharin?|A molecule found in the cell membrane that when the cell membrane invaginates forming a basket like structure.}}

{{hidden|List and describe the 3 main classifications of cell junctions.|1) Tight /occluding junctions - form a high resistance barrier to solute movement, and allows the cell to maintain polarity, 2) anchoring junctions / desmosomes - mechanically attach the cell and their cytoskeleton to other cells and the ECM (hemidesmosome), 3)communicating/gap junctions - mediate the passage of chemical or electrical signals from one cell to another.}}

{{hidden|What is the "unfolded protein response"?| Excess accumulation of misfolded protiens, which exceed the capacity of the ER to edit and degrade them, leads to the the ER stress response (UPR) that triggers cell death through apoptosis.}}

{{hidden|What cell organelle has a reactive hyperplasia with repeated exposure to phenobarbitol catabolism in the cytocrhome p450 system?|Smooth endoplasmic reticulum.}}

{{hidden|List three main functions of mitochondria.|1) Energy generation, 2) intermediate metabolism (instead of ATP make intemediate that can be used to make lipids, nucleic acids, and proteins), 3) Cell death ( necrosis & apoptosis)}}

{{hidden|List and describe the four extracellular cell-cell signaling pathways based on the distance the signal travels.|1)Paracrine (immediate vicinity), 2) Autocrine (cell affecting itself), 3) Synaptic (neurons sending neurotransmitters at synapse), 4) endocrine (signals released elsewhere into bloodstream).}}

{{hidden|What are the two characterizing features of stem cells?|Self renewal and asymmetric division (one daughter cell stays a stem cell)}}

{{hidden|What are the two types of stem cells?|embryonic stem cells (inner cell mass of the blastocyst, totipotent), and tissue/adult stem cells (found in stem cell niches associated with specialized tissues, limited repetoire of differentiation = multipotent)}}

{{hidden|What is the Warburg effect?|Increased cellular uptake of glucose and glutamine, increased glycolysis, and decreased oxidative phosphorylation by the cell.}}

{{hidden|Which CDKI's have selective effects on CDK4 and CDK6?|p15,p16,p17,and p19}}

{{hidden|List some examples of signal transduction pathways.|1) Receptor tyrosine kinases (RTKs), 2) Nonreceptor tyrosine kinase, 3) G-protein coupled receptors, 4) nuclear receptors, 5)Notch family receptors, 6) Wnt protein ligands (Frizzled family receptors).}}

{{hidden|Why does nuclear beta catenin occur in some neoplasms?|When Wnt ligand bins to frizzled it recruits Disheveled, this leads to the disruption of the wnt-ubiquitin complex, this stabilized pool of b-catening is then translocated to the nucleus forming a transcriptional complex}}

{{hidden|On Page 19 there is a table of growth factors involved in regeneration and repair, please review.|}}

{{hidden|Describe the function of cadherin.|}}

{{hidden|What are the functions of the extracellular matrix?|Mechanical support, control of cell proliferation, scaffolding for tissue renewal, establishment of tissue microenvironments}}

{{hidden|What are the two basic forms of the ECM?|interstitial matrix (fibrillar and non fibrillar collagen, fibronectin, elastin, proteoglycans, hyloronate, and other stuff), basement membrane (type IV collagen and laminin) }}

{{hidden|What are the three proteins groups in the ECM?|1) fibrous structural proteins (collagen, elastins), 2) water hydrated gels (proteoglycans and hyaluronan), 3) adhesive glycoproteins (connect ECM to each other and other cells)}}

{{hidden|Describe the structure of a protein that is dependent on vitamin C.|Collagen is composed of 3 seprate polypeptide chains braided into a rope like triple helix, lateral cross linking of the triple helices by lysyl oxidase (requires vitamin C) give it it's tensile strength. }}

{{hidden|List three non-fibrillar collagens.|Type IV -basement membrane, Type IX - Fibrillar associated collagen with interrupted triple helices (FACIT), Type VII (provides anchoring fibrils to basement membrane beneath skin)}}

{{hidden|Which structural protein is associated with Marfan syndrom?|Fibrillin synthetic defects, which wrap the elastin core. }}}}

== Chapter 2: Cellular Responses to Stress and Toxic Insults: Adaptation, Injury and Death ==

{{hidden|What are the four aspects of a disease?|
*1. Etiology
**Genetic - Inherited mutations and disease-associated gene variants, or polymorphisms
**Acquired - Infectious, nutritional, chemical and physical.
*2. Pathogenesis - The sequence of cellular, biochemical, and molecular events that follow the exposure of cells or tissues to an injurious agent.
*3. Morphological changes - The structural alterations in cells or tissues that are either characteristic of a disease or diagnostic of an etiologic process.
*4. Clinical Manifestations - Symptoms and signs of disease, as well as its clinical course and outcome}}

== Chapter 3 ==
== Chapter 4 ==
== Chapter 5 ==
{{hidden|MC cause of spontaneous abortion is ?|<center>[[ A demonstrable chromosomal abnormality.]]</center>}}

{{hidden|1% of all newborn infants possess a gross chromosomal abnormality and 5% of people <25y present with |<center>[[a genetic disease. ]]</center>}}

{{hidden|Mutation|<center>[[permanent change in the DNA, if affect germ cells are transmitted to the progeny ]]</center>}}

{{hidden|List and describe 4 broad categories of human genetic disorders:|<center>[[Disorders related to mutation sin single genes with large effects i. Usually follow classic Mendelian pattern of inheritance
ii. Often highly penetrant (large proportion of pop with gene has disease)
b. Chromosomal disorders
i. Structural or numerical alterations in autosomes and sex chromosomes
ii. Uncommon, high penetrance
c. Complex multigenic disorders
i. Interactions between multiple variant forms of genes and environmental factors (polymorphisms), poly genic means disease when many polymorphism present
d. Single gene disorders with nonclassic patterns of inheritance (not mendelian)
i. Disorders resulting from triplet repeat mutations
ii. Mutations in mitochondrial DNA
iii. Those influenced by genomic imprinting
iv. Those influenced by gonadal mosaicism]]</center>}}

{{hidden|List and describe the possible outcomes of a point mutation in a coding region?|[[a. Missense mutation – pt mutation changes amino acid code, conservative when the amino acid is preserved, non conservative when replaced with another amino acid, b. Nonsense mutation – makes a stop codon ]]</center>}}

{{hidden|List and describe the possible outcomes of point mutation or deletion in a non-coding region.|<center>[[a. Promoters/enhancers – interfere with binding of transcription factors, marker reduction or total lack of transcription, b. Introns – defective splicing > failure to make mature RNA > no translation]]</center>}}

{{hidden|List and describe the possible outcomes of deletions and insertions.|<center>[[a.Small coding: not multiple of three = frameshift, if multiple of 3 than add or del amino acids accordingly, often premature stop codon
i. Tay Sachs disease: 4 base pair insertion in Hexosaminidase A gene ]]}}

{{hidden|List and describe the possible outcomes of trinucleotide repeat mutations.|[[a. Usually G&C, dynamic and increase during gametogenesis, “RNA stutters”,b. Fragile X – CGG 250-4000, Huntinton’s Disease ]]}}

{{hidden|List and describe three examples of inheritance of single gene mutations|[[a. AD – manifested in the heterologous state, one parent of index case is usually affected, males and females affected and both can transmit conditioni. De novo cases may not have affected parentii. Penetrance = fraction of people with gene who have the traitiii. Variable expressivity = those with mutant gene have variety of phenotypesiv. Often age of onset is delayed so can reproduce before die from diseasev. Biochem mechanisms1. Reduced production of a protein or dysfunctional/inactive protein2. Involved in regulation of complex metabolic pathyway subject to feedback inhibition3. Key structural proteins (collagen and cytoskeleton of RBC)a. May be a dominant negative , e.g. osteogenesis imperfecta4. Gain of function are rare, 2 formsa. Increased in proteins normal function (excess enzyme activity)b. Huntinton’s diseas (abn protein accumulates, toxic to neurons)b. ARi. Largest category – both alleles at a locus are mutated1. Expression is uniform, complete penetrance common, early onset, unaffected carrier family members, mostly enzymesc. X Linkedi. All sex linked, and almost all are recessive , if Y Chromosome affected usually infertile males > no progenyii. Male expression b/c hemizygous, daughter carriers with variable phenotype because of lionization of 2nd X e.g G6DPiii. Dominant . vitamin D resistant rickets]]</center>}}

Stopped at P142

== Chapter 6 ==
== Chapter 7 ==
== Chapter 8 ==
== Chapter 9 ==
== Chapter 10 ==
== Chapter 11 ==
== Chapter 12 ==
== Chapter 13 ==
== Chapter 14 ==
== Chapter 15 ==
== Chapter 16 ==
== Chapter 17 ==
== Chapter 18 ==
== Chapter 19 ==
== Chapter 20 ==
== Chapter 21 ==
== Chapter 22 ==
== Chapter 23 ==
== Chapter 24 ==
== Chapter 25 ==
== Chapter 26 ==
== Chapter 27 ==
== Chapter 28 ==
== Chapter 29 ==

Robbins and Cotran 9th Edition Questions

2015-05-27T15:27:09Z

Yuanny: /* Chapter 2: Cellular Responses to Stress and Toxic Insults: Adaptation, Injury and Death */

== Chapter 1: The Cell as a Unit of Health and Disease==

{{hidden|How much of the human genome is coding and what does it code?|Of the 3.2b basepairs, there are 20,000 genes that comprise about 1.5% of the genome that code for proteins (enzymes, structural components, and signaling molecules used to assemble and maintain all the cells in the body}}

{{hidden|What do we think that the rest of the genome does?|80% of the genome binds proteins, implying that it is involved in regulating gene expression, related to the regulation of gene expression, often in a cell-type specific fashion.}}

{{hidden|List the major classes of functional non-protein-coding sequences found in the human genome.|1. Promoter & enhancer, 2. Chromatin binding site structures, 3. non-coding regulatory RNAs, 4. Mobile genetic elements (transposons), 5. telomeres, 6. centromers. }}

{{hidden|What are the two most common forms of DNA variation in the human genome?|1) Single nucleotide polymorphisms (SNPs), 2) copy number variations (CNVs)}}

{{hidden|What are the possible implications of SNPs.|1) regulatory = alters gene expression, 2) Correlation with disease states when in close proximity with altered genes, 3) association used to define linkage disequilibrium,?}}

{{hidden|Define epigenetics.|Heritable changes in gene expression which are not caused by alterations in DNA sequence.}}

{{hidden|List the 6 types of epigenetic changes.|1) Histone & histone modifying factors (Histones organize chromatin into heterochromatin and euchromatin, 2) histone methylation, 3) histone acteylation, 4)histone phosphorylation, 5) DNA methylation, 6) Chromatin organizing factors.}}

{{hidden|What is the function of micro-RNA (mi-RNA)?|It does not encode protein, instead they function primarily to modulate the translation of target mRNAs into their corresponding proteins, and are responsible for post-transcriptional silencing of gene expression.}}

{{hidden|What is knockdown technology?|The use of synthetic si-RNA (short RNA sequences) introduced into cells that serve as substrates for Dicer and interact with the RISC complex in a manner analogous to endogenous miRNAs, and are used to study gene function, and are being developed as therapeutic agents to silence pathogenic genes, e.g. oncogenic in neoplasms.}}

{{hidden|What is long non coding RNA?|Lnc-RNA modulate gene expression by binding to regions of chromatin, restricting RNA polymerase access to coding genes within the region, and may exceed the number of mRNA's by 10-20 fold.}}

{{hidden|What is XIST?|XIST is a lnc-RNA which is transcribed from the X-chromosome and plays an essential role in physiologic X chromosome inactivation, though not inactivated itself, it forms a repressive cloak on the X chromosome from which it is transcribed resulting in gene silencing.}}

{{hidden|What are the cellular housekeeping functions?|1) protection from the environment, 2) nutrient acquisition, 3) communication, 4) movement, 5) renewal of senescent molecules, 6) molecular catabolism, 7) energy generation.}}

{{hidden|List the cellular compartments and the role in the cell.|1) cytosol = metabolism, transport, protein translation, 2) Mitochondria = energy generation, apoptosis, 3) Rough ER = synthesis of membrane and secreted proteins, 4) Smooth ER / Golgi = protein modification, sorting, catabolism, 5)Nucleus = cell regulation, proliferation, DNA transcription, 6) Endosomes = intracellular transport and export, ingestion of extracellular substances, 7) Lysosomes = cellular catabolism, 8) peroxisomes = very long-chain fatty acid metabolism}}

{{hidden|Describe the basic structure and functions of the cell membrane.| The plasma membrane is composed of a lipid bilayer of phospholipids studded with a variety of proteins and glycoproteins involved in ion and metabolite transport, fluid phase and receptor-mediated uptake of macromolecules, cell-ligand/cell matrix/cell-cell interactions.}}

{{hidden|How are the large complexes in the plasma membrane formed?|They aggregate under the control of chaperone molecules in the RER or by lateral diffusion in the plasma membrane followed by complex formation in situ.}}

{{hidden|What are aquaporins?|Special integral membrane proteins which augment passive water transport in tissues where water is transported in large volumes.}}

{{hidden|How are channel and carrier proteins different?|Channel proteins created hydrophilic pores, permit rapid movement of solutes, restricted by size and charge, where Carrier proteins bind to their specific solutes and undergo a series of conformational changes to transfer the ligand across the membrane, relatively slow transport.}}

{{hidden|What is the "multidrug resistance (MDR) protein"?|A type of transporter ATPases which pumps polar compounds (e.g. chemo drugs) out of cells which may render cancer cells resistant to treatment.}}

{{hidden|What are the two fundamental mechanisms of fluid or macromolecules by the cell (endocytosis)?|1)Caveolae -invaginations of the plasma membrane, 2) Pinocytosis/receptor mediated endocytosis - macromolecules bind to receptor and membranes invaginate around it.}}

{{hidden|What is exocytosis?|It is the opposite process of pinocytosis, where the receptor bound macromolecule is move to the cell surface and released.}}

{{hidden|Describe the difference between phagocytosis and transcytosis.|In phagocytosis microbes are ingested forming phagosomes, which fuse with lysosomes and become phagylosomes, releasing undigested residual material when fusing again with the external membrane, in contrast transcytosis the materials are carried across the cell membrane unaltered.}}

{{hidden|List the three major classes of 3 cytoskeleton proteins.|1) Actin, 2)Intermediate filaments, 3)Microtubules}}

{{hidden|Describe actin.|Actin - 5 to 9nm diam fibrils, G-actin polymerized into F-actin, the form double strands helices, which interact with myosin (filamentous protein).}}

{{hidden|List the various intermediate filaments, which are 10nm in diameter.|1) Lamin A, B, and C (nuclear lamins of all cells, 2) Vimentin (mesenchymal), 3)Desmin (scaffold for actin/myosin), 4) Neurofilaments (axons of neurons), 5) Glial filament protein (glial cells), 6)Cytokeratins (acid and basic and vary based on cell type). }}

{{hidden|Describe microtubules.|Microtubules are 25nm diam fibrils of dimers of a and b tubulin, with a negative end embedded in the centrosome near the nucleus, the + end grows or shrinks as needed. There are kinesins and dyneins motors that move stuff around the cell, also found in cilia and flagella.}}

{{hidden|What is clatharin?|A molecule found in the cell membrane that when the cell membrane invaginates forming a basket like structure.}}

{{hidden|List and describe the 3 main classifications of cell junctions.|1) Tight /occluding junctions - form a high resistance barrier to solute movement, and allows the cell to maintain polarity, 2) anchoring junctions / desmosomes - mechanically attach the cell and their cytoskeleton to other cells and the ECM (hemidesmosome), 3)communicating/gap junctions - mediate the passage of chemical or electrical signals from one cell to another.}}

{{hidden|What is the "unfolded protein response"?| Excess accumulation of misfolded protiens, which exceed the capacity of the ER to edit and degrade them, leads to the the ER stress response (UPR) that triggers cell death through apoptosis.}}

{{hidden|What cell organelle has a reactive hyperplasia with repeated exposure to phenobarbitol catabolism in the cytocrhome p450 system?|Smooth endoplasmic reticulum.}}

{{hidden|List three main functions of mitochondria.|1) Energy generation, 2) intermediate metabolism (instead of ATP make intemediate that can be used to make lipids, nucleic acids, and proteins), 3) Cell death ( necrosis & apoptosis)}}

{{hidden|List and describe the four extracellular cell-cell signaling pathways based on the distance the signal travels.|1)Paracrine (immediate vicinity), 2) Autocrine (cell affecting itself), 3) Synaptic (neurons sending neurotransmitters at synapse), 4) endocrine (signals released elsewhere into bloodstream).}}

{{hidden|What are the two characterizing features of stem cells?|Self renewal and asymmetric division (one daughter cell stays a stem cell)}}

{{hidden|What are the two types of stem cells?|embryonic stem cells (inner cell mass of the blastocyst, totipotent), and tissue/adult stem cells (found in stem cell niches associated with specialized tissues, limited repetoire of differentiation = multipotent)}}

{{hidden|What is the Warburg effect?|Increased cellular uptake of glucose and glutamine, increased glycolysis, and decreased oxidative phosphorylation by the cell.}}

{{hidden|Which CDKI's have selective effects on CDK4 and CDK6?|p15,p16,p17,and p19}}

{{hidden|List some examples of signal transduction pathways.|1) Receptor tyrosine kinases (RTKs), 2) Nonreceptor tyrosine kinase, 3) G-protein coupled receptors, 4) nuclear receptors, 5)Notch family receptors, 6) Wnt protein ligands (Frizzled family receptors).}}

{{hidden|Why does nuclear beta catenin occur in some neoplasms?|When Wnt ligand bins to frizzled it recruits Disheveled, this leads to the disruption of the wnt-ubiquitin complex, this stabilized pool of b-catening is then translocated to the nucleus forming a transcriptional complex}}

{{hidden|On Page 19 there is a table of growth factors involved in regeneration and repair, please review.|}}

{{hidden|Describe the function of cadherin.|}}

{{hidden|What are the functions of the extracellular matrix?|Mechanical support, control of cell proliferation, scaffolding for tissue renewal, establishment of tissue microenvironments}}

{{hidden|What are the two basic forms of the ECM?|interstitial matrix (fibrillar and non fibrillar collagen, fibronectin, elastin, proteoglycans, hyloronate, and other stuff), basement membrane (type IV collagen and laminin) }}

{{hidden|What are the three proteins groups in the ECM?|1) fibrous structural proteins (collagen, elastins), 2) water hydrated gels (proteoglycans and hyaluronan), 3) adhesive glycoproteins (connect ECM to each other and other cells)}}

{{hidden|Describe the structure of a protein that is dependent on vitamin C.|Collagen is composed of 3 seprate polypeptide chains braided into a rope like triple helix, lateral cross linking of the triple helices by lysyl oxidase (requires vitamin C) give it it's tensile strength. }}

{{hidden|List three non-fibrillar collagens.|Type IV -basement membrane, Type IX - Fibrillar associated collagen with interrupted triple helices (FACIT), Type VII (provides anchoring fibrils to basement membrane beneath skin)}}

{{hidden|Which structural protein is associated with Marfan syndrom?|Fibrillin synthetic defects, which wrap the elastin core. }}

== Chapter 2: Cellular Responses to Stress and Toxic Insults: Adaptation, Injury and Death ==

{{hidden|What are the four aspects of a disease?|
*1. Etiology
**Genetic - Inherited mutations and disease-associated gene variants, or polymorphisms
**Acquired - Infectious, nutritional, chemical and physical.
*2. Pathogenesis - The sequence of cellular, biochemical, and molecular events that follow the exposure of cells or tissues to an injurious agent.
*3. Morphological changes - The structural alterations in cells or tissues that are either characteristic of a disease or diagnostic of an etiologic process.
*4. Clinical Manifestations - Symptoms and signs of disease, as well as its clinical course and outcome}}

== Chapter 3 ==
== Chapter 4 ==
== Chapter 5 ==
{{hidden|MC cause of spontaneous abortion is ?|<center>[[ A demonstrable chromosomal abnormality.]]</center>}}

{{hidden|1% of all newborn infants possess a gross chromosomal abnormality and 5% of people <25y present with |<center>[[a genetic disease. ]]</center>}}

{{hidden|Mutation|<center>[[permanent change in the DNA, if affect germ cells are transmitted to the progeny ]]</center>}}

{{hidden|List and describe 4 broad categories of human genetic disorders:|<center>[[Disorders related to mutation sin single genes with large effects i. Usually follow classic Mendelian pattern of inheritance
ii. Often highly penetrant (large proportion of pop with gene has disease)
b. Chromosomal disorders
i. Structural or numerical alterations in autosomes and sex chromosomes
ii. Uncommon, high penetrance
c. Complex multigenic disorders
i. Interactions between multiple variant forms of genes and environmental factors (polymorphisms), poly genic means disease when many polymorphism present
d. Single gene disorders with nonclassic patterns of inheritance (not mendelian)
i. Disorders resulting from triplet repeat mutations
ii. Mutations in mitochondrial DNA
iii. Those influenced by genomic imprinting
iv. Those influenced by gonadal mosaicism]]</center>}}

{{hidden|List and describe the possible outcomes of a point mutation in a coding region?|[[a. Missense mutation – pt mutation changes amino acid code, conservative when the amino acid is preserved, non conservative when replaced with another amino acid, b. Nonsense mutation – makes a stop codon ]]</center>}}

{{hidden|List and describe the possible outcomes of point mutation or deletion in a non-coding region.|<center>[[a. Promoters/enhancers – interfere with binding of transcription factors, marker reduction or total lack of transcription, b. Introns – defective splicing > failure to make mature RNA > no translation]]</center>}}

{{hidden|List and describe the possible outcomes of deletions and insertions.|<center>[[a.Small coding: not multiple of three = frameshift, if multiple of 3 than add or del amino acids accordingly, often premature stop codon
i. Tay Sachs disease: 4 base pair insertion in Hexosaminidase A gene ]]}}

{{hidden|List and describe the possible outcomes of trinucleotide repeat mutations.|[[a. Usually G&C, dynamic and increase during gametogenesis, “RNA stutters”,b. Fragile X – CGG 250-4000, Huntinton’s Disease ]]}}

{{hidden|List and describe three examples of inheritance of single gene mutations|[[a. AD – manifested in the heterologous state, one parent of index case is usually affected, males and females affected and both can transmit conditioni. De novo cases may not have affected parentii. Penetrance = fraction of people with gene who have the traitiii. Variable expressivity = those with mutant gene have variety of phenotypesiv. Often age of onset is delayed so can reproduce before die from diseasev. Biochem mechanisms1. Reduced production of a protein or dysfunctional/inactive protein2. Involved in regulation of complex metabolic pathyway subject to feedback inhibition3. Key structural proteins (collagen and cytoskeleton of RBC)a. May be a dominant negative , e.g. osteogenesis imperfecta4. Gain of function are rare, 2 formsa. Increased in proteins normal function (excess enzyme activity)b. Huntinton’s diseas (abn protein accumulates, toxic to neurons)b. ARi. Largest category – both alleles at a locus are mutated1. Expression is uniform, complete penetrance common, early onset, unaffected carrier family members, mostly enzymesc. X Linkedi. All sex linked, and almost all are recessive , if Y Chromosome affected usually infertile males > no progenyii. Male expression b/c hemizygous, daughter carriers with variable phenotype because of lionization of 2nd X e.g G6DPiii. Dominant . vitamin D resistant rickets]]</center>}}

Stopped at P142

== Chapter 6 ==
== Chapter 7 ==
== Chapter 8 ==
== Chapter 9 ==
== Chapter 10 ==
== Chapter 11 ==
== Chapter 12 ==
== Chapter 13 ==
== Chapter 14 ==
== Chapter 15 ==
== Chapter 16 ==
== Chapter 17 ==
== Chapter 18 ==
== Chapter 19 ==
== Chapter 20 ==
== Chapter 21 ==
== Chapter 22 ==
== Chapter 23 ==
== Chapter 24 ==
== Chapter 25 ==
== Chapter 26 ==
== Chapter 27 ==
== Chapter 28 ==
== Chapter 29 ==

Robbins and Cotran 9th Edition Questions

2015-05-27T15:25:59Z

Yuanny: /* Chapter 2: Cellular Responses to Stress and Toxic Insults: Adaptation, Injury and Death */

Robbins and Cotran 9th Edition Questions

2015-05-27T15:11:18Z

Yuanny: /* Cellular Responses to Stress and Toxic Insults: Adaptation, Injury and Death */

== Chapter 1: The Cell as a Unit of Health and Disease==

{{hidden|How much of the human genome is coding and what does it code?|Of the 3.2b basepairs, there are 20,000 genes that comprise about 1.5% of the genome that code for proteins (enzymes, structural components, and signaling molecules used to assemble and maintain all the cells in the body}}

{{hidden|What do we think that the rest of the genome does?|80% of the genome binds proteins, implying that it is involved in regulating gene expression, related to the regulation of gene expression, often in a cell-type specific fashion.}}

{{hidden|List the major classes of functional non-protein-coding sequences found in the human genome.|1. Promoter & enhancer, 2. Chromatin binding site structures, 3. non-coding regulatory RNAs, 4. Mobile genetic elements (transposons), 5. telomeres, 6. centromers. }}

{{hidden|What are the two most common forms of DNA variation in the human genome?|1) Single nucleotide polymorphisms (SNPs), 2) copy number variations (CNVs)}}

{{hidden|What are the possible implications of SNPs.|1) regulatory = alters gene expression, 2) Correlation with disease states when in close proximity with altered genes, 3) association used to define linkage disequilibrium,?}}

{{hidden|Define epigenetics.|Heritable changes in gene expression which are not caused by alterations in DNA sequence.}}

{{hidden|List the 6 types of epigenetic changes.|1) Histone & histone modifying factors (Histones organize chromatin into heterochromatin and euchromatin, 2) histone methylation, 3) histone acteylation, 4)histone phosphorylation, 5) DNA methylation, 6) Chromatin organizing factors.}}

{{hidden|What is the function of micro-RNA (mi-RNA)?|It does not encode protein, instead they function primarily to modulate the translation of target mRNAs into their corresponding proteins, and are responsible for post-transcriptional silencing of gene expression.}}

{{hidden|What is knockdown technology?|The use of synthetic si-RNA (short RNA sequences) introduced into cells that serve as substrates for Dicer and interact with the RISC complex in a manner analogous to endogenous miRNAs, and are used to study gene function, and are being developed as therapeutic agents to silence pathogenic genes, e.g. oncogenic in neoplasms.}}

{{hidden|What is long non coding RNA?|Lnc-RNA modulate gene expression by binding to regions of chromatin, restricting RNA polymerase access to coding genes within the region, and may exceed the number of mRNA's by 10-20 fold.}}

{{hidden|What is XIST?|XIST is a lnc-RNA which is transcribed from the X-chromosome and plays an essential role in physiologic X chromosome inactivation, though not inactivated itself, it forms a repressive cloak on the X chromosome from which it is transcribed resulting in gene silencing.}}

{{hidden|What are the cellular housekeeping functions?|1) protection from the environment, 2) nutrient acquisition, 3) communication, 4) movement, 5) renewal of senescent molecules, 6) molecular catabolism, 7) energy generation.}}

{{hidden|List the cellular compartments and the role in the cell.|1) cytosol = metabolism, transport, protein translation, 2) Mitochondria = energy generation, apoptosis, 3) Rough ER = synthesis of membrane and secreted proteins, 4) Smooth ER / Golgi = protein modification, sorting, catabolism, 5)Nucleus = cell regulation, proliferation, DNA transcription, 6) Endosomes = intracellular transport and export, ingestion of extracellular substances, 7) Lysosomes = cellular catabolism, 8) peroxisomes = very long-chain fatty acid metabolism}}

{{hidden|Describe the basic structure and functions of the cell membrane.| The plasma membrane is composed of a lipid bilayer of phospholipids studded with a variety of proteins and glycoproteins involved in ion and metabolite transport, fluid phase and receptor-mediated uptake of macromolecules, cell-ligand/cell matrix/cell-cell interactions.}}

{{hidden|How are the large complexes in the plasma membrane formed?|They aggregate under the control of chaperone molecules in the RER or by lateral diffusion in the plasma membrane followed by complex formation in situ.}}

{{hidden|What are aquaporins?|Special integral membrane proteins which augment passive water transport in tissues where water is transported in large volumes.}}

{{hidden|How are channel and carrier proteins different?|Channel proteins created hydrophilic pores, permit rapid movement of solutes, restricted by size and charge, where Carrier proteins bind to their specific solutes and undergo a series of conformational changes to transfer the ligand across the membrane, relatively slow transport.}}

{{hidden|What is the "multidrug resistance (MDR) protein"?|A type of transporter ATPases which pumps polar compounds (e.g. chemo drugs) out of cells which may render cancer cells resistant to treatment.}}

{{hidden|What are the two fundamental mechanisms of fluid or macromolecules by the cell (endocytosis)?|1)Caveolae -invaginations of the plasma membrane, 2) Pinocytosis/receptor mediated endocytosis - macromolecules bind to receptor and membranes invaginate around it.}}

{{hidden|What is exocytosis?|It is the opposite process of pinocytosis, where the receptor bound macromolecule is move to the cell surface and released.}}

{{hidden|Describe the difference between phagocytosis and transcytosis.|In phagocytosis microbes are ingested forming phagosomes, which fuse with lysosomes and become phagylosomes, releasing undigested residual material when fusing again with the external membrane, in contrast transcytosis the materials are carried across the cell membrane unaltered.}}

{{hidden|List the three major classes of 3 cytoskeleton proteins.|1) Actin, 2)Intermediate filaments, 3)Microtubules}}

{{hidden|Describe actin.|Actin - 5 to 9nm diam fibrils, G-actin polymerized into F-actin, the form double strands helices, which interact with myosin (filamentous protein).}}

{{hidden|List the various intermediate filaments, which are 10nm in diameter.|1) Lamin A, B, and C (nuclear lamins of all cells, 2) Vimentin (mesenchymal), 3)Desmin (scaffold for actin/myosin), 4) Neurofilaments (axons of neurons), 5) Glial filament protein (glial cells), 6)Cytokeratins (acid and basic and vary based on cell type). }}

{{hidden|Describe microtubules.|Microtubules are 25nm diam fibrils of dimers of a and b tubulin, with a negative end embedded in the centrosome near the nucleus, the + end grows or shrinks as needed. There are kinesins and dyneins motors that move stuff around the cell, also found in cilia and flagella.}}

{{hidden|What is clatharin?|A molecule found in the cell membrane that when the cell membrane invaginates forming a basket like structure.}}

{{hidden|List and describe the 3 main classifications of cell junctions.|1) Tight /occluding junctions - form a high resistance barrier to solute movement, and allows the cell to maintain polarity, 2) anchoring junctions / desmosomes - mechanically attach the cell and their cytoskeleton to other cells and the ECM (hemidesmosome), 3)communicating/gap junctions - mediate the passage of chemical or electrical signals from one cell to another.}}

{{hidden|What is the "unfolded protein response"?| Excess accumulation of misfolded protiens, which exceed the capacity of the ER to edit and degrade them, leads to the the ER stress response (UPR) that triggers cell death through apoptosis.}}

{{hidden|What cell organelle has a reactive hyperplasia with repeated exposure to phenobarbitol catabolism in the cytocrhome p450 system?|Smooth endoplasmic reticulum.}}

{{hidden|List three main functions of mitochondria.|1) Energy generation, 2) intermediate metabolism (instead of ATP make intemediate that can be used to make lipids, nucleic acids, and proteins), 3) Cell death ( necrosis & apoptosis)}}

{{hidden|List and describe the four extracellular cell-cell signaling pathways based on the distance the signal travels.|1)Paracrine (immediate vicinity), 2) Autocrine (cell affecting itself), 3) Synaptic (neurons sending neurotransmitters at synapse), 4) endocrine (signals released elsewhere into bloodstream).}}

{{hidden|What are the two characterizing features of stem cells?|Self renewal and asymmetric division (one daughter cell stays a stem cell)}}

{{hidden|What are the two types of stem cells?|embryonic stem cells (inner cell mass of the blastocyst, totipotent), and tissue/adult stem cells (found in stem cell niches associated with specialized tissues, limited repetoire of differentiation = multipotent)}}

{{hidden|What is the Warburg effect?|Increased cellular uptake of glucose and glutamine, increased glycolysis, and decreased oxidative phosphorylation by the cell.}}

{{hidden|Which CDKI's have selective effects on CDK4 and CDK6?|p15,p16,p17,and p19}}

{{hidden|List some examples of signal transduction pathways.|1) Receptor tyrosine kinases (RTKs), 2) Nonreceptor tyrosine kinase, 3) G-protein coupled receptors, 4) nuclear receptors, 5)Notch family receptors, 6) Wnt protein ligands (Frizzled family receptors).}}

{{hidden|Why does nuclear beta catenin occur in some neoplasms?|When Wnt ligand bins to frizzled it recruits Disheveled, this leads to the disruption of the wnt-ubiquitin complex, this stabilized pool of b-catening is then translocated to the nucleus forming a transcriptional complex}}

{{hidden|On Page 19 there is a table of growth factors involved in regeneration and repair, please review.|}}

{{hidden|Describe the function of cadherin.|}}

{{hidden|What are the functions of the extracellular matrix?|Mechanical support, control of cell proliferation, scaffolding for tissue renewal, establishment of tissue microenvironments}}

{{hidden|What are the two basic forms of the ECM?|interstitial matrix (fibrillar and non fibrillar collagen, fibronectin, elastin, proteoglycans, hyloronate, and other stuff), basement membrane (type IV collagen and laminin) }}

{{hidden|What are the three proteins groups in the ECM?|1) fibrous structural proteins (collagen, elastins), 2) water hydrated gels (proteoglycans and hyaluronan), 3) adhesive glycoproteins (connect ECM to each other and other cells)}}

{{hidden|Describe the structure of a protein that is dependent on vitamin C.|Collagen is composed of 3 seprate polypeptide chains braided into a rope like triple helix, lateral cross linking of the triple helices by lysyl oxidase (requires vitamin C) give it it's tensile strength. }}

{{hidden|List three non-fibrillar collagens.|Type IV -basement membrane, Type IX - Fibrillar associated collagen with interrupted triple helices (FACIT), Type VII (provides anchoring fibrils to basement membrane beneath skin)}}

{{hidden|Which structural protein is associated with Marfan syndrom?|Fibrillin synthetic defects, which wrap the elastin core. }}

== Chapter 2: Cellular Responses to Stress and Toxic Insults: Adaptation, Injury and Death ==

== Chapter 3 ==
== Chapter 4 ==
== Chapter 5 ==
{{hidden|MC cause of spontaneous abortion is ?|<center>[[ A demonstrable chromosomal abnormality.]]</center>}}

{{hidden|1% of all newborn infants possess a gross chromosomal abnormality and 5% of people <25y present with |<center>[[a genetic disease. ]]</center>}}

{{hidden|Mutation|<center>[[permanent change in the DNA, if affect germ cells are transmitted to the progeny ]]</center>}}

{{hidden|List and describe 4 broad categories of human genetic disorders:|<center>[[Disorders related to mutation sin single genes with large effects i. Usually follow classic Mendelian pattern of inheritance
ii. Often highly penetrant (large proportion of pop with gene has disease)
b. Chromosomal disorders
i. Structural or numerical alterations in autosomes and sex chromosomes
ii. Uncommon, high penetrance
c. Complex multigenic disorders
i. Interactions between multiple variant forms of genes and environmental factors (polymorphisms), poly genic means disease when many polymorphism present
d. Single gene disorders with nonclassic patterns of inheritance (not mendelian)
i. Disorders resulting from triplet repeat mutations
ii. Mutations in mitochondrial DNA
iii. Those influenced by genomic imprinting
iv. Those influenced by gonadal mosaicism]]</center>}}

{{hidden|List and describe the possible outcomes of a point mutation in a coding region?|[[a. Missense mutation – pt mutation changes amino acid code, conservative when the amino acid is preserved, non conservative when replaced with another amino acid, b. Nonsense mutation – makes a stop codon ]]</center>}}

{{hidden|List and describe the possible outcomes of point mutation or deletion in a non-coding region.|<center>[[a. Promoters/enhancers – interfere with binding of transcription factors, marker reduction or total lack of transcription, b. Introns – defective splicing > failure to make mature RNA > no translation]]</center>}}

{{hidden|List and describe the possible outcomes of deletions and insertions.|<center>[[a.Small coding: not multiple of three = frameshift, if multiple of 3 than add or del amino acids accordingly, often premature stop codon
i. Tay Sachs disease: 4 base pair insertion in Hexosaminidase A gene ]]}}

{{hidden|List and describe the possible outcomes of trinucleotide repeat mutations.|[[a. Usually G&C, dynamic and increase during gametogenesis, “RNA stutters”,b. Fragile X – CGG 250-4000, Huntinton’s Disease ]]}}

{{hidden|List and describe three examples of inheritance of single gene mutations|[[a. AD – manifested in the heterologous state, one parent of index case is usually affected, males and females affected and both can transmit conditioni. De novo cases may not have affected parentii. Penetrance = fraction of people with gene who have the traitiii. Variable expressivity = those with mutant gene have variety of phenotypesiv. Often age of onset is delayed so can reproduce before die from diseasev. Biochem mechanisms1. Reduced production of a protein or dysfunctional/inactive protein2. Involved in regulation of complex metabolic pathyway subject to feedback inhibition3. Key structural proteins (collagen and cytoskeleton of RBC)a. May be a dominant negative , e.g. osteogenesis imperfecta4. Gain of function are rare, 2 formsa. Increased in proteins normal function (excess enzyme activity)b. Huntinton’s diseas (abn protein accumulates, toxic to neurons)b. ARi. Largest category – both alleles at a locus are mutated1. Expression is uniform, complete penetrance common, early onset, unaffected carrier family members, mostly enzymesc. X Linkedi. All sex linked, and almost all are recessive , if Y Chromosome affected usually infertile males > no progenyii. Male expression b/c hemizygous, daughter carriers with variable phenotype because of lionization of 2nd X e.g G6DPiii. Dominant . vitamin D resistant rickets]]</center>}}

Stopped at P142

== Chapter 6 ==
== Chapter 7 ==
== Chapter 8 ==
== Chapter 9 ==
== Chapter 10 ==
== Chapter 11 ==
== Chapter 12 ==
== Chapter 13 ==
== Chapter 14 ==
== Chapter 15 ==
== Chapter 16 ==
== Chapter 17 ==
== Chapter 18 ==
== Chapter 19 ==
== Chapter 20 ==
== Chapter 21 ==
== Chapter 22 ==
== Chapter 23 ==
== Chapter 24 ==
== Chapter 25 ==
== Chapter 26 ==
== Chapter 27 ==
== Chapter 28 ==
== Chapter 29 ==

Robbins and Cotran 9th Edition Questions

2015-05-27T15:10:59Z

Yuanny: /* Chapter 2 */

== Chapter 1: The Cell as a Unit of Health and Disease==

{{hidden|How much of the human genome is coding and what does it code?|Of the 3.2b basepairs, there are 20,000 genes that comprise about 1.5% of the genome that code for proteins (enzymes, structural components, and signaling molecules used to assemble and maintain all the cells in the body}}

{{hidden|What do we think that the rest of the genome does?|80% of the genome binds proteins, implying that it is involved in regulating gene expression, related to the regulation of gene expression, often in a cell-type specific fashion.}}

{{hidden|List the major classes of functional non-protein-coding sequences found in the human genome.|1. Promoter & enhancer, 2. Chromatin binding site structures, 3. non-coding regulatory RNAs, 4. Mobile genetic elements (transposons), 5. telomeres, 6. centromers. }}

{{hidden|What are the two most common forms of DNA variation in the human genome?|1) Single nucleotide polymorphisms (SNPs), 2) copy number variations (CNVs)}}

{{hidden|What are the possible implications of SNPs.|1) regulatory = alters gene expression, 2) Correlation with disease states when in close proximity with altered genes, 3) association used to define linkage disequilibrium,?}}

{{hidden|Define epigenetics.|Heritable changes in gene expression which are not caused by alterations in DNA sequence.}}

{{hidden|List the 6 types of epigenetic changes.|1) Histone & histone modifying factors (Histones organize chromatin into heterochromatin and euchromatin, 2) histone methylation, 3) histone acteylation, 4)histone phosphorylation, 5) DNA methylation, 6) Chromatin organizing factors.}}

{{hidden|What is the function of micro-RNA (mi-RNA)?|It does not encode protein, instead they function primarily to modulate the translation of target mRNAs into their corresponding proteins, and are responsible for post-transcriptional silencing of gene expression.}}

{{hidden|What is knockdown technology?|The use of synthetic si-RNA (short RNA sequences) introduced into cells that serve as substrates for Dicer and interact with the RISC complex in a manner analogous to endogenous miRNAs, and are used to study gene function, and are being developed as therapeutic agents to silence pathogenic genes, e.g. oncogenic in neoplasms.}}

{{hidden|What is long non coding RNA?|Lnc-RNA modulate gene expression by binding to regions of chromatin, restricting RNA polymerase access to coding genes within the region, and may exceed the number of mRNA's by 10-20 fold.}}

{{hidden|What is XIST?|XIST is a lnc-RNA which is transcribed from the X-chromosome and plays an essential role in physiologic X chromosome inactivation, though not inactivated itself, it forms a repressive cloak on the X chromosome from which it is transcribed resulting in gene silencing.}}

{{hidden|What are the cellular housekeeping functions?|1) protection from the environment, 2) nutrient acquisition, 3) communication, 4) movement, 5) renewal of senescent molecules, 6) molecular catabolism, 7) energy generation.}}

{{hidden|List the cellular compartments and the role in the cell.|1) cytosol = metabolism, transport, protein translation, 2) Mitochondria = energy generation, apoptosis, 3) Rough ER = synthesis of membrane and secreted proteins, 4) Smooth ER / Golgi = protein modification, sorting, catabolism, 5)Nucleus = cell regulation, proliferation, DNA transcription, 6) Endosomes = intracellular transport and export, ingestion of extracellular substances, 7) Lysosomes = cellular catabolism, 8) peroxisomes = very long-chain fatty acid metabolism}}

{{hidden|Describe the basic structure and functions of the cell membrane.| The plasma membrane is composed of a lipid bilayer of phospholipids studded with a variety of proteins and glycoproteins involved in ion and metabolite transport, fluid phase and receptor-mediated uptake of macromolecules, cell-ligand/cell matrix/cell-cell interactions.}}

{{hidden|How are the large complexes in the plasma membrane formed?|They aggregate under the control of chaperone molecules in the RER or by lateral diffusion in the plasma membrane followed by complex formation in situ.}}

{{hidden|What are aquaporins?|Special integral membrane proteins which augment passive water transport in tissues where water is transported in large volumes.}}

{{hidden|How are channel and carrier proteins different?|Channel proteins created hydrophilic pores, permit rapid movement of solutes, restricted by size and charge, where Carrier proteins bind to their specific solutes and undergo a series of conformational changes to transfer the ligand across the membrane, relatively slow transport.}}

{{hidden|What is the "multidrug resistance (MDR) protein"?|A type of transporter ATPases which pumps polar compounds (e.g. chemo drugs) out of cells which may render cancer cells resistant to treatment.}}

{{hidden|What are the two fundamental mechanisms of fluid or macromolecules by the cell (endocytosis)?|1)Caveolae -invaginations of the plasma membrane, 2) Pinocytosis/receptor mediated endocytosis - macromolecules bind to receptor and membranes invaginate around it.}}

{{hidden|What is exocytosis?|It is the opposite process of pinocytosis, where the receptor bound macromolecule is move to the cell surface and released.}}

{{hidden|Describe the difference between phagocytosis and transcytosis.|In phagocytosis microbes are ingested forming phagosomes, which fuse with lysosomes and become phagylosomes, releasing undigested residual material when fusing again with the external membrane, in contrast transcytosis the materials are carried across the cell membrane unaltered.}}

{{hidden|List the three major classes of 3 cytoskeleton proteins.|1) Actin, 2)Intermediate filaments, 3)Microtubules}}

{{hidden|Describe actin.|Actin - 5 to 9nm diam fibrils, G-actin polymerized into F-actin, the form double strands helices, which interact with myosin (filamentous protein).}}

{{hidden|List the various intermediate filaments, which are 10nm in diameter.|1) Lamin A, B, and C (nuclear lamins of all cells, 2) Vimentin (mesenchymal), 3)Desmin (scaffold for actin/myosin), 4) Neurofilaments (axons of neurons), 5) Glial filament protein (glial cells), 6)Cytokeratins (acid and basic and vary based on cell type). }}

{{hidden|Describe microtubules.|Microtubules are 25nm diam fibrils of dimers of a and b tubulin, with a negative end embedded in the centrosome near the nucleus, the + end grows or shrinks as needed. There are kinesins and dyneins motors that move stuff around the cell, also found in cilia and flagella.}}

{{hidden|What is clatharin?|A molecule found in the cell membrane that when the cell membrane invaginates forming a basket like structure.}}

{{hidden|List and describe the 3 main classifications of cell junctions.|1) Tight /occluding junctions - form a high resistance barrier to solute movement, and allows the cell to maintain polarity, 2) anchoring junctions / desmosomes - mechanically attach the cell and their cytoskeleton to other cells and the ECM (hemidesmosome), 3)communicating/gap junctions - mediate the passage of chemical or electrical signals from one cell to another.}}

{{hidden|What is the "unfolded protein response"?| Excess accumulation of misfolded protiens, which exceed the capacity of the ER to edit and degrade them, leads to the the ER stress response (UPR) that triggers cell death through apoptosis.}}

{{hidden|What cell organelle has a reactive hyperplasia with repeated exposure to phenobarbitol catabolism in the cytocrhome p450 system?|Smooth endoplasmic reticulum.}}

{{hidden|List three main functions of mitochondria.|1) Energy generation, 2) intermediate metabolism (instead of ATP make intemediate that can be used to make lipids, nucleic acids, and proteins), 3) Cell death ( necrosis & apoptosis)}}

{{hidden|List and describe the four extracellular cell-cell signaling pathways based on the distance the signal travels.|1)Paracrine (immediate vicinity), 2) Autocrine (cell affecting itself), 3) Synaptic (neurons sending neurotransmitters at synapse), 4) endocrine (signals released elsewhere into bloodstream).}}

{{hidden|What are the two characterizing features of stem cells?|Self renewal and asymmetric division (one daughter cell stays a stem cell)}}

{{hidden|What are the two types of stem cells?|embryonic stem cells (inner cell mass of the blastocyst, totipotent), and tissue/adult stem cells (found in stem cell niches associated with specialized tissues, limited repetoire of differentiation = multipotent)}}

{{hidden|What is the Warburg effect?|Increased cellular uptake of glucose and glutamine, increased glycolysis, and decreased oxidative phosphorylation by the cell.}}

{{hidden|Which CDKI's have selective effects on CDK4 and CDK6?|p15,p16,p17,and p19}}

{{hidden|List some examples of signal transduction pathways.|1) Receptor tyrosine kinases (RTKs), 2) Nonreceptor tyrosine kinase, 3) G-protein coupled receptors, 4) nuclear receptors, 5)Notch family receptors, 6) Wnt protein ligands (Frizzled family receptors).}}

{{hidden|Why does nuclear beta catenin occur in some neoplasms?|When Wnt ligand bins to frizzled it recruits Disheveled, this leads to the disruption of the wnt-ubiquitin complex, this stabilized pool of b-catening is then translocated to the nucleus forming a transcriptional complex}}

{{hidden|On Page 19 there is a table of growth factors involved in regeneration and repair, please review.|}}

{{hidden|Describe the function of cadherin.|}}

{{hidden|What are the functions of the extracellular matrix?|Mechanical support, control of cell proliferation, scaffolding for tissue renewal, establishment of tissue microenvironments}}

{{hidden|What are the two basic forms of the ECM?|interstitial matrix (fibrillar and non fibrillar collagen, fibronectin, elastin, proteoglycans, hyloronate, and other stuff), basement membrane (type IV collagen and laminin) }}

{{hidden|What are the three proteins groups in the ECM?|1) fibrous structural proteins (collagen, elastins), 2) water hydrated gels (proteoglycans and hyaluronan), 3) adhesive glycoproteins (connect ECM to each other and other cells)}}

{{hidden|Describe the structure of a protein that is dependent on vitamin C.|Collagen is composed of 3 seprate polypeptide chains braided into a rope like triple helix, lateral cross linking of the triple helices by lysyl oxidase (requires vitamin C) give it it's tensile strength. }}

{{hidden|List three non-fibrillar collagens.|Type IV -basement membrane, Type IX - Fibrillar associated collagen with interrupted triple helices (FACIT), Type VII (provides anchoring fibrils to basement membrane beneath skin)}}

{{hidden|Which structural protein is associated with Marfan syndrom?|Fibrillin synthetic defects, which wrap the elastin core. }}

== Cellular Responses to Stress and Toxic Insults: Adaptation, Injury and Death ==

== Chapter 3 ==
== Chapter 4 ==
== Chapter 5 ==
{{hidden|MC cause of spontaneous abortion is ?|<center>[[ A demonstrable chromosomal abnormality.]]</center>}}

{{hidden|1% of all newborn infants possess a gross chromosomal abnormality and 5% of people <25y present with |<center>[[a genetic disease. ]]</center>}}

{{hidden|Mutation|<center>[[permanent change in the DNA, if affect germ cells are transmitted to the progeny ]]</center>}}

{{hidden|List and describe 4 broad categories of human genetic disorders:|<center>[[Disorders related to mutation sin single genes with large effects i. Usually follow classic Mendelian pattern of inheritance
ii. Often highly penetrant (large proportion of pop with gene has disease)
b. Chromosomal disorders
i. Structural or numerical alterations in autosomes and sex chromosomes
ii. Uncommon, high penetrance
c. Complex multigenic disorders
i. Interactions between multiple variant forms of genes and environmental factors (polymorphisms), poly genic means disease when many polymorphism present
d. Single gene disorders with nonclassic patterns of inheritance (not mendelian)
i. Disorders resulting from triplet repeat mutations
ii. Mutations in mitochondrial DNA
iii. Those influenced by genomic imprinting
iv. Those influenced by gonadal mosaicism]]</center>}}

{{hidden|List and describe the possible outcomes of a point mutation in a coding region?|[[a. Missense mutation – pt mutation changes amino acid code, conservative when the amino acid is preserved, non conservative when replaced with another amino acid, b. Nonsense mutation – makes a stop codon ]]</center>}}

{{hidden|List and describe the possible outcomes of point mutation or deletion in a non-coding region.|<center>[[a. Promoters/enhancers – interfere with binding of transcription factors, marker reduction or total lack of transcription, b. Introns – defective splicing > failure to make mature RNA > no translation]]</center>}}

{{hidden|List and describe the possible outcomes of deletions and insertions.|<center>[[a.Small coding: not multiple of three = frameshift, if multiple of 3 than add or del amino acids accordingly, often premature stop codon
i. Tay Sachs disease: 4 base pair insertion in Hexosaminidase A gene ]]}}

{{hidden|List and describe the possible outcomes of trinucleotide repeat mutations.|[[a. Usually G&C, dynamic and increase during gametogenesis, “RNA stutters”,b. Fragile X – CGG 250-4000, Huntinton’s Disease ]]}}

{{hidden|List and describe three examples of inheritance of single gene mutations|[[a. AD – manifested in the heterologous state, one parent of index case is usually affected, males and females affected and both can transmit conditioni. De novo cases may not have affected parentii. Penetrance = fraction of people with gene who have the traitiii. Variable expressivity = those with mutant gene have variety of phenotypesiv. Often age of onset is delayed so can reproduce before die from diseasev. Biochem mechanisms1. Reduced production of a protein or dysfunctional/inactive protein2. Involved in regulation of complex metabolic pathyway subject to feedback inhibition3. Key structural proteins (collagen and cytoskeleton of RBC)a. May be a dominant negative , e.g. osteogenesis imperfecta4. Gain of function are rare, 2 formsa. Increased in proteins normal function (excess enzyme activity)b. Huntinton’s diseas (abn protein accumulates, toxic to neurons)b. ARi. Largest category – both alleles at a locus are mutated1. Expression is uniform, complete penetrance common, early onset, unaffected carrier family members, mostly enzymesc. X Linkedi. All sex linked, and almost all are recessive , if Y Chromosome affected usually infertile males > no progenyii. Male expression b/c hemizygous, daughter carriers with variable phenotype because of lionization of 2nd X e.g G6DPiii. Dominant . vitamin D resistant rickets]]</center>}}

Stopped at P142

== Chapter 6 ==
== Chapter 7 ==
== Chapter 8 ==
== Chapter 9 ==
== Chapter 10 ==
== Chapter 11 ==
== Chapter 12 ==
== Chapter 13 ==
== Chapter 14 ==
== Chapter 15 ==
== Chapter 16 ==
== Chapter 17 ==
== Chapter 18 ==
== Chapter 19 ==
== Chapter 20 ==
== Chapter 21 ==
== Chapter 22 ==
== Chapter 23 ==
== Chapter 24 ==
== Chapter 25 ==
== Chapter 26 ==
== Chapter 27 ==
== Chapter 28 ==
== Chapter 29 ==

Cytogenetics Review Questions

2015-05-27T15:06:30Z

Yuanny: /* Unit 1 */

==Unit 1==
{{hidden| List the three broad categories of clinical indications for chromosomal analysis.|Prenatal, Constitutional, Cancer/Acquired}}

{{hidden|Which family members should have chromosomal analysis?|1. Both parents of a child with structural chromosome rearrangement, deletion, duplication, and 2. all family members at risk of having a chromosome rearrangement.}}

{{hidden|List 5 prenatal indications for cytogenetics analysis.|
*1. Advanced maternal age (Greater than 35 years old)
*2. Previous pregnancy with chromosomal disorder
*3. One parent is a known carrier (or other relative*)
*4. Couples at risk of x-linked disorders for which a molecular test is not available
*5. Fetal defects on ultrasound,
*6. Prenatal screen high risk pregnancies
*7. couples with 2+ spontaneous abortions
*8. infertility. }}

{{hidden|What are the indications for chromosomal analysis of products of conception?|1)Abortuses (missed abortions) of unknown reason, 2)Malformed stillbirths, 3)Stillbirth of undetermined etiology}}
{{hidden|Compare amniocentesis and chorionic villus sampling with regards to gestational age, complication rate, turn around time, and false results|}}
{{hidden|What are the clinical indications for tissue sampling instead of blood for cytogenetic analysis?|1)Suspicion of chromosomal mosaicism, 2) blood is not available (e.g. POC), 3) surgical or post-mortem tissue.}}
{{hidden|List 8 standard techniques for cytogenetics analysis.|1) Geimsa / G-Banding, 2) Quinacrin / Q-banding 3) Reverse / R-banding, 4)Centromere / C-banding, 5)NOR staining (nucleolus organizer regions), 6)DAPI staining, 7) Chromosomal breakage, 8) Sister chromatid Exchange (SCE)}}
{{hidden|List 5 Molecular cytogenetics techniques.|1)FISH (flourescence in situ hybridization), 2) Multi-colour FISH, 3) SKY (spectral karyotyping), 4) CGH (comparative genomic hybridization), 5) CGH array}}
{{hidden|What is g-banding?|Chromosomes are treated with trypsine and then stained with Geimsa (or wrights) which darkly stains the AT rich regions (heterochromatin), and lightly stains the GC rich regions of the chromosome.}}
{{hidden|Outline the general procedure for cytogenetics study.|1) cell culture at 37C 5%CO2 in medium (dividing and stimulation), 2) Chromosome elongation Thymidine BrdU, 3) Metaphase arrest with Colcemide, 4) Cell swelling with hypotonic KCl,* Hardening with acetic acid* 5) Fixation with Cournay's (Methanol: Acetic acid, 3:1), 6) Slide making (chromosome spread with ideal temperature and humidity), 7) Slide aging (air dry slide warmer), 8)Staining (G, Q, C, R-banding), 8) Molecular cytogenetic technique (FISH, multi-FISH, CGH, SKY, array CGH).}}
{{hidden|Broadly what at the three main morphological groups of chromosomes?|Metacentric, acrocentric, submetacentric.}}
{{hidden|What are the 4 minimum items included in a standard banding nomenclature?|1. Chromosome number, 2) short or long arm, 3) region on that arm, 4) band number within that region}}
{{hidden|What are the clinical indications for an individual to have chromosomal analysis?|1)suspected classic chromosome syndrome, 2) Mental retardation of undetermined etiology, 3) dysmophic features, 4) multiple congenital abnormalities, 5) abnormalities of sexual development, 6) ambiguous genitalia, 7)pubertal failure, 8)abnormalities of growth, 9) certain types of malignancies.}}
{{hidden|What is q-banding?|Chromosomes are prepared with quinacrine which produces flourescent bands in the AT rich regions, particularly useful in identifying polymorphisms on the acrocentric chromosomes ( ) and the Y chromosome.}}
{{hidden|What is R-banding?|Darkly stains the GC rich regions of the chromosome (Euchromatin), aka Reverse-banding, and is used to detect subtle deletions or rearrangements that may not be detected by Q or G banding.}}
{{hidden|What is C-banding?|C-Banding stains the constituitive heterochromatin that is localized to the pericentromeric regions of all chromosomes and on the distal long arm of Y. Used to identify pericentric inversions and polymorphisms in centromeric regions of 1,9,16, and Yq, as well as confirming translocations of Y}}
{{hidden|What is NOR?|NOR is a silver staining procedure which stains the nucleolus organizer regions of satellited chromosomes (used to study the size of stalks and satellites in the acrocentric chromosomes)}}
{{hidden|List the metacentric chromosomes.|}}
{{hidden|List the submetacentric chromosomes.|}}
{{hidden|List the acrocentric chromosomes.|}}
{{hidden|What is Bloom syndrome?|Bloom syndrome is a rare AR genetic disorder with a defect in the BLM gene with a phenotype of short stature, tendency to sunburn, increased risk of malignancy, reduced or absent fertility, and prone to sister chromatid exchange [[http://ghr.nlm.nih.gov/condition/bloom-syndrome]] }}
{{hidden|What is SCE (Sister chromatid exchange?|SCE (sister chromatid exchange) is the interchange of homologous segments between two chromatids of one chromosome, grow the cells under special conditions to produce a differential staining of sister chromatids.}}
{{hidden|What is DAPI staining?|DAPI staining produces bright flourescence of the heterochromatin regions of 1,9,16, and Y, as well as the centromere of 15, and is used to id marker chromosomes or translocations of Y.}}
{{hidden|Explain how chromosomal breakage studies are used to diagnose Fanconi's anemia.| Cultured cells are treated with DEB (Diepoxybutane) or mitomycin C to induce breakage, those cells with chromosomes prone to breakage are especially susceptible and this can be seen as gaps, breaks, deletions, triradial, quadriradial, dicentric, and complex figure in the metaphase.}}

==Unit 2==
{{hidden|Describe the 4 steps of mitosis.|Prophase, metaphase, anaphase, telophase}}
{{hidden|List the 8 steps of meiosis.|Meiosis 1(Prophase 1, Metaphase 1, Anaphase 1, Telophase 1), Meiosis 2( Prophase 2, Metaphase 2, Anaphase 2, Telophase 2).}}
{{hidden|What is the main difference between constitutional and acquired chromosome anomalies.|1) Constitutional affects the whole patient, acquired usually limited to 1 organ.}}
{{hidden|What at the three main categories of patient features associated with unbalanced constitutional chromosomal anomalies?]1) dysmophy, 2) Visceral malformations, 3) developmental/psychomotor delay.}}
{{hidden|What is meant by a homogeneous chromosomal anomaly?|Homogeneous chromosomal anomalies mean that all the cells STUDIED carry the anomaly, may be constitutional or acquired.}}
{{hidden|What is meant by a mosaic chromosomal anomaly?|Mosaic chromosomal anomalies mean that only some of the cells STUDIED carry the anomaly, may be constitutional or acquired.}}
{{hidden|What are chromosomal polymorphisms?|Chromosomal polymorphisms are variants of chromosomes that are widespread in a particular population which to date are not known to have any effect on the phenotype, they vary in size, position, and staining properties but must occur in heterochromatin regions usually near the centromere.}}
{{hidden|List 3 known chromosomal polymorphisms, according to ISCN 2013.|[[Chromosomal polymorphisms]]}}
{{hidden|Classify numerical abnormalities of chromosomes.|1) polyploidy (multiple complete sets of chromosomes, e.g. 3N), 2) Aneuploidy (monosomy (e.g. Turner's syndrome), trisomy (e.g. trisomy 18, 13, or 21), tetrasomy))}}
{{hidden|What are the four main types of abnormalities in chromosome structure?|1) Deletion, 2) duplication, 3) rearrangement (inversion or insertion), 4) translocation}}
{{hidden|What is the key difference between a balanced and an unbalanced chromosomal rearrangement?|Balanced translocations imply that there is no missing or excess genetic material, while unbalanced translocations have either missing or excess genetic material from that of a normal genotype.}}
{{hidden|List three types of balanced chromosomal rearrangements.|Translocation, inversion, insertion.}}
{{hidden|List three unbalanced numerical chromosomal rearrangements.|trisomy, monosomy, multiploidy}}
{{hidden|List 5 structural unbalanced chromosomal rearrangements.|deletion, duplication, derivative chromsome, recombination chromosome, marker chromosome, ring chromosome, Dm & HSR}}
{{hidden|What is the karyotype for a female infant with cri-du-chat?|46,XX,del(5)(p15.1)}}
==Unit 3==
{{hidden|What is FISH?|FISH is a molecular cytogenetic technique in which flourescently labelled DNA probes are hybridized to metaphase spreads or interphase nuclei.}}
{{hidden|When is interphase FISH more helpful than metaphase?|Interphase FISH is particularly useful in samples where there is poor culture growth such as bone marrow or cancer tissue.}}
{{hidden|What is the approximate resolution of cytogenetic FISH?|3-5Mb}}
{{hidden|What are the three types of FISH probes?|1)Probes for repetative sequences (Centromeres, telomeric sequences), 2) Unique sequence probes hybridized to a single copy of DNA sequences in a specific gene or chromosome, 3) Whole chromosome paints (or arms) which are cocktails of probes that are chromosome specific and cover the entire length.}}
{{hidden|List 7 applications of FISH technology?| 1) Microdeletion syndromes, 2) Characterization of chromosomal structural abnormalities, 3) identification of marker chromosomes, 4) Aneuploidy detection, 5) Cancer cytogenetics, 6) Gene mapping, 7)Rapid detection of sex chromosomes and the SRY gene}}
{{hidden|List 5 microdeletion syndromes.|[[List of Microdeletion Syndromes]]}}
{{hidden|Briefly describe Cri-du Chat Syndrome|}}
{{hidden|Describe 3 mechanisms by which uniparental disomy occurs.|1) Trisomic rescue (loss of a chromosome from a trisomic zygote), 2) monosomic rescue (duplication of a chromosome from a monosomic zygote), 3)Gamete complementation (fertilization of a gamete with two copies of a chromosome with no copies from other parent)}}
{{hidden|What is imprinting?|Normally we inherit one copy of each gene from each parent, some genes are only expressed when they are inherited paternally, some only when maternally, this differential expression based on inheritance is called imprinting, and changes generation to generation.}}
{{hidden|Which chromosomes are known to have imprinted genes?|Chromosomes 6,7,11,14,and 15.}}
{{hidden|Describe Prader-Willi Syndrome.|Features: hypotonia, obesity, developmental delay, hypogonadism, short stature, 70%: del(15q11-13), 25% uniparental disomy, 2%:other, diagnoses by FISH for microdeletion, or DNA methylation; due to absence of paternally derived PWS/AS gene }}
{{hidden|Briefly describe Williams Syndrome.|Deletion of one elastin allele (7q11.23 = 96% of cases), multi-system d/o characterized by: Growth & developmental delay, characteristic facies & personality, supra valvular stenosis, idiopathic infantile hypercalcemia (connective tissue / vascular)}}
{{hidden|Describe DeGeorge Syndrome.|95% 22q11.2 deletion, 5% FISH negative; AD inherit; 1) Conotruncal heart defects, 2)uropathy, 3)polyhydramnios,4)increased nuchal translucency, 5) IUGR, 6)thymic hypoplasia, 7) characteristic facies, 8) hypoparathyroidism, 9)MR/DD}}
{{hidden|What is SKY?|A chromosomal analysis technique that has the ability to paint each pair of chromosomes and the sex chromosomes a different flourescing colour.}}
{{hidden|What kinds of chromosomal transformations is SKY used for?|1) translocations, 2) insertions, 3)marker chromosome identification, 4) cancer tumour genetics}}
{{hidden|What are three limitations of SKY?|1) cannot detect del,dup,inv, 2) interpretation difficult if colours too similar}}
{{hidden|Explain the basic principle of Comparative Genomic Hybridization.|References genomes and the index genome are mixed, if the index genome substantially differs from the reference genome then there will be a neg signal loss or gain for that probe's flourescence, this can be used to determine if there is one allele in the index case that is missing or in excess compared to the reference genome.}}
{{hidden|How do CGH arrays work?|CGH arrays allow hundreds-thousands of probes to be used to compare the index and the reference genome, giving a complete chromosomal analysis that depends on the resolution of the probe.}}

==Unit 4==

==Miscellaneous==
{{hidden|What is Allerdice or Sandy Point Syndrome?|It is a chromosomal disorder discovered in Sandy Point, NL by Dr. Penny Allderdice, inv(3)(p25q21) characterized by affected offspring with multiple congenital anomalies with surviving children exhibiting severe growth and developmental delays.}}
{{hidden|What is the most common robertsonian translocation?|Translocation between the long arms of 13 and 14.}}
{{hidden|What is the most common non-robertsonian translocation?|t(11;22)(q23;q11)}}
{{hidden|What is a marker chromosome?|A structurally abnormal chromosome in which no part can be identified cytogenetically.}}
{{hidden|What is the most common chromosomal abnormality in humans?|Aneuploidy - about 5% of pregnancies.}}
{{hidden|What is the most common cause of triploidy?|Dispermy in 60%}}
{{hidden|What is the recurrence risk for parents of Down's syndrome child with a "free chromosome"?|1%}}
{{hidden|List 5 features of Trisomy 8.|}}
{{hidden|List 5 features of Trisomy 9.|}}
{{hidden|List 5 features of Trisomy 13.|}}
{{hidden|List 5 features of Trisomy 14.|}}
{{hidden|List 5 features of Trisomy 18.|}}
{{hidden|List 5 features of Trisomy 21.|}}
{{hidden|What is the most common outcome of a pregnancy when the parent has a balanced translocation?|Misscarriage}}

==Peripheral Blood Culture and Harvest==
{{hidden|
{{hidden|

Cytogenetics Review Questions

2015-05-27T15:04:31Z

Yuanny: /* Unit 1 */

==Unit 1==
{{hidden| List the three broad categories of clinical indications for chromosomal analysis.|Prenatal, Constitutional, Cancer/Acquired}}

{{hidden|Which family members should have chromosomal analysis?|1. Both parents of a child with structural chromosome rearrangement, deletion, duplication, and 2. all family members at risk of having a chromosome rearrangement.}}

{{hidden|List 5 prenatal indications for cytogenetics analysis.|1. Advanced maternal age (Greater than 35 years old), *2. Previous pregnancy with chromosomal disorder, 3. One parent is a known carrier (or other relative*), 4. Couples at risk of x-linked disorders for which a molecular test is not available, 5. Fetal defects on ultrasound, 6. Prenatal screen high risk pregnancies, 7. couples with 2+ spontaneous abortions, 8. infertility. }}
{{hidden|What are the indications for chromosomal analysis of products of conception?|1)Abortuses (missed abortions) of unknown reason, 2)Malformed stillbirths, 3)Stillbirth of undetermined etiology}}
{{hidden|Compare amniocentesis and chorionic villus sampling with regards to gestational age, complication rate, turn around time, and false results|}}
{{hidden|What are the clinical indications for tissue sampling instead of blood for cytogenetic analysis?|1)Suspicion of chromosomal mosaicism, 2) blood is not available (e.g. POC), 3) surgical or post-mortem tissue.}}
{{hidden|List 8 standard techniques for cytogenetics analysis.|1) Geimsa / G-Banding, 2) Quinacrin / Q-banding 3) Reverse / R-banding, 4)Centromere / C-banding, 5)NOR staining (nucleolus organizer regions), 6)DAPI staining, 7) Chromosomal breakage, 8) Sister chromatid Exchange (SCE)}}
{{hidden|List 5 Molecular cytogenetics techniques.|1)FISH (flourescence in situ hybridization), 2) Multi-colour FISH, 3) SKY (spectral karyotyping), 4) CGH (comparative genomic hybridization), 5) CGH array}}
{{hidden|What is g-banding?|Chromosomes are treated with trypsine and then stained with Geimsa (or wrights) which darkly stains the AT rich regions (heterochromatin), and lightly stains the GC rich regions of the chromosome.}}
{{hidden|Outline the general procedure for cytogenetics study.|1) cell culture at 37C 5%CO2 in medium (dividing and stimulation), 2) Chromosome elongation Thymidine BrdU, 3) Metaphase arrest with Colcemide, 4) Cell swelling with hypotonic KCl,* Hardening with acetic acid* 5) Fixation with Cournay's (Methanol: Acetic acid, 3:1), 6) Slide making (chromosome spread with ideal temperature and humidity), 7) Slide aging (air dry slide warmer), 8)Staining (G, Q, C, R-banding), 8) Molecular cytogenetic technique (FISH, multi-FISH, CGH, SKY, array CGH).}}
{{hidden|Broadly what at the three main morphological groups of chromosomes?|Metacentric, acrocentric, submetacentric.}}
{{hidden|What are the 4 minimum items included in a standard banding nomenclature?|1. Chromosome number, 2) short or long arm, 3) region on that arm, 4) band number within that region}}
{{hidden|What are the clinical indications for an individual to have chromosomal analysis?|1)suspected classic chromosome syndrome, 2) Mental retardation of undetermined etiology, 3) dysmophic features, 4) multiple congenital abnormalities, 5) abnormalities of sexual development, 6) ambiguous genitalia, 7)pubertal failure, 8)abnormalities of growth, 9) certain types of malignancies.}}
{{hidden|What is q-banding?|Chromosomes are prepared with quinacrine which produces flourescent bands in the AT rich regions, particularly useful in identifying polymorphisms on the acrocentric chromosomes ( ) and the Y chromosome.}}
{{hidden|What is R-banding?|Darkly stains the GC rich regions of the chromosome (Euchromatin), aka Reverse-banding, and is used to detect subtle deletions or rearrangements that may not be detected by Q or G banding.}}
{{hidden|What is C-banding?|C-Banding stains the constituitive heterochromatin that is localized to the pericentromeric regions of all chromosomes and on the distal long arm of Y. Used to identify pericentric inversions and polymorphisms in centromeric regions of 1,9,16, and Yq, as well as confirming translocations of Y}}
{{hidden|What is NOR?|NOR is a silver staining procedure which stains the nucleolus organizer regions of satellited chromosomes (used to study the size of stalks and satellites in the acrocentric chromosomes)}}
{{hidden|List the metacentric chromosomes.|}}
{{hidden|List the submetacentric chromosomes.|}}
{{hidden|List the acrocentric chromosomes.|}}
{{hidden|What is Bloom syndrome?|Bloom syndrome is a rare AR genetic disorder with a defect in the BLM gene with a phenotype of short stature, tendency to sunburn, increased risk of malignancy, reduced or absent fertility, and prone to sister chromatid exchange [[http://ghr.nlm.nih.gov/condition/bloom-syndrome]] }}
{{hidden|What is SCE (Sister chromatid exchange?|SCE (sister chromatid exchange) is the interchange of homologous segments between two chromatids of one chromosome, grow the cells under special conditions to produce a differential staining of sister chromatids.}}
{{hidden|What is DAPI staining?|DAPI staining produces bright flourescence of the heterochromatin regions of 1,9,16, and Y, as well as the centromere of 15, and is used to id marker chromosomes or translocations of Y.}}
{{hidden|Explain how chromosomal breakage studies are used to diagnose Fanconi's anemia.| Cultured cells are treated with DEB (Diepoxybutane) or mitomycin C to induce breakage, those cells with chromosomes prone to breakage are especially susceptible and this can be seen as gaps, breaks, deletions, triradial, quadriradial, dicentric, and complex figure in the metaphase.}}

==Unit 2==
{{hidden|Describe the 4 steps of mitosis.|Prophase, metaphase, anaphase, telophase}}
{{hidden|List the 8 steps of meiosis.|Meiosis 1(Prophase 1, Metaphase 1, Anaphase 1, Telophase 1), Meiosis 2( Prophase 2, Metaphase 2, Anaphase 2, Telophase 2).}}
{{hidden|What is the main difference between constitutional and acquired chromosome anomalies.|1) Constitutional affects the whole patient, acquired usually limited to 1 organ.}}
{{hidden|What at the three main categories of patient features associated with unbalanced constitutional chromosomal anomalies?]1) dysmophy, 2) Visceral malformations, 3) developmental/psychomotor delay.}}
{{hidden|What is meant by a homogeneous chromosomal anomaly?|Homogeneous chromosomal anomalies mean that all the cells STUDIED carry the anomaly, may be constitutional or acquired.}}
{{hidden|What is meant by a mosaic chromosomal anomaly?|Mosaic chromosomal anomalies mean that only some of the cells STUDIED carry the anomaly, may be constitutional or acquired.}}
{{hidden|What are chromosomal polymorphisms?|Chromosomal polymorphisms are variants of chromosomes that are widespread in a particular population which to date are not known to have any effect on the phenotype, they vary in size, position, and staining properties but must occur in heterochromatin regions usually near the centromere.}}
{{hidden|List 3 known chromosomal polymorphisms, according to ISCN 2013.|[[Chromosomal polymorphisms]]}}
{{hidden|Classify numerical abnormalities of chromosomes.|1) polyploidy (multiple complete sets of chromosomes, e.g. 3N), 2) Aneuploidy (monosomy (e.g. Turner's syndrome), trisomy (e.g. trisomy 18, 13, or 21), tetrasomy))}}
{{hidden|What are the four main types of abnormalities in chromosome structure?|1) Deletion, 2) duplication, 3) rearrangement (inversion or insertion), 4) translocation}}
{{hidden|What is the key difference between a balanced and an unbalanced chromosomal rearrangement?|Balanced translocations imply that there is no missing or excess genetic material, while unbalanced translocations have either missing or excess genetic material from that of a normal genotype.}}
{{hidden|List three types of balanced chromosomal rearrangements.|Translocation, inversion, insertion.}}
{{hidden|List three unbalanced numerical chromosomal rearrangements.|trisomy, monosomy, multiploidy}}
{{hidden|List 5 structural unbalanced chromosomal rearrangements.|deletion, duplication, derivative chromsome, recombination chromosome, marker chromosome, ring chromosome, Dm & HSR}}
{{hidden|What is the karyotype for a female infant with cri-du-chat?|46,XX,del(5)(p15.1)}}
==Unit 3==
{{hidden|What is FISH?|FISH is a molecular cytogenetic technique in which flourescently labelled DNA probes are hybridized to metaphase spreads or interphase nuclei.}}
{{hidden|When is interphase FISH more helpful than metaphase?|Interphase FISH is particularly useful in samples where there is poor culture growth such as bone marrow or cancer tissue.}}
{{hidden|What is the approximate resolution of cytogenetic FISH?|3-5Mb}}
{{hidden|What are the three types of FISH probes?|1)Probes for repetative sequences (Centromeres, telomeric sequences), 2) Unique sequence probes hybridized to a single copy of DNA sequences in a specific gene or chromosome, 3) Whole chromosome paints (or arms) which are cocktails of probes that are chromosome specific and cover the entire length.}}
{{hidden|List 7 applications of FISH technology?| 1) Microdeletion syndromes, 2) Characterization of chromosomal structural abnormalities, 3) identification of marker chromosomes, 4) Aneuploidy detection, 5) Cancer cytogenetics, 6) Gene mapping, 7)Rapid detection of sex chromosomes and the SRY gene}}
{{hidden|List 5 microdeletion syndromes.|[[List of Microdeletion Syndromes]]}}
{{hidden|Briefly describe Cri-du Chat Syndrome|}}
{{hidden|Describe 3 mechanisms by which uniparental disomy occurs.|1) Trisomic rescue (loss of a chromosome from a trisomic zygote), 2) monosomic rescue (duplication of a chromosome from a monosomic zygote), 3)Gamete complementation (fertilization of a gamete with two copies of a chromosome with no copies from other parent)}}
{{hidden|What is imprinting?|Normally we inherit one copy of each gene from each parent, some genes are only expressed when they are inherited paternally, some only when maternally, this differential expression based on inheritance is called imprinting, and changes generation to generation.}}
{{hidden|Which chromosomes are known to have imprinted genes?|Chromosomes 6,7,11,14,and 15.}}
{{hidden|Describe Prader-Willi Syndrome.|Features: hypotonia, obesity, developmental delay, hypogonadism, short stature, 70%: del(15q11-13), 25% uniparental disomy, 2%:other, diagnoses by FISH for microdeletion, or DNA methylation; due to absence of paternally derived PWS/AS gene }}
{{hidden|Briefly describe Williams Syndrome.|Deletion of one elastin allele (7q11.23 = 96% of cases), multi-system d/o characterized by: Growth & developmental delay, characteristic facies & personality, supra valvular stenosis, idiopathic infantile hypercalcemia (connective tissue / vascular)}}
{{hidden|Describe DeGeorge Syndrome.|95% 22q11.2 deletion, 5% FISH negative; AD inherit; 1) Conotruncal heart defects, 2)uropathy, 3)polyhydramnios,4)increased nuchal translucency, 5) IUGR, 6)thymic hypoplasia, 7) characteristic facies, 8) hypoparathyroidism, 9)MR/DD}}
{{hidden|What is SKY?|A chromosomal analysis technique that has the ability to paint each pair of chromosomes and the sex chromosomes a different flourescing colour.}}
{{hidden|What kinds of chromosomal transformations is SKY used for?|1) translocations, 2) insertions, 3)marker chromosome identification, 4) cancer tumour genetics}}
{{hidden|What are three limitations of SKY?|1) cannot detect del,dup,inv, 2) interpretation difficult if colours too similar}}
{{hidden|Explain the basic principle of Comparative Genomic Hybridization.|References genomes and the index genome are mixed, if the index genome substantially differs from the reference genome then there will be a neg signal loss or gain for that probe's flourescence, this can be used to determine if there is one allele in the index case that is missing or in excess compared to the reference genome.}}
{{hidden|How do CGH arrays work?|CGH arrays allow hundreds-thousands of probes to be used to compare the index and the reference genome, giving a complete chromosomal analysis that depends on the resolution of the probe.}}

==Unit 4==

==Miscellaneous==
{{hidden|What is Allerdice or Sandy Point Syndrome?|It is a chromosomal disorder discovered in Sandy Point, NL by Dr. Penny Allderdice, inv(3)(p25q21) characterized by affected offspring with multiple congenital anomalies with surviving children exhibiting severe growth and developmental delays.}}
{{hidden|What is the most common robertsonian translocation?|Translocation between the long arms of 13 and 14.}}
{{hidden|What is the most common non-robertsonian translocation?|t(11;22)(q23;q11)}}
{{hidden|What is a marker chromosome?|A structurally abnormal chromosome in which no part can be identified cytogenetically.}}
{{hidden|What is the most common chromosomal abnormality in humans?|Aneuploidy - about 5% of pregnancies.}}
{{hidden|What is the most common cause of triploidy?|Dispermy in 60%}}
{{hidden|What is the recurrence risk for parents of Down's syndrome child with a "free chromosome"?|1%}}
{{hidden|List 5 features of Trisomy 8.|}}
{{hidden|List 5 features of Trisomy 9.|}}
{{hidden|List 5 features of Trisomy 13.|}}
{{hidden|List 5 features of Trisomy 14.|}}
{{hidden|List 5 features of Trisomy 18.|}}
{{hidden|List 5 features of Trisomy 21.|}}
{{hidden|What is the most common outcome of a pregnancy when the parent has a balanced translocation?|Misscarriage}}

==Peripheral Blood Culture and Harvest==
{{hidden|
{{hidden|

Cytogenetics Review Questions

2015-05-27T15:03:53Z

Yuanny: /* Unit 1 */

==Unit 1==
{{hidden| List the three broad categories of clinical indications for chromosomal analysis.|Prenatal, Constitutional, Cancer/Acquired}}

{{hidden|Which family members should have chromosomal analysis?|1. Both parents of a child with structural chromosome rearrangement, deletion, duplication, and 2. all family members at risk of having a chromosome rearrangement.}}

{{hidden|List 5 prenatal indications for cytogenetics analysis.|1. Advanced maternal age (Greater than 35 years old), 2. Previous pregnancy with chromosomal disorder, 3. One parent is a known carrier (or other relative*), 4. Couples at risk of x-linked disorders for which a molecular test is not available, 5. Fetal defects on ultrasound, 6. Prenatal screen high risk pregnancies, 7. couples with 2+ spontaneous abortions, 8. infertility. }}
{{hidden|What are the indications for chromosomal analysis of products of conception?|1)Abortuses (missed abortions) of unknown reason, 2)Malformed stillbirths, 3)Stillbirth of undetermined etiology}}
{{hidden|Compare amniocentesis and chorionic villus sampling with regards to gestational age, complication rate, turn around time, and false results|}}
{{hidden|What are the clinical indications for tissue sampling instead of blood for cytogenetic analysis?|1)Suspicion of chromosomal mosaicism, 2) blood is not available (e.g. POC), 3) surgical or post-mortem tissue.}}
{{hidden|List 8 standard techniques for cytogenetics analysis.|1) Geimsa / G-Banding, 2) Quinacrin / Q-banding 3) Reverse / R-banding, 4)Centromere / C-banding, 5)NOR staining (nucleolus organizer regions), 6)DAPI staining, 7) Chromosomal breakage, 8) Sister chromatid Exchange (SCE)}}
{{hidden|List 5 Molecular cytogenetics techniques.|1)FISH (flourescence in situ hybridization), 2) Multi-colour FISH, 3) SKY (spectral karyotyping), 4) CGH (comparative genomic hybridization), 5) CGH array}}
{{hidden|What is g-banding?|Chromosomes are treated with trypsine and then stained with Geimsa (or wrights) which darkly stains the AT rich regions (heterochromatin), and lightly stains the GC rich regions of the chromosome.}}
{{hidden|Outline the general procedure for cytogenetics study.|1) cell culture at 37C 5%CO2 in medium (dividing and stimulation), 2) Chromosome elongation Thymidine BrdU, 3) Metaphase arrest with Colcemide, 4) Cell swelling with hypotonic KCl,* Hardening with acetic acid* 5) Fixation with Cournay's (Methanol: Acetic acid, 3:1), 6) Slide making (chromosome spread with ideal temperature and humidity), 7) Slide aging (air dry slide warmer), 8)Staining (G, Q, C, R-banding), 8) Molecular cytogenetic technique (FISH, multi-FISH, CGH, SKY, array CGH).}}
{{hidden|Broadly what at the three main morphological groups of chromosomes?|Metacentric, acrocentric, submetacentric.}}
{{hidden|What are the 4 minimum items included in a standard banding nomenclature?|1. Chromosome number, 2) short or long arm, 3) region on that arm, 4) band number within that region}}
{{hidden|What are the clinical indications for an individual to have chromosomal analysis?|1)suspected classic chromosome syndrome, 2) Mental retardation of undetermined etiology, 3) dysmophic features, 4) multiple congenital abnormalities, 5) abnormalities of sexual development, 6) ambiguous genitalia, 7)pubertal failure, 8)abnormalities of growth, 9) certain types of malignancies.}}
{{hidden|What is q-banding?|Chromosomes are prepared with quinacrine which produces flourescent bands in the AT rich regions, particularly useful in identifying polymorphisms on the acrocentric chromosomes ( ) and the Y chromosome.}}
{{hidden|What is R-banding?|Darkly stains the GC rich regions of the chromosome (Euchromatin), aka Reverse-banding, and is used to detect subtle deletions or rearrangements that may not be detected by Q or G banding.}}
{{hidden|What is C-banding?|C-Banding stains the constituitive heterochromatin that is localized to the pericentromeric regions of all chromosomes and on the distal long arm of Y. Used to identify pericentric inversions and polymorphisms in centromeric regions of 1,9,16, and Yq, as well as confirming translocations of Y}}
{{hidden|What is NOR?|NOR is a silver staining procedure which stains the nucleolus organizer regions of satellited chromosomes (used to study the size of stalks and satellites in the acrocentric chromosomes)}}
{{hidden|List the metacentric chromosomes.|}}
{{hidden|List the submetacentric chromosomes.|}}
{{hidden|List the acrocentric chromosomes.|}}
{{hidden|What is Bloom syndrome?|Bloom syndrome is a rare AR genetic disorder with a defect in the BLM gene with a phenotype of short stature, tendency to sunburn, increased risk of malignancy, reduced or absent fertility, and prone to sister chromatid exchange [[http://ghr.nlm.nih.gov/condition/bloom-syndrome]] }}
{{hidden|What is SCE (Sister chromatid exchange?|SCE (sister chromatid exchange) is the interchange of homologous segments between two chromatids of one chromosome, grow the cells under special conditions to produce a differential staining of sister chromatids.}}
{{hidden|What is DAPI staining?|DAPI staining produces bright flourescence of the heterochromatin regions of 1,9,16, and Y, as well as the centromere of 15, and is used to id marker chromosomes or translocations of Y.}}
{{hidden|Explain how chromosomal breakage studies are used to diagnose Fanconi's anemia.| Cultured cells are treated with DEB (Diepoxybutane) or mitomycin C to induce breakage, those cells with chromosomes prone to breakage are especially susceptible and this can be seen as gaps, breaks, deletions, triradial, quadriradial, dicentric, and complex figure in the metaphase.}}

==Unit 2==
{{hidden|Describe the 4 steps of mitosis.|Prophase, metaphase, anaphase, telophase}}
{{hidden|List the 8 steps of meiosis.|Meiosis 1(Prophase 1, Metaphase 1, Anaphase 1, Telophase 1), Meiosis 2( Prophase 2, Metaphase 2, Anaphase 2, Telophase 2).}}
{{hidden|What is the main difference between constitutional and acquired chromosome anomalies.|1) Constitutional affects the whole patient, acquired usually limited to 1 organ.}}
{{hidden|What at the three main categories of patient features associated with unbalanced constitutional chromosomal anomalies?]1) dysmophy, 2) Visceral malformations, 3) developmental/psychomotor delay.}}
{{hidden|What is meant by a homogeneous chromosomal anomaly?|Homogeneous chromosomal anomalies mean that all the cells STUDIED carry the anomaly, may be constitutional or acquired.}}
{{hidden|What is meant by a mosaic chromosomal anomaly?|Mosaic chromosomal anomalies mean that only some of the cells STUDIED carry the anomaly, may be constitutional or acquired.}}
{{hidden|What are chromosomal polymorphisms?|Chromosomal polymorphisms are variants of chromosomes that are widespread in a particular population which to date are not known to have any effect on the phenotype, they vary in size, position, and staining properties but must occur in heterochromatin regions usually near the centromere.}}
{{hidden|List 3 known chromosomal polymorphisms, according to ISCN 2013.|[[Chromosomal polymorphisms]]}}
{{hidden|Classify numerical abnormalities of chromosomes.|1) polyploidy (multiple complete sets of chromosomes, e.g. 3N), 2) Aneuploidy (monosomy (e.g. Turner's syndrome), trisomy (e.g. trisomy 18, 13, or 21), tetrasomy))}}
{{hidden|What are the four main types of abnormalities in chromosome structure?|1) Deletion, 2) duplication, 3) rearrangement (inversion or insertion), 4) translocation}}
{{hidden|What is the key difference between a balanced and an unbalanced chromosomal rearrangement?|Balanced translocations imply that there is no missing or excess genetic material, while unbalanced translocations have either missing or excess genetic material from that of a normal genotype.}}
{{hidden|List three types of balanced chromosomal rearrangements.|Translocation, inversion, insertion.}}
{{hidden|List three unbalanced numerical chromosomal rearrangements.|trisomy, monosomy, multiploidy}}
{{hidden|List 5 structural unbalanced chromosomal rearrangements.|deletion, duplication, derivative chromsome, recombination chromosome, marker chromosome, ring chromosome, Dm & HSR}}
{{hidden|What is the karyotype for a female infant with cri-du-chat?|46,XX,del(5)(p15.1)}}
==Unit 3==
{{hidden|What is FISH?|FISH is a molecular cytogenetic technique in which flourescently labelled DNA probes are hybridized to metaphase spreads or interphase nuclei.}}
{{hidden|When is interphase FISH more helpful than metaphase?|Interphase FISH is particularly useful in samples where there is poor culture growth such as bone marrow or cancer tissue.}}
{{hidden|What is the approximate resolution of cytogenetic FISH?|3-5Mb}}
{{hidden|What are the three types of FISH probes?|1)Probes for repetative sequences (Centromeres, telomeric sequences), 2) Unique sequence probes hybridized to a single copy of DNA sequences in a specific gene or chromosome, 3) Whole chromosome paints (or arms) which are cocktails of probes that are chromosome specific and cover the entire length.}}
{{hidden|List 7 applications of FISH technology?| 1) Microdeletion syndromes, 2) Characterization of chromosomal structural abnormalities, 3) identification of marker chromosomes, 4) Aneuploidy detection, 5) Cancer cytogenetics, 6) Gene mapping, 7)Rapid detection of sex chromosomes and the SRY gene}}
{{hidden|List 5 microdeletion syndromes.|[[List of Microdeletion Syndromes]]}}
{{hidden|Briefly describe Cri-du Chat Syndrome|}}
{{hidden|Describe 3 mechanisms by which uniparental disomy occurs.|1) Trisomic rescue (loss of a chromosome from a trisomic zygote), 2) monosomic rescue (duplication of a chromosome from a monosomic zygote), 3)Gamete complementation (fertilization of a gamete with two copies of a chromosome with no copies from other parent)}}
{{hidden|What is imprinting?|Normally we inherit one copy of each gene from each parent, some genes are only expressed when they are inherited paternally, some only when maternally, this differential expression based on inheritance is called imprinting, and changes generation to generation.}}
{{hidden|Which chromosomes are known to have imprinted genes?|Chromosomes 6,7,11,14,and 15.}}
{{hidden|Describe Prader-Willi Syndrome.|Features: hypotonia, obesity, developmental delay, hypogonadism, short stature, 70%: del(15q11-13), 25% uniparental disomy, 2%:other, diagnoses by FISH for microdeletion, or DNA methylation; due to absence of paternally derived PWS/AS gene }}
{{hidden|Briefly describe Williams Syndrome.|Deletion of one elastin allele (7q11.23 = 96% of cases), multi-system d/o characterized by: Growth & developmental delay, characteristic facies & personality, supra valvular stenosis, idiopathic infantile hypercalcemia (connective tissue / vascular)}}
{{hidden|Describe DeGeorge Syndrome.|95% 22q11.2 deletion, 5% FISH negative; AD inherit; 1) Conotruncal heart defects, 2)uropathy, 3)polyhydramnios,4)increased nuchal translucency, 5) IUGR, 6)thymic hypoplasia, 7) characteristic facies, 8) hypoparathyroidism, 9)MR/DD}}
{{hidden|What is SKY?|A chromosomal analysis technique that has the ability to paint each pair of chromosomes and the sex chromosomes a different flourescing colour.}}
{{hidden|What kinds of chromosomal transformations is SKY used for?|1) translocations, 2) insertions, 3)marker chromosome identification, 4) cancer tumour genetics}}
{{hidden|What are three limitations of SKY?|1) cannot detect del,dup,inv, 2) interpretation difficult if colours too similar}}
{{hidden|Explain the basic principle of Comparative Genomic Hybridization.|References genomes and the index genome are mixed, if the index genome substantially differs from the reference genome then there will be a neg signal loss or gain for that probe's flourescence, this can be used to determine if there is one allele in the index case that is missing or in excess compared to the reference genome.}}
{{hidden|How do CGH arrays work?|CGH arrays allow hundreds-thousands of probes to be used to compare the index and the reference genome, giving a complete chromosomal analysis that depends on the resolution of the probe.}}

==Unit 4==

==Miscellaneous==
{{hidden|What is Allerdice or Sandy Point Syndrome?|It is a chromosomal disorder discovered in Sandy Point, NL by Dr. Penny Allderdice, inv(3)(p25q21) characterized by affected offspring with multiple congenital anomalies with surviving children exhibiting severe growth and developmental delays.}}
{{hidden|What is the most common robertsonian translocation?|Translocation between the long arms of 13 and 14.}}
{{hidden|What is the most common non-robertsonian translocation?|t(11;22)(q23;q11)}}
{{hidden|What is a marker chromosome?|A structurally abnormal chromosome in which no part can be identified cytogenetically.}}
{{hidden|What is the most common chromosomal abnormality in humans?|Aneuploidy - about 5% of pregnancies.}}
{{hidden|What is the most common cause of triploidy?|Dispermy in 60%}}
{{hidden|What is the recurrence risk for parents of Down's syndrome child with a "free chromosome"?|1%}}
{{hidden|List 5 features of Trisomy 8.|}}
{{hidden|List 5 features of Trisomy 9.|}}
{{hidden|List 5 features of Trisomy 13.|}}
{{hidden|List 5 features of Trisomy 14.|}}
{{hidden|List 5 features of Trisomy 18.|}}
{{hidden|List 5 features of Trisomy 21.|}}
{{hidden|What is the most common outcome of a pregnancy when the parent has a balanced translocation?|Misscarriage}}

==Peripheral Blood Culture and Harvest==
{{hidden|
{{hidden|

Cytogenetics Review Questions

2015-05-27T15:03:13Z

Yuanny: /* Unit 1 */

==Unit 1==
{{hidden| List the three broad categories of clinical indications for chromosomal analysis.|Prenatal, Constitutional, Cancer/Acquired}}

{{hidden|Which family members should have chromosomal analysis?|1. Both parents of a child with structural chromosome rearrangement, deletion, duplication, and 2. all family members at risk of having a chromosome rearrangement.}}

{{hidden|List 5 prenatal indications for cytogenetics analysis.|
1. Advanced maternal age (Greater than 35 years old),
2. Previous pregnancy with chromosomal disorder,
3. One parent is a known carrier (or other relative*), 4. Couples at risk of x-linked disorders for which a molecular test is not available, 5. Fetal defects on ultrasound, 6. Prenatal screen high risk pregnancies, 7. couples with 2+ spontaneous abortions, 8. infertility. }}
{{hidden|What are the indications for chromosomal analysis of products of conception?|1)Abortuses (missed abortions) of unknown reason, 2)Malformed stillbirths, 3)Stillbirth of undetermined etiology}}
{{hidden|Compare amniocentesis and chorionic villus sampling with regards to gestational age, complication rate, turn around time, and false results|}}
{{hidden|What are the clinical indications for tissue sampling instead of blood for cytogenetic analysis?|1)Suspicion of chromosomal mosaicism, 2) blood is not available (e.g. POC), 3) surgical or post-mortem tissue.}}
{{hidden|List 8 standard techniques for cytogenetics analysis.|1) Geimsa / G-Banding, 2) Quinacrin / Q-banding 3) Reverse / R-banding, 4)Centromere / C-banding, 5)NOR staining (nucleolus organizer regions), 6)DAPI staining, 7) Chromosomal breakage, 8) Sister chromatid Exchange (SCE)}}
{{hidden|List 5 Molecular cytogenetics techniques.|1)FISH (flourescence in situ hybridization), 2) Multi-colour FISH, 3) SKY (spectral karyotyping), 4) CGH (comparative genomic hybridization), 5) CGH array}}
{{hidden|What is g-banding?|Chromosomes are treated with trypsine and then stained with Geimsa (or wrights) which darkly stains the AT rich regions (heterochromatin), and lightly stains the GC rich regions of the chromosome.}}
{{hidden|Outline the general procedure for cytogenetics study.|1) cell culture at 37C 5%CO2 in medium (dividing and stimulation), 2) Chromosome elongation Thymidine BrdU, 3) Metaphase arrest with Colcemide, 4) Cell swelling with hypotonic KCl,* Hardening with acetic acid* 5) Fixation with Cournay's (Methanol: Acetic acid, 3:1), 6) Slide making (chromosome spread with ideal temperature and humidity), 7) Slide aging (air dry slide warmer), 8)Staining (G, Q, C, R-banding), 8) Molecular cytogenetic technique (FISH, multi-FISH, CGH, SKY, array CGH).}}
{{hidden|Broadly what at the three main morphological groups of chromosomes?|Metacentric, acrocentric, submetacentric.}}
{{hidden|What are the 4 minimum items included in a standard banding nomenclature?|1. Chromosome number, 2) short or long arm, 3) region on that arm, 4) band number within that region}}
{{hidden|What are the clinical indications for an individual to have chromosomal analysis?|1)suspected classic chromosome syndrome, 2) Mental retardation of undetermined etiology, 3) dysmophic features, 4) multiple congenital abnormalities, 5) abnormalities of sexual development, 6) ambiguous genitalia, 7)pubertal failure, 8)abnormalities of growth, 9) certain types of malignancies.}}
{{hidden|What is q-banding?|Chromosomes are prepared with quinacrine which produces flourescent bands in the AT rich regions, particularly useful in identifying polymorphisms on the acrocentric chromosomes ( ) and the Y chromosome.}}
{{hidden|What is R-banding?|Darkly stains the GC rich regions of the chromosome (Euchromatin), aka Reverse-banding, and is used to detect subtle deletions or rearrangements that may not be detected by Q or G banding.}}
{{hidden|What is C-banding?|C-Banding stains the constituitive heterochromatin that is localized to the pericentromeric regions of all chromosomes and on the distal long arm of Y. Used to identify pericentric inversions and polymorphisms in centromeric regions of 1,9,16, and Yq, as well as confirming translocations of Y}}
{{hidden|What is NOR?|NOR is a silver staining procedure which stains the nucleolus organizer regions of satellited chromosomes (used to study the size of stalks and satellites in the acrocentric chromosomes)}}
{{hidden|List the metacentric chromosomes.|}}
{{hidden|List the submetacentric chromosomes.|}}
{{hidden|List the acrocentric chromosomes.|}}
{{hidden|What is Bloom syndrome?|Bloom syndrome is a rare AR genetic disorder with a defect in the BLM gene with a phenotype of short stature, tendency to sunburn, increased risk of malignancy, reduced or absent fertility, and prone to sister chromatid exchange [[http://ghr.nlm.nih.gov/condition/bloom-syndrome]] }}
{{hidden|What is SCE (Sister chromatid exchange?|SCE (sister chromatid exchange) is the interchange of homologous segments between two chromatids of one chromosome, grow the cells under special conditions to produce a differential staining of sister chromatids.}}
{{hidden|What is DAPI staining?|DAPI staining produces bright flourescence of the heterochromatin regions of 1,9,16, and Y, as well as the centromere of 15, and is used to id marker chromosomes or translocations of Y.}}
{{hidden|Explain how chromosomal breakage studies are used to diagnose Fanconi's anemia.| Cultured cells are treated with DEB (Diepoxybutane) or mitomycin C to induce breakage, those cells with chromosomes prone to breakage are especially susceptible and this can be seen as gaps, breaks, deletions, triradial, quadriradial, dicentric, and complex figure in the metaphase.}}

==Unit 2==
{{hidden|Describe the 4 steps of mitosis.|Prophase, metaphase, anaphase, telophase}}
{{hidden|List the 8 steps of meiosis.|Meiosis 1(Prophase 1, Metaphase 1, Anaphase 1, Telophase 1), Meiosis 2( Prophase 2, Metaphase 2, Anaphase 2, Telophase 2).}}
{{hidden|What is the main difference between constitutional and acquired chromosome anomalies.|1) Constitutional affects the whole patient, acquired usually limited to 1 organ.}}
{{hidden|What at the three main categories of patient features associated with unbalanced constitutional chromosomal anomalies?]1) dysmophy, 2) Visceral malformations, 3) developmental/psychomotor delay.}}
{{hidden|What is meant by a homogeneous chromosomal anomaly?|Homogeneous chromosomal anomalies mean that all the cells STUDIED carry the anomaly, may be constitutional or acquired.}}
{{hidden|What is meant by a mosaic chromosomal anomaly?|Mosaic chromosomal anomalies mean that only some of the cells STUDIED carry the anomaly, may be constitutional or acquired.}}
{{hidden|What are chromosomal polymorphisms?|Chromosomal polymorphisms are variants of chromosomes that are widespread in a particular population which to date are not known to have any effect on the phenotype, they vary in size, position, and staining properties but must occur in heterochromatin regions usually near the centromere.}}
{{hidden|List 3 known chromosomal polymorphisms, according to ISCN 2013.|[[Chromosomal polymorphisms]]}}
{{hidden|Classify numerical abnormalities of chromosomes.|1) polyploidy (multiple complete sets of chromosomes, e.g. 3N), 2) Aneuploidy (monosomy (e.g. Turner's syndrome), trisomy (e.g. trisomy 18, 13, or 21), tetrasomy))}}
{{hidden|What are the four main types of abnormalities in chromosome structure?|1) Deletion, 2) duplication, 3) rearrangement (inversion or insertion), 4) translocation}}
{{hidden|What is the key difference between a balanced and an unbalanced chromosomal rearrangement?|Balanced translocations imply that there is no missing or excess genetic material, while unbalanced translocations have either missing or excess genetic material from that of a normal genotype.}}
{{hidden|List three types of balanced chromosomal rearrangements.|Translocation, inversion, insertion.}}
{{hidden|List three unbalanced numerical chromosomal rearrangements.|trisomy, monosomy, multiploidy}}
{{hidden|List 5 structural unbalanced chromosomal rearrangements.|deletion, duplication, derivative chromsome, recombination chromosome, marker chromosome, ring chromosome, Dm & HSR}}
{{hidden|What is the karyotype for a female infant with cri-du-chat?|46,XX,del(5)(p15.1)}}
==Unit 3==
{{hidden|What is FISH?|FISH is a molecular cytogenetic technique in which flourescently labelled DNA probes are hybridized to metaphase spreads or interphase nuclei.}}
{{hidden|When is interphase FISH more helpful than metaphase?|Interphase FISH is particularly useful in samples where there is poor culture growth such as bone marrow or cancer tissue.}}
{{hidden|What is the approximate resolution of cytogenetic FISH?|3-5Mb}}
{{hidden|What are the three types of FISH probes?|1)Probes for repetative sequences (Centromeres, telomeric sequences), 2) Unique sequence probes hybridized to a single copy of DNA sequences in a specific gene or chromosome, 3) Whole chromosome paints (or arms) which are cocktails of probes that are chromosome specific and cover the entire length.}}
{{hidden|List 7 applications of FISH technology?| 1) Microdeletion syndromes, 2) Characterization of chromosomal structural abnormalities, 3) identification of marker chromosomes, 4) Aneuploidy detection, 5) Cancer cytogenetics, 6) Gene mapping, 7)Rapid detection of sex chromosomes and the SRY gene}}
{{hidden|List 5 microdeletion syndromes.|[[List of Microdeletion Syndromes]]}}
{{hidden|Briefly describe Cri-du Chat Syndrome|}}
{{hidden|Describe 3 mechanisms by which uniparental disomy occurs.|1) Trisomic rescue (loss of a chromosome from a trisomic zygote), 2) monosomic rescue (duplication of a chromosome from a monosomic zygote), 3)Gamete complementation (fertilization of a gamete with two copies of a chromosome with no copies from other parent)}}
{{hidden|What is imprinting?|Normally we inherit one copy of each gene from each parent, some genes are only expressed when they are inherited paternally, some only when maternally, this differential expression based on inheritance is called imprinting, and changes generation to generation.}}
{{hidden|Which chromosomes are known to have imprinted genes?|Chromosomes 6,7,11,14,and 15.}}
{{hidden|Describe Prader-Willi Syndrome.|Features: hypotonia, obesity, developmental delay, hypogonadism, short stature, 70%: del(15q11-13), 25% uniparental disomy, 2%:other, diagnoses by FISH for microdeletion, or DNA methylation; due to absence of paternally derived PWS/AS gene }}
{{hidden|Briefly describe Williams Syndrome.|Deletion of one elastin allele (7q11.23 = 96% of cases), multi-system d/o characterized by: Growth & developmental delay, characteristic facies & personality, supra valvular stenosis, idiopathic infantile hypercalcemia (connective tissue / vascular)}}
{{hidden|Describe DeGeorge Syndrome.|95% 22q11.2 deletion, 5% FISH negative; AD inherit; 1) Conotruncal heart defects, 2)uropathy, 3)polyhydramnios,4)increased nuchal translucency, 5) IUGR, 6)thymic hypoplasia, 7) characteristic facies, 8) hypoparathyroidism, 9)MR/DD}}
{{hidden|What is SKY?|A chromosomal analysis technique that has the ability to paint each pair of chromosomes and the sex chromosomes a different flourescing colour.}}
{{hidden|What kinds of chromosomal transformations is SKY used for?|1) translocations, 2) insertions, 3)marker chromosome identification, 4) cancer tumour genetics}}
{{hidden|What are three limitations of SKY?|1) cannot detect del,dup,inv, 2) interpretation difficult if colours too similar}}
{{hidden|Explain the basic principle of Comparative Genomic Hybridization.|References genomes and the index genome are mixed, if the index genome substantially differs from the reference genome then there will be a neg signal loss or gain for that probe's flourescence, this can be used to determine if there is one allele in the index case that is missing or in excess compared to the reference genome.}}
{{hidden|How do CGH arrays work?|CGH arrays allow hundreds-thousands of probes to be used to compare the index and the reference genome, giving a complete chromosomal analysis that depends on the resolution of the probe.}}

==Unit 4==

==Miscellaneous==
{{hidden|What is Allerdice or Sandy Point Syndrome?|It is a chromosomal disorder discovered in Sandy Point, NL by Dr. Penny Allderdice, inv(3)(p25q21) characterized by affected offspring with multiple congenital anomalies with surviving children exhibiting severe growth and developmental delays.}}
{{hidden|What is the most common robertsonian translocation?|Translocation between the long arms of 13 and 14.}}
{{hidden|What is the most common non-robertsonian translocation?|t(11;22)(q23;q11)}}
{{hidden|What is a marker chromosome?|A structurally abnormal chromosome in which no part can be identified cytogenetically.}}
{{hidden|What is the most common chromosomal abnormality in humans?|Aneuploidy - about 5% of pregnancies.}}
{{hidden|What is the most common cause of triploidy?|Dispermy in 60%}}
{{hidden|What is the recurrence risk for parents of Down's syndrome child with a "free chromosome"?|1%}}
{{hidden|List 5 features of Trisomy 8.|}}
{{hidden|List 5 features of Trisomy 9.|}}
{{hidden|List 5 features of Trisomy 13.|}}
{{hidden|List 5 features of Trisomy 14.|}}
{{hidden|List 5 features of Trisomy 18.|}}
{{hidden|List 5 features of Trisomy 21.|}}
{{hidden|What is the most common outcome of a pregnancy when the parent has a balanced translocation?|Misscarriage}}

==Peripheral Blood Culture and Harvest==
{{hidden|
{{hidden|

Cytogenetics Review Questions

2015-05-27T15:02:49Z

Yuanny: /* Unit 1 */

==Unit 1==
{{hidden| List the three broad categories of clinical indications for chromosomal analysis.|Prenatal, Constitutional, Cancer/Acquired}}

{{hidden|Which family members should have chromosomal analysis?|1. Both parents of a child with structural chromosome rearrangement, deletion, duplication, and 2. all family members at risk of having a chromosome rearrangement.}}

{{hidden|List 5 prenatal indications for cytogenetics analysis.|1. Advanced maternal age (Greater than 35 years old), 2. Previous pregnancy with chromosomal disorder, 3. One parent is a known carrier (or other relative*), 4. Couples at risk of x-linked disorders for which a molecular test is not available, 5. Fetal defects on ultrasound, 6. Prenatal screen high risk pregnancies, 7. couples with 2+ spontaneous abortions, 8. infertility. }}
{{hidden|What are the indications for chromosomal analysis of products of conception?|1)Abortuses (missed abortions) of unknown reason, 2)Malformed stillbirths, 3)Stillbirth of undetermined etiology}}
{{hidden|Compare amniocentesis and chorionic villus sampling with regards to gestational age, complication rate, turn around time, and false results|}}
{{hidden|What are the clinical indications for tissue sampling instead of blood for cytogenetic analysis?|1)Suspicion of chromosomal mosaicism, 2) blood is not available (e.g. POC), 3) surgical or post-mortem tissue.}}
{{hidden|List 8 standard techniques for cytogenetics analysis.|1) Geimsa / G-Banding, 2) Quinacrin / Q-banding 3) Reverse / R-banding, 4)Centromere / C-banding, 5)NOR staining (nucleolus organizer regions), 6)DAPI staining, 7) Chromosomal breakage, 8) Sister chromatid Exchange (SCE)}}
{{hidden|List 5 Molecular cytogenetics techniques.|1)FISH (flourescence in situ hybridization), 2) Multi-colour FISH, 3) SKY (spectral karyotyping), 4) CGH (comparative genomic hybridization), 5) CGH array}}
{{hidden|What is g-banding?|Chromosomes are treated with trypsine and then stained with Geimsa (or wrights) which darkly stains the AT rich regions (heterochromatin), and lightly stains the GC rich regions of the chromosome.}}
{{hidden|Outline the general procedure for cytogenetics study.|1) cell culture at 37C 5%CO2 in medium (dividing and stimulation), 2) Chromosome elongation Thymidine BrdU, 3) Metaphase arrest with Colcemide, 4) Cell swelling with hypotonic KCl,* Hardening with acetic acid* 5) Fixation with Cournay's (Methanol: Acetic acid, 3:1), 6) Slide making (chromosome spread with ideal temperature and humidity), 7) Slide aging (air dry slide warmer), 8)Staining (G, Q, C, R-banding), 8) Molecular cytogenetic technique (FISH, multi-FISH, CGH, SKY, array CGH).}}
{{hidden|Broadly what at the three main morphological groups of chromosomes?|Metacentric, acrocentric, submetacentric.}}
{{hidden|What are the 4 minimum items included in a standard banding nomenclature?|1. Chromosome number, 2) short or long arm, 3) region on that arm, 4) band number within that region}}
{{hidden|What are the clinical indications for an individual to have chromosomal analysis?|1)suspected classic chromosome syndrome, 2) Mental retardation of undetermined etiology, 3) dysmophic features, 4) multiple congenital abnormalities, 5) abnormalities of sexual development, 6) ambiguous genitalia, 7)pubertal failure, 8)abnormalities of growth, 9) certain types of malignancies.}}
{{hidden|What is q-banding?|Chromosomes are prepared with quinacrine which produces flourescent bands in the AT rich regions, particularly useful in identifying polymorphisms on the acrocentric chromosomes ( ) and the Y chromosome.}}
{{hidden|What is R-banding?|Darkly stains the GC rich regions of the chromosome (Euchromatin), aka Reverse-banding, and is used to detect subtle deletions or rearrangements that may not be detected by Q or G banding.}}
{{hidden|What is C-banding?|C-Banding stains the constituitive heterochromatin that is localized to the pericentromeric regions of all chromosomes and on the distal long arm of Y. Used to identify pericentric inversions and polymorphisms in centromeric regions of 1,9,16, and Yq, as well as confirming translocations of Y}}
{{hidden|What is NOR?|NOR is a silver staining procedure which stains the nucleolus organizer regions of satellited chromosomes (used to study the size of stalks and satellites in the acrocentric chromosomes)}}
{{hidden|List the metacentric chromosomes.|}}
{{hidden|List the submetacentric chromosomes.|}}
{{hidden|List the acrocentric chromosomes.|}}
{{hidden|What is Bloom syndrome?|Bloom syndrome is a rare AR genetic disorder with a defect in the BLM gene with a phenotype of short stature, tendency to sunburn, increased risk of malignancy, reduced or absent fertility, and prone to sister chromatid exchange [[http://ghr.nlm.nih.gov/condition/bloom-syndrome]] }}
{{hidden|What is SCE (Sister chromatid exchange?|SCE (sister chromatid exchange) is the interchange of homologous segments between two chromatids of one chromosome, grow the cells under special conditions to produce a differential staining of sister chromatids.}}
{{hidden|What is DAPI staining?|DAPI staining produces bright flourescence of the heterochromatin regions of 1,9,16, and Y, as well as the centromere of 15, and is used to id marker chromosomes or translocations of Y.}}
{{hidden|Explain how chromosomal breakage studies are used to diagnose Fanconi's anemia.| Cultured cells are treated with DEB (Diepoxybutane) or mitomycin C to induce breakage, those cells with chromosomes prone to breakage are especially susceptible and this can be seen as gaps, breaks, deletions, triradial, quadriradial, dicentric, and complex figure in the metaphase.}}

==Unit 2==
{{hidden|Describe the 4 steps of mitosis.|Prophase, metaphase, anaphase, telophase}}
{{hidden|List the 8 steps of meiosis.|Meiosis 1(Prophase 1, Metaphase 1, Anaphase 1, Telophase 1), Meiosis 2( Prophase 2, Metaphase 2, Anaphase 2, Telophase 2).}}
{{hidden|What is the main difference between constitutional and acquired chromosome anomalies.|1) Constitutional affects the whole patient, acquired usually limited to 1 organ.}}
{{hidden|What at the three main categories of patient features associated with unbalanced constitutional chromosomal anomalies?]1) dysmophy, 2) Visceral malformations, 3) developmental/psychomotor delay.}}
{{hidden|What is meant by a homogeneous chromosomal anomaly?|Homogeneous chromosomal anomalies mean that all the cells STUDIED carry the anomaly, may be constitutional or acquired.}}
{{hidden|What is meant by a mosaic chromosomal anomaly?|Mosaic chromosomal anomalies mean that only some of the cells STUDIED carry the anomaly, may be constitutional or acquired.}}
{{hidden|What are chromosomal polymorphisms?|Chromosomal polymorphisms are variants of chromosomes that are widespread in a particular population which to date are not known to have any effect on the phenotype, they vary in size, position, and staining properties but must occur in heterochromatin regions usually near the centromere.}}
{{hidden|List 3 known chromosomal polymorphisms, according to ISCN 2013.|[[Chromosomal polymorphisms]]}}
{{hidden|Classify numerical abnormalities of chromosomes.|1) polyploidy (multiple complete sets of chromosomes, e.g. 3N), 2) Aneuploidy (monosomy (e.g. Turner's syndrome), trisomy (e.g. trisomy 18, 13, or 21), tetrasomy))}}
{{hidden|What are the four main types of abnormalities in chromosome structure?|1) Deletion, 2) duplication, 3) rearrangement (inversion or insertion), 4) translocation}}
{{hidden|What is the key difference between a balanced and an unbalanced chromosomal rearrangement?|Balanced translocations imply that there is no missing or excess genetic material, while unbalanced translocations have either missing or excess genetic material from that of a normal genotype.}}
{{hidden|List three types of balanced chromosomal rearrangements.|Translocation, inversion, insertion.}}
{{hidden|List three unbalanced numerical chromosomal rearrangements.|trisomy, monosomy, multiploidy}}
{{hidden|List 5 structural unbalanced chromosomal rearrangements.|deletion, duplication, derivative chromsome, recombination chromosome, marker chromosome, ring chromosome, Dm & HSR}}
{{hidden|What is the karyotype for a female infant with cri-du-chat?|46,XX,del(5)(p15.1)}}
==Unit 3==
{{hidden|What is FISH?|FISH is a molecular cytogenetic technique in which flourescently labelled DNA probes are hybridized to metaphase spreads or interphase nuclei.}}
{{hidden|When is interphase FISH more helpful than metaphase?|Interphase FISH is particularly useful in samples where there is poor culture growth such as bone marrow or cancer tissue.}}
{{hidden|What is the approximate resolution of cytogenetic FISH?|3-5Mb}}
{{hidden|What are the three types of FISH probes?|1)Probes for repetative sequences (Centromeres, telomeric sequences), 2) Unique sequence probes hybridized to a single copy of DNA sequences in a specific gene or chromosome, 3) Whole chromosome paints (or arms) which are cocktails of probes that are chromosome specific and cover the entire length.}}
{{hidden|List 7 applications of FISH technology?| 1) Microdeletion syndromes, 2) Characterization of chromosomal structural abnormalities, 3) identification of marker chromosomes, 4) Aneuploidy detection, 5) Cancer cytogenetics, 6) Gene mapping, 7)Rapid detection of sex chromosomes and the SRY gene}}
{{hidden|List 5 microdeletion syndromes.|[[List of Microdeletion Syndromes]]}}
{{hidden|Briefly describe Cri-du Chat Syndrome|}}
{{hidden|Describe 3 mechanisms by which uniparental disomy occurs.|1) Trisomic rescue (loss of a chromosome from a trisomic zygote), 2) monosomic rescue (duplication of a chromosome from a monosomic zygote), 3)Gamete complementation (fertilization of a gamete with two copies of a chromosome with no copies from other parent)}}
{{hidden|What is imprinting?|Normally we inherit one copy of each gene from each parent, some genes are only expressed when they are inherited paternally, some only when maternally, this differential expression based on inheritance is called imprinting, and changes generation to generation.}}
{{hidden|Which chromosomes are known to have imprinted genes?|Chromosomes 6,7,11,14,and 15.}}
{{hidden|Describe Prader-Willi Syndrome.|Features: hypotonia, obesity, developmental delay, hypogonadism, short stature, 70%: del(15q11-13), 25% uniparental disomy, 2%:other, diagnoses by FISH for microdeletion, or DNA methylation; due to absence of paternally derived PWS/AS gene }}
{{hidden|Briefly describe Williams Syndrome.|Deletion of one elastin allele (7q11.23 = 96% of cases), multi-system d/o characterized by: Growth & developmental delay, characteristic facies & personality, supra valvular stenosis, idiopathic infantile hypercalcemia (connective tissue / vascular)}}
{{hidden|Describe DeGeorge Syndrome.|95% 22q11.2 deletion, 5% FISH negative; AD inherit; 1) Conotruncal heart defects, 2)uropathy, 3)polyhydramnios,4)increased nuchal translucency, 5) IUGR, 6)thymic hypoplasia, 7) characteristic facies, 8) hypoparathyroidism, 9)MR/DD}}
{{hidden|What is SKY?|A chromosomal analysis technique that has the ability to paint each pair of chromosomes and the sex chromosomes a different flourescing colour.}}
{{hidden|What kinds of chromosomal transformations is SKY used for?|1) translocations, 2) insertions, 3)marker chromosome identification, 4) cancer tumour genetics}}
{{hidden|What are three limitations of SKY?|1) cannot detect del,dup,inv, 2) interpretation difficult if colours too similar}}
{{hidden|Explain the basic principle of Comparative Genomic Hybridization.|References genomes and the index genome are mixed, if the index genome substantially differs from the reference genome then there will be a neg signal loss or gain for that probe's flourescence, this can be used to determine if there is one allele in the index case that is missing or in excess compared to the reference genome.}}
{{hidden|How do CGH arrays work?|CGH arrays allow hundreds-thousands of probes to be used to compare the index and the reference genome, giving a complete chromosomal analysis that depends on the resolution of the probe.}}

==Unit 4==

==Miscellaneous==
{{hidden|What is Allerdice or Sandy Point Syndrome?|It is a chromosomal disorder discovered in Sandy Point, NL by Dr. Penny Allderdice, inv(3)(p25q21) characterized by affected offspring with multiple congenital anomalies with surviving children exhibiting severe growth and developmental delays.}}
{{hidden|What is the most common robertsonian translocation?|Translocation between the long arms of 13 and 14.}}
{{hidden|What is the most common non-robertsonian translocation?|t(11;22)(q23;q11)}}
{{hidden|What is a marker chromosome?|A structurally abnormal chromosome in which no part can be identified cytogenetically.}}
{{hidden|What is the most common chromosomal abnormality in humans?|Aneuploidy - about 5% of pregnancies.}}
{{hidden|What is the most common cause of triploidy?|Dispermy in 60%}}
{{hidden|What is the recurrence risk for parents of Down's syndrome child with a "free chromosome"?|1%}}
{{hidden|List 5 features of Trisomy 8.|}}
{{hidden|List 5 features of Trisomy 9.|}}
{{hidden|List 5 features of Trisomy 13.|}}
{{hidden|List 5 features of Trisomy 14.|}}
{{hidden|List 5 features of Trisomy 18.|}}
{{hidden|List 5 features of Trisomy 21.|}}
{{hidden|What is the most common outcome of a pregnancy when the parent has a balanced translocation?|Misscarriage}}

==Peripheral Blood Culture and Harvest==
{{hidden|
{{hidden|

Cytogenetics Review Questions

2015-05-27T15:02:38Z

Yuanny: /* Unit 1 */

==Unit 1==
{{hidden| List the three broad categories of clinical indications for chromosomal analysis.|Prenatal, Constitutional, Cancer/Acquired}}

{{hidden|Which family members should have chromosomal analysis?|1. Both parents of a child with structural chromosome rearrangement, deletion, duplication, and 2. all family members at risk of having a chromosome rearrangement.}}

{{hidden|List 5 prenatal indications for cytogenetics analysis.|1. Advanced maternal age (Greater than 35 years old), 2. Previous pregnancy with chromosomal disorder, 3. One parent is a known carrier (or other relative*), 4. Couples at risk of x-linked disorders for which a molecular test is not available, 5. Fetal defects on ultrasound, 6. Prenatal screen high risk pregnancies, 7. couples with 2+ spontaneous abortions, 8. infertility. }}

{{hidden|What are the indications for chromosomal analysis of products of conception?|1)Abortuses (missed abortions) of unknown reason, 2)Malformed stillbirths, 3)Stillbirth of undetermined etiology}}
{{hidden|Compare amniocentesis and chorionic villus sampling with regards to gestational age, complication rate, turn around time, and false results|}}
{{hidden|What are the clinical indications for tissue sampling instead of blood for cytogenetic analysis?|1)Suspicion of chromosomal mosaicism, 2) blood is not available (e.g. POC), 3) surgical or post-mortem tissue.}}
{{hidden|List 8 standard techniques for cytogenetics analysis.|1) Geimsa / G-Banding, 2) Quinacrin / Q-banding 3) Reverse / R-banding, 4)Centromere / C-banding, 5)NOR staining (nucleolus organizer regions), 6)DAPI staining, 7) Chromosomal breakage, 8) Sister chromatid Exchange (SCE)}}
{{hidden|List 5 Molecular cytogenetics techniques.|1)FISH (flourescence in situ hybridization), 2) Multi-colour FISH, 3) SKY (spectral karyotyping), 4) CGH (comparative genomic hybridization), 5) CGH array}}
{{hidden|What is g-banding?|Chromosomes are treated with trypsine and then stained with Geimsa (or wrights) which darkly stains the AT rich regions (heterochromatin), and lightly stains the GC rich regions of the chromosome.}}
{{hidden|Outline the general procedure for cytogenetics study.|1) cell culture at 37C 5%CO2 in medium (dividing and stimulation), 2) Chromosome elongation Thymidine BrdU, 3) Metaphase arrest with Colcemide, 4) Cell swelling with hypotonic KCl,* Hardening with acetic acid* 5) Fixation with Cournay's (Methanol: Acetic acid, 3:1), 6) Slide making (chromosome spread with ideal temperature and humidity), 7) Slide aging (air dry slide warmer), 8)Staining (G, Q, C, R-banding), 8) Molecular cytogenetic technique (FISH, multi-FISH, CGH, SKY, array CGH).}}
{{hidden|Broadly what at the three main morphological groups of chromosomes?|Metacentric, acrocentric, submetacentric.}}
{{hidden|What are the 4 minimum items included in a standard banding nomenclature?|1. Chromosome number, 2) short or long arm, 3) region on that arm, 4) band number within that region}}
{{hidden|What are the clinical indications for an individual to have chromosomal analysis?|1)suspected classic chromosome syndrome, 2) Mental retardation of undetermined etiology, 3) dysmophic features, 4) multiple congenital abnormalities, 5) abnormalities of sexual development, 6) ambiguous genitalia, 7)pubertal failure, 8)abnormalities of growth, 9) certain types of malignancies.}}
{{hidden|What is q-banding?|Chromosomes are prepared with quinacrine which produces flourescent bands in the AT rich regions, particularly useful in identifying polymorphisms on the acrocentric chromosomes ( ) and the Y chromosome.}}
{{hidden|What is R-banding?|Darkly stains the GC rich regions of the chromosome (Euchromatin), aka Reverse-banding, and is used to detect subtle deletions or rearrangements that may not be detected by Q or G banding.}}
{{hidden|What is C-banding?|C-Banding stains the constituitive heterochromatin that is localized to the pericentromeric regions of all chromosomes and on the distal long arm of Y. Used to identify pericentric inversions and polymorphisms in centromeric regions of 1,9,16, and Yq, as well as confirming translocations of Y}}
{{hidden|What is NOR?|NOR is a silver staining procedure which stains the nucleolus organizer regions of satellited chromosomes (used to study the size of stalks and satellites in the acrocentric chromosomes)}}
{{hidden|List the metacentric chromosomes.|}}
{{hidden|List the submetacentric chromosomes.|}}
{{hidden|List the acrocentric chromosomes.|}}
{{hidden|What is Bloom syndrome?|Bloom syndrome is a rare AR genetic disorder with a defect in the BLM gene with a phenotype of short stature, tendency to sunburn, increased risk of malignancy, reduced or absent fertility, and prone to sister chromatid exchange [[http://ghr.nlm.nih.gov/condition/bloom-syndrome]] }}
{{hidden|What is SCE (Sister chromatid exchange?|SCE (sister chromatid exchange) is the interchange of homologous segments between two chromatids of one chromosome, grow the cells under special conditions to produce a differential staining of sister chromatids.}}
{{hidden|What is DAPI staining?|DAPI staining produces bright flourescence of the heterochromatin regions of 1,9,16, and Y, as well as the centromere of 15, and is used to id marker chromosomes or translocations of Y.}}
{{hidden|Explain how chromosomal breakage studies are used to diagnose Fanconi's anemia.| Cultured cells are treated with DEB (Diepoxybutane) or mitomycin C to induce breakage, those cells with chromosomes prone to breakage are especially susceptible and this can be seen as gaps, breaks, deletions, triradial, quadriradial, dicentric, and complex figure in the metaphase.}}

==Unit 2==
{{hidden|Describe the 4 steps of mitosis.|Prophase, metaphase, anaphase, telophase}}
{{hidden|List the 8 steps of meiosis.|Meiosis 1(Prophase 1, Metaphase 1, Anaphase 1, Telophase 1), Meiosis 2( Prophase 2, Metaphase 2, Anaphase 2, Telophase 2).}}
{{hidden|What is the main difference between constitutional and acquired chromosome anomalies.|1) Constitutional affects the whole patient, acquired usually limited to 1 organ.}}
{{hidden|What at the three main categories of patient features associated with unbalanced constitutional chromosomal anomalies?]1) dysmophy, 2) Visceral malformations, 3) developmental/psychomotor delay.}}
{{hidden|What is meant by a homogeneous chromosomal anomaly?|Homogeneous chromosomal anomalies mean that all the cells STUDIED carry the anomaly, may be constitutional or acquired.}}
{{hidden|What is meant by a mosaic chromosomal anomaly?|Mosaic chromosomal anomalies mean that only some of the cells STUDIED carry the anomaly, may be constitutional or acquired.}}
{{hidden|What are chromosomal polymorphisms?|Chromosomal polymorphisms are variants of chromosomes that are widespread in a particular population which to date are not known to have any effect on the phenotype, they vary in size, position, and staining properties but must occur in heterochromatin regions usually near the centromere.}}
{{hidden|List 3 known chromosomal polymorphisms, according to ISCN 2013.|[[Chromosomal polymorphisms]]}}
{{hidden|Classify numerical abnormalities of chromosomes.|1) polyploidy (multiple complete sets of chromosomes, e.g. 3N), 2) Aneuploidy (monosomy (e.g. Turner's syndrome), trisomy (e.g. trisomy 18, 13, or 21), tetrasomy))}}
{{hidden|What are the four main types of abnormalities in chromosome structure?|1) Deletion, 2) duplication, 3) rearrangement (inversion or insertion), 4) translocation}}
{{hidden|What is the key difference between a balanced and an unbalanced chromosomal rearrangement?|Balanced translocations imply that there is no missing or excess genetic material, while unbalanced translocations have either missing or excess genetic material from that of a normal genotype.}}
{{hidden|List three types of balanced chromosomal rearrangements.|Translocation, inversion, insertion.}}
{{hidden|List three unbalanced numerical chromosomal rearrangements.|trisomy, monosomy, multiploidy}}
{{hidden|List 5 structural unbalanced chromosomal rearrangements.|deletion, duplication, derivative chromsome, recombination chromosome, marker chromosome, ring chromosome, Dm & HSR}}
{{hidden|What is the karyotype for a female infant with cri-du-chat?|46,XX,del(5)(p15.1)}}
==Unit 3==
{{hidden|What is FISH?|FISH is a molecular cytogenetic technique in which flourescently labelled DNA probes are hybridized to metaphase spreads or interphase nuclei.}}
{{hidden|When is interphase FISH more helpful than metaphase?|Interphase FISH is particularly useful in samples where there is poor culture growth such as bone marrow or cancer tissue.}}
{{hidden|What is the approximate resolution of cytogenetic FISH?|3-5Mb}}
{{hidden|What are the three types of FISH probes?|1)Probes for repetative sequences (Centromeres, telomeric sequences), 2) Unique sequence probes hybridized to a single copy of DNA sequences in a specific gene or chromosome, 3) Whole chromosome paints (or arms) which are cocktails of probes that are chromosome specific and cover the entire length.}}
{{hidden|List 7 applications of FISH technology?| 1) Microdeletion syndromes, 2) Characterization of chromosomal structural abnormalities, 3) identification of marker chromosomes, 4) Aneuploidy detection, 5) Cancer cytogenetics, 6) Gene mapping, 7)Rapid detection of sex chromosomes and the SRY gene}}
{{hidden|List 5 microdeletion syndromes.|[[List of Microdeletion Syndromes]]}}
{{hidden|Briefly describe Cri-du Chat Syndrome|}}
{{hidden|Describe 3 mechanisms by which uniparental disomy occurs.|1) Trisomic rescue (loss of a chromosome from a trisomic zygote), 2) monosomic rescue (duplication of a chromosome from a monosomic zygote), 3)Gamete complementation (fertilization of a gamete with two copies of a chromosome with no copies from other parent)}}
{{hidden|What is imprinting?|Normally we inherit one copy of each gene from each parent, some genes are only expressed when they are inherited paternally, some only when maternally, this differential expression based on inheritance is called imprinting, and changes generation to generation.}}
{{hidden|Which chromosomes are known to have imprinted genes?|Chromosomes 6,7,11,14,and 15.}}
{{hidden|Describe Prader-Willi Syndrome.|Features: hypotonia, obesity, developmental delay, hypogonadism, short stature, 70%: del(15q11-13), 25% uniparental disomy, 2%:other, diagnoses by FISH for microdeletion, or DNA methylation; due to absence of paternally derived PWS/AS gene }}
{{hidden|Briefly describe Williams Syndrome.|Deletion of one elastin allele (7q11.23 = 96% of cases), multi-system d/o characterized by: Growth & developmental delay, characteristic facies & personality, supra valvular stenosis, idiopathic infantile hypercalcemia (connective tissue / vascular)}}
{{hidden|Describe DeGeorge Syndrome.|95% 22q11.2 deletion, 5% FISH negative; AD inherit; 1) Conotruncal heart defects, 2)uropathy, 3)polyhydramnios,4)increased nuchal translucency, 5) IUGR, 6)thymic hypoplasia, 7) characteristic facies, 8) hypoparathyroidism, 9)MR/DD}}
{{hidden|What is SKY?|A chromosomal analysis technique that has the ability to paint each pair of chromosomes and the sex chromosomes a different flourescing colour.}}
{{hidden|What kinds of chromosomal transformations is SKY used for?|1) translocations, 2) insertions, 3)marker chromosome identification, 4) cancer tumour genetics}}
{{hidden|What are three limitations of SKY?|1) cannot detect del,dup,inv, 2) interpretation difficult if colours too similar}}
{{hidden|Explain the basic principle of Comparative Genomic Hybridization.|References genomes and the index genome are mixed, if the index genome substantially differs from the reference genome then there will be a neg signal loss or gain for that probe's flourescence, this can be used to determine if there is one allele in the index case that is missing or in excess compared to the reference genome.}}
{{hidden|How do CGH arrays work?|CGH arrays allow hundreds-thousands of probes to be used to compare the index and the reference genome, giving a complete chromosomal analysis that depends on the resolution of the probe.}}

==Unit 4==

==Miscellaneous==
{{hidden|What is Allerdice or Sandy Point Syndrome?|It is a chromosomal disorder discovered in Sandy Point, NL by Dr. Penny Allderdice, inv(3)(p25q21) characterized by affected offspring with multiple congenital anomalies with surviving children exhibiting severe growth and developmental delays.}}
{{hidden|What is the most common robertsonian translocation?|Translocation between the long arms of 13 and 14.}}
{{hidden|What is the most common non-robertsonian translocation?|t(11;22)(q23;q11)}}
{{hidden|What is a marker chromosome?|A structurally abnormal chromosome in which no part can be identified cytogenetically.}}
{{hidden|What is the most common chromosomal abnormality in humans?|Aneuploidy - about 5% of pregnancies.}}
{{hidden|What is the most common cause of triploidy?|Dispermy in 60%}}
{{hidden|What is the recurrence risk for parents of Down's syndrome child with a "free chromosome"?|1%}}
{{hidden|List 5 features of Trisomy 8.|}}
{{hidden|List 5 features of Trisomy 9.|}}
{{hidden|List 5 features of Trisomy 13.|}}
{{hidden|List 5 features of Trisomy 14.|}}
{{hidden|List 5 features of Trisomy 18.|}}
{{hidden|List 5 features of Trisomy 21.|}}
{{hidden|What is the most common outcome of a pregnancy when the parent has a balanced translocation?|Misscarriage}}

==Peripheral Blood Culture and Harvest==
{{hidden|
{{hidden|

Robbins and Cotran 9th Edition Questions

2015-05-19T14:18:50Z

Yuanny: /* Chapter 1: The Cell as a Unit of Health and Disease */

== Chapter 1: The Cell as a Unit of Health and Disease==

{{hidden|How much of the human genome is coding and what does it code?|Of the 3.2b basepairs, there are 20,000 genes that comprise about 1.5% of the genome that code for proteins (enzymes, structural components, and signaling molecules used to assemble and maintain all the cells in the body}}

{{hidden|What do we think that the rest of the genome does?|[[80% of the genome binds proteins, implying that it is involved in regulating gene expression, related to the regulation of gene expression, often in a cell-type specific fashion.]]}}

{{hidden|List the major classes of functional non-protein-coding sequences found in the human genome.|[[1. Promoter & enhancer, 2. Chromatin binding site structures, 3. non-coding regulatory RNAs, 4. Mobile genetic elements (transposons), 5. telomeres, 6. centromers. ]]}}

{{hidden|What are the two most common forms of DNA variation in the human genome?|[[1) Single nucleotide polymorphisms (SNPs), 2) copy number variations (CNVs)]]}}

{{hidden|What are the possible implications of SNPs.|[[1) regulatory = alters gene expression, 2) Correlation with disease states when in close proximity with altered genes, 3) association used to define linkage disequilibrium,?]]}}

{{hidden|Define epigenetics.|[[Heritable changes in gene expression which are not caused by alterations in DNA sequence.]]}}

{{hidden|List the 6 types of epigenetic changes.|[[1) Histone & histone modifying factors (Histones organize chromatin into heterochromatin and euchromatin, 2) histone methylation, 3) histone acteylation, 4)histone phosphorylation, 5) DNA methylation, 6) Chromatin organizing factors.]]}}

{{hidden|What is the function of micro-RNA (mi-RNA)?|[[It does not encode protein, instead they function primarily to modulate the translation of target mRNAs into their corresponding proteins, and are responsible for post-transcriptional silencing of gene expression.]]}}

{{hidden|What is knockdown technology?|[[The use of synthetic si-RNA (short RNA sequences) introduced into cells that serve as substrates for Dicer and interact with the RISC complex in a manner analogous to endogenous miRNAs, and are used to study gene function, and are being developed as therapeutic agents to silence pathogenic genes, e.g. oncogenic in neoplasms.]]}}

{{hidden|What is long non coding RNA?|[[ Lnc-RNA modulate gene expression by binding to regions of chromatin, restricting RNA polymerase access to coding genes within the region, and may exceed the number of mRNA's by 10-20 fold.]]}}

{{hidden|What is XIST?|[[XIST is a lnc-RNA which is transcribed from the X-chromosome and plays an essential role in physiologic X chromosome inactivation, though not inactivated itself, it forms a repressive cloak on the X chromosome from which it is transcribed resulting in gene silencing.]]}}

{{hidden|What are the cellular housekeeping functions?|[[ 1) protection from the environment, 2) nutrient acquisition, 3) communication, 4) movement, 5) renewal of senescent molecules, 6) molecular catabolism, 7) energy generation.]]}}

{{hidden|List the cellular compartments and the role in the cell.|[[1) cytosol = metabolism, transport, protein translation, 2) Mitochondria = energy generation, apoptosis, 3) Rough ER = synthesis of membrane and secreted proteins, 4) Smooth ER / Golgi = protein modification, sorting, catabolism, 5)Nucleus = cell regulation, proliferation, DNA transcription, 6) Endosomes = intracellular transport and export, ingestion of extracellular substances, 7) Lysosomes = cellular catabolism, 8) peroxisomes = very long-chain fatty acid metabolism]]}}

{{hidden|Describe the basic structure and functions of the cell membrane.|[[ The plasma membrane is composed of a lipid bilayer of phospholipids studded with a variety of proteins and glycoproteins involved in ion and metabolite transport, fluid phase and receptor-mediated uptake of macromolecules, cell-ligand/cell matrix/cell-cell interactions.]]}}

{{hidden|How are the large complexes in the plasma membrane formed?|They aggregate under the control of chaperone molecules in the RER or by lateral diffusion in the plasma membrane followed by complex formation in situ.]]}}

{{hidden|What are aquaporins?|[[Special integral membrane proteins which augment passive water transport in tissues where water is transported in large volumes.]]}}

{{hidden|How are channel and carrier proteins different?|Channel proteins created hydrophilic pores, permit rapid movement of solutes, restricted by size and charge, where Carrier proteins bind to their specific solutes and undergo a series of conformational changes to transfer the ligand across the membrane, relatively slow transport.]]}}

{{hidden|What is the "multidrug resistance (MDR) protein"?|[[A type of transporter ATPases which pumps polar compounds (e.g. chemo drugs) out of cells which may render cancer cells resistant to treatment.]]}}

{{hidden|What are the two fundamental mechanisms of fluid or macromolecules by the cell (endocytosis)?|[[1)Caveolae -invaginations of the plasma membrane, 2) Pinocytosis/receptor mediated endocytosis - macromolecules bind to receptor and membranes invaginate around it.]]}}

{{hidden|What is exocytosis?|[[It is the opposite process of pinocytosis, where the receptor bound macromolecule is move to the cell surface and released.]]}}

{{hidden|Describe the difference between phagocytosis and transcytosis.|[[In phagocytosis microbes are ingested forming phagosomes, which fuse with lysosomes and become phagylosomes, releasing undigested residual material when fusing again with the external membrane, in contrast transcytosis the materials are carried across the cell membrane unaltered.]]}}

{{hidden|List the three major classes of 3 cytoskeleton proteins.|[[1) Actin, 2)Intermediate filaments, 3)Microtubules]]}}

{{hidden|Describe actin.|[[Actin - 5 to 9nm diam fibrils, G-actin polymerized into F-actin, the form double strands helices, which interact with myosin (filamentous protein).]]}}

{{hidden|List the various intermediate filaments, which are 10nm in diameter.|[[1) Lamin A, B, and C (nuclear lamins of all cells, 2) Vimentin (mesenchymal), 3)Desmin (scaffold for actin/myosin), 4) Neurofilaments (axons of neurons), 5) Glial filament protein (glial cells), 6)Cytokeratins (acid and basic and vary based on cell type). ]]}}

{{hidden|Describe microtubules.|[[ Microtubules are 25nm diam fibrils of dimers of a and b tubulin, with a negative end embedded in the centrosome near the nucleus, the + end grows or shrinks as needed. There are kinesins and dyneins motors that move stuff around the cell, also found in cilia and flagella.]]}}

{{hidden|What is clatharin?|[[A molecule found in the cell membrane that when the cell membrane invaginates forming a basket like structure.]]}}

{{hidden|List and describe the 3 main classifications of cell junctions.|[[1) Tight /occluding junctions - form a high resistance barrier to solute movement, and allows the cell to maintain polarity, 2) anchoring junctions / desmosomes - mechanically attach the cell and their cytoskeleton to other cells and the ECM (hemidesmosome), 3)communicating/gap junctions - mediate the passage of chemical or electrical signals from one cell to another.]]}}

{{hidden|What is the "unfolded protein response"?| Excess accumulation of misfolded protiens, which exceed the capacity of the ER to edit and degrade them, leads to the the ER stress response (UPR) that triggers cell death through apoptosis.]]}}

{{hidden|What cell organelle has a reactive hyperplasia with repeated exposure to phenobarbitol catabolism in the cytocrhome p450 system?|[[Smooth endoplasmic reticulum.]]}}

{{hidden|List three main functions of mitochondria.|[[1) Energy generation, 2) intermediate metabolism (instead of ATP make intemediate that can be used to make lipids, nucleic acids, and proteins), 3) Cell death ( necrosis & apoptosis)]]}}

{{hidden|List and describe the four extracellular cell-cell signaling pathways based on the distance the signal travels.|[[1)Paracrine (immediate vicinity), 2) Autocrine (cell affecting itself), 3) Synaptic (neurons sending neurotransmitters at synapse), 4) endocrine (signals released elsewhere into bloodstream).]]}}

{{hidden|What are the two characterizing features of stem cells?|[[Self renewal and asymmetric division (one daughter cell stays a stem cell)]]}}

{{hidden|What are the two types of stem cells?|[[embryonic stem cells (inner cell mass of the blastocyst, totipotent), and tissue/adult stem cells (found in stem cell niches associated with specialized tissues, limited repetoire of differentiation = multipotent)]]}}

{{hidden|What is the Warburg effect?|[[Increased cellular uptake of glucose and glutamine, increased glycolysis, and decreased oxidative phosphorylation by the cell.]]}}

{{hidden|Which CDKI's have selective effects on CDK4 and CDK6?|[[p15,p16,p17,and p19]]}}

{{hidden|List some examples of signal transduction pathways.|[[1) Receptor tyrosine kinases (RTKs), 2) Nonreceptor tyrosine kinase, 3) G-protein coupled receptors, 4) nuclear receptors, 5)Notch family receptors, 6) Wnt protein ligands (Frizzled family receptors).]]}}

{{hidden|Why does nuclear beta catenin occur in some neoplasms?|[[When Wnt ligand bins to frizzled it recruits Disheveled, this leads to the disruption of the wnt-ubiquitin complex, this stabilized pool of b-catening is then translocated to the nucleus forming a transcriptional complex]]}}

{{hidden|On Page 19 there is a table of growth factors involved in regeneration and repair, please review.|[[]]}}

{{hidden|Describe the function of cadherin.|[[]]}}

{{hidden|What are the functions of the extracellular matrix?|[[Mechanical support, control of cell proliferation, scaffolding for tissue renewal, establishment of tissue microenvironments]]}}

{{hidden|What are the two basic forms of the ECM?|[[interstitial matrix (fibrillar and non fibrillar collagen, fibronectin, elastin, proteoglycans, hyloronate, and other stuff), basement membrane (type IV collagen and laminin) ]]}}

{{hidden|What are the three proteins groups in the ECM?|[[1) fibrous structural proteins (collagen, elastins), 2) water hydrated gels (proteoglycans and hyaluronan), 3) adhesive glycoproteins (connect ECM to each other and other cells)]]}}

{{hidden|Describe the structure of a protein that is dependent on vitamin C.|[[Collagen is composed of 3 seprate polypeptide chains braided into a rope like triple helix, lateral cross linking of the triple helices by lysyl oxidase (requires vitamin C) give it it's tensile strength. ]]}}

{{hidden|List three non-fibrillar collagens.|[[Type IV -basement membrane, Type IX - Fibrillar associated collagen with interrupted triple helices (FACIT), Type VII (provides anchoring fibrils to basement membrane beneath skin)]]}}

{{hidden|Which structural protein is associated with Marfan syndrom?|[[Fibrillin synthetic defects, which wrap the elastin core. ]]}}

== Chapter 2 ==
== Chapter 3 ==
== Chapter 4 ==
== Chapter 5 ==
{{hidden|MC cause of spontaneous abortion is ?|<center>[[ A demonstrable chromosomal abnormality.]]</center>}}

{{hidden|1% of all newborn infants possess a gross chromosomal abnormality and 5% of people <25y present with |<center>[[a genetic disease. ]]</center>}}

{{hidden|Mutation|<center>[[permanent change in the DNA, if affect germ cells are transmitted to the progeny ]]</center>}}

{{hidden|List and describe 4 broad categories of human genetic disorders:|<center>[[Disorders related to mutation sin single genes with large effects i. Usually follow classic Mendelian pattern of inheritance
ii. Often highly penetrant (large proportion of pop with gene has disease)
b. Chromosomal disorders
i. Structural or numerical alterations in autosomes and sex chromosomes
ii. Uncommon, high penetrance
c. Complex multigenic disorders
i. Interactions between multiple variant forms of genes and environmental factors (polymorphisms), poly genic means disease when many polymorphism present
d. Single gene disorders with nonclassic patterns of inheritance (not mendelian)
i. Disorders resulting from triplet repeat mutations
ii. Mutations in mitochondrial DNA
iii. Those influenced by genomic imprinting
iv. Those influenced by gonadal mosaicism]]</center>}}

{{hidden|List and describe the possible outcomes of a point mutation in a coding region?|[[a. Missense mutation – pt mutation changes amino acid code, conservative when the amino acid is preserved, non conservative when replaced with another amino acid, b. Nonsense mutation – makes a stop codon ]]</center>}}

{{hidden|List and describe the possible outcomes of point mutation or deletion in a non-coding region.|<center>[[a. Promoters/enhancers – interfere with binding of transcription factors, marker reduction or total lack of transcription, b. Introns – defective splicing > failure to make mature RNA > no translation]]</center>}}

{{hidden|List and describe the possible outcomes of deletions and insertions.|<center>[[a.Small coding: not multiple of three = frameshift, if multiple of 3 than add or del amino acids accordingly, often premature stop codon
i. Tay Sachs disease: 4 base pair insertion in Hexosaminidase A gene ]]}}

{{hidden|List and describe the possible outcomes of trinucleotide repeat mutations.|[[a. Usually G&C, dynamic and increase during gametogenesis, “RNA stutters”,b. Fragile X – CGG 250-4000, Huntinton’s Disease ]]}}

{{hidden|List and describe three examples of inheritance of single gene mutations|[[a. AD – manifested in the heterologous state, one parent of index case is usually affected, males and females affected and both can transmit conditioni. De novo cases may not have affected parentii. Penetrance = fraction of people with gene who have the traitiii. Variable expressivity = those with mutant gene have variety of phenotypesiv. Often age of onset is delayed so can reproduce before die from diseasev. Biochem mechanisms1. Reduced production of a protein or dysfunctional/inactive protein2. Involved in regulation of complex metabolic pathyway subject to feedback inhibition3. Key structural proteins (collagen and cytoskeleton of RBC)a. May be a dominant negative , e.g. osteogenesis imperfecta4. Gain of function are rare, 2 formsa. Increased in proteins normal function (excess enzyme activity)b. Huntinton’s diseas (abn protein accumulates, toxic to neurons)b. ARi. Largest category – both alleles at a locus are mutated1. Expression is uniform, complete penetrance common, early onset, unaffected carrier family members, mostly enzymesc. X Linkedi. All sex linked, and almost all are recessive , if Y Chromosome affected usually infertile males > no progenyii. Male expression b/c hemizygous, daughter carriers with variable phenotype because of lionization of 2nd X e.g G6DPiii. Dominant . vitamin D resistant rickets]]</center>}}

Stopped at P142

== Chapter 6 ==
== Chapter 7 ==
== Chapter 8 ==
== Chapter 9 ==
== Chapter 10 ==
== Chapter 11 ==
== Chapter 12 ==
== Chapter 13 ==
== Chapter 14 ==
== Chapter 15 ==
== Chapter 16 ==
== Chapter 17 ==
== Chapter 18 ==
== Chapter 19 ==
== Chapter 20 ==
== Chapter 21 ==
== Chapter 22 ==
== Chapter 23 ==
== Chapter 24 ==
== Chapter 25 ==
== Chapter 26 ==
== Chapter 27 ==
== Chapter 28 ==
== Chapter 29 ==

Libre Pathology talk:Study Group

2015-05-14T10:57:11Z

Yuanny: /* Robbins and Cotran Chapter 5 9th Edition */

==Michael's thoughts on the exam==
*I wrote it and passed it in 2012. I also did the American exam the same year and passed that.
*The pass rate for the FRCPC exam is pretty high.
**2009-2011 it was 96+/-3.9% for Canadian medical school grads on their first attempt.

===Written===
*I though it was picking at details. Some things are very relevant to practise... other less so.
**The pocketbook version of [[Robbins]] covers most of it.

===Practical (slide) exam===
*You should know the answer almost immediately.
**If you don't know, write something down and move on.
*It is set to broadly cover everything.
*If it isn't a [[spot diagnosis]]... it should not be on.
*Somethings are PGY2/PGY3 stuff. One should not overthink things.
*Anecdotally, the first impression is usually the right one.
**I think one should stick with the first impression.

===Gross exam===
*Go with the most probable if you're uncertain.
*I worked through the ''Atlas of Gross Pathology with Histologic Correlation'' (see [[Pathology books]] for the reference).
**I am not sure this is necessary... but I thought it was useful.
*Flickr.com/Google images has a lot to offer in this respect.
*[[Gross spot diagnosis]].

===Forensic exam===
*I thought this was tricky... and I liked forensics.
*Residents that took the exam prior to me said the same.

===Cytology exam===
*Some of the cases have several images.
*I remember being confused... the first three images were from one case. I remember thinking... I have the same diagnosis three times.
*Like the forensics and gross sections - this section isn't too long. From an exam strategy point-of-view, this makes it less likely that a diagnosis is repeated.

===Oral exam===
*I think this is to test if you are safe and useful.
**By "safe" I mean: knowing your limits and consulting with a colleague when appropriate.
**By "useful" I mean: you don't need to consult on everything.
*The examiners ask a pre-determined list of questions.
**Questions may depend on one another and, in fairness, they are told to redirect you.
***Example: You see a lung biopsy with hyaline material... and you go down the fibrosis route-- but it is really amyloidosis.
****The examiners will say something like "how would one work-up suspected amyloid?" or "lets assume this is amyloid..."
*If you're a Canadian resident, you cannot be examined by someone within your residency program.
*As far as I know, examiners are told to be stone-faced, i.e. show no emotion.
*Some of the cases were very straight forward.
*I didn't think anything was really exotic.

[[User:Michael|Michael]] ([[User talk:Michael|talk]]) 23:43, 25 October 2014 (EDT)

== Short answer questions on genetics and molecular pathology. ==

These are some questions I came up with that are plausible to me... let me know if they are out to lunch.

===UNIT 1===
{{hidden|List three differences between DNA and RNA.|[[DNA (double stranded, thymine, deoxyribose, more stable; RNA single stranded, ribose, uracil]]}}

{{hidden|What are the three stop codons?|[UAA, UGA, UAG]]}}

{{hidden|Where does transcription begin?|[[promoters at the 5' end before the coding region]]}}

{{hidden|List 2 enzymes necessary for transcription and their function. |[[helicase, polymerase]]}}

{{hidden|List and describe three post transcription modifications of RNA.|[[Splicing, cappping, 3'polyadenylation, ]]}}

{{hidden| Why is alternative splicing important?|[[Using the basic construction blocks of coding sequences allows a large variety of recombinations, more efficient coding (e.g. creating functions to call))]]}}

{{hidden|List three differences between somatic and germline mutations. |<center>[[Somatic: not passed on to progeny, only tumour or particular tissue cells with mutation, Germline: passed onto progeny, all cells have mutation * unless mosaicism or chimerism]]</center>}}

{{hidden|What is the difference between a missense and a non-sense mutation?|<center>[[Missense the new base pair does not change the amino acid found in the protein at that location, non-sense changes the amino acid in the protein at that location]]</center>}}
{{hidden|Define a frameshift mutation. |<center>[[deletion of a non-multiple of 3 which causes all further trinucleotide combinations to no longer code for the correct amino acid, often results in a premature stop codon]]</center>}}
{{hidden|Why are inversion mutations difficult to detect?|<center>[[When the are smal, e.g. only a few base pairs]]</center>}}
{{hidden|Describe the potential sequelae of a translocation mutation. |<center>[[when a segment on one chromosome is transferred to another, make a gene non-functional or can result in a fusion gene]]</center>}}

===UNIT 2===
{{hidden|Translate the following: c.1524_1527delCGTA.|<center>[[a small deletion of CGTA between the 1524 and 1527 base pairs]]</center>}}
{{hidden|List 5 features of SNPs.|<center>[[most common DNA sequence variation in humans, must occur in >=1% of a particular population, frequency of SNPs varies by groups, but responsible for >90% of human genetic variation, an can be found in any region of genome]]</center>}}
{{hidden|Define a regulatory SNP and a synonymous SNP?|<center>[[Regulatory SNP: occur in non-coding regions e.g. promoters where they affect mRNA expression and stability, as occur in the splice site where can result in abnormal protein production]]</center>}}
{{hidden|What is the difference between a microstalellite and a minisattelite?|<center>[[Microsatellite = stretches of DNA with sequences of 2-4 base pairs repeated a few dozen times (STRP), minisatellite = variable number of tandem repeats 10-100bp in lenght]]</center>}}
{{hidden|Describe Hardy-Weinberg Equilibrium?|<center>[[Mathematical probability function to describe allelic and genotype frequency in a random mating scenario]]</center>}}
{{hidden|What factors can disrupt the H-W equilibrium?|<center>[[non random mating, migration, genetic drift, founder effects, mutation, natural selection]]</center>}}
{{hidden|What is linkage disequilibrium?|<center>[[The closer two genes are together on the chromosome the more likely they are to be found toghether in a population, during meiosis some exchange of material happens between the two chromosomes]]</center>}}

===UNIT 3===
{{hidden|What are the three major steps of PCR?|<center>[[denaturing, primer annealing, strand extending]]</center>}}
{{hidden|What is the hallmark of PCR?|<center>[[The cycling at different temperatures, in the presence of key reaction components to traget and exponentially amplify a specific DNA target sequence]]</center>}}
{{hidden|What factors affect the method of genotyping chosen?|<center>[[throughput, type of variants that can be genotyped, equipment and costs, TAT, technical expertise, and multiplex ability]]</center>}}
{{hidden|Define sensitivity, specificity, positive predictive value and negative predictive value. |<center>[[Sensitivity = probability of a positive test in a disease, specificity = probability of a negative dest in a non-diseased patient ]]</center>}}
{{hidden|Define reproducibility and accuracy of an analytical test. |<center>[[Reproducability = probability of the test repeatedly producing the same reults in the same person, Accuracy = the degree to which the observed genotype matches the true genotype]]</center>}}
{{hidden|Describe briefly Sanger sequencing.|<center>[[DIdeoxynucleotides are used in a mix with deoxynucleotides, the Di*** terminate the chain, and so you get all possible lengths of chains so then you put them all in order and you can read (based on weight) which one is at each position]]</center>}}
{{hidden|Describe briefly how Taqman automated genotyping is used for allele detection. |<center>[[Microsatellite instability]]</center>}}
{{hidden|How are DNA microarrays used to identify drug disposition or responses?|<center>[[Microsatellite instability]]</center>}}

===UNIT 4===
{{hidden|Describe the procedure for submitting FFPE slides for KRAS for colorectal cancer.|<center>[[Microsatellite instability]]</center>}}
{{hidden|Compare and contrast uniplex versus multiplex genotyping. |<center>[[Microsatellite instability]]</center>}}
{{hidden|Compare and contrast conventional vs massively parallel sequencing. |<center>[[Microsatellite instability]]</center>}}
{{hidden|What is multiplex ligation-dependent ligation (MLPA)?|<center>[[Microsatellite instability]]</center>}}
{{hidden|What is fragment analysis?|<center>[[Microsatellite instability]]</center>}}
{{hidden|Compare and contrast RT-PCR vs qRTPCR.|<center>[[Microsatellite instability]]</center>}}
{{hidden|What is MSI?|<center>[[Microsatellite instability]]</center>}}
{{hidden|What is methylation analysis?|<center>[[Microsatellite instability]]</center>}}

===UNIT 5===
{{hidden|What are the four test features required to be documented by the CLIA?|<center>[[Microsatellite instability]]</center>}}
{{hidden|What are "in vitro diagnostics" vs "laboratory developed tests"?|<center>[[Microsatellite instability]]</center>}}
{{hidden|What does validation mean? |<center>[[Microsatellite instability]]</center>}}
{{hidden|What are the four performance characteristics that need to be verified for FDA cleared/approved tests?|<center>[[Microsatellite instability]]</center>}}
{{hidden|What are the six performance characteristics that need to be verified for FDA cleared LDTs or modified FDA cleared/approved tests?|<center>[[Microsatellite instability]]</center>}}

===UNIT 6===
{{hidden|List the components of a molecular pathology report.|<center>[[Microsatellite instability]]</center>}}
{{hidden|Define analytical sensitivity and clinical sensitivity. |<center>[[Microsatellite instability]]</center>}}
{{hidden|What should be said in a report of a molecular test on a patient for residual disease if no previous positive assay was confirmed?|<center>[[Microsatellite instability]]</center>}}
{{hidden|Define ammended report versus addendum report.|<center>[[Microsatellite instability]]</center>}}
{{hidden|Whose responsibility is it to sythesize the test results with other clinico-pathological information?|<center>[[Microsatellite instability]]</center>}}
{{hidden|How long are cytogenetic reports required to be kept by CAP?|<center>[[Microsatellite instability]]</center>}}
{{hidden|What is the recommended process to use test results if an assay is not yet validated for clinical use?|<center>[[Microsatellite instability]]</center>}}
{{hidden|Give three examples of "grey areas" which warrant discretion of professionals involved to use a non-validated test?|<center>[[Microsatellite instability]]</center>}}
{{hidden|What reference standard is available for gene nomenclature?|<center>[[Microsatellite instability]]</center>}}
{{hidden|Create a table of the most common gene rearrangements associated with heme and soft tissue diseases. |<center>[[Microsatellite instability]]</center>}}
{{hidden|What is a "DNA fingerprint" and what can it be used for?|<center>[[A method that examines multiple areas of short tandem repeats to identify paternity, mosaicism, chimerism, and identity in forensics cases]]</center>}}

===Robbins and Cotran Chapter 5 9th Edition===

{{hidden|MC cause of spontaneous abortion is ?|<center>[[ A demonstrable chromosomal abnormality.]]</center>}}

{{hidden|1% of all newborn infants possess a gross chromosomal abnormality and 5% of people <25y present with |<center>[[a genetic disease. ]]</center>}}

{{hidden|Mutation|<center>[[permanent change in the DNA, if affect germ cells are transmitted to the progeny ]]</center>}}

{{hidden|List and describe 4 broad categories of human genetic disorders:|<center>[[Disorders related to mutation sin single genes with large effects i. Usually follow classic Mendelian pattern of inheritance
ii. Often highly penetrant (large proportion of pop with gene has disease)
b. Chromosomal disorders
i. Structural or numerical alterations in autosomes and sex chromosomes
ii. Uncommon, high penetrance
c. Complex multigenic disorders
i. Interactions between multiple variant forms of genes and environmental factors (polymorphisms), poly genic means disease when many polymorphism present
d. Single gene disorders with nonclassic patterns of inheritance (not mendelian)
i. Disorders resulting from triplet repeat mutations
ii. Mutations in mitochondrial DNA
iii. Those influenced by genomic imprinting
iv. Those influenced by gonadal mosaicism]]</center>}}

{{hidden|List and describe the possible outcomes of a point mutation in a coding region?|<center>[[a. Missense mutation – pt mutation changes amino acid code, conservative when the amino acid is preserved, non conservative when replaced with another amino acid
b. Nonsense mutation – makes a stop codon ]]</center>}}

{{hidden|List and describe the possible outcomes of point mutation or deletion in a non-coding region.|<center>[[a. Promoters/enhancers – interfere with binding of transcription factors, marker reduction or total lack of transcription, b. Introns – defective splicing > failure to make mature RNA > no translation]]</center>}}
{{hidden|List and describe the possible outcomes of deletions and insertions.|<center>[[a. Small coding: not multiple of three = frameshift, if multiple of 3 than add or del amino acids accordingly, often premature stop codon
i. Tay Sachs disease: 4 base pair insertion in Hexosaminidase A gene
{{hidden|List and describe the possible outcomes of trinucleotide repeat mutations.
a. Usually G&C, dynamic and increase during gametogenesis, “RNA stutters”
b. Fragile X – CGG 250-4000, Huntinton’s Disease * See Neuropath Notes]]</center>}}

{{hidden|List and describe three examples of inheritance of single gene mutations
a. AD – manifested in the heterologous state, one parent of index case is usually affected, males and females affected and both can transmit condition
i. De novo cases may not have affected parent
ii. Penetrance = fraction of people with gene who have the trait
iii. Variable expressivity = those with mutant gene have variety of phenotypes
iv. Often age of onset is delayed so can reproduce before die from disease
v. Biochem mechanisms
1. Reduced production of a protein or dysfunctional/inactive protein
2. Involved in regulation of complex metabolic pathyway subject to feedback inhibition
3. Key structural proteins (collagen and cytoskeleton of RBC)
a. May be a dominant negative , e.g. osteogenesis imperfecta
4. Gain of function are rare, 2 forms
a. Increased in proteins normal function (excess enzyme activity)
b. Huntinton’s diseas (abn protein accumulates, toxic to neurons)
b. AR
i. Largest category – both alleles at a locus are mutated
1. Expression is uniform, complete penetrance common, early onset, unaffected carrier family members, mostly enzymes
c. X Linked
i. All sex linked, and almost all are recessive , if Y Chromosome affected usually infertile males > no progeny
ii. Male expression b/c hemizygous, daughter carriers with variable phenotype because of lionization of 2nd X e.g G6DP
iii. Dominant . vitamin D resistant rickets]]</center>}}
Stopped at P142

Molecular Genetic Diagnosis
1. List three basic molecular diagnostic techniques
a. Karyotyping
b. Southern blot
c. Sanger DNA sequencing
d. Polymerase chain reaction
2. Constitutional vs somatic mutations.

===Discussion===
Hi Michael, I've started, but mostly just with the questions for now, as I study I will keep working on it. Can you help me, maybe we can make additional discussion pages for each of my "study" exams,e.g. molecular, robbins chapters, cap protocols etc. This is just like LaTEX!!!

:I hope to get a few other ppl involved. I am just thinking about how to organize the pages. [[User:Michael|Michael]] ([[User talk:Michael|talk]]) 04:52, 14 May 2015 (EDT)

Libre Pathology talk:Study Group

2015-05-14T10:54:31Z

Yuanny: /* UNIT 2 */

==Michael's thoughts on the exam==
*I wrote it and passed it in 2012. I also did the American exam the same year and passed that.
*The pass rate for the FRCPC exam is pretty high.
**2009-2011 it was 96+/-3.9% for Canadian medical school grads on their first attempt.

===Written===
*I though it was picking at details. Some things are very relevant to practise... other less so.
**The pocketbook version of [[Robbins]] covers most of it.

===Practical (slide) exam===
*You should know the answer almost immediately.
**If you don't know, write something down and move on.
*It is set to broadly cover everything.
*If it isn't a [[spot diagnosis]]... it should not be on.
*Somethings are PGY2/PGY3 stuff. One should not overthink things.
*Anecdotally, the first impression is usually the right one.
**I think one should stick with the first impression.

===Gross exam===
*Go with the most probable if you're uncertain.
*I worked through the ''Atlas of Gross Pathology with Histologic Correlation'' (see [[Pathology books]] for the reference).
**I am not sure this is necessary... but I thought it was useful.
*Flickr.com/Google images has a lot to offer in this respect.
*[[Gross spot diagnosis]].

===Forensic exam===
*I thought this was tricky... and I liked forensics.
*Residents that took the exam prior to me said the same.

===Cytology exam===
*Some of the cases have several images.
*I remember being confused... the first three images were from one case. I remember thinking... I have the same diagnosis three times.
*Like the forensics and gross sections - this section isn't too long. From an exam strategy point-of-view, this makes it less likely that a diagnosis is repeated.

===Oral exam===
*I think this is to test if you are safe and useful.
**By "safe" I mean: knowing your limits and consulting with a colleague when appropriate.
**By "useful" I mean: you don't need to consult on everything.
*The examiners ask a pre-determined list of questions.
**Questions may depend on one another and, in fairness, they are told to redirect you.
***Example: You see a lung biopsy with hyaline material... and you go down the fibrosis route-- but it is really amyloidosis.
****The examiners will say something like "how would one work-up suspected amyloid?" or "lets assume this is amyloid..."
*If you're a Canadian resident, you cannot be examined by someone within your residency program.
*As far as I know, examiners are told to be stone-faced, i.e. show no emotion.
*Some of the cases were very straight forward.
*I didn't think anything was really exotic.

[[User:Michael|Michael]] ([[User talk:Michael|talk]]) 23:43, 25 October 2014 (EDT)

== Short answer questions on genetics and molecular pathology. ==

These are some questions I came up with that are plausible to me... let me know if they are out to lunch.

===UNIT 1===
{{hidden|List three differences between DNA and RNA.|[[DNA (double stranded, thymine, deoxyribose, more stable; RNA single stranded, ribose, uracil]]}}

{{hidden|What are the three stop codons?|[UAA, UGA, UAG]]}}

{{hidden|Where does transcription begin?|[[promoters at the 5' end before the coding region]]}}

{{hidden|List 2 enzymes necessary for transcription and their function. |[[helicase, polymerase]]}}

{{hidden|List and describe three post transcription modifications of RNA.|[[Splicing, cappping, 3'polyadenylation, ]]}}

{{hidden| Why is alternative splicing important?|[[Using the basic construction blocks of coding sequences allows a large variety of recombinations, more efficient coding (e.g. creating functions to call))]]}}

{{hidden|List three differences between somatic and germline mutations. |<center>[[Somatic: not passed on to progeny, only tumour or particular tissue cells with mutation, Germline: passed onto progeny, all cells have mutation * unless mosaicism or chimerism]]</center>}}

{{hidden|What is the difference between a missense and a non-sense mutation?|<center>[[Missense the new base pair does not change the amino acid found in the protein at that location, non-sense changes the amino acid in the protein at that location]]</center>}}
{{hidden|Define a frameshift mutation. |<center>[[deletion of a non-multiple of 3 which causes all further trinucleotide combinations to no longer code for the correct amino acid, often results in a premature stop codon]]</center>}}
{{hidden|Why are inversion mutations difficult to detect?|<center>[[When the are smal, e.g. only a few base pairs]]</center>}}
{{hidden|Describe the potential sequelae of a translocation mutation. |<center>[[when a segment on one chromosome is transferred to another, make a gene non-functional or can result in a fusion gene]]</center>}}

===UNIT 2===
{{hidden|Translate the following: c.1524_1527delCGTA.|<center>[[a small deletion of CGTA between the 1524 and 1527 base pairs]]</center>}}
{{hidden|List 5 features of SNPs.|<center>[[most common DNA sequence variation in humans, must occur in >=1% of a particular population, frequency of SNPs varies by groups, but responsible for >90% of human genetic variation, an can be found in any region of genome]]</center>}}
{{hidden|Define a regulatory SNP and a synonymous SNP?|<center>[[Regulatory SNP: occur in non-coding regions e.g. promoters where they affect mRNA expression and stability, as occur in the splice site where can result in abnormal protein production]]</center>}}
{{hidden|What is the difference between a microstalellite and a minisattelite?|<center>[[Microsatellite = stretches of DNA with sequences of 2-4 base pairs repeated a few dozen times (STRP), minisatellite = variable number of tandem repeats 10-100bp in lenght]]</center>}}
{{hidden|Describe Hardy-Weinberg Equilibrium?|<center>[[Mathematical probability function to describe allelic and genotype frequency in a random mating scenario]]</center>}}
{{hidden|What factors can disrupt the H-W equilibrium?|<center>[[non random mating, migration, genetic drift, founder effects, mutation, natural selection]]</center>}}
{{hidden|What is linkage disequilibrium?|<center>[[The closer two genes are together on the chromosome the more likely they are to be found toghether in a population, during meiosis some exchange of material happens between the two chromosomes]]</center>}}

===UNIT 3===
{{hidden|What are the three major steps of PCR?|<center>[[denaturing, primer annealing, strand extending]]</center>}}
{{hidden|What is the hallmark of PCR?|<center>[[The cycling at different temperatures, in the presence of key reaction components to traget and exponentially amplify a specific DNA target sequence]]</center>}}
{{hidden|What factors affect the method of genotyping chosen?|<center>[[throughput, type of variants that can be genotyped, equipment and costs, TAT, technical expertise, and multiplex ability]]</center>}}
{{hidden|Define sensitivity, specificity, positive predictive value and negative predictive value. |<center>[[Sensitivity = probability of a positive test in a disease, specificity = probability of a negative dest in a non-diseased patient ]]</center>}}
{{hidden|Define reproducibility and accuracy of an analytical test. |<center>[[Reproducability = probability of the test repeatedly producing the same reults in the same person, Accuracy = the degree to which the observed genotype matches the true genotype]]</center>}}
{{hidden|Describe briefly Sanger sequencing.|<center>[[DIdeoxynucleotides are used in a mix with deoxynucleotides, the Di*** terminate the chain, and so you get all possible lengths of chains so then you put them all in order and you can read (based on weight) which one is at each position]]</center>}}
{{hidden|Describe briefly how Taqman automated genotyping is used for allele detection. |<center>[[Microsatellite instability]]</center>}}
{{hidden|How are DNA microarrays used to identify drug disposition or responses?|<center>[[Microsatellite instability]]</center>}}

===UNIT 4===
{{hidden|Describe the procedure for submitting FFPE slides for KRAS for colorectal cancer.|<center>[[Microsatellite instability]]</center>}}
{{hidden|Compare and contrast uniplex versus multiplex genotyping. |<center>[[Microsatellite instability]]</center>}}
{{hidden|Compare and contrast conventional vs massively parallel sequencing. |<center>[[Microsatellite instability]]</center>}}
{{hidden|What is multiplex ligation-dependent ligation (MLPA)?|<center>[[Microsatellite instability]]</center>}}
{{hidden|What is fragment analysis?|<center>[[Microsatellite instability]]</center>}}
{{hidden|Compare and contrast RT-PCR vs qRTPCR.|<center>[[Microsatellite instability]]</center>}}
{{hidden|What is MSI?|<center>[[Microsatellite instability]]</center>}}
{{hidden|What is methylation analysis?|<center>[[Microsatellite instability]]</center>}}

===UNIT 5===
{{hidden|What are the four test features required to be documented by the CLIA?|<center>[[Microsatellite instability]]</center>}}
{{hidden|What are "in vitro diagnostics" vs "laboratory developed tests"?|<center>[[Microsatellite instability]]</center>}}
{{hidden|What does validation mean? |<center>[[Microsatellite instability]]</center>}}
{{hidden|What are the four performance characteristics that need to be verified for FDA cleared/approved tests?|<center>[[Microsatellite instability]]</center>}}
{{hidden|What are the six performance characteristics that need to be verified for FDA cleared LDTs or modified FDA cleared/approved tests?|<center>[[Microsatellite instability]]</center>}}

===UNIT 6===
{{hidden|List the components of a molecular pathology report.|<center>[[Microsatellite instability]]</center>}}
{{hidden|Define analytical sensitivity and clinical sensitivity. |<center>[[Microsatellite instability]]</center>}}
{{hidden|What should be said in a report of a molecular test on a patient for residual disease if no previous positive assay was confirmed?|<center>[[Microsatellite instability]]</center>}}
{{hidden|Define ammended report versus addendum report.|<center>[[Microsatellite instability]]</center>}}
{{hidden|Whose responsibility is it to sythesize the test results with other clinico-pathological information?|<center>[[Microsatellite instability]]</center>}}
{{hidden|How long are cytogenetic reports required to be kept by CAP?|<center>[[Microsatellite instability]]</center>}}
{{hidden|What is the recommended process to use test results if an assay is not yet validated for clinical use?|<center>[[Microsatellite instability]]</center>}}
{{hidden|Give three examples of "grey areas" which warrant discretion of professionals involved to use a non-validated test?|<center>[[Microsatellite instability]]</center>}}
{{hidden|What reference standard is available for gene nomenclature?|<center>[[Microsatellite instability]]</center>}}
{{hidden|Create a table of the most common gene rearrangements associated with heme and soft tissue diseases. |<center>[[Microsatellite instability]]</center>}}
{{hidden|What is a "DNA fingerprint" and what can it be used for?|<center>[[A method that examines multiple areas of short tandem repeats to identify paternity, mosaicism, chimerism, and identity in forensics cases]]</center>}}

===Robbins and Cotran Chapter 5 9th Edition===

{{hidden|MC cause of spontaneous abortion is ?|<center>[[ A demonstrable chromosomal abnormality.]]</center>}}

{{hidden|1% of all newborn infants possess a gross chromosomal abnormality and 5% of people <25y present with |<center>[[a genetic disease. ]]</center>}}

{{hidden|Mutation|<center>[[permanent change in the DNA, if affect germ cells are transmitted to the progeny ]]</center>}}

{{hidden|List and describe 4 broad categories of human genetic disorders:|<center>[[Disorders related to mutation sin single genes with large effects i. Usually follow classic Mendelian pattern of inheritance
ii. Often highly penetrant (large proportion of pop with gene has disease)
b. Chromosomal disorders
i. Structural or numerical alterations in autosomes and sex chromosomes
ii. Uncommon, high penetrance
c. Complex multigenic disorders
i. Interactions between multiple variant forms of genes and environmental factors (polymorphisms), poly genic means disease when many polymorphism present
d. Single gene disorders with nonclassic patterns of inheritance (not mendelian)
i. Disorders resulting from triplet repeat mutations
ii. Mutations in mitochondrial DNA
iii. Those influenced by genomic imprinting
iv. Those influenced by gonadal mosaicism]]</center>}}

{{hidden|List and describe the possible outcomes of a point mutation in a coding region?|<center>[[a. Missense mutation – pt mutation changes amino acid code, conservative when the amino acid is preserved, non conservative when replaced with another amino acid
b. Nonsense mutation – makes a stop codon ]]</center>}}

{{hidden|List and describe the possible outcomes of point mutation or deletion in a non-coding region.|<center>[[a. Promoters/enhancers – interfere with binding of transcription factors, marker reduction or total lack of transcription, b. Introns – defective splicing > failure to make mature RNA > no translation]]</center>}}
{{hidden|List and describe the possible outcomes of deletions and insertions.|<center>[[a. Small coding: not multiple of three = frameshift, if multiple of 3 than add or del amino acids accordingly, often premature stop codon
i. Tay Sachs disease: 4 base pair insertion in Hexosaminidase A gene
{{hidden|List and describe the possible outcomes of trinucleotide repeat mutations.
a. Usually G&C, dynamic and increase during gametogenesis, “RNA stutters”
b. Fragile X – CGG 250-4000, Huntinton’s Disease * See Neuropath Notes
{{hidden|List and describe three examples of inheritance of single gene mutations
a. AD – manifested in the heterologous state, one parent of index case is usually affected, males and females affected and both can transmit condition
i. De novo cases may not have affected parent
ii. Penetrance = fraction of people with gene who have the trait
iii. Variable expressivity = those with mutant gene have variety of phenotypes
iv. Often age of onset is delayed so can reproduce before die from disease
v. Biochem mechanisms
1. Reduced production of a protein or dysfunctional/inactive protein
2. Involved in regulation of complex metabolic pathyway subject to feedback inhibition
3. Key structural proteins (collagen and cytoskeleton of RBC)
a. May be a dominant negative , e.g. osteogenesis imperfecta
4. Gain of function are rare, 2 forms
a. Increased in proteins normal function (excess enzyme activity)
b. Huntinton’s diseas (abn protein accumulates, toxic to neurons)
b. AR
i. Largest category – both alleles at a locus are mutated
1. Expression is uniform, complete penetrance common, early onset, unaffected carrier family members, mostly enzymes
c. X Linked
i. All sex linked, and almost all are recessive , if Y Chromosome affected usually infertile males > no progeny
ii. Male expression b/c hemizygous, daughter carriers with variable phenotype because of lionization of 2nd X e.g G6DP
iii. Dominant . vitamin D resistant rickets]]</center>}}
Stopped at P142

Molecular Genetic Diagnosis
1. List three basic molecular diagnostic techniques
a. Karyotyping
b. Southern blot
c. Sanger DNA sequencing
d. Polymerase chain reaction
2. Constitutional vs somatic mutations.

===Discussion===
Hi Michael, I've started, but mostly just with the questions for now, as I study I will keep working on it. Can you help me, maybe we can make additional discussion pages for each of my "study" exams,e.g. molecular, robbins chapters, cap protocols etc. This is just like LaTEX!!!

:I hope to get a few other ppl involved. I am just thinking about how to organize the pages. [[User:Michael|Michael]] ([[User talk:Michael|talk]]) 04:52, 14 May 2015 (EDT)

Prostate cancer

2014-12-13T13:52:54Z

Yuanny:

{{ Infobox diagnosis
| Name = Prostate carcinoma
| Image = Prostate cancer with Gleason pattern 4 low mag.jpg
| Width =
| Caption = Prostate carcinoma. [[H&E stain]].
| Micro = major criteria: abnormal architecture (increased gland density, usu. small circular glands, "infiltrative growth" pattern), basal cells lost, cytological abnormalities (nuclear enlargement, nucleoli); minor criteria: nuclear hyperchromasia, wispy blue mucin, pink amorphous secretions, intraluminal crystalloid, amphophilic cytoplasm, adjacent [[HGPIN]], mitoses
| Subtypes =
| LMDDx = [[high-grade prostatic intraepithelial neoplasia]], [[atypical small acinar proliferation]] (biopsy only), [[prostatic atrophy]], [[seminal vesicle]], [[basal cell hyperplasia of the prostate|basal cell hyperplasia]], others
| Stains =
| IHC = PSA +ve, PSAP +ve, AMACR +ve, p63 -ve, CK34betaE12 -ve
| EM =
| Molecular = +/-[[BRCA1]] mutation (genetic predisposition), +/-[[BRCA2]] mutation (genetic predisposition)
| IF =
| Gross = usu. posterior aspect of the prostate - often not apparent at gross
| Grossing = [[prostate biopsy]], [[prostate chips]], [[radical prostatectomy]]
| Site = [[prostate gland]]
| Assdx =
| Syndromes =
| Clinicalhx =
| Signs = firm, nodular prostate on digital rectal exam
| Symptoms = often asymptomatic
| Prevalence = very common
| Bloodwork = PSA elevated (common)
| Rads = hypoechoic areas, no apparent abnormality
| Endoscopy =
| Prognosis = good-to-poor (depends on [[Gleason score]] and [[stage]])
| Other =
| ClinDDx = [[prostatitis]], [[nodular hyperplasia of the prostate]]
| Tx = observation (common for low-grade, low tumour burden), radiation or radical prostatectomy
}}
This article deals with '''prostate [[cancer]]'''.

The vast majority of prostate cancers are carcinomas and could be labelled '''prostatic carcinoma'''. Most prostatic carcinomas are gland forming; thus, they can be labelled '''prostatic [[adenocarcinoma]]''' or '''adenocarcinoma of the prostate'''.

Benign pathology of the prostate gland, and prostate histology and anatomy are dealt with in the ''[[prostate gland]]'' article.

=Conventional prostate cancer=
==General==
*Very common.
*Increasing incidence with age - the age in years is an approximation of the percentage of men with prostate cancer.<ref>{{cite journal |author=Sakr WA, Haas GP, Cassin BF, Pontes JE, Crissman JD |title=The frequency of carcinoma and intraepithelial neoplasia of the prostate in young male patients |journal=J. Urol. |volume=150 |issue=2 Pt 1 |pages=379–85 |year=1993 |month=August |pmid=8326560 |doi= |url=}}</ref>{{fact}}
*Usually an indolent course - most old men die with prostate cancer ''not'' from prostate cancer.

*Risk increased with a [[BRCA1]] or [[BRCA2]] mutation<ref name=pmid23747895>{{Cite journal | last1 = Li | first1 = D. | last2 = Kumaraswamy | first2 = E. | last3 = Harlan-Williams | first3 = LM. | last4 = Jensen | first4 = RA. | title = The role of BRCA1 and BRCA2 in prostate cancer. | journal = Front Biosci (Landmark Ed) | volume = 18 | issue = | pages = 1445-59 | month = | year = 2013 | doi = | PMID = 23747895 }}</ref> - families have a mix of [[breast cancer]] and prostate cancer.
**BRCA2 mutation risk >8x for men over 65 years old.<ref name=pmid22522501>{{Cite journal | last1 = Castro | first1 = E. | last2 = Eeles | first2 = R. | title = The role of BRCA1 and BRCA2 in prostate cancer. | journal = Asian J Androl | volume = 14 | issue = 3 | pages = 409-14 | month = May | year = 2012 | doi = 10.1038/aja.2011.150 | PMID = 22522501 }}</ref>
**A BRCA2 founder mutation is described in French Canadians.<Ref name=pmid23318356>{{Cite journal | last1 = Taherian | first1 = N. | last2 = Hamel | first2 = N. | last3 = Bégin | first3 = LR. | last4 = Bismar | first4 = TA. | last5 = Goldgar | first5 = DE. | last6 = Feng | first6 = BJ. | last7 = Foulkes | first7 = WD. | title = Familial prostate cancer: the damage done and lessons learnt. | journal = Nat Rev Urol | volume = 10 | issue = 2 | pages = 116-22 | month = Feb | year = 2013 | doi = 10.1038/nrurol.2012.257 | PMID = 23318356 }}</ref>

===Management===
====Dirty first approximation====
*The management changes between [[Gleason score]] 6, 7 and 8.

Typically, the implications are:
* Gleason 6: observation ''or'' radioactive seeds; surgery if patient wants.
* Gleason 7: do something -- surgery ''or'' radiation therapy.
* Gleason 8+: bad cancer -- do something quickly!

Bottom line:
*You want to be sure when you call something Gleason pattern 4.

====Observational strategies====
*Delay of definitive treatment (surgery ''or'' radiation).
*Common in the management of prostate cancer.

Classification:<ref name=pmid23126653>{{Cite journal | last1 = Ip | first1 = S. | last2 = Dahabreh | first2 = IJ. | last3 = Chung | first3 = M. | last4 = Yu | first4 = WW. | last5 = Balk | first5 = EM. | last6 = Iovin | first6 = RC. | last7 = Mathew | first7 = P. | last8 = Luongo | first8 = T. | last9 = Dvorak | first9 = T. | title = An evidence review of active surveillance in men with localized prostate cancer. | journal = Evid Rep Technol Assess (Full Rep) | volume = | issue = 204 | pages = 1-341 | month = Dec | year = 2011 | doi = | PMID = 23126653 | url = http://www.ncbi.nlm.nih.gov/books/NBK83054/ }}</ref>
*Active surveillance (AS).
**Low risk of progression.
**May get definitive treatment later.
*Watchful waiting (WW).
**Higher risk of progression.

Note:
*There is no agreed upon set of criteria for active surveillance, and the large number of criteria out there vary significantly.<ref name=pmid22314081>{{Cite journal | last1 = Palisaar | first1 = JR. | last2 = Noldus | first2 = J. | last3 = Löppenberg | first3 = B. | last4 = von Bodman | first4 = C. | last5 = Sommerer | first5 = F. | last6 = Eggert | first6 = T. | title = Comprehensive report on prostate cancer misclassification by 16 currently used low-risk and active surveillance criteria. | journal = BJU Int | volume = 110 | issue = 6 Pt B | pages = E172-81 | month = Sep | year = 2012 | doi = 10.1111/j.1464-410X.2012.10935.x | PMID = 22314081 }}</ref>

=====Active surveillance=====
The ''Klotz'' criteria for active surveillance - pathologic factors only:<ref name=pmid22314081/><ref>{{Cite journal | last1 = Klotz | first1 = L. | title = Active surveillance for prostate cancer: for whom? | journal = J Clin Oncol | volume = 23 | issue = 32 | pages = 8165-9 | month = Nov | year = 2005 | doi = 10.1200/JCO.2005.03.3134 | PMID = 16278468 }}</ref>
*Gleason score 6 or less.
*All biopsies cores < 50% involvement.
*One or two cores involved.<ref>URL: [http://www.active-surveillance.com/laurence-klotz-md/ http://www.active-surveillance.com/laurence-klotz-md/]. Accessed on: 12 July 2013.</ref><ref name=pmid23548978>{{Cite journal | last1 = Klotz | first1 = L. | title = Active surveillance: patient selection. | journal = Curr Opin Urol | volume = 23 | issue = 3 | pages = 239-44 | month = May | year = 2013 | doi = 10.1097/MOU.0b013e32835f8f6b | PMID = 23548978 }}</ref><ref name=pmid22891078>{{Cite journal | last1 = Klotz | first1 = L. | title = Active surveillance for low-risk prostate cancer. | journal = F1000 Med Rep | volume = 4 | issue = | pages = 16 | month = | year = 2012 | doi = 10.3410/M4-16 | PMID = 22891078 | PMC = 3412317 }}</ref>
Clinical criteria:
*PSA <= 10 ng/mL.<ref name=pmid22314081/>

==Gross==
*Prostate cancer is uncommonly apparent on gross.
*Classic location: posterior aspect of the prostate.

===Radiology===
*Hypoechoic areas = suspicious for cancer.
**It seems that size of the area matters.
***Small hypoechoic areas (<0.2 cm3) have cancer less than 4% of the time.<ref name=pmid9933054>{{Cite journal | last1 = Fleshner | first1 = NE. | last2 = O'Sullivan | first2 = M. | last3 = Premdass | first3 = C. | last4 = Fair | first4 = WR. | title = Clinical significance of small (less than 0.2 cm3) hypoechoic lesions in men with normal digital rectal examinations and prostate-specific antigen levels less than 10 ng/mL. | journal = Urology | volume = 53 | issue = 2 | pages = 356-8 | month = Feb | year = 1999 | doi = | PMID = 9933054 }}</ref>
***One study suggests hypoechoic lesions tend to have a worse outcome;<ref name=pmid22920545>{{Cite journal | last1 = Nakano Junqueira | first1 = VC. | last2 = Zogbi | first2 = O. | last3 = Cologna | first3 = A. | last4 = Dos Reis | first4 = RB. | last5 = Tucci | first5 = S. | last6 = Reis | first6 = LO. | last7 = Westphalen | first7 = AC. | last8 = Muglia | first8 = VF. | title = Is a visible (hypoechoic) lesion at biopsy an independent predictor of prostate cancer outcome? | journal = Ultrasound Med Biol | volume = 38 | issue = 10 | pages = 1689-94 | month = Oct | year = 2012 | doi = 10.1016/j.ultrasmedbio.2012.06.006 | PMID = 22920545 }}</ref> however, this is not supported by an older study.<ref name=pmid1688955>{{Cite journal | last1 = Devonec | first1 = M. | last2 = Fendler | first2 = JP. | last3 = Monsallier | first3 = M. | last4 = Mouriquand | first4 = P. | last5 = Maquet | first5 = JH. | last6 = Mestas | first6 = JL. | last7 = Dutrieux-Berger | first7 = N. | last8 = Perrin | first8 = P. | title = The significance of the prostatic hypoechoic area: results in 226 ultrasonically guided prostatic biopsies. | journal = J Urol | volume = 143 | issue = 2 | pages = 316-9 | month = Feb | year = 1990 | doi = | PMID = 1688955 }}</ref>

===Prostatectomy grossing===
{{Main|Radical prostatectomy}}

===Cytoprostatectomy grossing===
*Limited sampling of the prostate may lead to undersampling error.<ref name=pmid11182038>{{Cite journal | last1 = Cindolo | first1 = L. | last2 = Benincasa | first2 = G. | last3 = Autorino | first3 = R. | last4 = Domizio | first4 = S. | last5 = De Rosa | first5 = G. | last6 = Testa | first6 = G. | last7 = D'Armiento | first7 = M. | last8 = Altieri | first8 = V. | title = Prevalence of silent prostatic adenocarcinoma in 165 patients undergone cystoprostatectomy: a retrospective study. | journal = Oncol Rep | volume = 8 | issue = 2 | pages = 269-71 | month = | year = | doi = | PMID = 11182038 }}</ref>

==Microscopic==
===Criteria as a list===
Major criteria (the ABCs of prostate pathology):<ref name=pmid17213347>{{cite journal |author=Humphrey PA |title=Diagnosis of adenocarcinoma in prostate needle biopsy tissue |journal=J. Clin. Pathol. |volume=60 |issue=1 |pages=35–42 |year=2007 |month=January |pmid=17213347 |pmc=1860598 |doi=10.1136/jcp.2005.036442 |url=http://www.ncbi.nlm.nih.gov/pmc/articles/PMC1860598/?tool=pubmed}}</ref>
#Architecture.
#*Increased gland density.
#*Small circular glands.
#**In rare subtypes - large branching glands.
#*"Infiltrative growth" pattern - malignant glands between benign ones.
#**Image: [http://www.nature.com/modpathol/journal/v17/n3/fig_tab/3800050f1.html#figure-title Infiltrative growth pattern (nature.com)].
#Basal cells lacking.
#Cytological abnormalities:
#*Nuclear enlargement (subtle).
#*[[Nucleoli]] (prominent).

Minor criteria:<ref name=pmid17213347/>
#Nuclear hyperchromasia.
#Wispy blue mucin.
#*Image: [http://www.nature.com/modpathol/journal/v17/n3/fig_tab/3800050f3.html#figure-title Wispy blue mucin (nature.com)] - from Epstein.<ref name=pmid14739905>{{cite journal |author=Epstein JI |title=Diagnosis and reporting of limited adenocarcinoma of the prostate on needle biopsy |journal=Mod. Pathol. |volume=17 |issue=3 |pages=307–15 |year=2004 |month=March |pmid=14739905 |doi=10.1038/modpathol.3800050 |url=http://www.nature.com/modpathol/journal/v17/n3/full/3800050a.html}}</ref>
#Pink amorphous secretions.
#*Image: [http://www.nature.com/modpathol/journal/v17/n3/fig_tab/3800050f11.html Pink amorphous secretions (nature.com)] - from Epstein.<ref name=pmid14739905>{{cite journal |author=Epstein JI |title=Diagnosis and reporting of limited adenocarcinoma of the prostate on needle biopsy |journal=Mod. Pathol. |volume=17 |issue=3 |pages=307–15 |year=2004 |month=March |pmid=14739905 |doi=10.1038/modpathol.3800050 |url=http://www.nature.com/modpathol/journal/v17/n3/full/3800050a.html}}</ref>
#Intraluminal crystalloid.
#*Image: [http://www.nature.com/modpathol/journal/v17/n3/fig_tab/3800050f4.html#figure-title Intraluminal crystalloid (nature.com)] - from Epstein.<ref name=pmid14739905/>
#Amphophilic cytoplasm.
#*Amphopilic is said to be ''bluish-red''<ref>URL: [http://pancreaticcancer2000.com/page1.htm http://pancreaticcancer2000.com/page1.htm]. Accessed on: 3 June 2010.</ref> -- though might also be described as ''blue-grey''.
#**Image: [http://www.webpathology.com/image.asp?n=4&Case=20 Amphophilic cytoplasm is prostate carcinoma].
#Adjacent [[HGPIN]].
#Mitoses - quite rare.

Extent/quantity criteria:
*There is no agreed upon minimum number of glands; however, one paper suggests that agreement among experts is low with 5 or less glands.<ref name=pmid20061936>{{Cite journal | last1 = Van der Kwast | first1 = TH. | last2 = Evans | first2 = A. | last3 = Lockwood | first3 = G. | last4 = Tkachuk | first4 = D. | last5 = Bostwick | first5 = DG. | last6 = Epstein | first6 = JI. | last7 = Humphrey | first7 = PA. | last8 = Montironi | first8 = R. | last9 = Van Leenders | first9 = GJ. | title = Variability in diagnostic opinion among pathologists for single small atypical foci in prostate biopsies. | journal = Am J Surg Pathol | volume = 34 | issue = 2 | pages = 169-77 | month = Feb | year = 2010 | doi = 10.1097/PAS.0b013e3181c7997b | PMID = 20061936 }}</ref>
**Thus, it has been suggested that six or more glands should be present to diagnose cancer.<ref name=pmid20061936/>

Pathognomonic features of prostate carcinoma:<ref>{{Cite journal | last1 = Egevad | first1 = L. | last2 = Allsbrook | first2 = WC. | last3 = Epstein | first3 = JI. | title = Current practice of diagnosis and reporting of prostate cancer on needle biopsy among genitourinary pathologists. | journal = Hum Pathol | volume = 37 | issue = 3 | pages = 292-7 | month = Mar | year = 2006 | doi = | PMID = 16613324 }}</ref>
#Perineural invasion.
#*Must be circumferential (>95% of circumference{{fact}}).
#Glomeruloid bodies.
#Collagenous micronodules.

<gallery>
Image: Intraluminal eosinophilic crystalloid of prostate gland - high mag.jpg| Intraluminal eosinophilic crystalloid - high mag. (WC)
</gallery>

===Divided into high and low power===
====Low power features====
*Architecture is the '''key''' to diagnosing low grade cancer.
**Back-to-back glands or crowding of glands -- think low grade cancer (Gleason pattern 3).
**Sharp transition between gland border and lumen.
***Loss of epithelial folding at the epithelium-gland lumen interface - "punched-out" appearance.
**Eosinophilic debris within the gland lumen (pink amorphous secretions, intraluminal crystalloid).
**Blue-tinged acellular material within the gland lumen (mucin) -- uncommon.
**"Infiltrative": small round/oval (malignant) glands (approx. 5 cells across) interspersed with larger (benign) glands that are 2-3 times larger.

====High power features====
*Nuclear changes.
**Hyperchromatic nuclei (like in HGPIN).
**Nuclear enlargement, mild (10%?).
***Difficult to appreciate (if cancer isn't side-by-side with normal prostate).
***Difficult/impossible to see at low power.
*"Large" nucleoli.
**Visible on intermediate and high power (100x / 200x magnification).
***May be difficult to see - especially if light intensity is low or the staining is of poor quality.
***One should not use 400x to look for nucleoli (it is a waste of time + you risk over-calling something benign).
**"Large" is rarely precisely quantified; 3 micrometres has been suggested as "large" based on one study.<ref name=pmid1688728>{{Cite journal | last1 = Kelemen | first1 = PR. | last2 = Buschmann | first2 = RJ. | last3 = Weisz-Carrington | first3 = P. | title = Nucleolar prominence as a diagnostic variable in prostatic carcinoma. | journal = Cancer | volume = 65 | issue = 4 | pages = 1017-20 | month = Feb | year = 1990 | doi = | PMID = 1688728 }}</ref>
***Three micrometres is a little more than 1/3 of [[RBC]] diameter.
*Loss of basal cells - diagnostic feature.
**Like in [[breast pathology]] (where one looks for loss of myoepithelial cells) - this may be difficult to see.

Notes:
*Mitoses are not a common feature.
**If you find them the lesion is probably high-grade.
**Generally, it isn't worth looking for them.

===Mimics===
Mimics of prostate adenocarcinoma:<ref>{{Ref TPoSP|100-3}}</ref>
{| class="wikitable sortable"
! Entity
! Key feature
! Detailed microscopic
! Other
! Image
|-
| Adenosis ([[AKA]] ''atypical adenomatous hyperplasia'')
| gradual transition between normal & small gland (NOT two populations)
| many small glands, lack nuclear size variation, basal layer present
| nucleoli may be present; may need to do p63 or 34betaE12 to find basal layer
| [http://webpathology.com/image.asp?case=21&n=3 AAH (webpathology.com)]
|-
| Sclerosing adenosis
| gradual transition between normal & small gland (NOT two populations), fibrosis
| many small glands, lack nuclear size variation, basal layer present
| analogous to [[sclerosing adenosis of the breast]]{{fact}}
| [http://webpathology.com/image.asp?case=21&n=8 Sclerosing adenosis (webpathology.com)]
|-
| [[atrophy of the prostate|Atrophy]]
| sharp angulation of gland
| nuclear hyperchromasia, scant cytoplasm
| may appear right beside non-atrophic tissue
| [[Image:Atrophic_prostatic_glands_--_high_mag.jpg|thumb|150px|center| Prostatic atrophy. (WC)]]
|-
| [[Basal cell hyperplasia of the prostate|Basal cell hyperplasia]]
| two distinct cell populations (in epithelial component)
| abundant epithelial cells; nucleoli in pale ('blue') nuclei of basal cells, glandular cell nuclei darker ('purple')
| vaguely similar to epithelial hyperplasia of usual type (EHUT) in breast
| [[Image:Basal_cell_hyperplasia_of_the_prostate_--_high_mag.jpg|thumb|150px|center| Prostatic BCH. (WC)]]
|-
| [[Bulbourethral gland]]
| no nuclear atypia
| clear cytoplasm
| apex of prostate
| [[Image:Bulbourethral gland -- very high mag.jpg |thumb|150px|center| Bulbourethral gland. (WC)]]
|-
| [[Seminal vesicles]] / ejaculatory ducts
| lipofuscin (yellow granular material in cytoplasm), smudge cells (smeared appearance + hyperchromatic)
| fern-like arrangement of epithelium (low power), nucleoli, surrounded by muscle, +/- nuclear inclusions
| involvement by cancer changes staging, lipofuscin may be present in prostate, often has marked nuc. size var.; location: usu. base of prostate
| [[Image:Seminal_vesicle_high_mag.jpg |thumb|150px|center|Seminal vesicles. (WC)]]
|-
| [[Radiation effect]]
| marked nuclear size variation
| increased stroma (fibrosis), lack nucleoli ???
| history of Rx; uniform nuc. size with Hx of Rx should raise susp. of cancer
| [http://webpathology.com/image.asp?case=97&n=6 Radiation changes (webpathology.com)], [http://webpathology.com/image.asp?case=97&n=7 Radiation changes (webpathology.com)]
|-
| Prostatitis
| inflammatory cells (lymphocytes, plasma cells, PMNs)
| no nuclear atypia, normal gland arch.
| clinical mimic of cancer (elevated PSA); usu. not a problem for the pathologist
| [[Image:Inflammation_of_prostate.jpg|thumb|150px|center| Prostatic inflammation. (WC)]]
|-
| [[Vasitis nodosa]]
| sperm within ducts, clinical history (usu. post-[[vasectomy]])
| small tubules, nucleoli common, mild atypia, may "invade" vessels, track along nerves
| mimics metastatic prostate carcinoma, IHC stains: PSA-, PSAP-
| [[Image:Vasitis nodosa -11- intermed mag.jpg|thumb|150px|center| VN. (WC)]]
|}
Memory device: '''AAABBRS''' = atrophy, adenosis, adenosis (sclerosing), basal cell hyperplasia, bulbourethral gland, radiation, seminal vesicles.

===Gleason grading system===
====Overview====
*This system is only one any one talks about and there is consensus on how it is done.<ref name=pmid16096414>{{Cite journal | last1 = Epstein | first1 = JI. | last2 = Allsbrook | first2 = WC. | last3 = Amin | first3 = MB. | last4 = Egevad | first4 = LL. | title = The 2005 International Society of Urological Pathology (ISUP) Consensus Conference on Gleason Grading of Prostatic Carcinoma. | journal = Am J Surg Pathol | volume = 29 | issue = 9 | pages = 1228-42 | month = Sep | year = 2005 | doi = | PMID = 16096414 }}</ref>
*Score range: 6-10.
**Technically 2-10... but almost no one uses 2-5.
*Reported on biopsy (and [[TURP]]) as: (primary pattern) + (secondary pattern ''or'' tertiary pattern with the highest grade) = sum.
**e.g. ''Gleason score 3+4=7'' means: pattern 3 is present and dominant, pattern 4 is the remainder of the tumour - but present in a lesser amount than pattern 3.
*Reported as on prostatectomies as: (primary pattern) + (secondary pattern) = sum, (tertiary pattern)

*Tertiary Gleason pattern - definition: a pattern that is seen in than 5% of the tumour (volume), that is higher grade than the two dominant patterns.<ref name=Ref_GUP72>{{Ref GUP|72}}</ref>
**The presence of a tertiary patterns adversely affect the prognosis; however, the prognosis is not as bad as when the tertiary pattern is the secondary pattern, i.e. 3+4 tertiary 5 has a better prognosis than 3+5 (with some small amount of pattern 4).<ref name=Ref_GUP72>{{Ref GUP|72}}</ref>

Testing yourself:
*There is a nice test-yourself quiz from Johns Hopkins: [http://162.129.103.34/prostate/ http://162.129.103.34/prostate/].
**It was studied in a paper by Kronz et al.<ref name=pmid11014569>{{Cite journal | last1 = Kronz | first1 = JD. | last2 = Silberman | first2 = MA. | last3 = Allsbrook | first3 = WC. | last4 = Bastacky | first4 = SI. | last5 = Burks | first5 = RT. | last6 = Cina | first6 = SJ. | last7 = Mills | first7 = SE. | last8 = Ross | first8 = JS. | last9 = Sakr | first9 = WA. | last10 = Tomaszewski | first10 = JE. | last11 = True | first11 = LD. | last12 = Ulbright | first12 = TM. | last13 = Weinstein | first13 = MW. | last14 = Yantiss | first14 = RK. | last15 = Young | first15 = RH. | last16 = Epstein | first16 = JI. | title = Pathology residents' use of a Web-based tutorial to improve Gleason grading of prostate carcinoma on needle biopsies. | journal = Hum Pathol | volume = 31 | issue = 9 | pages = 1044-50 | month = Sep | year = 2000 | doi = 10.1053/hupa.2000.16278 | PMID = 11014569 }}</ref>

====Examples====
*A biopsy with 80% pattern 4, 16% pattern 3 and 4% pattern 5... would be reported as: 4+5=9.
*A biopsy with 92% pattern 4, and 8% pattern 3... would be reported as: 4+3=7.
*A biopsy with 98% pattern 4, and 2% pattern 3... would be reported as: 4+4=8.
*A prostatectomy with 80% pattern 4, 16% pattern 3 and 4% pattern 5... would be reported as: 4+3=7 with tertiary pattern 5.

====Gleason pattern 1 & 2====
*Use strongly discouraged by a number of GU pathology experts.

Notes:
*Gleason pattern 1 - probably represents what today would be called ''adenosis''.
**Should never be used.
*Gleason pattern 2 - used by few GU pathology experts occasionally.
**Generally, should '''not''' be diagnosed on core biopsies.<ref name=pmid20006878>{{Cite journal | last1 = Epstein | first1 = JI. | title = An update of the Gleason grading system. | journal = J Urol | volume = 183 | issue = 2 | pages = 433-40 | month = Feb | year = 2010 | doi = 10.1016/j.juro.2009.10.046 | PMID = 20006878 }}</ref>

====Gleason pattern 3====
*Glands smaller than normal prostate glands + loss of epithelial folding.
*Can draw a line around each gland.
*May have ''gland branching''.
**Glands have a X, U, V or Y shape.

Notes:
*Gland lumina should be seen.
*All ''cribriform'' is now, generally, classified as Gleason pattern 4.<ref name=pmid20006878>{{cite journal |author=Epstein JI |title=An update of the Gleason grading system |journal=J. Urol. |volume=183 |issue=2 |pages=433–40 |year=2010 |month=February |pmid=20006878 |doi=10.1016/j.juro.2009.10.046 |url=}}</ref>

====Gleason pattern 4====
*Loss of gland lumina.
*Gland fusion.
*Benign looking cords ('hypernephroid pattern').
*Cribriform.
*Glomeruloid pattern - resembles a glomerulus.

Notes:
*One gland is not enough to call Gleason 4.

=====Images=====
<gallery>
Image:Prostate_cancer_with_Gleason_pattern_4_low_mag.jpg | Gleason pattern 4 - cribriform. (WC)
Image:Gleason_4_and_5_intermed_mag.jpg | Gleason pattern 4 - small glands & Gleason pattern 5 - single cells. (WC)
</gallery>
www:
*[http://www.nature.com/modpathol/journal/v17/n3/fig_tab/3800050f9.html#figure-title Glomeruloid pattern (nature.com)].

====Gleason pattern 5====
*Sheets.
**Must be differentiated from [[intraductal carcinoma of the prostate|intraductal growth]] (which like in the breast are well circumscribed nests).
*Single cells.
**May be confused with stromal/lymphocytic infiltration.
***Look for nucleoli, cells should be round (prostatic stroma cells are spindle cells).
*Cords (strands).
**Line of cells.
**Should not be intermixed with clumps of cells (pattern 4).
*Nests of cells with [[necrosis]] (at the centre) (comedonecrosis) ''or'' (intraluminal) necrosis in a cribriform pattern.<ref name=pmid16096414/>
**Necrosis:
***Nuclear changes:
****Karyorrhexis (nuclear fragmentation).
****Pynosis (nuclear shrinkage).
****Karyolysis (nuclear dissolution).
***Cell ghosts (cells without a nucleus).

Notes:
*Pattern 5 may be under-diagnosed.
*Single cells is the most commonly missed pattern.<ref name=pmid21997691>{{Cite journal | last1 = Fajardo | first1 = DA. | last2 = Miyamoto | first2 = H. | last3 = Miller | first3 = JS. | last4 = Lee | first4 = TK. | last5 = Epstein | first5 = JI. | title = Identification of Gleason pattern 5 on prostatic needle core biopsy: frequency of underdiagnosis and relation to morphology. | journal = Am J Surg Pathol | volume = 35 | issue = 11 | pages = 1706-11 | month = Nov | year = 2011 | doi = 10.1097/PAS.0b013e318228571d | PMID = 21997691 }}
</ref>

=====Images=====
<gallery>
Image:Gleason_4_and_5_intermed_mag.jpg | Gleason pattern 4 - small glands (left) & Gleason pattern 5 - single cells (right). (WC)
</gallery>
www:
*[http://www.webpathology.com/image.asp?n=17&Case=20 Gleason pattern 5 - sheeting (webpathology.com)].

====Special types====
Special types of prostate cancer have suggested Gleason patterns:<ref name=pmid14976541>{{cite journal |author=Grignon DJ |title=Unusual subtypes of prostate cancer |journal=Mod. Pathol. |volume=17 |issue=3 |pages=316–27 |year=2004 |month=March |pmid=14976541 |doi=10.1038/modpathol.3800052 |url=}}</ref>
{| class="wikitable sortable" style="margin-left:auto;margin-right:auto"
! Special type
! Gleason pattern
! Comment
|-
|Ductal carcinoma
| 4
| may be graded 3 or 5<ref name=bostwicklabs>URL: [https://www.bostwicklaboratories.com/global/physicians/medical-library/articles/gleason-grading.aspx https://www.bostwicklaboratories.com/global/physicians/medical-library/articles/gleason-grading.aspx]. Accessed on: 26 November 2011.</ref>
|-
|Mucinous carcinoma
| 4, dependent on morphology<ref name=pmid18487999>{{Cite journal | last1 = Osunkoya | first1 = AO. | last2 = Adsay | first2 = NV. | last3 = Cohen | first3 = C. | last4 = Epstein | first4 = JI. | last5 = Smith | first5 = SL. | title = MUC2 expression in primary mucinous and nonmucinous adenocarcinoma of the prostate: an analysis of 50 cases on radical prostatectomy. | journal = Mod Pathol | volume = 21 | issue = 7 | pages = 789-94 | month = Jul | year = 2008 | doi = 10.1038/modpathol.2008.47 | PMID = 18487999 }}</ref><ref name=pmid18300802>{{Cite journal | last1 = Osunkoya | first1 = AO. | last2 = Nielsen | first2 = ME. | last3 = Epstein | first3 = JI. | title = Prognosis of mucinous adenocarcinoma of the prostate treated by radical prostatectomy: a study of 47 cases. | journal = Am J Surg Pathol | volume = 32 | issue = 3 | pages = 468-72 | month = Mar | year = 2008 | doi = 10.1097/PAS.0b013e3181589f72 | PMID = 18300802 }}</ref>
| may be graded 4<ref name=pmid14976541/>
|-
|Sarcomatoid carcinoma
| 5
| glands graded separately
|-
|Signet ring cell carcinoma
| 5
|
|-
|Small cell carcinoma
| not graded
| may be graded 5<ref name=bostwicklabs/>
|-
|[[Adenosquamous carcinoma|Adenosquamous]] and [[squamous carcinoma]]
| not graded
|
|-
|[[Lymphoepithelioma-like carcinoma]]
| not graded
|
|-
|[[Adenoid cystic carcinoma]]
| not graded
|
|-
|[[Urothelial carcinoma]]
| not graded
|
|-
|Undifferentiated carcinoma, NOS
| not graded
|
|}

How to remember the ones that aren't graded - think of '''Ur''' '''L'''ung carcinomas ('''Ur'''othelial carcinoma, '''L'''ymphoepithelioma-like carcinoma):
*Small cell carcinoma.
*Squamous cell carcinoma.
*Adenosquamous carcinoma.
*Adenoid cystic carcinoma.

====Biopsy-prostatectomy concordance of Gleason score====
*Discordance is common.
**Upgrade on prostatectomy: 25-40%.
**Downgrade on prostatectomy: 5-15%.

Selected studies on concordance:
{| class="wikitable sortable" style="margin-left:auto;margin-right:auto"
! Study
! Upgrade
! Downgrade
! Notes
|-
| Sfoungaristos et al.<ref name=pmid22277633>{{Cite journal | last1 = Sfoungaristos | first1 = S. | last2 = Perimenis | first2 = P. | title = Clinical and pathological variables that predict changes in tumour grade after radical prostatectomy in patients with prostate cancer. | journal = Can Urol Assoc J | volume = | issue = | pages = 1-5 | month = Jan | year = 2012 | doi = 10.5489/cuaj.11067 | PMID = 22277633 }}</ref>
| 42.1%
| 13.7%
| high volume of tumour predicts upgrade
|-
| Thomas et al.<ref name=pmid21592293>{{Cite journal | last1 = Thomas | first1 = C. | last2 = Pfirrmann | first2 = K. | last3 = Pieles | first3 = F. | last4 = Bogumil | first4 = A. | last5 = Gillitzer | first5 = R. | last6 = Wiesner | first6 = C. | last7 = Thüroff | first7 = JW. | last8 = Melchior | first8 = SW. | title = Predictors for clinically relevant Gleason score upgrade in patients undergoing radical prostatectomy. | journal = BJU Int | volume = 109 | issue = 2 | pages = 214-9 | month = Jan | year = 2012 | doi = 10.1111/j.1464-410X.2011.10187.x | PMID = 21592293 }}</ref>
| 38.1%
| 4.7%
|
|-
| Truesdale et al.<ref name=pmid20840549>{{Cite journal | last1 = Truesdale | first1 = MD. | last2 = Cheetham | first2 = PJ. | last3 = Turk | first3 = AT. | last4 = Sartori | first4 = S. | last5 = Hruby | first5 = GW. | last6 = Dinneen | first6 = EP. | last7 = Benson | first7 = MC. | last8 = Badani | first8 = KK. | title = Gleason score concordance on biopsy-confirmed prostate cancer: is pathological re-evaluation necessary prior to radical prostatectomy? | journal = BJU Int | volume = 107 | issue = 5 | pages = 749-54 | month = Mar | year = 2011 | doi = 10.1111/j.1464-410X.2010.09570.x | PMID = 20840549 }}</ref>
| 23%
| 11%
|
|}

=====Sign out=====
=====Upgrading=====
<pre>
Gleason score upgrading on prostatectomy is considered relatively common; it is reported
to occur in 23% to 42.1% of cases.[1][2]

1. BJU Int. 2011 107 (5): 749-54.
2. Can Urol Assoc J. 2012 Jan 24:1-5.
</pre>

=====Downgrading=====
<pre>
Gleason score downgrading on prostatectomy is considered uncommon; however, it is reported
in 4.7% to 13.7% of cases.[1][2]

1. BJU Int. 2012 Jan; 109(2):214-9.
2. Can Urol Assoc J. 2012 Jan; 24;1-5.
</pre>

=====Order of Gleason score components changed=====
<pre>
COMMENT:
The change in the order of the Gleason score components (3+4 on prostatectomy
versus 4+3 on core biopsy) may be explained by sampling.
</pre>

===Staging parameters, margins and more===
====Surgical margins====
{{Main|Surgical margins}}
*Positive is ''tumour touching ink''.† <ref name=pmid22578729>{{Cite journal | last1 = Lu | first1 = J. | last2 = Wirth | first2 = GJ. | last3 = Wu | first3 = S. | last4 = Chen | first4 = J. | last5 = Dahl | first5 = DM. | last6 = Olumi | first6 = AF. | last7 = Young | first7 = RH. | last8 = McDougal | first8 = WS. | last9 = Wu | first9 = CL. | title = A close surgical margin after radical prostatectomy is an independent predictor of recurrence. | journal = J Urol | volume = 188 | issue = 1 | pages = 91-7 | month = Jul | year = 2012 | doi = 10.1016/j.juro.2012.02.2565 | PMID = 22578729 }}</ref>
**"Close" margins (<0.1 mm) have an increased recurrence risk.<ref name=pmid22578729/>

Notes:
*Surgical margin - where the surgeon cut.
**It is possible to have EPE without a positive margin.
**It is possible to have a positive margin without EPE.
* † Epstein says not touching may be enough, as tumour close to the margin is damaged from the surgery.<ref>URL: [http://urology.jhu.edu/newsletter/prostate_cancer410.php http://urology.jhu.edu/newsletter/prostate_cancer410.php]. Accessed on: 26 March 2013.</ref>

=====Rates and implication=====
Positivity rate varies substantially (13-44%):
*Norway: 26% -- strong dependence on surgeon volume (18% high case load vs. 44% low case load).<ref name=pmid22860630>{{Cite journal | last1 = Steinsvik | first1 = EA. | last2 = Axcrona | first2 = K. | last3 = Angelsen | first3 = A. | last4 = Beisland | first4 = C. | last5 = Dahl | first5 = A. | last6 = Eri | first6 = LM. | last7 = Haug | first7 = ES. | last8 = Svindland | first8 = A. | last9 = Fosså | first9 = S. | title = Does a surgeon's annual radical prostatectomy volume predict the risk of positive surgical margins and urinary incontinence at one-year follow-up? - Findings from a prospective national study. | journal = Scand J Urol Nephrol | volume = | issue = | pages = | month = Aug | year = 2012 | doi = 10.3109/00365599.2012.707684 | PMID = 22860630 }}</ref>
*France: 13-17% -- PSA and prostate size predictors of positivity.<ref name=pmid22860572>{{Cite journal | last1 = Koutlidis | first1 = N. | last2 = Mourey | first2 = E. | last3 = Champigneulle | first3 = J. | last4 = Mangin | first4 = P. | last5 = Cormier | first5 = L. | title = Robot-assisted or pure laparoscopic nerve-sparing radical prostatectomy: What is the optimal procedure for the surgical margins? A single center experience. | journal = Int J Urol | volume = | issue = | pages = | month = Jul | year = 2012 | doi = 10.1111/j.1442-2042.2012.03102.x | PMID = 22860572 }}</ref>

Note:
*Stage and grade (Gleason score) seem to have less impact than surgeons volume on margin positivity rate.<ref name=pmid22860630/>

The impact of positive margins:
*Significant modest negative affect on long-term outcome in node negative cancers (pT2-4 pN0).<ref name=pmid22901983>{{Cite journal | last1 = Mauermann | first1 = J. | last2 = Fradet | first2 = V. | last3 = Lacombe | first3 = L. | last4 = Dujardin | first4 = T. | last5 = Tiguert | first5 = R. | last6 = Tetu | first6 = B. | last7 = Fradet | first7 = Y. | title = The Impact of Solitary and Multiple Positive Surgical Margins on Hard Clinical End Points in 1712 Adjuvant Treatment-Naive pT2-4 N0 Radical Prostatectomy Patients. | journal = Eur Urol | volume = | issue = | pages = | month = Aug | year = 2012 | doi = 10.1016/j.eururo.2012.08.002 | PMID = 22901983 }}</ref>
*Weaker impact than stage and Gleason score.<ref>{{Cite journal | last1 = Chalfin | first1 = HJ. | last2 = Dinizo | first2 = M. | last3 = Trock | first3 = BJ. | last4 = Feng | first4 = Z. | last5 = Partin | first5 = AW. | last6 = Walsh | first6 = PC. | last7 = Humphreys | first7 = E. | last8 = Han | first8 = M. | title = Impact of surgical margin status on prostate-cancer-specific mortality. | journal = BJU Int | volume = | issue = | pages = | month = Jul | year = 2012 | doi = 10.1111/j.1464-410X.2012.11371.x | PMID = 22788795 }}</ref>
*Bladder neck margin positivity may change the T-stage - see below.

=====Bladder neck margin=====
:[[AKA]] ''invasion of the bladder neck''.<ref name=pmid19914651/>
*Bladder neck margin positivity typically is '''pT3a'''.<ref name=pmid23225909>{{Cite journal | last1 = Chung | first1 = MS. | last2 = Lee | first2 = SH. | last3 = Lee | first3 = DH. | last4 = Chung | first4 = BH. | title = Evaluation of the 7th American Joint Committee on cancer TNM staging system for prostate cancer in point of classification of bladder neck invasion. | journal = Jpn J Clin Oncol | volume = 43 | issue = 2 | pages = 184-8 | month = Feb | year = 2013 | doi = 10.1093/jjco/hys196 | PMID = 23225909 }</ref>
*Seen in approximately 1% of prostatectomies.<ref name=pmid19914651>{{Cite journal | last1 = Pierorazio | first1 = PM. | last2 = Epstein | first2 = JI. | last3 = Humphreys | first3 = E. | last4 = Han | first4 = M. | last5 = Walsh | first5 = PC. | last6 = Partin | first6 = AW. | title = The significance of a positive bladder neck margin after radical prostatectomy: the American Joint Committee on Cancer Pathological Stage T4 designation is not warranted. | journal = J Urol | volume = 183 | issue = 1 | pages = 151-7 | month = Jan | year = 2010 | doi = 10.1016/j.juro.2009.08.138 | PMID = 19914651 }}</ref>

====Extraprostatic extension====
:Abbreviated ''EPE''.

=====General=====
*Extraprostatic extension (EPE) is difficult to assess in prostatectomy specimens.<ref name=pmid20802467>{{Cite journal | last1 = Magi-Galluzzi | first1 = C. | last2 = Evans | first2 = AJ. | last3 = Delahunt | first3 = B. | last4 = Epstein | first4 = JI. | last5 = Griffiths | first5 = DF. | last6 = van der Kwast | first6 = TH. | last7 = Montironi | first7 = R. | last8 = Wheeler | first8 = TM. | last9 = Srigley | first9 = JR. | title = International Society of Urological Pathology (ISUP) Consensus Conference on Handling and Staging of Radical Prostatectomy Specimens. Working group 3: extraprostatic extension, lymphovascular invasion and locally advanced disease. | journal = Mod Pathol | volume = 24 | issue = 1 | pages = 26-38 | month = Jan | year = 2011 | doi = 10.1038/modpathol.2010.158 | PMID = 20802467 }}</ref>
**The prostate does NOT have a well defined capsule.
***Intraobserver agreement for EPE is fair-moderate and lower than for the surgical margin.<ref name=pmid18708939>{{Cite journal | last1 = Evans | first1 = AJ. | last2 = Henry | first2 = PC. | last3 = Van der Kwast | first3 = TH. | last4 = Tkachuk | first4 = DC. | last5 = Watson | first5 = K. | last6 = Lockwood | first6 = GA. | last7 = Fleshner | first7 = NE. | last8 = Cheung | first8 = C. | last9 = Belanger | first9 = EC. | last10 = Amin | first10 = MB. | last11 = Boccon-Gibod | first11 = L. | last12 = Bostwick | first12 = DG. | last13 = Egevad | first13 = L. | last14 = Epstein | first14 = JI. | last15 = Grignon | first15 = DJ. | last16 = Jones | first16 = EC. | last17 = Montironi | first17 = R. | last18 = Moussa | first18 = M. | last19 = Sweet | first19 = JM. | last20 = Trpkov | first20 = K. | last21 = Wheeler | first21 = TM. | last22 = Srigley | first22 = JR. | title = Interobserver variability between expert urologic pathologists for extraprostatic extension and surgical margin status in radical prostatectomy specimens. | journal = Am J Surg Pathol | volume = 32 | issue = 10 | pages = 1503-12 | month = Oct | year = 2008 | doi = 10.1097/PAS.0b013e31817fb3a0 | PMID = 18708939 }}</ref>
*EPE, typically, upstages tumours from T2x to T3a.

=====Prostatectomy specimens=====
EPE is present in a prostatectomy if there is either:
#A "significant bulge" in the contour of the prostate at low power ''and'' no fibromuscular tissue surrounding the malignant cells.
#Malignant cells directly adjacent to peri-prostatic adipose tissue.

Note:
*The apex of the prostate gland may have some skeletal muscle. Thus, it is difficult to define extension at this site. EPE is not called at the apex by some pathologists; however, it is generally believed to exist.<ref name=pmid20802467/>

=====Prostate biopsy=====
EPE is present in prostate biopsy if:
*Tumour touches adipose tissue.<ref name=pmid17707261>{{Cite journal | last1 = Epstein | first1 = JI. | last2 = Srigley | first2 = J. | last3 = Grignon | first3 = D. | last4 = Humphrey | first4 = P. | title = Recommendations for the reporting of prostate carcinoma. | journal = Hum Pathol | volume = 38 | issue = 9 | pages = 1305-9 | month = Sep | year = 2007 | doi = 10.1016/j.humpath.2007.05.015 | PMID = 17707261 }}</ref>

======Images======
<gallery>
Image: Prostate carcinoma with extraprostatic extension -- intermed mag.jpg | EPE - intermed. mag.
Image: Prostate carcinoma with extraprostatic extension -- high mag.jpg | EPE - high mag.
</gallery>

====Seminal vesicle invasion====
:Abbreviated ''SVI''.
General:
*Typically upstages to pT3b.
*Associations:<ref name=pmid23194127>{{Cite journal | last1 = Sapre | first1 = N. | last2 = Pedersen | first2 = J. | last3 = Hong | first3 = MK. | last4 = Harewood | first4 = L. | last5 = Peters | first5 = J. | last6 = Costello | first6 = AJ. | last7 = Hovens | first7 = CM. | last8 = Corcoran | first8 = NM. | title = Re-evaluating the biological significance of seminal vesicle invasion (SVI) in locally advanced prostate cancer. | journal = BJU Int | volume = 110 Suppl 4 | issue = | pages = 58-63 | month = Dec | year = 2012 | doi = 10.1111/j.1464-410X.2012.11477.x | PMID = 23194127 }}</ref>
**Most SVI is by direct extension ~90%.
**Approximately 20% of patients with pT3x have SVI.
**Usually associated with a large tumour volume (22% versus 12%).

Microscopic:
*Tumour '''must''' be in the muscle surrounding the epithelial component; tumour in the adventitia (the loose connective tissue surrounding the seminal vesicles) does not count.<ref name=Ref_Lester3_409>{{Ref Lester3|409}}</ref><ref name=pmid20818343>{{Cite journal | last1 = Berney | first1 = DM. | last2 = Wheeler | first2 = TM. | last3 = Grignon | first3 = DJ. | last4 = Epstein | first4 = JI. | last5 = Griffiths | first5 = DF. | last6 = Humphrey | first6 = PA. | last7 = van der Kwast | first7 = T. | last8 = Montironi | first8 = R. | last9 = Delahunt | first9 = B. | title = International Society of Urological Pathology (ISUP) Consensus Conference on Handling and Staging of Radical Prostatectomy Specimens. Working group 4: seminal vesicles and lymph nodes. | journal = Mod Pathol | volume = 24 | issue = 1 | pages = 39-47 | month = Jan | year = 2011 | doi = 10.1038/modpathol.2010.160 | PMID = 20818343 }}</ref>

Notes:
*Invasion of the adventitia (only) would quality as EPE; this is, usually, T3a.
*Immunostains useful to separate prostate carcinoma from [[SV]] are discussed in the ''[[seminal vesicle]]'' article.
*It is not possible to differentiate the ''seminal vesicles'' and ''ejaculatory ducts'' based only on histology; thus, on biopsy one can generally comment only on ''seminal vesicle/ejaculatory duct invasion''.

====Lymph node metastases====
{{Main|Lymph node metastasis}}
*Essentially never happens in Gleason score 6 cancers.
**A study of over 14,000 Gleason score <=6 cases found 22 cases with lymph node metastases -- all of the 19 cases available for review were determined to have a higher Gleason score and some Gleason pattern 4 or 5.<ref name=pmid22531173>{{Cite journal | last1 = Ross | first1 = HM. | last2 = Kryvenko | first2 = ON. | last3 = Cowan | first3 = JE. | last4 = Simko | first4 = JP. | last5 = Wheeler | first5 = TM. | last6 = Epstein | first6 = JI. | title = Do adenocarcinomas of the prostate with Gleason score (GS) ≤6 have the potential to metastasize to lymph nodes? | journal = Am J Surg Pathol | volume = 36 | issue = 9 | pages = 1346-52 | month = Sep | year = 2012 | doi = 10.1097/PAS.0b013e3182556dcd | PMID = 22531173 }}</ref>

====Perineural invasion====
{{Main|Perineural invasion}}
*''Not'' a staging parameter.
*Seen in approximately 20% of core biopsies.<ref name=pmid16096404>{{Cite journal | last1 = Ali | first1 = TZ. | last2 = Epstein | first2 = JI. | title = Perineural involvement by benign prostatic glands on needle biopsy. | journal = Am J Surg Pathol | volume = 29 | issue = 9 | pages = 1159-63 | month = Sep | year = 2005 | doi = | PMID = 16096404 }}</ref>
*Complete wrapping of a nerve by epithelium is considered pathognomonic for cancer.<ref name=pmid10435561>{{Cite journal | last1 = Baisden | first1 = BL. | last2 = Kahane | first2 = H. | last3 = Epstein | first3 = JI. | title = Perineural invasion, mucinous fibroplasia, and glomerulations: diagnostic features of limited cancer on prostate needle biopsy. | journal = Am J Surg Pathol | volume = 23 | issue = 8 | pages = 918-24 | month = Aug | year = 1999 | doi = | PMID = 10435561 }}</ref><ref name=pmid16096404/>

Note:
*Occasionally, benign glands are found perineural.<ref name=pmid16096404/>
**These should ''not'' completely wrap around the nerve and should be cytologically benign.

==IHC==
===General recommendations===
ISUP consensus statement:<ref name=pmid25025364>{{cite journal |author=Amin MB, Epstein JI, Ulbright TM, ''et al.'' |title=Best practices recommendations in the application of immunohistochemistry in urologic pathology: report from the international society of urological pathology consensus conference |journal=Am. J. Surg. Pathol. |volume=38 |issue=8 |pages=1017–22 |year=2014 |month=August |pmid=25025364 |doi=10.1097/PAS.0000000000000254 |url=}}</ref>
*Should ''not'' be used if cancer is obvious.
*Should ''not'' be used if it isn't going change the clinical management.

===Prostate markers===
*PSA (prostate specific antigen) +ve.
*PSAP (prostatic specific acid phosphatase) +ve. †
*P501S +ve. ‡
*NKX3.1 +ve. ‡

Notes:
*† PSAP may be positive in hindgut [[neuroendocrine tumour]]s.<ref name=pmid>{{Cite journal | last1 = Azumi | first1 = N. | last2 = Traweek | first2 = ST. | last3 = Battifora | first3 = H. | title = Prostatic acid phosphatase in carcinoid tumors. Immunohistochemical and immunoblot studies. | journal = Am J Surg Pathol | volume = 15 | issue = 8 | pages = 785-90 | month = Aug | year = 1991 | doi = | PMID = 1712549 }}</ref>
*‡ P501S and NKX3.1 are considered second line markers.<ref name=pmid25025364/>
*Prostate carcinoma is typically CK7 -ve and CK20 -ve; however, in high [[Gleason score]] cancers focal positivity of these markers can be seen.<ref name=pmid11888088>{{Cite journal | last1 = Goldstein | first1 = NS. | title = Immunophenotypic characterization of 225 prostate adenocarcinomas with intermediate or high Gleason scores. | journal = Am J Clin Pathol | volume = 117 | issue = 3 | pages = 471-7 | month = Mar | year = 2002 | doi = 10.1309/G6PR-Y774-X738-FG2K | PMID = 11888088 }}</ref>
**CK7: >25-50% staining seen in ~5% of cases.
***>50% staining with CK7 is not report.
**CK20: >25-50% staining seen in ~10% of cases.
***>50% staining with CK20 is not reported.

===Benign prostate versus neoplastic prostate===
*AMACR +ve.
*p63 -ve.
*HMWCK (34betaE12) -ve.

Combination immunostains:
*''PIN-4'' -- consists of: CK5 + CK14 + p63 + P504S (AMACR).<ref>URL: [http://biocare.net/wp-content/uploads/225DS.pdf http://biocare.net/wp-content/uploads/225DS.pdf]. Accessed on: 18 October 2011.</ref><ref>URL: [http://www.antibodies-online.com/antibody/308235/anti-PIN-4+p63+Cytokeratin+HMW+p504S++AMACR/ http://www.antibodies-online.com/antibody/308235/anti-PIN-4+p63+Cytokeratin+HMW+p504S++AMACR/]. Accessed on: 18 October 2011.</ref><ref>URL: [http://www.webpathology.com/image.asp?case=96&n=5 http://www.webpathology.com/image.asp?case=96&n=5]. Accessed on: 18 October 2011.</ref>
**[[AKA]] ''PIN''.
**[[AKA]] ''CAP''.
***Why '''CAP'''?
****A. '''CA'''ncer of the '''P'''rostate.

Other IHC stains:
*AR +ve -- in prostate confined cancer.
**Usu. -ve in LN +ve disease.<ref name=pmid20878946>{{Cite journal | last1 = Fleischmann | first1 = A. | last2 = Rocha | first2 = C. | last3 = Schobinger | first3 = S. | last4 = Seiler | first4 = R. | last5 = Wiese | first5 = B. | last6 = Thalmann | first6 = GN. | title = Androgen receptors are differentially expressed in Gleason patterns of prostate cancer and down-regulated in matched lymph node metastases. | journal = Prostate | volume = 71 | issue = 5 | pages = 453-60 | month = Apr | year = 2011 | doi = 10.1002/pros.21259 | PMID = 20878946 }}</ref>

====Prostate carcinoma versus urothelial carcinoma====
The ISUP panel recommends:<ref name=pmid25025364>{{cite journal |author=Amin MB, Epstein JI, Ulbright TM, ''et al.'' |title=Best practices recommendations in the application of immunohistochemistry in urologic pathology: report from the international society of urological pathology consensus conference |journal=Am. J. Surg. Pathol. |volume=38 |issue=8 |pages=1017–22 |year=2014 |month=August |pmid=25025364 |doi=10.1097/PAS.0000000000000254 |url=}}</ref>
*PSA +ve (-ve in UCC).
*GATA3 -ve (+ve in UCC).

Another panel - if GATA3 isn't available:
*Prostate: PSA +ve, p63 -ve, HWMCK -ve.
*Urothelial: p63 +ve, HWMCK +ve, PSA -ve.

Notes:
*AMACR not useful; it is positive in ~50% of [[UCC]].<ref name=pmid16315020>{{Cite journal | last1 = Langner | first1 = C. | last2 = Rupar | first2 = G. | last3 = Leibl | first3 = S. | last4 = Hutterer | first4 = G. | last5 = Chromecki | first5 = T. | last6 = Hoefler | first6 = G. | last7 = Rehak | first7 = P. | last8 = Zigeuner | first8 = R. | title = Alpha-methylacyl-CoA racemase (AMACR/P504S) protein expression in urothelial carcinoma of the upper urinary tract correlates with tumour progression. | journal = Virchows Arch | volume = 448 | issue = 3 | pages = 325-30 | month = Mar | year = 2006 | doi = 10.1007/s00428-005-0129-6 | PMID = 16315020 }}</ref>
*CK7 and CK20 are typically negative in prostate carcinoma, and classically positive in urothelial carcinoma.

===Rate of utilization===
*Dependent on practise setting.
**One tertiary academic institution uses it on ~ 40% of cases.<ref>{{Cite journal | last1 = Watson | first1 = K. | last2 = Wang | first2 = C. | last3 = Yilmaz | first3 = A. | last4 = Bismar | first4 = TA. | last5 = Trpkov | first5 = K. | title = Use of immunohistochemistry in routine workup of prostate needle biopsies: a tertiary academic institution experience. | journal = Arch Pathol Lab Med | volume = 137 | issue = 4 | pages = 541-5 | month = Apr | year = 2013 | doi = 10.5858/arpa.2012-0145-OA | PMID = 23273390 }}</ref>

==Molecular changes in prostate cancer==
A fusion gene between ''TMPRSS2'' and ''ERG'' is described.<ref name=pmid20478527>{{cite journal | author = Yu J, Yu J, Mani RS, Cao Q, Brenner CJ, Cao X, Wang X, Wu L, Li J, Hu M, Gong Y, Cheng H, Laxman B, Vellaichamy A, Shankar S, Li Y, Dhanasekaran SM, Morey R, Barrette T, Lonigro RJ, Tomlins SA, Varambally S, Qin ZS, Chinnaiyan AM | title = An Integrated Network of Androgen Receptor, Polycomb, and TMPRSS2-ERG Gene Fusions in Prostate Cancer Progression | journal = Cancer Cell | volume = 17 | issue = 5 | pages = 443–54 | year = 2010 | month = May | pmid = 20478527 | pmc = 2874722 | doi = 10.1016/j.ccr.2010.03.018 | url = }}</ref><ref name=omim602060>{{OMIM|602060}}</ref>
*Both genes are on chromosome 21.
*Currently ''not'' used diagnostically.
*Fusion gene seen in approximately 50% of prostate cancer.<ref name=omim602060>{{OMIM|602060}}</ref>
*A subset of ''TMPRSS2-ERG'' known as ''2+Edel'' (seen in ~7% of all prostate cancer cases) predicts poor survival.<ref name=pmid17637754>{{Cite journal | last1 = Attard | first1 = G. | last2 = Clark | first2 = J. | last3 = Ambroisine | first3 = L. | last4 = Fisher | first4 = G. | last5 = Kovacs | first5 = G. | last6 = Flohr | first6 = P. | last7 = Berney | first7 = D. | last8 = Foster | first8 = CS. | last9 = Fletcher | first9 = A. | title = Duplication of the fusion of TMPRSS2 to ERG sequences identifies fatal human prostate cancer. | journal = Oncogene | volume = 27 | issue = 3 | pages = 253-63 | month = Jan | year = 2008 | doi = 10.1038/sj.onc.1210640 | PMID = 17637754 }}</ref>

==Sign out==
===Prostatectomy specimens===
*A prostatectomy that appears to be negative should be worked-up. This is discuss in the ''[[negative prostatectomy]]'' article.
*[http://www.cap.org/apps/cap.portal?_nfpb=true&cntvwrPtlt_actionOverride=/portlets/contentViewer/show&_windowLabel=cntvwrPtlt&cntvwrPtlt{actionForm.contentReference}=committees/cancer/cancer_protocols/protocols_index.html&_pageLabel=cntvwr CAP checklist].

<pre>
A. LYMPH NODES, RIGHT PELVIC, EXCISION:
- ONE LYMPH NODE NEGATIVE FOR MALIGNANCY ( 0 POSITIVE / 1 ).

B. LYMPH NODES, LEFT PELVIC, EXCISION:
- ONE LYMPH NODE NEGATIVE FOR MALIGNANCY ( 0 POSITIVE / 1 ).

C. PROSTATE GLAND AND SEMINAL VESICLES, RADICAL PROSTATECTOMY:
- ADENOCARCINOMA, GLEASON SCORE 7/10 (3+4), pT2c pN0.
-- SURGICAL MARGINS NEGATIVE.
-- PLEASE SEE TUMOUR SUMMARY.
</pre>

===Transurethral resection of prostate===
<pre>
PROSTATE TISSUE, TRANSURETHRAL RESECTION OF PROSTATE (TURP):
- ADENOCARCINOMA, GLEASON SCORE 7/10 (3+4);
- APPROXIMATELY 5% OF TISSUE INVOLVED;
- PLEASE SEE TUMOUR SUMMARY.

TUMOUR SUMMARY - TRANSURETHRAL RESECTION OF PROSTATE (TURP).

PROCEDURE: TRANSURETHRAL PROSTATIC RESECTION.
SPECIMEN SIZE: WEIGHT: 10 GRAMS.
HISTOLOGIC TYPE: ADENOCARCINOMA (ACINAR, NOT OTHERWISE SPECIFIED).

HISTOLOGIC GRADING:
PRIMARY PATTERN: 3.
SECONDARY PATTERN: 4 (40% OF TUMOUR).
TOTAL GLEASON SCORE: 7 (3+4).

TUMOUR QUANTITATION - PERCENTAGE OF PROSTATIC TISSUE INVOLVED BY TUMOUR: 80 %.

PERIPROSTATIC FAT INVASION: NOT IDENTIFIED.
SEMINAL VESICLE INVASION: NOT IDENTIFIED.
LYMPH-VASCULAR INVASION: NOT IDENTIFIED.
PERINEURAL INVASION: NOT IDENTIFIED.

ADDITIONAL PATHOLOGIC FINDINGS:
HIGH-GRADE PROSTATIC INTRAEPITHELIAL NEOPLASIA (HGPIN).
NODULAR PROSTATIC HYPERPLASIA.
CHRONIC INFLAMMATION.
</pre>

<pre>
PROSTATE TISSUE, TRANSURETHRAL RESECTION OF THE PROSTATE (TURP):
- ADENOCARCINOMA, GLEASON SCORE 6/10 (3+3);
- APPROXIMATELY 5% OF TISSUE INVOLVED;
- PLEASE SEE TUMOUR SUMMARY.
</pre>

===Biopsy specimens===
Important elements - a list:<ref name=pmid17213347/>
#Type of cancer, e.g. "prostatic adenocarcinoma, acinar type".
#Gleason score including primary and secondary pattern, e.g. "Gleason score 3+4=7".
#Number of cores and number involved, e.g. "2/3 cores involved by cancer".
#Percent area involved, i.e. how much of the core is cancer, e.g. "75% of specimen is tumour". ‡
#Percent area involved that is Gleason pattern 4 or 5, e.g. "25% of the tumour is Gleason pattern 4 or 5".
#Presence of [[perineural invasion]].
#Presence of extension into fat (extraprostatic extension).

Notes:
*‡ "Percent area involved" may seem like an odd thing to request 'cause it is sampling dependent, i.e. if the radiologist sticks the biopsy needle deeper into the lesion more of the core is positive, but urologists think it is important -- more important than perineural invasion.<ref name=pmid15223967>{{cite journal |author=Rubin MA, Bismar TA, Curtis S, Montie JE |title=Prostate needle biopsy reporting: how are the surgical members of the Society of Urologic Oncology using pathology reports to guide treatment of prostate cancer patients? |journal=Am. J. Surg. Pathol. |volume=28 |issue=7 |pages=946–52 |year=2004 |month=July |pmid=15223967 |doi= |url=}}</ref>
**There is disagreement on how one should measure patchy cancer (cancer when there is interspersed normal). Epstein believes one should include the interspersed benign if the cancer is patchy, as the groupings of tumour likely join out of the plane of section.<ref name=pmid21788055>{{Cite journal | last1 = Epstein | first1 = JI. | title = Prognostic significance of tumor volume in radical prostatectomy and needle biopsy specimens. | journal = J Urol | volume = 186 | issue = 3 | pages = 790-7 | month = Sep | year = 2011 | doi = 10.1016/j.juro.2011.02.2695 | PMID = 21788055 }}</ref>
**A review by Epstein on the topic of tumour volume suggests it does not have predictive value in multivariante analyses.<ref name=pmid21788055/>
**The biopsy tumour volume is a predictor of Gleason score upgrading on prostatectomy.<ref name=pmid22688447>{{Cite journal | last1 = Fu | first1 = Q. | last2 = Moul | first2 = JW. | last3 = Bañez | first3 = LL. | last4 = Sun | first4 = L. | last5 = Mouraviev | first5 = V. | last6 = Xie | first6 = D. | last7 = Polascik | first7 = TJ. | title = Association between percentage of tumor involvement and Gleason score upgrading in low-risk prostate cancer. | journal = Med Oncol | volume = 29 | issue = 5 | pages = 3339-44 | month = Dec | year = 2012 | doi = 10.1007/s12032-012-0270-4 | PMID = 22688447 }}</ref>

====Completely negative====
<pre>
A. PROSTATE, RIGHT LATERAL SUPERIOR, BIOPSY:
- BENIGN PROSTATE TISSUE.

B. PROSTATE, RIGHT MEDIAL SUPERIOR, BIOPSY:
- BENIGN PROSTATE TISSUE.

C. PROSTATE, RIGHT LATERAL MIDZONE, BIOPSY:
- BENIGN PROSTATE TISSUE.

D. PROSTATE, RIGHT MEDIAL MIDZONE, BIOPSY:
- BENIGN PROSTATE TISSUE.

E. PROSTATE, RIGHT LATERAL INTERIOR, BIOPSY:
- BENIGN PROSTATE TISSUE.

F. PROSTATE, RIGHT MEDIAL INFERIOR, BIOPSY:
- BENIGN PROSTATE TISSUE.

G. PROSTATE, LEFT LATERAL SUPERIOR, BIOPSY:
- BENIGN PROSTATE TISSUE.

H. PROSTATE, LEFT MEDIAL SUPERIOR, BIOPSY:
- BENIGN PROSTATE TISSUE.

I. PROSTATE, LEFT LATERAL MIDZONE, BIOPSY:
- BENIGN PROSTATE TISSUE.

J. PROSTATE, LEFT MEDIAL MIDZONE, BIOPSY:
- BENIGN PROSTATE TISSUE.

K. PROSTATE, LEFT LATERAL INTERIOR, BIOPSY:
- BENIGN PROSTATE TISSUE.

L. PROSTATE, LEFT MEDIAL INFERIOR, BIOPSY:
- BENIGN PROSTATE TISSUE.
</pre>

====Negative biopsy in surveillance====
<pre>
COMMENT:
The previous results are noted. The absence of cancer in this biopsy may
be due to sampling.
</pre>

====No glands====
<pre>
F. PROSTATE, RIGHT MEDIAL MIDZONE, BIOPSY:
- BENIGN FIBROMUSCULAR TISSUE;
- NO PROSTATIC GLANDULAR TISSUE PRESENT.
</pre>

====Inflammation====
<pre>
G. PROSTATE, LEFT LATERAL SUPERIOR, BIOPSY:
- BENIGN PROSTATE TISSUE;
- FOCAL CHRONIC INFLAMMATION.
</pre>

<pre>
F. PROSTATE, RIGHT MEDIAL MIDZONE, BIOPSY:
- BENIGN PROSTATE TISSUE;
- CHRONIC INFLAMMATION.
</pre>

<pre>
F. PROSTATE, RIGHT MEDIAL MIDZONE, BIOPSY:
- BENIGN PROSTATE TISSUE;
- ACUTE AND CHRONIC INFLAMMATION.
</pre>

====Positive====
<pre>
F. PROSTATE, RIGHT MEDIAL INFERIOR, BIOPSY:
- ADENOCARCINOMA, GLEASON SCORE 6/10 (3+3);
- 1/1 CORE INVOLVED; APPROXIMATELY 5% OF TISSUE INVOLVED.
</pre>

<pre>
F. PROSTATE, RIGHT MEDIAL INFERIOR, BIOPSY:
- ADENOCARCINOMA, GLEASON SCORE 6/10 (3+3);
- 1/1 CORE INVOLVED; APPROXIMATELY 25% OF TISSUE INVOLVED;
- PERINEURAL INVASION PRESENT.
</pre>

<pre>
G. PROSTATE, LEFT LATERAL SUPERIOR, BIOPSY:
- ADENOCARCINOMA, GLEASON SCORE 7/10 (4+3);
- 1/1 CORE INVOLVED; APPROXIMATELY 5% OF TISSUE INVOLVED;
- PERINEURAL INVASION PRESENT.
</pre>

<pre>
H. PROSTATE, LEFT MEDIAL SUPERIOR, BIOPSY:
- ADENOCARCINOMA, GLEASON SCORE 8/10 (4+4);
- 1/1 CORE INVOLVED; APPROXIMATELY 15% OF TISSUE INVOLVED.
</pre>

<pre>
H. PROSTATE, LEFT MEDIAL SUPERIOR, BIOPSY:
- ADENOCARCINOMA, GLEASON SCORE 8/10 (4+4);
- 1/1 CORE INVOLVED; APPROXIMATELY 15% OF TISSUE INVOLVED;
- PERINEURAL INVASION PRESENT.
</pre>

=====Tumour summaries=====
*These are not completely without controversy.
*It should be noted that treatment is driven by the highest Gleason score.{{fact}}

<pre>
TUMOUR SUMMARY - PROSTATE CORE BIOPSIES:
- HISTOLOGIC TYPE: ADENOCARCINOMA (ACINAR, NOT OTHERWISE SPECIFIED).
- TOTAL GLEASON SCORE: 7.
- PRIMARY PATTERN: 4.
- SECONDARY PATTERN: 3.
- PERCENT OF TUMOUR WITH PATTERN HIGHER THAN GRADE 3: 75%.

- NUMBER OF CORES POSITIVE: 10.
- TOTAL NUMBER OF CORES: 12.
- TOTAL LINEAR MILLIMETERS OF NEEDLE CORE TISSUE: 152 MM.
- PERCENT OF NEEDLE CORE TISSUE THAT IS TUMOUR: 44%.

- PERIPROSTATIC FAT INVASION: NOT IDENTIFIED.
- SEMINAL VESICLE INVASION: SEMINAL VESICLE NOT IDENTIFIED.
- LYMPHOVASCULAR INVASION: NOT IDENTIFIED.
- PERINEURAL INVASION: PRESENT.

- ADDITIONAL FINDINGS: HIGH-GRADE PROSTATIC INTRAEPITHELIAL NEOPLASIA, CHRONIC INFLAMMATION (FOCAL).
</pre>

<pre>
TUMOUR SUMMARY - PROSTATE CORE BIOPSIES:
- HISTOLOGIC TYPE: ADENOCARCINOMA (ACINAR, NOT OTHERWISE SPECIFIED).
- HIGHEST GLEASON SCORE: 8 (4+4).
- SUMMARY GLEASON SCORE: 7 (4+3).
- PERCENT OF TUMOUR WITH PATTERN 4: 55%.
- PERCENT OF TUMOUR WITH PATTERN 5: 0%.

- NUMBER OF CORES POSITIVE: 12.
- TOTAL NUMBER OF CORES: 12.
- TOTAL LINEAR MILLIMETERS OF NEEDLE CORE TISSUE: 178 MM.
- PERCENT OF NEEDLE CORE TISSUE THAT IS TUMOUR: 80%.

- PERINEURAL INVASION: PRESENT.
- PERIPROSTATIC FAT INVASION: PRESENT.
- LYMPHOVASCULAR INVASION: NOT IDENTIFIED.
- SEMINAL VESICLE INVASION: NOT IDENTIFIED.
</pre>

===Seminal vesicle/ejaculatory duct invasion on biopsy===
<pre>
COMMENT:
The seminal vesicles and ejaculatory ducts have the same histology; thus, it is not
usually possible to confidently differentiate them in a needle biopsy.

SV/ED invasion was demonstrated with CK7, CK34betaE12/AMACR, PSA and p63 immunostaining.
The tumour is PSA and AMACR positive.
</pre>

=Intraductal spread of prostate cancer=
==Intraductal carcinoma of the prostate==
*[[AKA]] ''[[intraductal carcinoma]]''.
*[[AKA]] ''intraductal prostate carcinoma''.
===General===
*Associated with a poor prognosis.<ref name=pmid19246509>{{Cite journal | last1 = Henry | first1 = PC. | last2 = Evans | first2 = AJ. | title = Intraductal carcinoma of the prostate: a distinct histopathological entity with important prognostic implications. | journal = J Clin Pathol | volume = 62 | issue = 7 | pages = 579-83 | month = Jul | year = 2009 | doi = 10.1136/jcp.2009.065003 | PMID = 19246509 }}</ref>
*Strong association with aggressive invasive carcinomas on prostatectomy when identified in isolation on biopsy.<ref name=pmid20723921>{{Cite journal | last1 = Robinson | first1 = BD. | last2 = Epstein | first2 = JI. | title = Intraductal carcinoma of the prostate without invasive carcinoma on needle biopsy: emphasis on radical prostatectomy findings. | journal = J Urol | volume = 184 | issue = 4 | pages = 1328-33 | month = Oct | year = 2010 | doi = 10.1016/j.juro.2010.06.017 | PMID = 20723921 }}</ref>

===Microscopic===
====Major criteria====
Required major criteria:<ref name=pmid22692290>{{Cite journal | last1 = Shah | first1 = RB. | last2 = Zhou | first2 = M. | title = Atypical cribriform lesions of the prostate: clinical significance, differential diagnosis and current concept of intraductal carcinoma of the prostate. | journal = Adv Anat Pathol | volume = 19 | issue = 4 | pages = 270-8 | month = Jul | year = 2012 | doi = 10.1097/PAP.0b013e31825c6c0e | PMID = 22692290 }}</ref><ref name=pmid17616999>{{Cite journal | last1 = Cohen | first1 = RJ. | last2 = Wheeler | first2 = TM. | last3 = Bonkhoff | first3 = H. | last4 = Rubin | first4 = MA. | title = A proposal on the identification, histologic reporting, and implications of intraductal prostatic carcinoma. | journal = Arch Pathol Lab Med | volume = 131 | issue = 7 | pages = 1103-9 | month = Jul | year = 2007 | doi = 10.1043/1543-2165(2007)131[1103:APOTIH]2.0.CO;2 | PMID = 17616999 }}</ref>
#Glands 2x normal (peripheral zone) glands.
#Basal cells present (proven by IHC).
#"Cytologically malignant cells" = nuclear hyperchromasia, nuclear enlargement, nucleoli.
#Fills the lumen ("expansile") but does not have to be "solid".
#*Solid = no spaces between the cells.

Additional (major) criterion:<ref name=pmid22692290/>
*Comedo[[necrosis]].

====Minor criteria====
Minor criteria:<ref name=pmid22692290/>
#Branching of ducts at right angles.
#Rounded/smooth gland outlines.
#Two cell populations:
#*Malignant population (enlarged nuclei with hyperchromasia and nucleoli) = peripheral location in gland.
#*Benign population (smaller nuclei, no nucleoli) = central location in gland.

DDx:
*[[High-grade prostatic intraepithelial neoplasia]] (HGPIN).
*Invasive [[prostate adenocarcinoma]].

===IHC===
Features - basal cells present:
*CK34betaE12 +ve.
*p63 +ve.

=Unusual forms of prostate cancer=
==Prostatic ductal adenocarcinoma==
*[[AKA]] ''ductal adenocarcinoma of the prostate''.
*[[AKA]] ''prostatic adenocarcinoma, large duct type''.
===General===
*Sometimes it is referred to as ''endometrioid'' or ''endometrial'' adenocarcinoma; both terms are discouraged.<ref name=pmid18773743>{{Cite journal | last1 = Samaratunga | first1 = H. | last2 = Delahunt | first2 = B. | title = Ductal adenocarcinoma of the prostate: current opinion and controversies. | journal = Anal Quant Cytol Histol | volume = 30 | issue = 4 | pages = 237-46 | month = Aug | year = 2008 | doi = | PMID = 18773743 }}</ref>
*Not completely uncontroversial - may represent ''acinar adenocarcinoma'' with periurethral ducts involvement.<ref name=pmid10403300>{{Cite journal | last1 = Bock | first1 = BJ. | last2 = Bostwick | first2 = DG. | title = Does prostatic ductal adenocarcinoma exist? | journal = Am J Surg Pathol | volume = 23 | issue = 7 | pages = 781-5 | month = Jul | year = 1999 | doi = | PMID = 10403300 }}</ref>
*More aggressive than conventional (acinar) prostate carcinoma.

===Microscopic===
Features:<ref name=Ref_GUP88>{{Ref GUP|88}}</ref>
#Pseudostratified (crowded appearing) columnar (or cigar-shaped) nuclei - '''key feature'''.
#*Vaguely resembles [[colonic adenocarcinoma]].
#Compatible architecture:
#*Papillary.
#*Cribriform.
#*Single gland (large glands).
#*Endometrioid - vaguely looks like [[endometrioid endometrial carcinoma]] (with back-to-back glands).
#>= 50% of tumour.<ref name=pmid21383610/>{{fact}}
#*If ductal component <50%, it is a conventional (acinar) adenocarcinoma with a ductal component.

Notes:
*Proportion of ductal component should be quantified:
**<10% ductal component of no prognostic significance.<ref name=pmid21383610>{{Cite journal | last1 = Amin | first1 = A. | last2 = Epstein | first2 = JI. | title = Pathologic stage of prostatic ductal adenocarcinoma at radical prostatectomy: effect of percentage of the ductal component and associated grade of acinar adenocarcinoma. | journal = Am J Surg Pathol | volume = 35 | issue = 4 | pages = 615-9 | month = Apr | year = 2011 | doi = 10.1097/PAS.0b013e31820eb25b | PMID = 21383610 }}</ref>

Images:
*[http://path.upmc.edu/cases/case203.html Prostatic ductal adenocarcinoma - several images (upmc.edu)].
*[http://path.upmc.edu/cases/case711.html Prostatic ductal adenocarcinoma - another case - several images (upmc.edu)].
*[http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3024288/figure/F1/ Prostatic ductal adenocarcinoma - F1 (nih.gov)].
*[http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3024288/figure/F2/ Prostatic ductal adenocarcinoma - F2 (nih.gov)].
*[http://www.webpathology.com/image.asp?case=23&n=6 Prostatic ductal adenocarcinoma (webpathology.com)].
*[http://www.webpathology.com/image.asp?n=7&Case=23 Prostatic ductal adenocarcinoma (webpathology.com)].

===IHC===
Features:<ref name=pmid22583364>{{Cite journal | last1 = Tarján | first1 = M. | last2 = Lenngren | first2 = A. | last3 = Hellberg | first3 = D. | last4 = Tot | first4 = T. | title = Immunohistochemical verification of ductal differentiation in prostate cancer. | journal = APMIS | volume = 120 | issue = 6 | pages = 510-8 | month = Jun | year = 2012 | doi = 10.1111/j.1600-0463.2011.02862.x | PMID = 22583364 }}</ref>
*p53 +ve in ~ 75% of cases.
*Ki-67 high in ~ 70% of cases.
*Chromogranin A +ve (cytoplasm) in ~ 70% of cases.

Others:<ref name=pmid20368883>{{Cite journal | last1 = Kumar | first1 = A. | last2 = Mukherjee | first2 = SD. | title = Metastatic ductal carcinoma of the prostate: a rare variant responding to a common treatment. | journal = Can Urol Assoc J | volume = 4 | issue = 2 | pages = E50-4 | month = Apr | year = 2010 | doi = | PMID = 20368883 }}</ref>
*PSA +ve.

==PIN-like prostatic ductal adenocarcinoma==
===General===
*Recently described.<ref name=pmid16607376>{{Cite journal | last1 = Hameed | first1 = O. | last2 = Humphrey | first2 = PA. | title = Stratified epithelium in prostatic adenocarcinoma: a mimic of high-grade prostatic intraepithelial neoplasia. | journal = Mod Pathol | volume = 19 | issue = 7 | pages = 899-906 | month = Jul | year = 2006 | doi = 10.1038/modpathol.3800601 | PMID = 16607376 }}</ref><ref name=pmid20438402>{{Cite journal | last1 = Lee | first1 = TK. | last2 = Miller | first2 = JS. | last3 = Epstein | first3 = JI. | title = Rare histological patterns of prostatic ductal adenocarcinoma. | journal = Pathology | volume = 42 | issue = 4 | pages = 319-24 | month = Jun | year = 2010 | doi = 10.3109/00313021003767314 | PMID = 20438402 }}</ref>
*May be confused with [[prostatic intraepithelial neoplasia]] (PIN).

===Microscopic===
Features:<ref name=pmid16607376>{{Cite journal | last1 = Hameed | first1 = O. | last2 = Humphrey | first2 = PA. | title = Stratified epithelium in prostatic adenocarcinoma: a mimic of high-grade prostatic intraepithelial neoplasia. | journal = Mod Pathol | volume = 19 | issue = 7 | pages = 899-906 | month = Jul | year = 2006 | doi = 10.1038/modpathol.3800601 | PMID = 16607376 }}</ref>
*Stratified malignant epithelium.

Note:
*Vaguely similar to a tubular adenoma of the colon.

DDx:
*[[HGPIN]].

Image:
*[http://www.nature.com/modpathol/journal/v19/n7/fig_tab/3800601f1.html#figure-title PIN-like adenocarcinoma (nature.com)].

==Foamy gland carcinoma==
*[[AKA]] ''foamy gland adenocarcinoma''.<ref name=pmid19033862>{{Cite journal | last1 = Zhao | first1 = J. | last2 = Epstein | first2 = JI. | title = High-grade foamy gland prostatic adenocarcinoma on biopsy or transurethral resection: a morphologic study of 55 cases. | journal = Am J Surg Pathol | volume = 33 | issue = 4 | pages = 583-90 | month = Apr | year = 2009 | doi = 10.1097/PAS.0b013e31818a5c6c | PMID = 19033862 }}</ref>
{{Main|Foamy gland carcinoma}}

==Atrophic prostate carcinoma==
*[[AKA]] ''atrophic carcinoma''.
{{Main|Atrophic prostate carcinoma}}

==Mucinous prostate carcinoma==
===General===
*Rare.
*Most often Gleason 3+4 ~ 80% in one series of 47 cases.<ref name=pmid18300802>{{Cite journal | last1 = Osunkoya | first1 = AO. | last2 = Nielsen | first2 = ME. | last3 = Epstein | first3 = JI. | title = Prognosis of mucinous adenocarcinoma of the prostate treated by radical prostatectomy: a study of 47 cases. | journal = Am J Surg Pathol | volume = 32 | issue = 3 | pages = 468-72 | month = Mar | year = 2008 | doi = 10.1097/PAS.0b013e3181589f72 | PMID = 18300802 }}</ref>

Gleason pattern:
*In the past, it has been suggested that the mucinous component be assigned ''Gleason pattern 4''.<ref name=pmid14976541>{{cite journal |author=Grignon DJ |title=Unusual subtypes of prostate cancer |journal=Mod. Pathol. |volume=17 |issue=3 |pages=316–27 |year=2004 |month=March |pmid=14976541 |doi=10.1038/modpathol.3800052 |url=}}</ref>
*The prognosis is similar or may be better than the conventional type of prostate cancer in a large series;<ref name=pmid18300802/> thus, it seems reasonable to grade based on the pattern (as advocated by some experts<ref name=pmid18487999>{{Cite journal | last1 = Osunkoya | first1 = AO. | last2 = Adsay | first2 = NV. | last3 = Cohen | first3 = C. | last4 = Epstein | first4 = JI. | last5 = Smith | first5 = SL. | title = MUC2 expression in primary mucinous and nonmucinous adenocarcinoma of the prostate: an analysis of 50 cases on radical prostatectomy. | journal = Mod Pathol | volume = 21 | issue = 7 | pages = 789-94 | month = Jul | year = 2008 | doi = 10.1038/modpathol.2008.47 | PMID = 18487999 }}</ref>).

===Microscopic===
Features:
*Cytologically malignant cells floating in mucin.
*> 25% of tumour mucinous.<ref name=pmid14976541>{{cite journal |author=Grignon DJ |title=Unusual subtypes of prostate cancer |journal=Mod. Pathol. |volume=17 |issue=3 |pages=316–27 |year=2004 |month=March |pmid=14976541 |doi=10.1038/modpathol.3800052 |url=}}</ref>
**Two studies suggests '''>=''' 25%.<ref>{{cite journal |author=Osunkoya AO, Nielsen ME, Epstein JI |title=Prognosis of mucinous adenocarcinoma of the prostate treated by radical prostatectomy: a study of 47 cases |journal=Am. J. Surg. Pathol. |volume=32 |issue=3 |pages=468–72 |year=2008 |month=March |pmid=18300802 |doi=10.1097/PAS.0b013e3181589f72 |url=}}</ref><ref name=pmid23060063>{{Cite journal | last1 = Bohman | first1 = KD. | last2 = Osunkoya | first2 = AO. | title = Mucin-producing tumors and tumor-like lesions involving the prostate: a comprehensive review. | journal = Adv Anat Pathol | volume = 19 | issue = 6 | pages = 374-87 | month = Nov | year = 2012 | doi = 10.1097/PAP.0b013e318271a361 | PMID = 23060063 }}</ref>

Notes:
*[[Mucinous carcinoma]] - percentage required to call varies by site.

DDx:
*Metastatic [[mucinous carcinoma]].
*Mucinous adenocarcinoma of the prostatic urethra - analogous to the mucinous adenocarcinoma of the [[urinary bladder]].<ref name=pmid23060063/>

==Pseudohyperplastic prostatic adenocarcinoma==
*[[AKA]] ''pseudohyperplastic adenocarcinoma''.
===General===
*Rare.

===Microscopic===
Features:<ref name=Ref_GUP77>{{Ref GUP|77}}</ref><ref name=pmid14688829>{{cite journal |author=Arista-Nasr J, Martinez-Benitez B, Valdes S, Hernández M, Bornstein-Quevedo L |title=Pseudohyperplastic prostatic adenocarcinoma in transurethral resections of the prostate |journal=Pathol. Oncol. Res. |volume=9 |issue=4 |pages=232–5 |year=2003 |pmid=14688829 |doi=PAOR.2003.9.4.0232 |url=}}</ref>
*Medium to large glands with an atypical morphology - '''key low power feature''':
**Papillary or pseudopapillary infoldings, luminal undulations, branching or cystic dilatation.
*Nuclear features of conventional prostate cancer (nucleoli, nuclear enlargement).

====Images====
*[http://www.webpathology.com/image.asp?n=29&Case=23 Pseudohyperplastic adenocarcinoma (webpathology.com)].
*[http://www.nature.com/modpathol/journal/v17/n3/fig_tab/3800050f13.html Pseudohyperplastic prostatic adenocarcinoma (nature.com)].

Notes:
*Usually associated with conventional (acinar) prostate adenocarcinoma.
*Pale abundant cytoplasm - similar to normal prostate.

==Prostatic signet ring cell carcinoma==
{{Main|Signet ring cell carcinoma}}
===General===
*Very rare - 9 cases in a series of 29,783 prostate cancer cases.<ref name=pmid21123640>{{Cite journal | last1 = Warner | first1 = JN. | last2 = Nakamura | first2 = LY. | last3 = Pacelli | first3 = A. | last4 = Humphreys | first4 = MR. | last5 = Castle | first5 = EP. | title = Primary signet ring cell carcinoma of the prostate. | journal = Mayo Clin Proc | volume = 85 | issue = 12 | pages = 1130-6 | month = Dec | year = 2010 | doi = 10.4065/mcp.2010.0463 | PMID = 21123640 }}</ref>
*Criteria vary - percentage of SRCs required for Dx varies from 20% to 50%.<ref name=pmid21123640/>

===Microscopic===
Features:
*Signet ring cells - see ''[[basics]]'' article.

DDx:
*Acinar adenocarcinoma - Gleason pattern 4 with very small glands.

====Images====
*[http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2996149/figure/F1/ Prostatic SRCC (nih.gov)].
*[http://www.nature.com/modpathol/journal/v17/n3/fig_tab/3800052f7.html#figure-title Prostatic SRCC (nature.com)].
*[http://www.nature.com/modpathol/journal/v17/n3/fig_tab/3800052f8.html Prostatic SRCC (nature.com)].
*[http://www.webpathology.com/image.asp?case=23&n=34 Prostatic SRCC (webpathology.com)] - looks like ''acinar adenocarcinoma''.

===Stains===
*Alcian blue-PAS stain +ve.
*[[PAS stain|PAS]] -- 50% of cases +ve.<ref name=pmid21123640/>
*[[Alcian blue stain|Alcian blue]] -- 44% of cases +ve.<ref name=pmid21123640/>

==Sarcomatoid prostate carcinoma==
*[[AKA]] ''carcinosarcoma''.
===General===
*Rare.

===Microscopic===
Features:<ref name=Ref_GUP80>{{Ref GUP|77 & 80}}</ref>
*Biphasic tumour:
*#Spindle cells (sarcomatous component).
*#*May include components of: [[osteosarcoma]], [[chondrosarcoma]] and/or [[rhabdomyosarcoma]].
*#Glandular component (like conventional prostate carcinoma).

===IHC===
Features - typical:<ref name=Ref_GUP80>{{Ref GUP|77 & 80}}</ref>
*PSA +ve.
*Keratin +ve.

==Small cell carcinoma of the prostate gland==
{{Main|Small cell carcinoma}}
===General===
*Very rare.<ref name=pmid22110988>{{Cite journal | last1 = Furtado | first1 = P. | last2 = Lima | first2 = MV. | last3 = Nogueira | first3 = C. | last4 = Franco | first4 = M. | last5 = Tavora | first5 = F. | title = Review of small cell carcinomas of the prostate. | journal = Prostate Cancer | volume = 2011 | issue = | pages = 543272 | month = | year = 2011 | doi = 10.1155/2011/543272 | PMID = 22110988 }}</ref>
*Most common small cell carcinoma outside of the lung.<ref name=pmid22110988/>
*Poor prognosis.

===Microscopic===
Features:
*Small cells with:
**Nuclear moulding.
**Stippled chromatin.
**High [[NC ratio]].
*+/-High-grade acinar adenocarcinoma, i.e. conventional prostate carcinoma, seen in ~50% of cases.<ref name=pmid22110988/>

Notes:
*Similar to [[small cell carcinoma of the lung]].
*High-grade squamoid component favours metastatic [[urothelial carcinoma]].
**UCC usu. HWCK +ve.

DDx:
*[[Small cell carcinoma of the urinary bladder]].
*[[Lymphoma]], large cell.
*Other [[small round cell tumours]].

Images:
*[http://www.webpathology.com/image.asp?case=23&n=25 SmCC of the prostate - low mag. (webpathology.com)].
*[http://www.webpathology.com/image.asp?case=23&n=26 SmCC of the prostate - high mag. (webpathology.com)].
*[http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3200299/figure/fig1/ SmCC of the prostate - low mag. (nih.gov)].
*[http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3200299/figure/fig3/ SmCC of the prostate - high mag. (nih.gov)].

===IHC===
Features:<ref name=pmid22110988/>
*PSA weak +ve/-ve.
*Chromogranin +ve.

==Adenoid cystic/basal cell carcinoma of the prostate==
*Abbreviated ''ACBCC''.
===General===
*Rare.
*Typically indolent - may be aggressive.<ref name=pmid14657711>{{Cite journal | last1 = Iczkowski | first1 = KA. | last2 = Ferguson | first2 = KL. | last3 = Grier | first3 = DD. | last4 = Hossain | first4 = D. | last5 = Banerjee | first5 = SS. | last6 = McNeal | first6 = JE. | last7 = Bostwick | first7 = DG. | title = Adenoid cystic/basal cell carcinoma of the prostate: clinicopathologic findings in 19 cases. | journal = Am J Surg Pathol | volume = 27 | issue = 12 | pages = 1523-9 | month = Dec | year = 2003 | doi = | PMID = 14657711 }}</ref>

===Microscopic===
Features:
*[[Adenoid cystic carcinoma]]-like and [[basal cell adenoma]]-like:
**Nests of cells that have round spaces filled by whispy blue mucin.
**Dense collagenous stroma.


===IHC===
*HER2/neu +ve (strong).<ref name=pmid17142577>{{Cite journal | last1 = Iczkowski | first1 = KA. | last2 = Montironi | first2 = R. | title = Adenoid cystic/basal cell carcinoma of the prostate strongly expresses HER-2/neu. | journal = J Clin Pathol | volume = 59 | issue = 12 | pages = 1327-30 | month = Dec | year = 2006 | doi = 10.1136/jcp.2005.035147 | PMID = 17142577 }}</ref>

=Metastatic disease and other cancers of the prostate=
==Urothelial carcinoma==
{{Main|Urothelial carcinoma}} {{Main|Urothelium}}
:''Prostatic urothelial carcinoma'' redirects here.
===General===
*Spreads from the [[urinary bladder]] usually - common.<ref name=pmid22520044>{{Cite journal | last1 = Huguet | first1 = J. | title = [Prostatic involvement by urothelial carcinoma in patients with bladder cancer and their implications in the clinical practice]. | journal = Actas Urol Esp | volume = 36 | issue = 9 | pages = 545-53 | month = Oct | year = 2012 | doi = 10.1016/j.acuro.2012.02.005 | PMID = 22520044 }}</ref>
*Identified by endoscopic loop biopsy.<ref name=pmid17338657>{{Cite journal | last1 = Liedberg | first1 = F. | last2 = Chebil | first2 = G. | last3 = Månsson | first3 = W. | title = Urothelial carcinoma in the prostatic urethra and prostate: current controversies. | journal = Expert Rev Anticancer Ther | volume = 7 | issue = 3 | pages = 383-90 | month = Mar | year = 2007 | doi = 10.1586/14737140.7.3.383 | PMID = 17338657 }}</ref>

Treatment:<ref name=pmid17338657/>
*[[Cytoprostatectomy]] - stromal invasion ''or'' extensive intraductal involvement.
*Endoscopic resection and BCG - limited extent without stromal invasion.

===Microscopic===
Features:
*Divided into tumours with:
*#Stromal invasion.
*#Without stromal invasion.

Notes:
*Stromal involvement common ~ 75% of cases.<ref name=pmid23250619>{{Cite journal | last1 = Ichihara | first1 = K. | last2 = Masumori | first2 = N. | last3 = Kitamura | first3 = H. | last4 = Hasegawa | first4 = T. | last5 = Tsukamoto | first5 = T. | title = Clinical outcomes of urothelial carcinoma of the prostate detected in radical cystectomy specimens. | journal = Int J Clin Oncol | volume = | issue = | pages = | month = Dec | year = 2012 | doi = 10.1007/s10147-012-0508-3 | PMID = 23250619 }}</ref>

===Sign out===
<pre>
PROSTATE TISSUE, TRANSURETHRAL RESECTION:
- HIGH-GRADE UROTHELIAL CARCINOMA WITH FOCAL STROMAL INVASION, AND EXTENSIVE
INTRADUCTAL SPREAD IN FRAGMENTS WITH BENIGN PROSTATIC GLANDS.
</pre>

=See also=
*[[Prostate gland]].
*[[Genitourinary pathology]]

=References=
{{Reflist|2}}

[[Category:Genitourinary pathology]]

Dermal cysts

2014-07-28T13:03:41Z

Yuanny: /* Sign out */

'''Dermal cysts''', also '''skin cysts''', are common in [[dermatopathology]]. Dermatopathologists can diagnose 'em.

=Overview=
Common types:<ref name=Ref_TN2007_D5>{{Ref TN2007| D5}}</ref>
*[[Epidermal cyst]] (sebaceous cyst) -- most common.
*[[pilar cyst|Pilar (trichilemmal) cyst]].
*[[Dermoid cyst]].
*[[Ganglion cyst]].
*Milicem.

==Epidermal necrosis==
*This may be cystic. It is covered in the ''[[epidermal necrosis]]'' article, which covers [[erythema multiforme]], [[Steven-Johnson syndrome]] and [[toxic epidermal necrolysis]].

=Common cysts=
==Venous lake==
===General===
*Dilated vein.

Clinical:
*Blanch with pressure.<ref>URL: [http://dermatlas.med.jhmi.edu/derm/IndexDisplay.cfm?ImageID=-969536424 http://dermatlas.med.jhmi.edu/derm/IndexDisplay.cfm?ImageID=-969536424]. Accessed on: 13 August 2012.</ref>

===Gross===
*Purple/blue spot.

Images:
*[http://dermatlas.med.jhmi.edu/derm/IndexDisplay.cfm?ImageID=-969536424 Venous lake (jhmi.edu)].<ref name=jhmi_vl>URL: [http://dermatlas.med.jhmi.edu/derm/result.cfm?Diagnosis=605386295 http://dermatlas.med.jhmi.edu/derm/result.cfm?Diagnosis=605386295]. Accessed on: 13 August 2012.</ref>
*[http://dermatlas.med.jhmi.edu/derm/IndexDisplay.cfm?ImageID=-881531868 Venous lake (jhmi.edu)].<ref name=jhmi_vl>URL: [http://dermatlas.med.jhmi.edu/derm/result.cfm?Diagnosis=605386295 http://dermatlas.med.jhmi.edu/derm/result.cfm?Diagnosis=605386295]. Accessed on: 13 August 2012.</ref>

===Microscopic===
Features:<ref>Weedon's Skin Pathology. 3rd Ed. P.895.</ref>
*Lined by endothelium.
*Blood in lumen.
*+/-Fibrin in lumen.
*+/-[[Solar elastosis]] - very common.<ref name=Ref_Derm551>{{Ref Derm|551}}</ref>

DDx:
*[[Angiokeratoma]].
**Ectatic superficial dermal vessels.
**Irregular [[acanthosis]].
**Longer rete ridges.
*[[Cherry hemangioma]].<ref name=Ref_Derm551>{{Ref Derm|551}}</ref>

Images:
*[http://dermatlas.med.jhmi.edu/derm/IndexDisplay.cfm?ImageID=1982738883 Venous lake (jhmi.edu)].<ref name=jhmi_vl>URL: [http://dermatlas.med.jhmi.edu/derm/result.cfm?Diagnosis=605386295 http://dermatlas.med.jhmi.edu/derm/result.cfm?Diagnosis=605386295]. Accessed on: 13 August 2012.</ref>
*[http://www.dermpedia.org/case-type/9?page=63 Venous lake (dermpedia.org)].<ref>URL: [http://www.dermpedia.org/case/70-year-old-woman-with-nose-lesion http://www.dermpedia.org/case/70-year-old-woman-with-nose-lesion]. Accessed on: 21 June 2013.</ref>
*[http://www.surgicalpathologyatlas.com/glfusion/mediagallery/media.php?s=20080802172033945 Venous lake (surgical pathologyatlas.com)].

===Sign out===
<pre>
SKIN LESION, RIGHT CHEEK, BIOPSY:
- VENOUS LAKE.
- SOLAR ELASTOSIS.
- NEGATIVE FOR NEVUS.
</pre>

==Epidermal inclusion cyst==
{{Main|Epidermal inclusion cyst}}

==Pilar cyst==
*[[AKA]] ''trichilemmal cyst''.
{{Main|Pilar cyst}}

==Dermoid cyst==
===General===
*Benign.
*Congenital [[choristoma]]s.<ref name=dc_uiowa>Gandhi N, Syed NA, Alen R. Dermoid Cyst. EyeRounds.org. posted July 26, 2010; Available from: [http://www.EyeRounds.org/cases/115-dermoid-cyst.htm http://www.EyeRounds.org/cases/115-dermoid-cyst.htm]. Accessed on: 22 September 2011.</ref>
*May be found in the [[ovary]].

===Microscopic===
Features:<ref name=dc_uiowa>Gandhi N, Syed NA, Alen R. Dermoid Cyst. EyeRounds.org. posted July 26, 2010; Available from: [http://www.EyeRounds.org/cases/115-dermoid-cyst.htm http://www.EyeRounds.org/cases/115-dermoid-cyst.htm]. Accessed on: 22 September 2011.</ref><ref name=Ref_PCPBoD8_596>{{Ref PCPBoD8|596}}</ref>
*Cyst lined by normal (keratinized) skin with adnexal structure (hair follicles, sweat glands, sebaceous glands).

DDx:
*[[Epidermal cyst]] - no adnexal structures.

Images:
*[http://webeye.ophth.uiowa.edu/eyeforum/cases-i/case115/larger/Figure3.jpg Dermoid cyst - low mag. (uiowa.edu)].<ref name=dc_uiowa>Gandhi N, Syed NA, Alen R. Dermoid Cyst. EyeRounds.org. posted July 26, 2010; Available from: [http://www.EyeRounds.org/cases/115-dermoid-cyst.htm http://www.EyeRounds.org/cases/115-dermoid-cyst.htm]. Accessed on: 22 September 2011.</ref>
*[http://webeye.ophth.uiowa.edu/eyeforum/cases-i/case115/larger/Figure4.jpg Dermoid cyst - intermed. mag. (uiowa.edu)].

===Sign out===
<pre>
SKIN CYST, RIGHT LATERAL ORBIT, EXCISION:
- DERMOID CYST
- NEGATIVE FOR MALIGNANCY.
</pre>

==Pilonidal cyst==
*[[AKA]] ''pilonidal sinus''.
*[[AKA]] ''pilonidal disease''.<ref>URL: [http://emedicine.medscape.com/article/788127-overview http://emedicine.medscape.com/article/788127-overview]. Accessed on: 10 September 2012.</ref>

===General===
*Benign.
*Young adults (late teens, early twenties) - usu. men.<ref>URL: [http://www.nhs.uk/conditions/Pilonidal-sinus/Pages/Introduction.aspx http://www.nhs.uk/conditions/Pilonidal-sinus/Pages/Introduction.aspx]. Accessed on: 10 September 2012.</ref>

===Gross===
*Usually at gluteal folds.
**Uncommon: axilla, genital region, umbilicus, scalp.<ref name=Ref_Derm326>{{Ref Derm|326}}</ref>

===Microscopic===
Features:<ref name=Ref_Derm326>{{Ref Derm|326}}</ref>
*Cyst or pseudocyst into the deep dermis.
**May be lined by squamous epithelium with inflammation +/-[[pseudoepitheliomatous hyperplasia]].
*Neutrophils.
*[[Granuloma|Granulomatous inflammation]].

DDx:
*[[Squamous cell carcinoma of the skin]] with inflammation.<ref name=pmid19482585>{{Cite journal | last1 = Chatzis | first1 = I. | last2 = Noussios | first2 = G. | last3 = Katsourakis | first3 = A. | last4 = Chatzitheoklitos | first4 = E. | title = Squamous cell carcinoma related to long standing pilonidal-disease. | journal = Eur J Dermatol | volume = 19 | issue = 4 | pages = 408-9 | month = | year = | doi = 10.1684/ejd.2009.0705 | PMID = 19482585 }}</ref>
*Infection.

===Sign out===
<pre>
SKIN LESION (PILONIDAL SINUS), EXCISION:
- PILONIDAL SINUS.
- NEGATIVE FOR MALIGNANCY.
</pre>

<pre>
LESION (PILONIDAL SINUS), EXCISION:
- SKIN WITH PILONIDAL SINUS, CHRONIC INFLAMMATION AND SCARRING.
- NEGATIVE FOR MALIGNANCY.
</pre>

====Micro====
The section shows hair-bearing skin with a deep sinus tract containing large clusters of neutrophils, abundant plasma cells, hemosiderin-laden macrophages, eosinophils and multinucleated giant cells. The core of the lesion is, focally, well-vascularized. At the edge of the lesion is fibrotic tissue with plump fibroblasts. Benign, fibrofatty tissue with scant inflammation completely surrounds the tract, in the plane of section; however, it is focally fragmented. There is no squamous lining within the sinus. No nuclear atypia is identified.

=====Alternate=====
The section shows hair-bearing skin with a deep sinus containing large clusters of neutrophils, abundant plasma cells, hemosiderin-laden macrophages and multinucleated giant cells. Benign fibrofatty tissue with scant inflammation completely surrounds the lesion in the plane of section. There is no squamous lining within the sinus. No nuclear atypia is identified.

=====Sinus versus cyst=====
The section shows hair-bearing skin with a cyst/sinus lined by benign squamous epithelium containing keratin. The surrounding dermis has a mixed inflammatory infiltrate, predominantly consisting of plasma cells and lymphocytes. Multinucleated giant cells are present. No significant nuclear atypia is identified.

=Less common=
==Steatocystoma==
{{Main|Steatocystoma}}

==Digital mucous cyst==
*[[AKA]] ''digital synovial cyst''.<ref name=dermpedia>URL: [http://www.dermpedia.org/dermpedia-textbook/digital-mucous-myxoid-cyst http://www.dermpedia.org/dermpedia-textbook/digital-mucous-myxoid-cyst]. Accessed on: 17 January 2012.</ref>
*[[AKA]] ''digital myxoid pseudocyst''.<ref name=dermpedia/>
===General===
*Dome-shaped [[papule]].

===Microscopic===
Features:<ref name=dermpedia>URL: [http://www.dermpedia.org/dermpedia-textbook/digital-mucous-myxoid-cyst http://www.dermpedia.org/dermpedia-textbook/digital-mucous-myxoid-cyst]. Accessed on: 17 January 2012.</ref>
*Mucous in superficial dermis - '''key feature'''.
*No epithelial lining; it is a pseudocyst.

Note:
*Mucin = glycolated proteins; may be part of mucous.
*Mucous = slippery secretion.
**Some split hairs over the "u" - "mucus" vs. "mucous".<ref>URL: [http://dictionary.reference.com/browse/mucous http://dictionary.reference.com/browse/mucous]. Accessed on: 8 January 2012.</ref><ref>URL: [http://dictionary.reference.com/browse/mucus http://dictionary.reference.com/browse/mucus]. Accessed on: 8 January 2012.</ref>

DDx:
*[[Focal cutaneous mucinosis]].
*[[Ganglion cyst]].

Images:
*[http://www.dermpedia.org/files/images/Digital_mucous_cyst_2.jpg Digital mucous cyst (dermpedia.org)].<ref name=dermpedia>URL: [http://www.dermpedia.org/dermpedia-textbook/digital-mucous-myxoid-cyst http://www.dermpedia.org/dermpedia-textbook/digital-mucous-myxoid-cyst]. Accessed on: 17 January 2012.</ref>
*[http://www.dermpedia.org/files/images/Untitled89.jpg Digital mucous cyst (dermpedia.org)].<ref>URL: [http://www.dermpedia.org/case/digital-mucous-cyst-ganglion-type http://www.dermpedia.org/case/digital-mucous-cyst-ganglion-type]. Accessed on: 5 July 2013.</ref>

===Sign out===
<pre>
LESION, LEFT INDEX FINGER, EXCISION:
- DIGITAL MUCOUS CYST.
</pre>

==Apocrine cystadenoma==
===General===
*Uncommon.

===Microscopic===
Features:<ref name=Ref_Derm316>{{Ref Derm|316}}</ref>
*Multiloculated.
*Apocrine differentiation: columnar epithelium +/- apical snouts.
*Solid areas of epithelial proliferation.
*Papillary projections into the cyst.

Images:
*[http://alf3.urz.unibas.ch/pathopic/e/getpic-fra.cfm?id=7292 Apocrine cystadenoma (unibas.ch)].
*[http://www.flickr.com/photos/40764007@N08/6499470691/ Apocrine cystadenoma (flickr.com)].

=See also=
*[[Non-malignant skin disease]]
*[[Dermatopathology introduction]]

=References=
{{reflist|2}}

[[Category:Non-malignant skin disease]]
[[Category:Dermatopathology]]

Dermal cysts

2014-07-28T12:54:23Z

Yuanny: /* Sign out */

'''Dermal cysts''', also '''skin cysts''', are common in [[dermatopathology]]. Dermatopathologists can diagnose 'em.

=Overview=
Common types:<ref name=Ref_TN2007_D5>{{Ref TN2007| D5}}</ref>
*[[Epidermal cyst]] (sebaceous cyst) -- most common.
*[[pilar cyst|Pilar (trichilemmal) cyst]].
*[[Dermoid cyst]].
*[[Ganglion cyst]].
*Milicem.

==Epidermal necrosis==
*This may be cystic. It is covered in the ''[[epidermal necrosis]]'' article, which covers [[erythema multiforme]], [[Steven-Johnson syndrome]] and [[toxic epidermal necrolysis]].

=Common cysts=
==Venous lake==
===General===
*Dilated vein.

Clinical:
*Blanch with pressure.<ref>URL: [http://dermatlas.med.jhmi.edu/derm/IndexDisplay.cfm?ImageID=-969536424 http://dermatlas.med.jhmi.edu/derm/IndexDisplay.cfm?ImageID=-969536424]. Accessed on: 13 August 2012.</ref>

===Gross===
*Purple/blue spot.

Images:
*[http://dermatlas.med.jhmi.edu/derm/IndexDisplay.cfm?ImageID=-969536424 Venous lake (jhmi.edu)].<ref name=jhmi_vl>URL: [http://dermatlas.med.jhmi.edu/derm/result.cfm?Diagnosis=605386295 http://dermatlas.med.jhmi.edu/derm/result.cfm?Diagnosis=605386295]. Accessed on: 13 August 2012.</ref>
*[http://dermatlas.med.jhmi.edu/derm/IndexDisplay.cfm?ImageID=-881531868 Venous lake (jhmi.edu)].<ref name=jhmi_vl>URL: [http://dermatlas.med.jhmi.edu/derm/result.cfm?Diagnosis=605386295 http://dermatlas.med.jhmi.edu/derm/result.cfm?Diagnosis=605386295]. Accessed on: 13 August 2012.</ref>

===Microscopic===
Features:<ref>Weedon's Skin Pathology. 3rd Ed. P.895.</ref>
*Lined by endothelium.
*Blood in lumen.
*+/-Fibrin in lumen.
*+/-[[Solar elastosis]] - very common.<ref name=Ref_Derm551>{{Ref Derm|551}}</ref>

DDx:
*[[Angiokeratoma]].
**Ectatic superficial dermal vessels.
**Irregular [[acanthosis]].
**Longer rete ridges.
*[[Cherry hemangioma]].<ref name=Ref_Derm551>{{Ref Derm|551}}</ref>

Images:
*[http://dermatlas.med.jhmi.edu/derm/IndexDisplay.cfm?ImageID=1982738883 Venous lake (jhmi.edu)].<ref name=jhmi_vl>URL: [http://dermatlas.med.jhmi.edu/derm/result.cfm?Diagnosis=605386295 http://dermatlas.med.jhmi.edu/derm/result.cfm?Diagnosis=605386295]. Accessed on: 13 August 2012.</ref>
*[http://www.dermpedia.org/case-type/9?page=63 Venous lake (dermpedia.org)].<ref>URL: [http://www.dermpedia.org/case/70-year-old-woman-with-nose-lesion http://www.dermpedia.org/case/70-year-old-woman-with-nose-lesion]. Accessed on: 21 June 2013.</ref>
*[http://www.surgicalpathologyatlas.com/glfusion/mediagallery/media.php?s=20080802172033945 Venous lake (surgical pathologyatlas.com)].

===Sign out===
<pre>
SKIN LESION, RIGHT CHEEK, BIOPSY:
- VENOUS LAKE.
- SOLAR ELASTOSIS.
- NEGATIVE FOR NEVUS.
</pre>

==Epidermal inclusion cyst==
{{Main|Epidermal inclusion cyst}}

==Pilar cyst==
*[[AKA]] ''trichilemmal cyst''.
{{Main|Pilar cyst}}

==Dermoid cyst==
===General===
*Benign.
*Congenital [[choristoma]]s.<ref name=dc_uiowa>Gandhi N, Syed NA, Alen R. Dermoid Cyst. EyeRounds.org. posted July 26, 2010; Available from: [http://www.EyeRounds.org/cases/115-dermoid-cyst.htm http://www.EyeRounds.org/cases/115-dermoid-cyst.htm]. Accessed on: 22 September 2011.</ref>
*May be found in the [[ovary]].

===Microscopic===
Features:<ref name=dc_uiowa>Gandhi N, Syed NA, Alen R. Dermoid Cyst. EyeRounds.org. posted July 26, 2010; Available from: [http://www.EyeRounds.org/cases/115-dermoid-cyst.htm http://www.EyeRounds.org/cases/115-dermoid-cyst.htm]. Accessed on: 22 September 2011.</ref><ref name=Ref_PCPBoD8_596>{{Ref PCPBoD8|596}}</ref>
*Cyst lined by normal (keratinized) skin with adnexal structure (hair follicles, sweat glands, sebaceous glands).

DDx:
*[[Epidermal cyst]] - no adnexal structures.

Images:
*[http://webeye.ophth.uiowa.edu/eyeforum/cases-i/case115/larger/Figure3.jpg Dermoid cyst - low mag. (uiowa.edu)].<ref name=dc_uiowa>Gandhi N, Syed NA, Alen R. Dermoid Cyst. EyeRounds.org. posted July 26, 2010; Available from: [http://www.EyeRounds.org/cases/115-dermoid-cyst.htm http://www.EyeRounds.org/cases/115-dermoid-cyst.htm]. Accessed on: 22 September 2011.</ref>
*[http://webeye.ophth.uiowa.edu/eyeforum/cases-i/case115/larger/Figure4.jpg Dermoid cyst - intermed. mag. (uiowa.edu)].

===Sign out===
<pre>
SKIN CYST, BACK, EXCISION:
- DERMOID CYST
- NEGATIVE FOR MALIGNANCY.
</pre>

==Pilonidal cyst==
*[[AKA]] ''pilonidal sinus''.
*[[AKA]] ''pilonidal disease''.<ref>URL: [http://emedicine.medscape.com/article/788127-overview http://emedicine.medscape.com/article/788127-overview]. Accessed on: 10 September 2012.</ref>

===General===
*Benign.
*Young adults (late teens, early twenties) - usu. men.<ref>URL: [http://www.nhs.uk/conditions/Pilonidal-sinus/Pages/Introduction.aspx http://www.nhs.uk/conditions/Pilonidal-sinus/Pages/Introduction.aspx]. Accessed on: 10 September 2012.</ref>

===Gross===
*Usually at gluteal folds.
**Uncommon: axilla, genital region, umbilicus, scalp.<ref name=Ref_Derm326>{{Ref Derm|326}}</ref>

===Microscopic===
Features:<ref name=Ref_Derm326>{{Ref Derm|326}}</ref>
*Cyst or pseudocyst into the deep dermis.
**May be lined by squamous epithelium with inflammation +/-[[pseudoepitheliomatous hyperplasia]].
*Neutrophils.
*[[Granuloma|Granulomatous inflammation]].

DDx:
*[[Squamous cell carcinoma of the skin]] with inflammation.<ref name=pmid19482585>{{Cite journal | last1 = Chatzis | first1 = I. | last2 = Noussios | first2 = G. | last3 = Katsourakis | first3 = A. | last4 = Chatzitheoklitos | first4 = E. | title = Squamous cell carcinoma related to long standing pilonidal-disease. | journal = Eur J Dermatol | volume = 19 | issue = 4 | pages = 408-9 | month = | year = | doi = 10.1684/ejd.2009.0705 | PMID = 19482585 }}</ref>
*Infection.

===Sign out===
<pre>
SKIN LESION (PILONIDAL SINUS), EXCISION:
- PILONIDAL SINUS.
- NEGATIVE FOR MALIGNANCY.
</pre>

<pre>
LESION (PILONIDAL SINUS), EXCISION:
- SKIN WITH PILONIDAL SINUS, CHRONIC INFLAMMATION AND SCARRING.
- NEGATIVE FOR MALIGNANCY.
</pre>

====Micro====
The section shows hair-bearing skin with a deep sinus tract containing large clusters of neutrophils, abundant plasma cells, hemosiderin-laden macrophages, eosinophils and multinucleated giant cells. The core of the lesion is, focally, well-vascularized. At the edge of the lesion is fibrotic tissue with plump fibroblasts. Benign, fibrofatty tissue with scant inflammation completely surrounds the tract, in the plane of section; however, it is focally fragmented. There is no squamous lining within the sinus. No nuclear atypia is identified.

=====Alternate=====
The section shows hair-bearing skin with a deep sinus containing large clusters of neutrophils, abundant plasma cells, hemosiderin-laden macrophages and multinucleated giant cells. Benign fibrofatty tissue with scant inflammation completely surrounds the lesion in the plane of section. There is no squamous lining within the sinus. No nuclear atypia is identified.

=====Sinus versus cyst=====
The section shows hair-bearing skin with a cyst/sinus lined by benign squamous epithelium containing keratin. The surrounding dermis has a mixed inflammatory infiltrate, predominantly consisting of plasma cells and lymphocytes. Multinucleated giant cells are present. No significant nuclear atypia is identified.

=Less common=
==Steatocystoma==
{{Main|Steatocystoma}}

==Digital mucous cyst==
*[[AKA]] ''digital synovial cyst''.<ref name=dermpedia>URL: [http://www.dermpedia.org/dermpedia-textbook/digital-mucous-myxoid-cyst http://www.dermpedia.org/dermpedia-textbook/digital-mucous-myxoid-cyst]. Accessed on: 17 January 2012.</ref>
*[[AKA]] ''digital myxoid pseudocyst''.<ref name=dermpedia/>
===General===
*Dome-shaped [[papule]].

===Microscopic===
Features:<ref name=dermpedia>URL: [http://www.dermpedia.org/dermpedia-textbook/digital-mucous-myxoid-cyst http://www.dermpedia.org/dermpedia-textbook/digital-mucous-myxoid-cyst]. Accessed on: 17 January 2012.</ref>
*Mucous in superficial dermis - '''key feature'''.
*No epithelial lining; it is a pseudocyst.

Note:
*Mucin = glycolated proteins; may be part of mucous.
*Mucous = slippery secretion.
**Some split hairs over the "u" - "mucus" vs. "mucous".<ref>URL: [http://dictionary.reference.com/browse/mucous http://dictionary.reference.com/browse/mucous]. Accessed on: 8 January 2012.</ref><ref>URL: [http://dictionary.reference.com/browse/mucus http://dictionary.reference.com/browse/mucus]. Accessed on: 8 January 2012.</ref>

DDx:
*[[Focal cutaneous mucinosis]].
*[[Ganglion cyst]].

Images:
*[http://www.dermpedia.org/files/images/Digital_mucous_cyst_2.jpg Digital mucous cyst (dermpedia.org)].<ref name=dermpedia>URL: [http://www.dermpedia.org/dermpedia-textbook/digital-mucous-myxoid-cyst http://www.dermpedia.org/dermpedia-textbook/digital-mucous-myxoid-cyst]. Accessed on: 17 January 2012.</ref>
*[http://www.dermpedia.org/files/images/Untitled89.jpg Digital mucous cyst (dermpedia.org)].<ref>URL: [http://www.dermpedia.org/case/digital-mucous-cyst-ganglion-type http://www.dermpedia.org/case/digital-mucous-cyst-ganglion-type]. Accessed on: 5 July 2013.</ref>

===Sign out===
<pre>
LESION, LEFT INDEX FINGER, EXCISION:
- DIGITAL MUCOUS CYST.
</pre>

==Apocrine cystadenoma==
===General===
*Uncommon.

===Microscopic===
Features:<ref name=Ref_Derm316>{{Ref Derm|316}}</ref>
*Multiloculated.
*Apocrine differentiation: columnar epithelium +/- apical snouts.
*Solid areas of epithelial proliferation.
*Papillary projections into the cyst.

Images:
*[http://alf3.urz.unibas.ch/pathopic/e/getpic-fra.cfm?id=7292 Apocrine cystadenoma (unibas.ch)].
*[http://www.flickr.com/photos/40764007@N08/6499470691/ Apocrine cystadenoma (flickr.com)].

=See also=
*[[Non-malignant skin disease]]
*[[Dermatopathology introduction]]

=References=
{{reflist|2}}

[[Category:Non-malignant skin disease]]
[[Category:Dermatopathology]]

Cases

2014-07-07T11:34:55Z

Yuanny: /* Cases */

'''Cases''', also '''learning with simulated cases''' and '''interactive cases''', is a part of [[onlinepathology]] that is focused on individual specimens.

The cases presented usually do not exactly mirror the details behind the pictures. The reason they aren't exactly like real life is: real life often isn't a good test, e.g. if the requisition say ''Peutz-Jeghers syndrome'' and the specimen is ''polyps''... it isn't hard to diagnose the Peutz-Jeghers polyps.

==Objective==
The objective here is to simulate the decision making in pathology practise.

There are opportunities to look for more history, order [[special stains]], order [[immunostains]], order molecular testing for translocations, and ask a colleague -- before clicking on ''diagnosis'' to see if one is correct.

==Cases==
{| class="wikitable sortable"
! Case #
! Tease
! Subspecialty
! Difficulty
|-
| [[Case 1]]
| enlarged inguinal lymph node
| [[:Category:Cases in lymph node pathology|Lymph node pathology]]
| {{Hide |header=|content=[[:Category:Cases in lymph node pathology - fellow and expert|Fellow and expert]] }}
|-
| [[Case 2]]
| duodenal mass
| [[:Category:Cases in gastrointestinal pathology|Gastrointestinal pathology]]
| {{Hide |header=|content=[[:Category:Cases in gastrointestinal pathology - senior|Senior]] }}
|-
| [[Case 3]]
| renal mass
| [[:Category:Cases in genitourinary pathology|Genitourinary pathology]]
| {{Hide |header=|content=[[:Category:Cases in genitourinary pathology - senior|Senior]] }}
|-
| [[Case 4]]
| renal mass
| [[:Category:Cases in genitourinary pathology|Genitourinary pathology]]
| {{Hide |header=|content=[[:Category:Cases in genitourinary pathology - senior|Senior]] }}
|-
| [[Case 5]]
| cerebellar mass
| [[:Category:Cases in neuropathology|Neuropathology]]
| {{Hide |header=|content=[[:Category:Cases in neuropathology - junior|Junior]] }}
|-
| [[Case 6]]
| testicular mass
| [[:Category:Cases in genitourinary pathology|Genitourinary pathology]]
| {{Hide |header=|content=[[:Category:Cases in genitourinary pathology - junior|Junior]] }}
|-
| [[Case 7]]
| cervical lymphadenopathy
| [[:Category:Cases in lymph node pathology|Lymph node pathology]]
| {{Hide |header=|content=[[:Category:Cases in lymph node pathology - senior|Senior]] }}
|-
| [[Case 8]]
| cervical mass
| [[:Category:Cases in gynecologic pathology|Gynecologic pathology]]
| {{Hide |header=|content=[[:Category:Cases in gynecologic pathology - senior|Senior]] }}
|-
| [[Case 9]]
| brown esophageal ulcers
| [[:Category:Cases in gastrointestinal pathology|Gastrointestinal pathology]]
| {{Hide |header=|content=[[:Category:Cases in gastrointestinal pathology - senior|Senior]] }}
|-
| [[Case 10]]
| colon biopsy - diarrhea
| [[:Category:Cases in gastrointestinal pathology|Gastrointestinal pathology]]
| {{Hide |header=|content=[[:Category:Cases in gastrointestinal pathology - junior|Junior]] }}
|-
| [[Case 11]]
| pons - multi-organ dysfunction and stroke
| [[:Category:Cases in neuropathology|Neuropathology]]
| {{Hide |header=|content=[[:Category:Cases in neuropathology - senior|Senior]] }}
|-
| [[Case 12]]
| colon biopsy - diarrhea
| [[:Category:Cases in gastrointestinal pathology|Gastrointestinal pathology]]
| {{Hide |header=|content=[[:Category:Cases in gastrointestinal pathology - junior|Junior]] }}
|-
| [[Case 13]]
| renal mass
| [[:Category:Cases in genitourinary pathology|Genitourinary pathology]]
| {{Hide |header=|content=[[:Category:Cases in genitourinary pathology - senior|Senior]] }}
|-
| [[Case 14]]
| terminal ileum - hematochezia & diarrhea
| [[:Category:Cases in gastrointestinal pathology|Gastrointestinal pathology]]
| {{Hide |header=|content=[[:Category:Cases in gastrointestinal pathology - senior|Senior]] }}
|-
| [[Case 15]]
| duodenum - older man, weight loss
| [[:Category:Cases in gastrointestinal pathology|Gastrointestinal pathology]]
| {{Hide |header=|content=[[:Category:Cases in gastrointestinal pathology - junior|Junior]] }}
|-
| [[Case 16]]
| elbow lesion
| [[:Category:Cases in dermatopathology|Dermatopathology]]
| {{Hide |header=|content=[[:Category:Cases in dermatopathology - junior|Junior]] }}
|-
| [[Case 17]]
| colonic polyp
| [[:Category:Cases in gastrointestinal pathology|Gastrointestinal pathology]]
| {{Hide |header=|content=[[:Category:Cases in gastrointestinal pathology - senior|Senior]] }}
|-
| [[Case 18]]
| dome-shaped papules
| [[:Category:Cases in dermatopathology|Dermatopathology]]
| {{Hide |header=|content=[[:Category:Cases in dermatopathology - junior|Junior]] }}
|-
| [[Case 19]]
| vas deferens
| [[:Category:Cases in genitourinary pathology|Genitourinary pathology]]
| {{Hide |header=|content=[[:Category:Cases in genitourinary pathology - senior|Senior]] }}
|-
| [[Case 20]]
| failure to progress
| [[:Category:Cases in placental pathology|Placental pathology]]
| {{Hide |header=|content=[[:Category:Cases in placental pathology - junior|Junior]] }}
|-
| [[Case 21]]
| thyroid mass in young woman
| [[:Category:Cases in endocrine pathology|Endocrine pathology]]
| {{Hide |header=|content=[[:Category:Cases in endocrine pathology - junior|Junior]] }}
|-
| [[Case 22]]
| parotid mass
| [[:Category:Cases in head and neck pathology|Head and neck pathology]]
| {{Hide |header=|content=[[:Category:Cases in head and neck pathology - senior|Senior]] }}
|-
| [[Case 23]]
| 6 month old with chronic diarrhea
| [[:Category:Cases in pediatric pathology|Pediatric pathology]]
| {{Hide |header=|content=[[:Category:Cases in pediatric pathology - fellow and expert|Fellow and expert]] }}
|-
| [[Case 24]]
| breast of a young man
| [[:Category:Cases in breast pathology|Breast pathology]]
| {{Hide |header=|content=[[:Category:Cases in breast pathology - junior|Junior]] }}
|-
| [[Case 25]]
| breast mass
| [[:Category:Cases in breast pathology|Breast pathology]]
| {{Hide |header=|content=[[:Category:Cases in breast pathology - junior|Junior]] }}
|-
| [[Case 26]]
| bladder mass
| [[:Category:Cases in genitourinary pathology|Genitourinary pathology]]
| {{Hide |header=|content=[[:Category:Cases in genitourinary pathology - senior|Senior]] }}
|-
| [[Case 27]]
| skin with brown patches
| [[:Category:Cases in dermatopathology|Dermatopathology]]
| {{Hide |header=|content=[[:Category:Cases in dermatopathology - senior|Senior]] }}
|-
| [[Case 28]]
| woman with dyspnea
| [[:Category:Cases in pulmonary pathology|Pulmonary pathology]]
| {{Hide |header=|content=[[:Category:Cases in pulmonary pathology - senior|Senior]] }}
|-
| [[Case 29]]
| atrial mass
| [[:Category:Cases in cardiovascular pathology|Cardiovascular pathology]]
| {{Hide |header=|content=[[:Category:Cases in cardiovascular pathology - junior|Junior]] }}
|-
| [[Case 30]]
| anasarca and renal failure
| [[:Category:Cases in medical kidney pathology|Medical kidney pathology]]
| {{Hide |header=|content=[[:Category:Cases in medical kidney pathology - senior|Senior]] }}
|-
| [[Case 31]]
| scalp lesion
| [[:Category:Cases in dermatopathology|Dermatopathology]]
| {{Hide |header=|content=[[:Category:Cases in dermatopathology - senior|Senior]] }}
|-
| [[Case 32]]
| sudden death
| [[:Category:Cases in cardiovascular pathology|Cardiovascular pathology]]
| {{Hide |header=|content=[[:Category:Cases in cardiovascular pathology - senior|Senior]] }}
|-
| [[Case 33]]
| aortic valve mass
| [[:Category:Cases in cardiovascular pathology|Cardiovascular pathology]]
| {{Hide |header=|content=[[:Category:Cases in cardiovascular pathology - junior|Junior]] }}
|-
| [[Case 34]]
| "appendicitis"
| [[:Category:Cases in gastrointestinal pathology|Gastrointestinal pathology]]
| {{Hide |header=|content=[[:Category:Cases in gastrointestinal pathology - junior|Junior]] }}
|-
| [[Case 35]]
| RLQ abdominal pain with nausea & vomiting
| [[:Category:Cases in gastrointestinal pathology|Gastrointestinal pathology]]
| {{Hide |header=|content=[[:Category:Cases in gastrointestinal pathology - senior|Senior]] }}
|-
| [[Case 36]]
| routine pap test
| [[:Category:Cases in cytopathology|Cytopathology]]
| {{Hide |header=|content=[[:Category:Cases in cytopathology - junior|Junior]] }}
|-
| [[Case 37]]
| left arm lesion
| [[:Category:Cases in dermatopathology|Dermatopathology]]
| {{Hide |header=|content=[[:Category:Cases in dermatopathology - senior|Senior]] }}
|-
| [[Case 38]]
| screening colon
| [[:Category:Cases in gastrointestinal pathology|Gastrointestinal pathology]]
| {{Hide |header=|content=[[:Category:Cases in gastrointestinal pathology - junior|Junior]] }}
|-
| [[Case 39]]
| colonic polyp
| [[:Category:Cases in gastrointestinal pathology|Gastrointestinal pathology]]
| {{Hide |header=|content=[[:Category:Cases in gastrointestinal pathology - junior|Junior]] }}
|-
| [[Case 40]]
| stomach with large polyp
| [[:Category:Cases in gastrointestinal pathology|Gastrointestinal pathology]]
| {{Hide |header=|content=[[:Category:Cases in gastrointestinal pathology - senior|Senior]] }}
|-
| [[Case 41]]
| parotid mass
| [[:Category:Cases in head and neck pathology|Head and neck pathology]]
| {{Hide |header=|content=[[:Category:Cases in head and neck pathology - junior|Junior]] }}
|-
| [[Case 42]]
| parotid mass
| [[:Category:Cases in head and neck pathology|Head and neck pathology]]
| {{Hide |header=|content=[[:Category:Cases in head and neck pathology - junior|Junior]] }}
|-
| [[Case 43]]
| parotid mass
| [[:Category:Cases in head and neck pathology|Head and neck pathology]]
| {{Hide |header=|content=[[:Category:Cases in head and neck pathology - junior|Junior]] }}
|-
| [[Case 44]]
| placental lesion - white
| [[:Category:Cases in placental pathology|Placental pathology]]
| {{Hide |header=|content=[[:Category:Cases in placental pathology - junior|Junior]] }}
|-
| [[Case 45]]
| large ovarian mass
| [[:Category:Cases in gynecologic pathology|Gynecologic pathology]]
| {{Hide |header=|content=[[:Category:Cases in gynecologic pathology - senior|Senior]] }}
|-
| [[Case 46]]
| painful lesion, buttock
| [[:Category:Cases in soft tissue pathology|Soft tissue pathology]]
| {{Hide |header=|content=[[:Category:Cases in soft tissue pathology - senior|Senior]] }}
|-
| [[Case 47]]
| face lesion
| [[:Category:Cases in dermatopathology|Dermatopathology]]
| {{Hide |header=|content=[[:Category:Cases in dermatopathology - junior|Junior]] }}
|-
| [[Case 48]]
| colon lesion
| [[:Category:Cases in gastrointestinal pathology|Gastrointestinal pathology]]
| {{Hide |header=|content=[[:Category:Cases in gastrointestinal pathology - junior|Junior]] }}
|-
| [[Case 49]]
| eroded GI lesion
| [[:Category:Cases in gastrointestinal pathology|Gastrointestinal pathology]]
| {{Hide |header=|content=[[:Category:Cases in gastrointestinal pathology - junior|Junior]] }}
|-
| [[Case 50]]
| acute appendicitis
| [[:Category:Cases in gastrointestinal pathology|Gastrointestinal pathology]]
| {{Hide |header=|content=[[:Category:Cases in gastrointestinal pathology - junior|Junior]] }}
|-
| [[Case 51]]
| thyroid mass
| [[:Category:Cases in head and neck pathology|Head and neck pathology]]
| {{Hide |header=|content=[[:Category:Cases in head and neck pathology - senior|Senior]] }}
|-
| [[Case 52]]
| left lung mass
| [[:Category:Cases in pulmonary pathology|Pulmonary pathology]]
| {{Hide |header=|content=[[:Category:Cases in pulmonary pathology - junior|Junior]] }}
|-
| [[Case 53]]
| right lung biopsy
| [[:Category:Cases in pulmonary pathology|Pulmonary pathology]]
| {{Hide |header=|content=[[:Category:Cases in pulmonary pathology - junior|Junior]] }}
|-
| [[Case 54]]
| airspace disease unresponsive to antimicrobials
| [[:Category:Cases in pulmonary pathology|Pulmonary pathology]]
| {{Hide |header=|content=[[:Category:Cases in pulmonary pathology - senior|Senior]] }}
|-
| [[Case 55]]
| skin lesion
| [[:Category:Cases in dermatopathology|Dermatopathology]]
| {{Hide |header=|content=[[:Category:Cases in dermatopathology - junior|Junior]] }}
|-
| [[Case 56]]
| swelling at the angle of the jaw
| [[:Category:Cases in head and neck pathology|Head and neck pathology]]
| {{Hide |header=|content=[[:Category:Cases in head and neck pathology - junior|Junior]] }}
|-
| [[Case 57]]
| cervical biopsy
| [[:Category:Cases in gynecologic pathology|Gynecologic pathology]]
| {{Hide |header=|content=[[:Category:Cases in gynecologic pathology - junior|Junior]] }}
|-
| [[Case 58]]
| testicular mass
| [[:Category:Cases in genitourinary pathology|Genitourinary pathology]]
| {{Hide |header=|content=[[:Category:Cases in genitourinary pathology - junior|Junior]] }}
|-
| [[Case 59]]
| lymph node from a sigmoidectomy
| [[:Category:Cases in lymph node pathology|Lymph node pathology]]
| {{Hide |header=|content=[[:Category:Cases in lymph node pathology - junior|Junior]] }}
|-
| [[Case 60]]
| sigmoid polyp
| [[:Category:Cases in gastrointestinal pathology|Gastrointestinal pathology]]
| {{Hide |header=|content=[[:Category:Cases in gastrointestinal pathology - junior|Junior]] }}
|-
| [[Case 61]]
| rectal polyp
| [[:Category:Cases in gastrointestinal pathology|Gastrointestinal pathology]]
| {{Hide |header=|content=[[:Category:Cases in gastrointestinal pathology - junior|Junior]] }}
|-
| [[Case 62]]
| rectal polyp
| [[:Category:Cases in gastrointestinal pathology|Gastrointestinal pathology]]
| {{Hide |header=|content=[[:Category:Cases in gastrointestinal pathology - senior|Senior]] }}
|-
| [[Case 63]]
| urinary bladder lesion
| [[:Category:Cases in genitourinary pathology|Genitourinary pathology]]
| {{Hide |header=|content=[[:Category:Cases in genitourinary pathology - junior|Junior]] }}
|-
| [[Case 64]]
| kidney mass
| [[:Category:Cases in genitourinary pathology|Genitourinary pathology]]
| {{Hide |header=|content=[[:Category:Cases in genitourinary pathology - junior|Junior]] }}
|-
| [[Case 65]]
| dyspepsia in a young man
| [[:Category:Cases in gastrointestinal pathology|Gastrointestinal pathology]]
| {{Hide |header=|content=[[:Category:Cases in genitourinary pathology - junior|Junior]] }}
|-
| [[Case 66]]
| Uterine mass
| [[:Category:Cases in gynecologic pathology|Gynecologic pathology]]
| {{Hide |header=|content=[[:Category:Cases in Gynecologic pathology - junior|Junior]] }}
|-
| [[Case 67]]
| Lymph node/Colon Cancer
| [[:Category:Cases in lymph node pathology|Lymph node pathology]]
| {{Hide |header=|content=[[:Category:Cases in Lymph node pathology - junior|Junior]] }}
|-
| [[Case 68]]
| Lung biopsy
| [[:Category:Cases in pulmonary pathology|Pulmonary pathology]]
| {{Hide |header=|content=[[:Category:Cases in pulmonary pathology - junior|Junior]] }}
|-
| [[Case 69]]
| Back lesion
| [[:Category:Cases in dermatopathology|Dermatopathology]]
| {{Hide |header=|content=[[:Category:Cases in dermatopathology - junior|Junior]] }}
|-
| [[Case 70]]
| Stomach biopsy
| [[:Category:Cases in gastrointestinal pathology|Gastrointestinal pathology]]
| {{Hide |header=|content=[[:Category:Cases in gastrointestinal pathology - junior|Junior]] }}
|-
| [[Case 71]]
| Lung biopsy
| [[:Category:Cases in pulmonary pathology|Pulmonary pathology]]
| {{Hide |header=|content=[[:Category:Cases in pulmonary pathology - junior|Junior]] }}
|-
| [[Case 72]]
| Ureteral mass
| [[:Category:Cases in genitourinary pathology|Genitourinary pathology]]
| {{Hide |header=|content=[[:Category:Cases in genitourinary pathology - junior|Junior]] }}
|-
| [[Case 73]]
| Ovarian mass
| [[:Category:Cases in gynecologic pathology|Gynecologic pathology]]
| {{Hide |header=|content=[[:Category:Cases in gynecologic pathology - senior|Senior]] }}
|-
| [[Case 74]]
| Ovarian mass
| [[:Category:Cases in gynecologic pathology|Gynecologic pathology]]
| {{Hide |header=|content=[[:Category:Cases in gynecologic pathology - senior|Senior]] }}
|-
| [[Case 75]]
| Arm lesion
| [[:Category:Cases in dermatopathology|Dermatopathology]]
| {{Hide |header=|content=[[:Category:Cases in dermatopathology - junior|Junior]] }}

|}

==See also==
*[[Case how-to]].
*[[Case:Notes]]

[[Category:Cases]]

Case 75

2014-07-06T01:01:08Z

Yuanny: /* Diagnosis */

===Provided clinical history===
56 year old man, skin lesion

===Site===
Skin

===Primary image===
[[Image: Solar elastosis - intermed mag.jpg |500px|link=|center|]]
<center>Low magnification. [[H&E stain]].</center>

{{hidden|Intermediate magnification|[[Image: Solar elastosis - high mag.jpg |500px|link=|center|]]
<center>Intermediate magnification. [[H&E stain]].</center>}}

===Differential diagnosis===
{{hidden|Differential diagnosis|<center>[[Actinic keratosis]], [[Basal cell carcinoma]], [[Solar elastosis]],[[Squamous cell carcinoma]]</center>}}

===Additional tests===
====More history====
{{hidden|More history|<center>Patient spends a lot of time hiking outdoors</center>}}

====Ask a colleague====
{{hidden|Ask a colleague|<center>Very benign lesion, commonly seen as a result of sun damage</center>}}

====Stains====
{{Case Stains
| blank=Dr Torres would ask why!
| alcpas=
| alc1=
| alc25=
| aur=
| biel=
| bili=
| iron=
| congored=
| cresylv=
| dieterle=
| diffquik=
| fontana=
| gallyas=
| giemsa=
| gms=
| gomori=
| gram=
| gremelius=
| jms=
| jones=
| kinyoun=
| luxol=
| masson=
| mmas=
| movat=
| mucicar=
| oilredo=
| orecein=
| pas=
| pasd=
| pasf=
| ptah=
| prussian=
| reticulin=
| sudanblackb=
| toluidine=
| verhoeff=
| vonkossa=
| warthinstarry=
| zn=
}}
====IHC====
{{Case IHC
| blank=Dr Torres would ask why!
| a1at=
| acth=
| ae1ae3=
| afp=
| alk1=
| amacr=
| ar=
| b2microglobulin=
| b72_3=
| bcatenin=
| bcl2=
| bcl6=
| bclxl=
| c3=
| calcitonin=
| calponin=
| calretinin=
| cam5p2=
| cd10=
| cd117=
| cd138=
| cd15=
| cd1a=
| cd20=
| cd21=
| cd23=
| cd3=
| cd30=
| cd31=
| cd34=
| cd35=
| cd4=
| cd43=
| cd45=
| cd45=
| cd5=
| cd56=
| cd57=
| cd68=
| cd7=
| cd79a=
| cd8=
| cd99=
| cdx2=
| cea=
| chromo=
| chromo=
| ck17=
| ck19=
| ck20=
| ck34be12=
| ck5_6=
| ck7=
| cmv=
| cmyc=
| cyclin_d1=
| d2_40=
| desmin=
| dog1=
| ebv=
| ema=
| erpr=
| f_viii=
| f_xiiia=
| fascin=
| fsh=
| gastrin=
| gcdfp=
| gfap=
| gh=
| glucagon=
| glypican3=
| hbme1=
| hbv_core=
| hbv_surf=
| hcaldesmon=
| hcg=
| helicobacter=
| hepatocyte=
| her2=
| hhv8=
| hmb45=
| hnf1beta=
| hpv=
| hsv1=
| hsv2=
| Idh-1=
| inhibin=
| insulin=
| kappa=
| ki67=
| lambda=
| leu7=
| lga=
| lgg=
| lgm=
| lh=
| lysozyme=
| mammogl=
| mcv=
| melanin_a=
| mitf=
| mum1=
| myleoperox=
| myo_d1=
| myog=
| myog=
| nf=
| nse=
| oct3_4=
| p16=
| p53= +ve
| p57=
| p63=
| panker=
| pax2=
| pax5=
| pax8=
| pcna=
| pdgfr=
| plap=
| pnl-2c=
| prolactin=
| psa=
| psap=
| rcc=
| s100=
| sma=
| somatsatin=
| synapto=
| tdt=
| tfe3=
| thyrogl=
| toxopl=
| tsh=
| ttf1=
| ubiquitin=
| uchl1=
| ulex_europe=
| vim=
| vip=
| vzv=
| wt1=
}}
====Chromosomal translocations====
{{Case Translocations
| blank=Dr Torres would ask why!
| t1_13=
| t2_13=
| t8_14=
| t9_22bcr_abl=
| t9_22chn_ews=
| t11_14=
| t11_22dsrct=
| t11_22ews=
| t12_15=
| t12_16afh=
| t12_16liposar=
| t12_22=
| t14_18=
| t15_17=
| t16_21=
| t17_22=
| t21_22=
| tx_1=
| tx_17=
| tx_18=
}}

===Diagnosis===
{{hidden|Diagnosis|<center>[[Solar elastosis]]</center>}}
 

===Other cases===
{{Cases navigation}}

__NOTOC__

[[Category:Cases]]
[[Category:Cases in dermatopathology]]
[[Category:Cases difficulty 1]]
[[Category:Cases in dermatopathology - junior]]

Case 75

2014-07-06T01:00:32Z

Yuanny:

===Provided clinical history===
56 year old man, skin lesion

===Site===
Skin

===Primary image===
[[Image: Solar elastosis - intermed mag.jpg |500px|link=|center|]]
<center>Low magnification. [[H&E stain]].</center>

{{hidden|Intermediate magnification|[[Image: Solar elastosis - high mag.jpg |500px|link=|center|]]
<center>Intermediate magnification. [[H&E stain]].</center>}}

===Differential diagnosis===
{{hidden|Differential diagnosis|<center>[[Actinic keratosis]], [[Basal cell carcinoma]], [[Solar elastosis]],[[Squamous cell carcinoma]]</center>}}

===Additional tests===
====More history====
{{hidden|More history|<center>Patient spends a lot of time hiking outdoors</center>}}

====Ask a colleague====
{{hidden|Ask a colleague|<center>Very benign lesion, commonly seen as a result of sun damage</center>}}

====Stains====
{{Case Stains
| blank=Dr Torres would ask why!
| alcpas=
| alc1=
| alc25=
| aur=
| biel=
| bili=
| iron=
| congored=
| cresylv=
| dieterle=
| diffquik=
| fontana=
| gallyas=
| giemsa=
| gms=
| gomori=
| gram=
| gremelius=
| jms=
| jones=
| kinyoun=
| luxol=
| masson=
| mmas=
| movat=
| mucicar=
| oilredo=
| orecein=
| pas=
| pasd=
| pasf=
| ptah=
| prussian=
| reticulin=
| sudanblackb=
| toluidine=
| verhoeff=
| vonkossa=
| warthinstarry=
| zn=
}}
====IHC====
{{Case IHC
| blank=Dr Torres would ask why!
| a1at=
| acth=
| ae1ae3=
| afp=
| alk1=
| amacr=
| ar=
| b2microglobulin=
| b72_3=
| bcatenin=
| bcl2=
| bcl6=
| bclxl=
| c3=
| calcitonin=
| calponin=
| calretinin=
| cam5p2=
| cd10=
| cd117=
| cd138=
| cd15=
| cd1a=
| cd20=
| cd21=
| cd23=
| cd3=
| cd30=
| cd31=
| cd34=
| cd35=
| cd4=
| cd43=
| cd45=
| cd45=
| cd5=
| cd56=
| cd57=
| cd68=
| cd7=
| cd79a=
| cd8=
| cd99=
| cdx2=
| cea=
| chromo=
| chromo=
| ck17=
| ck19=
| ck20=
| ck34be12=
| ck5_6=
| ck7=
| cmv=
| cmyc=
| cyclin_d1=
| d2_40=
| desmin=
| dog1=
| ebv=
| ema=
| erpr=
| f_viii=
| f_xiiia=
| fascin=
| fsh=
| gastrin=
| gcdfp=
| gfap=
| gh=
| glucagon=
| glypican3=
| hbme1=
| hbv_core=
| hbv_surf=
| hcaldesmon=
| hcg=
| helicobacter=
| hepatocyte=
| her2=
| hhv8=
| hmb45=
| hnf1beta=
| hpv=
| hsv1=
| hsv2=
| Idh-1=
| inhibin=
| insulin=
| kappa=
| ki67=
| lambda=
| leu7=
| lga=
| lgg=
| lgm=
| lh=
| lysozyme=
| mammogl=
| mcv=
| melanin_a=
| mitf=
| mum1=
| myleoperox=
| myo_d1=
| myog=
| myog=
| nf=
| nse=
| oct3_4=
| p16=
| p53= +ve
| p57=
| p63=
| panker=
| pax2=
| pax5=
| pax8=
| pcna=
| pdgfr=
| plap=
| pnl-2c=
| prolactin=
| psa=
| psap=
| rcc=
| s100=
| sma=
| somatsatin=
| synapto=
| tdt=
| tfe3=
| thyrogl=
| toxopl=
| tsh=
| ttf1=
| ubiquitin=
| uchl1=
| ulex_europe=
| vim=
| vip=
| vzv=
| wt1=
}}
====Chromosomal translocations====
{{Case Translocations
| blank=Dr Torres would ask why!
| t1_13=
| t2_13=
| t8_14=
| t9_22bcr_abl=
| t9_22chn_ews=
| t11_14=
| t11_22dsrct=
| t11_22ews=
| t12_15=
| t12_16afh=
| t12_16liposar=
| t12_22=
| t14_18=
| t15_17=
| t16_21=
| t17_22=
| t21_22=
| tx_1=
| tx_17=
| tx_18=
}}

===Diagnosis===
{{hidden|Diagnosis|<center>Solar elastosis</center>}}
 
===Other cases===
{{Cases navigation}}

__NOTOC__

[[Category:Cases]]
[[Category:Cases in dermatopathology]]
[[Category:Cases difficulty 1]]
[[Category:Cases in dermatopathology - junior]]

Cases

2014-07-06T00:53:28Z

Yuanny:

'''Cases''', also '''learning with simulated cases''' and '''interactive cases''', is a part of [[onlinepathology]] that is focused on individual specimens.

The cases presented usually do not exactly mirror the details behind the pictures. The reason they aren't exactly like real life is: real life often isn't a good test, e.g. if the requisition say ''Peutz-Jeghers syndrome'' and the specimen is ''polyps''... it isn't hard to diagnose the Peutz-Jeghers polyps.

==Objective==
The objective here is to simulate the decision making in pathology practise.

There are opportunities to look for more history, order [[special stains]], order [[immunostains]], order molecular testing for translocations, and ask a colleague -- before clicking on ''diagnosis'' to see if one is correct.

==Cases==
{| class="wikitable sortable"
! Case #
! Tease
! Subspecialty
! Difficulty
|-
| [[Case 1]]
| enlarged inguinal lymph node
| [[:Category:Cases in lymph node pathology|Lymph node pathology]]
| {{Hide |header=|content=[[:Category:Cases in lymph node pathology - fellow and expert|Fellow and expert]] }}
|-
| [[Case 2]]
| duodenal mass
| [[:Category:Cases in gastrointestinal pathology|Gastrointestinal pathology]]
| {{Hide |header=|content=[[:Category:Cases in gastrointestinal pathology - senior|Senior]] }}
|-
| [[Case 3]]
| renal mass
| [[:Category:Cases in genitourinary pathology|Genitourinary pathology]]
| {{Hide |header=|content=[[:Category:Cases in genitourinary pathology - senior|Senior]] }}
|-
| [[Case 4]]
| renal mass
| [[:Category:Cases in genitourinary pathology|Genitourinary pathology]]
| {{Hide |header=|content=[[:Category:Cases in genitourinary pathology - senior|Senior]] }}
|-
| [[Case 5]]
| cerebellar mass
| [[:Category:Cases in neuropathology|Neuropathology]]
| {{Hide |header=|content=[[:Category:Cases in neuropathology - junior|Junior]] }}
|-
| [[Case 6]]
| testicular mass
| [[:Category:Cases in genitourinary pathology|Genitourinary pathology]]
| {{Hide |header=|content=[[:Category:Cases in genitourinary pathology - junior|Junior]] }}
|-
| [[Case 7]]
| cervical lymphadenopathy
| [[:Category:Cases in lymph node pathology|Lymph node pathology]]
| {{Hide |header=|content=[[:Category:Cases in lymph node pathology - senior|Senior]] }}
|-
| [[Case 8]]
| cervical mass
| [[:Category:Cases in gynecologic pathology|Gynecologic pathology]]
| {{Hide |header=|content=[[:Category:Cases in gynecologic pathology - senior|Senior]] }}
|-
| [[Case 9]]
| brown esophageal ulcers
| [[:Category:Cases in gastrointestinal pathology|Gastrointestinal pathology]]
| {{Hide |header=|content=[[:Category:Cases in gastrointestinal pathology - senior|Senior]] }}
|-
| [[Case 10]]
| colon biopsy - diarrhea
| [[:Category:Cases in gastrointestinal pathology|Gastrointestinal pathology]]
| {{Hide |header=|content=[[:Category:Cases in gastrointestinal pathology - junior|Junior]] }}
|-
| [[Case 11]]
| pons - multi-organ dysfunction and stroke
| [[:Category:Cases in neuropathology|Neuropathology]]
| {{Hide |header=|content=[[:Category:Cases in neuropathology - senior|Senior]] }}
|-
| [[Case 12]]
| colon biopsy - diarrhea
| [[:Category:Cases in gastrointestinal pathology|Gastrointestinal pathology]]
| {{Hide |header=|content=[[:Category:Cases in gastrointestinal pathology - junior|Junior]] }}
|-
| [[Case 13]]
| renal mass
| [[:Category:Cases in genitourinary pathology|Genitourinary pathology]]
| {{Hide |header=|content=[[:Category:Cases in genitourinary pathology - senior|Senior]] }}
|-
| [[Case 14]]
| terminal ileum - hematochezia & diarrhea
| [[:Category:Cases in gastrointestinal pathology|Gastrointestinal pathology]]
| {{Hide |header=|content=[[:Category:Cases in gastrointestinal pathology - senior|Senior]] }}
|-
| [[Case 15]]
| duodenum - older man, weight loss
| [[:Category:Cases in gastrointestinal pathology|Gastrointestinal pathology]]
| {{Hide |header=|content=[[:Category:Cases in gastrointestinal pathology - junior|Junior]] }}
|-
| [[Case 16]]
| elbow lesion
| [[:Category:Cases in dermatopathology|Dermatopathology]]
| {{Hide |header=|content=[[:Category:Cases in dermatopathology - junior|Junior]] }}
|-
| [[Case 17]]
| colonic polyp
| [[:Category:Cases in gastrointestinal pathology|Gastrointestinal pathology]]
| {{Hide |header=|content=[[:Category:Cases in gastrointestinal pathology - senior|Senior]] }}
|-
| [[Case 18]]
| dome-shaped papules
| [[:Category:Cases in dermatopathology|Dermatopathology]]
| {{Hide |header=|content=[[:Category:Cases in dermatopathology - junior|Junior]] }}
|-
| [[Case 19]]
| vas deferens
| [[:Category:Cases in genitourinary pathology|Genitourinary pathology]]
| {{Hide |header=|content=[[:Category:Cases in genitourinary pathology - senior|Senior]] }}
|-
| [[Case 20]]
| failure to progress
| [[:Category:Cases in placental pathology|Placental pathology]]
| {{Hide |header=|content=[[:Category:Cases in placental pathology - junior|Junior]] }}
|-
| [[Case 21]]
| thyroid mass in young woman
| [[:Category:Cases in endocrine pathology|Endocrine pathology]]
| {{Hide |header=|content=[[:Category:Cases in endocrine pathology - junior|Junior]] }}
|-
| [[Case 22]]
| parotid mass
| [[:Category:Cases in head and neck pathology|Head and neck pathology]]
| {{Hide |header=|content=[[:Category:Cases in head and neck pathology - senior|Senior]] }}
|-
| [[Case 23]]
| 6 month old with chronic diarrhea
| [[:Category:Cases in pediatric pathology|Pediatric pathology]]
| {{Hide |header=|content=[[:Category:Cases in pediatric pathology - fellow and expert|Fellow and expert]] }}
|-
| [[Case 24]]
| breast of a young man
| [[:Category:Cases in breast pathology|Breast pathology]]
| {{Hide |header=|content=[[:Category:Cases in breast pathology - junior|Junior]] }}
|-
| [[Case 25]]
| breast mass
| [[:Category:Cases in breast pathology|Breast pathology]]
| {{Hide |header=|content=[[:Category:Cases in breast pathology - junior|Junior]] }}
|-
| [[Case 26]]
| bladder mass
| [[:Category:Cases in genitourinary pathology|Genitourinary pathology]]
| {{Hide |header=|content=[[:Category:Cases in genitourinary pathology - senior|Senior]] }}
|-
| [[Case 27]]
| skin with brown patches
| [[:Category:Cases in dermatopathology|Dermatopathology]]
| {{Hide |header=|content=[[:Category:Cases in dermatopathology - senior|Senior]] }}
|-
| [[Case 28]]
| woman with dyspnea
| [[:Category:Cases in pulmonary pathology|Pulmonary pathology]]
| {{Hide |header=|content=[[:Category:Cases in pulmonary pathology - senior|Senior]] }}
|-
| [[Case 29]]
| atrial mass
| [[:Category:Cases in cardiovascular pathology|Cardiovascular pathology]]
| {{Hide |header=|content=[[:Category:Cases in cardiovascular pathology - junior|Junior]] }}
|-
| [[Case 30]]
| anasarca and renal failure
| [[:Category:Cases in medical kidney pathology|Medical kidney pathology]]
| {{Hide |header=|content=[[:Category:Cases in medical kidney pathology - senior|Senior]] }}
|-
| [[Case 31]]
| scalp lesion
| [[:Category:Cases in dermatopathology|Dermatopathology]]
| {{Hide |header=|content=[[:Category:Cases in dermatopathology - senior|Senior]] }}
|-
| [[Case 32]]
| sudden death
| [[:Category:Cases in cardiovascular pathology|Cardiovascular pathology]]
| {{Hide |header=|content=[[:Category:Cases in cardiovascular pathology - senior|Senior]] }}
|-
| [[Case 33]]
| aortic valve mass
| [[:Category:Cases in cardiovascular pathology|Cardiovascular pathology]]
| {{Hide |header=|content=[[:Category:Cases in cardiovascular pathology - junior|Junior]] }}
|-
| [[Case 34]]
| "appendicitis"
| [[:Category:Cases in gastrointestinal pathology|Gastrointestinal pathology]]
| {{Hide |header=|content=[[:Category:Cases in gastrointestinal pathology - junior|Junior]] }}
|-
| [[Case 35]]
| RLQ abdominal pain with nausea & vomiting
| [[:Category:Cases in gastrointestinal pathology|Gastrointestinal pathology]]
| {{Hide |header=|content=[[:Category:Cases in gastrointestinal pathology - senior|Senior]] }}
|-
| [[Case 36]]
| routine pap test
| [[:Category:Cases in cytopathology|Cytopathology]]
| {{Hide |header=|content=[[:Category:Cases in cytopathology - junior|Junior]] }}
|-
| [[Case 37]]
| left arm lesion
| [[:Category:Cases in dermatopathology|Dermatopathology]]
| {{Hide |header=|content=[[:Category:Cases in dermatopathology - senior|Senior]] }}
|-
| [[Case 38]]
| screening colon
| [[:Category:Cases in gastrointestinal pathology|Gastrointestinal pathology]]
| {{Hide |header=|content=[[:Category:Cases in gastrointestinal pathology - junior|Junior]] }}
|-
| [[Case 39]]
| colonic polyp
| [[:Category:Cases in gastrointestinal pathology|Gastrointestinal pathology]]
| {{Hide |header=|content=[[:Category:Cases in gastrointestinal pathology - junior|Junior]] }}
|-
| [[Case 40]]
| stomach with large polyp
| [[:Category:Cases in gastrointestinal pathology|Gastrointestinal pathology]]
| {{Hide |header=|content=[[:Category:Cases in gastrointestinal pathology - senior|Senior]] }}
|-
| [[Case 41]]
| parotid mass
| [[:Category:Cases in head and neck pathology|Head and neck pathology]]
| {{Hide |header=|content=[[:Category:Cases in head and neck pathology - junior|Junior]] }}
|-
| [[Case 42]]
| parotid mass
| [[:Category:Cases in head and neck pathology|Head and neck pathology]]
| {{Hide |header=|content=[[:Category:Cases in head and neck pathology - junior|Junior]] }}
|-
| [[Case 43]]
| parotid mass
| [[:Category:Cases in head and neck pathology|Head and neck pathology]]
| {{Hide |header=|content=[[:Category:Cases in head and neck pathology - junior|Junior]] }}
|-
| [[Case 44]]
| placental lesion - white
| [[:Category:Cases in placental pathology|Placental pathology]]
| {{Hide |header=|content=[[:Category:Cases in placental pathology - junior|Junior]] }}
|-
| [[Case 45]]
| large ovarian mass
| [[:Category:Cases in gynecologic pathology|Gynecologic pathology]]
| {{Hide |header=|content=[[:Category:Cases in gynecologic pathology - senior|Senior]] }}
|-
| [[Case 46]]
| painful lesion, buttock
| [[:Category:Cases in soft tissue pathology|Soft tissue pathology]]
| {{Hide |header=|content=[[:Category:Cases in soft tissue pathology - senior|Senior]] }}
|-
| [[Case 47]]
| face lesion
| [[:Category:Cases in dermatopathology|Dermatopathology]]
| {{Hide |header=|content=[[:Category:Cases in dermatopathology - junior|Junior]] }}
|-
| [[Case 48]]
| colon lesion
| [[:Category:Cases in gastrointestinal pathology|Gastrointestinal pathology]]
| {{Hide |header=|content=[[:Category:Cases in gastrointestinal pathology - junior|Junior]] }}
|-
| [[Case 49]]
| eroded GI lesion
| [[:Category:Cases in gastrointestinal pathology|Gastrointestinal pathology]]
| {{Hide |header=|content=[[:Category:Cases in gastrointestinal pathology - junior|Junior]] }}
|-
| [[Case 50]]
| acute appendicitis
| [[:Category:Cases in gastrointestinal pathology|Gastrointestinal pathology]]
| {{Hide |header=|content=[[:Category:Cases in gastrointestinal pathology - junior|Junior]] }}
|-
| [[Case 51]]
| thyroid mass
| [[:Category:Cases in head and neck pathology|Head and neck pathology]]
| {{Hide |header=|content=[[:Category:Cases in head and neck pathology - senior|Senior]] }}
|-
| [[Case 52]]
| left lung mass
| [[:Category:Cases in pulmonary pathology|Pulmonary pathology]]
| {{Hide |header=|content=[[:Category:Cases in pulmonary pathology - junior|Junior]] }}
|-
| [[Case 53]]
| right lung biopsy
| [[:Category:Cases in pulmonary pathology|Pulmonary pathology]]
| {{Hide |header=|content=[[:Category:Cases in pulmonary pathology - junior|Junior]] }}
|-
| [[Case 54]]
| airspace disease unresponsive to antimicrobials
| [[:Category:Cases in pulmonary pathology|Pulmonary pathology]]
| {{Hide |header=|content=[[:Category:Cases in pulmonary pathology - senior|Senior]] }}
|-
| [[Case 55]]
| skin lesion
| [[:Category:Cases in dermatopathology|Dermatopathology]]
| {{Hide |header=|content=[[:Category:Cases in dermatopathology - junior|Junior]] }}
|-
| [[Case 56]]
| swelling at the angle of the jaw
| [[:Category:Cases in head and neck pathology|Head and neck pathology]]
| {{Hide |header=|content=[[:Category:Cases in head and neck pathology - junior|Junior]] }}
|-
| [[Case 57]]
| cervical biopsy
| [[:Category:Cases in gynecologic pathology|Gynecologic pathology]]
| {{Hide |header=|content=[[:Category:Cases in gynecologic pathology - junior|Junior]] }}
|-
| [[Case 58]]
| testicular mass
| [[:Category:Cases in genitourinary pathology|Genitourinary pathology]]
| {{Hide |header=|content=[[:Category:Cases in genitourinary pathology - junior|Junior]] }}
|-
| [[Case 59]]
| lymph node from a sigmoidectomy
| [[:Category:Cases in lymph node pathology|Lymph node pathology]]
| {{Hide |header=|content=[[:Category:Cases in lymph node pathology - junior|Junior]] }}
|-
| [[Case 60]]
| sigmoid polyp
| [[:Category:Cases in gastrointestinal pathology|Gastrointestinal pathology]]
| {{Hide |header=|content=[[:Category:Cases in gastrointestinal pathology - junior|Junior]] }}
|-
| [[Case 61]]
| rectal polyp
| [[:Category:Cases in gastrointestinal pathology|Gastrointestinal pathology]]
| {{Hide |header=|content=[[:Category:Cases in gastrointestinal pathology - junior|Junior]] }}
|-
| [[Case 62]]
| rectal polyp
| [[:Category:Cases in gastrointestinal pathology|Gastrointestinal pathology]]
| {{Hide |header=|content=[[:Category:Cases in gastrointestinal pathology - senior|Senior]] }}
|-
| [[Case 63]]
| urinary bladder lesion
| [[:Category:Cases in genitourinary pathology|Genitourinary pathology]]
| {{Hide |header=|content=[[:Category:Cases in genitourinary pathology - junior|Junior]] }}
|-
| [[Case 64]]
| kidney mass
| [[:Category:Cases in genitourinary pathology|Genitourinary pathology]]
| {{Hide |header=|content=[[:Category:Cases in genitourinary pathology - junior|Junior]] }}
|-
| [[Case 65]]
| dyspepsia in a young man
| [[:Category:Cases in gastrointestinal pathology|Gastrointestinal pathology]]
| {{Hide |header=|content=[[:Category:Cases in genitourinary pathology - junior|Junior]] }}
|-
| [[Case 66]]
| Uterine mass
| [[:Category:Cases in gynecologic pathology|Gynecologic pathology]]
| {{Hide |header=|content=[[:Category:Cases in Gynecologic pathology - junior|Junior]] }}
|-
| [[Case 67]]
| Lymph node/Colon Cancer
| [[:Category:Cases in lymph node pathology|Lymph node pathology]]
| {{Hide |header=|content=[[:Category:Cases in Lymph node pathology - junior|Junior]] }}
|-
| [[Case 68]]
| Lung Bx
| [[:Category:Cases in pulmonary pathology|Pulmonary pathology]]
| {{Hide |header=|content=[[:Category:Cases in pulmonary pathology - junior|Junior]] }}
|-
| [[Case 69]]
| Back lesion
| [[:Category:Cases in dermatopathology|Dermatopathology]]
| {{Hide |header=|content=[[:Category:Cases in dermatopathology - junior|Junior]] }}
|-
| [[Case 70]]
| Stomach biopsy
| [[:Category:Cases in gastrointestinal pathology|Gastrointestinal pathology]]
| {{Hide |header=|content=[[:Category:Cases in gastrointestinal pathology - junior|Junior]] }}
|-
| [[Case 71]]
| Lung Bx
| [[:Category:Cases in pulmonary pathology|Pulmonary pathology]]
| {{Hide |header=|content=[[:Category:Cases in pulmonary pathology - junior|Junior]] }}
|-
| [[Case 72]]
| Ureteral mass
| [[:Category:Cases in genitourinary pathology|Genitourinary pathology]]
| {{Hide |header=|content=[[:Category:Cases in genitourinary pathology - junior|Junior]] }}
|-
| [[Case 73]]
| Ovarian mass
| [[:Category:Cases in gynecologic pathology|Gynecologic pathology]]
| {{Hide |header=|content=[[:Category:Cases in gynecologic pathology - senior|Senior]] }}
|-
| [[Case 74]]
| Ovarian mass
| [[:Category:Cases in gynecologic pathology|Gynecologic pathology]]
| {{Hide |header=|content=[[:Category:Cases in gynecologic pathology - senior|Senior]] }}
|-
| [[Case 75]]
| Arm Lesion
| [[:Category:Cases in dermatopathology|Dermatopathology]]
| {{Hide |header=|content=[[:Category:Cases in dermatopathology - junior|Junior]] }}

|}

==See also==
*[[Case how-to]].
*[[Case:Notes]]

[[Category:Cases]]

Case 74

2014-07-06T00:20:37Z

Yuanny: /* Other cases */

===Provided clinical history===
46 year old man/woman, asymptomatic, incidental finding

===Site===
Ovary

===Primary image===
[[Image: Brenner tumour intermed mag.jpg |500px|link=|center|]]
<center>Low magnification. [[H&E stain]].</center>

{{hidden|Intermediate magnification|[[Image: Brenner tumour high mag.jpg |500px|link=|center|]]
<center>Intermediate magnification. [[H&E stain]].</center>}}

{{hidden|High magnification|[[Image: Brenner tumour high mag cropped.jpg |500px|link=|center|]]
<center>High magnification. [[H&E stain]].</center>}}

===Differential diagnosis===
{{hidden|Differential diagnosis|<center>[[Ovarian fibroma]], [[Thecoma]], [[Brenner tumour]]</center>}}

===Additional tests===
====More history====
{{hidden|More history|<center>Patient has an unremarkable history</center>}}

====Ask a colleague====
{{hidden|Ask a colleague|<center>This is a very Benign lesion</center>}}

====Stains====
{{Case Stains
| blank=Dr Torres would ask why!
| alcpas=
| alc1=
| alc25=
| aur=
| biel=
| bili=
| iron=
| congored=
| cresylv=
| dieterle=
| diffquik=
| fontana=
| gallyas=
| giemsa=
| gms=
| gomori=
| gram=
| gremelius=
| jms=
| jones=
| kinyoun=
| luxol=
| masson=
| mmas=
| movat=
| mucicar=
| oilredo=
| orecein=
| pas=
| pasd=
| pasf=
| ptah=
| prussian=
| reticulin=
| sudanblackb=
| toluidine=
| verhoeff=
| vonkossa=
| warthinstarry=
| zn=
}}
====IHC====
{{Case IHC
| blank=Dr Torres would ask why!
| a1at=
| acth=
| ae1ae3=
| afp=
| alk1=
| amacr=
| ar= +ve
| b2microglobulin=
| b72_3=
| bcatenin=
| bcl2=
| bcl6=
| bclxl=
| c3=
| calcitonin=
| calponin=
| calretinin= -ve
| cam5p2=
| cd10=
| cd117=
| cd138=
| cd15=
| cd1a=
| cd20=
| cd21=
| cd23=
| cd3=
| cd30=
| cd31=
| cd34=
| cd35=
| cd4=
| cd43=
| cd45=
| cd45=
| cd5=
| cd56=
| cd57=
| cd68=
| cd7=
| cd79a=
| cd8=
| cd99=
| cdx2=
| cea=
| chromo=
| chromo=
| ck17=
| ck19=
| ck20= -ve
| ck34be12=
| ck5_6=
| ck7= +ve
| cmv=
| cmyc=
| cyclin_d1=
| d2_40=
| desmin=
| dog1=
| ebv=
| ema=
| erpr=
| f_viii=
| f_xiiia=
| fascin=
| fsh=
| gastrin=
| gcdfp=
| gfap=
| gh=
| glucagon=
| glypican3=
| hbme1=
| hbv_core=
| hbv_surf=
| hcaldesmon=
| hcg=
| helicobacter=
| hepatocyte=
| her2=
| hhv8=
| hmb45=
| hnf1beta=
| hpv=
| hsv1=
| hsv2=
| Idh-1=
| inhibin=
| insulin=
| kappa=
| ki67=
| lambda=
| leu7=
| lga=
| lgg=
| lgm=
| lh=
| lysozyme=
| mammogl=
| mcv=
| melanin_a=
| mitf=
| mum1=
| myleoperox=
| myo_d1=
| myog=
| myog=
| nf=
| nse=
| oct3_4=
| p16=
| p53=
| p57=
| p63=
| panker=
| pax2=
| pax5=
| pax8=
| pcna=
| pdgfr=
| plap=
| pnl-2c=
| prolactin=
| psa=
| psap=
| rcc=
| s100=
| sma=
| somatsatin=
| synapto=
| tdt=
| tfe3=
| thyrogl=
| toxopl=
| tsh=
| ttf1=
| ubiquitin=
| uchl1=
| ulex_europe=
| vim=
| vip=
| vzv=
| wt1=
}}
====Chromosomal translocations====
{{Case Translocations
| blank=Dr Torres would ask why!
| t1_13=
| t2_13=
| t8_14=
| t9_22bcr_abl=
| t9_22chn_ews=
| t11_14=
| t11_22dsrct=
| t11_22ews=
| t12_15=
| t12_16afh=
| t12_16liposar=
| t12_22=
| t14_18=
| t15_17=
| t16_21=
| t17_22=
| t21_22=
| tx_1=
| tx_17=
| tx_18=
}}

===Diagnosis===
{{hidden|Diagnosis|<center>[[Brenner tumour]]</center>}}
 

===Other cases===
{{Cases navigation}}

__NOTOC__

[[Category:Cases]]
[[Category:Cases in gynecologic pathology]]
[[Category:Cases difficulty 3]]
[[Category:Cases in gynecologic pathology - senior]]

Case 74

2014-07-06T00:14:43Z

Yuanny: /* Diagnosis */

===Provided clinical history===
46 year old man/woman, asymptomatic, incidental finding

===Site===
Ovary

===Primary image===
[[Image: Brenner tumour intermed mag.jpg |500px|link=|center|]]
<center>Low magnification. [[H&E stain]].</center>

{{hidden|Intermediate magnification|[[Image: Brenner tumour high mag.jpg |500px|link=|center|]]
<center>Intermediate magnification. [[H&E stain]].</center>}}

{{hidden|High magnification|[[Image: Brenner tumour high mag cropped.jpg |500px|link=|center|]]
<center>High magnification. [[H&E stain]].</center>}}

===Differential diagnosis===
{{hidden|Differential diagnosis|<center>[[Ovarian fibroma]], [[Thecoma]], [[Brenner tumour]]</center>}}

===Additional tests===
====More history====
{{hidden|More history|<center>Patient has an unremarkable history</center>}}

====Ask a colleague====
{{hidden|Ask a colleague|<center>This is a very Benign lesion</center>}}

====Stains====
{{Case Stains
| blank=Dr Torres would ask why!
| alcpas=
| alc1=
| alc25=
| aur=
| biel=
| bili=
| iron=
| congored=
| cresylv=
| dieterle=
| diffquik=
| fontana=
| gallyas=
| giemsa=
| gms=
| gomori=
| gram=
| gremelius=
| jms=
| jones=
| kinyoun=
| luxol=
| masson=
| mmas=
| movat=
| mucicar=
| oilredo=
| orecein=
| pas=
| pasd=
| pasf=
| ptah=
| prussian=
| reticulin=
| sudanblackb=
| toluidine=
| verhoeff=
| vonkossa=
| warthinstarry=
| zn=
}}
====IHC====
{{Case IHC
| blank=Dr Torres would ask why!
| a1at=
| acth=
| ae1ae3=
| afp=
| alk1=
| amacr=
| ar= +ve
| b2microglobulin=
| b72_3=
| bcatenin=
| bcl2=
| bcl6=
| bclxl=
| c3=
| calcitonin=
| calponin=
| calretinin= -ve
| cam5p2=
| cd10=
| cd117=
| cd138=
| cd15=
| cd1a=
| cd20=
| cd21=
| cd23=
| cd3=
| cd30=
| cd31=
| cd34=
| cd35=
| cd4=
| cd43=
| cd45=
| cd45=
| cd5=
| cd56=
| cd57=
| cd68=
| cd7=
| cd79a=
| cd8=
| cd99=
| cdx2=
| cea=
| chromo=
| chromo=
| ck17=
| ck19=
| ck20= -ve
| ck34be12=
| ck5_6=
| ck7= +ve
| cmv=
| cmyc=
| cyclin_d1=
| d2_40=
| desmin=
| dog1=
| ebv=
| ema=
| erpr=
| f_viii=
| f_xiiia=
| fascin=
| fsh=
| gastrin=
| gcdfp=
| gfap=
| gh=
| glucagon=
| glypican3=
| hbme1=
| hbv_core=
| hbv_surf=
| hcaldesmon=
| hcg=
| helicobacter=
| hepatocyte=
| her2=
| hhv8=
| hmb45=
| hnf1beta=
| hpv=
| hsv1=
| hsv2=
| Idh-1=
| inhibin=
| insulin=
| kappa=
| ki67=
| lambda=
| leu7=
| lga=
| lgg=
| lgm=
| lh=
| lysozyme=
| mammogl=
| mcv=
| melanin_a=
| mitf=
| mum1=
| myleoperox=
| myo_d1=
| myog=
| myog=
| nf=
| nse=
| oct3_4=
| p16=
| p53=
| p57=
| p63=
| panker=
| pax2=
| pax5=
| pax8=
| pcna=
| pdgfr=
| plap=
| pnl-2c=
| prolactin=
| psa=
| psap=
| rcc=
| s100=
| sma=
| somatsatin=
| synapto=
| tdt=
| tfe3=
| thyrogl=
| toxopl=
| tsh=
| ttf1=
| ubiquitin=
| uchl1=
| ulex_europe=
| vim=
| vip=
| vzv=
| wt1=
}}
====Chromosomal translocations====
{{Case Translocations
| blank=Dr Torres would ask why!
| t1_13=
| t2_13=
| t8_14=
| t9_22bcr_abl=
| t9_22chn_ews=
| t11_14=
| t11_22dsrct=
| t11_22ews=
| t12_15=
| t12_16afh=
| t12_16liposar=
| t12_22=
| t14_18=
| t15_17=
| t16_21=
| t17_22=
| t21_22=
| tx_1=
| tx_17=
| tx_18=
}}

===Diagnosis===
{{hidden|Diagnosis|<center>[[Brenner tumour]]</center>}}
 

===Other cases===
{{Cases navigation}}

__NOTOC__

[[Category:Cases]]



[[Category:Cases difficulty 4]]

Case 74

2014-07-06T00:13:56Z

Yuanny: /* Diagnosis */

===Provided clinical history===
46 year old man/woman, asymptomatic, incidental finding

===Site===
Ovary

===Primary image===
[[Image: Brenner tumour intermed mag.jpg |500px|link=|center|]]
<center>Low magnification. [[H&E stain]].</center>

{{hidden|Intermediate magnification|[[Image: Brenner tumour high mag.jpg |500px|link=|center|]]
<center>Intermediate magnification. [[H&E stain]].</center>}}

{{hidden|High magnification|[[Image: Brenner tumour high mag cropped.jpg |500px|link=|center|]]
<center>High magnification. [[H&E stain]].</center>}}

===Differential diagnosis===
{{hidden|Differential diagnosis|<center>[[Ovarian fibroma]], [[Thecoma]], [[Brenner tumour]]</center>}}

===Additional tests===
====More history====
{{hidden|More history|<center>Patient has an unremarkable history</center>}}

====Ask a colleague====
{{hidden|Ask a colleague|<center>This is a very Benign lesion</center>}}

====Stains====
{{Case Stains
| blank=Dr Torres would ask why!
| alcpas=
| alc1=
| alc25=
| aur=
| biel=
| bili=
| iron=
| congored=
| cresylv=
| dieterle=
| diffquik=
| fontana=
| gallyas=
| giemsa=
| gms=
| gomori=
| gram=
| gremelius=
| jms=
| jones=
| kinyoun=
| luxol=
| masson=
| mmas=
| movat=
| mucicar=
| oilredo=
| orecein=
| pas=
| pasd=
| pasf=
| ptah=
| prussian=
| reticulin=
| sudanblackb=
| toluidine=
| verhoeff=
| vonkossa=
| warthinstarry=
| zn=
}}
====IHC====
{{Case IHC
| blank=Dr Torres would ask why!
| a1at=
| acth=
| ae1ae3=
| afp=
| alk1=
| amacr=
| ar= +ve
| b2microglobulin=
| b72_3=
| bcatenin=
| bcl2=
| bcl6=
| bclxl=
| c3=
| calcitonin=
| calponin=
| calretinin= -ve
| cam5p2=
| cd10=
| cd117=
| cd138=
| cd15=
| cd1a=
| cd20=
| cd21=
| cd23=
| cd3=
| cd30=
| cd31=
| cd34=
| cd35=
| cd4=
| cd43=
| cd45=
| cd45=
| cd5=
| cd56=
| cd57=
| cd68=
| cd7=
| cd79a=
| cd8=
| cd99=
| cdx2=
| cea=
| chromo=
| chromo=
| ck17=
| ck19=
| ck20= -ve
| ck34be12=
| ck5_6=
| ck7= +ve
| cmv=
| cmyc=
| cyclin_d1=
| d2_40=
| desmin=
| dog1=
| ebv=
| ema=
| erpr=
| f_viii=
| f_xiiia=
| fascin=
| fsh=
| gastrin=
| gcdfp=
| gfap=
| gh=
| glucagon=
| glypican3=
| hbme1=
| hbv_core=
| hbv_surf=
| hcaldesmon=
| hcg=
| helicobacter=
| hepatocyte=
| her2=
| hhv8=
| hmb45=
| hnf1beta=
| hpv=
| hsv1=
| hsv2=
| Idh-1=
| inhibin=
| insulin=
| kappa=
| ki67=
| lambda=
| leu7=
| lga=
| lgg=
| lgm=
| lh=
| lysozyme=
| mammogl=
| mcv=
| melanin_a=
| mitf=
| mum1=
| myleoperox=
| myo_d1=
| myog=
| myog=
| nf=
| nse=
| oct3_4=
| p16=
| p53=
| p57=
| p63=
| panker=
| pax2=
| pax5=
| pax8=
| pcna=
| pdgfr=
| plap=
| pnl-2c=
| prolactin=
| psa=
| psap=
| rcc=
| s100=
| sma=
| somatsatin=
| synapto=
| tdt=
| tfe3=
| thyrogl=
| toxopl=
| tsh=
| ttf1=
| ubiquitin=
| uchl1=
| ulex_europe=
| vim=
| vip=
| vzv=
| wt1=
}}
====Chromosomal translocations====
{{Case Translocations
| blank=Dr Torres would ask why!
| t1_13=
| t2_13=
| t8_14=
| t9_22bcr_abl=
| t9_22chn_ews=
| t11_14=
| t11_22dsrct=
| t11_22ews=
| t12_15=
| t12_16afh=
| t12_16liposar=
| t12_22=
| t14_18=
| t15_17=
| t16_21=
| t17_22=
| t21_22=
| tx_1=
| tx_17=
| tx_18=
}}

===Diagnosis===
{{hidden|Diagnosis|<center>[[Brenner tumor]]</center>}}
 

===Other cases===
{{Cases navigation}}

__NOTOC__

[[Category:Cases]]



[[Category:Cases difficulty 4]]

Case 74

2014-07-06T00:13:35Z

Yuanny:

===Provided clinical history===
46 year old man/woman, asymptomatic, incidental finding

===Site===
Ovary

===Primary image===
[[Image: Brenner tumour intermed mag.jpg |500px|link=|center|]]
<center>Low magnification. [[H&E stain]].</center>

{{hidden|Intermediate magnification|[[Image: Brenner tumour high mag.jpg |500px|link=|center|]]
<center>Intermediate magnification. [[H&E stain]].</center>}}

{{hidden|High magnification|[[Image: Brenner tumour high mag cropped.jpg |500px|link=|center|]]
<center>High magnification. [[H&E stain]].</center>}}

===Differential diagnosis===
{{hidden|Differential diagnosis|<center>[[Ovarian fibroma]], [[Thecoma]], [[Brenner tumour]]</center>}}

===Additional tests===
====More history====
{{hidden|More history|<center>Patient has an unremarkable history</center>}}

====Ask a colleague====
{{hidden|Ask a colleague|<center>This is a very Benign lesion</center>}}

====Stains====
{{Case Stains
| blank=Dr Torres would ask why!
| alcpas=
| alc1=
| alc25=
| aur=
| biel=
| bili=
| iron=
| congored=
| cresylv=
| dieterle=
| diffquik=
| fontana=
| gallyas=
| giemsa=
| gms=
| gomori=
| gram=
| gremelius=
| jms=
| jones=
| kinyoun=
| luxol=
| masson=
| mmas=
| movat=
| mucicar=
| oilredo=
| orecein=
| pas=
| pasd=
| pasf=
| ptah=
| prussian=
| reticulin=
| sudanblackb=
| toluidine=
| verhoeff=
| vonkossa=
| warthinstarry=
| zn=
}}
====IHC====
{{Case IHC
| blank=Dr Torres would ask why!
| a1at=
| acth=
| ae1ae3=
| afp=
| alk1=
| amacr=
| ar= +ve
| b2microglobulin=
| b72_3=
| bcatenin=
| bcl2=
| bcl6=
| bclxl=
| c3=
| calcitonin=
| calponin=
| calretinin= -ve
| cam5p2=
| cd10=
| cd117=
| cd138=
| cd15=
| cd1a=
| cd20=
| cd21=
| cd23=
| cd3=
| cd30=
| cd31=
| cd34=
| cd35=
| cd4=
| cd43=
| cd45=
| cd45=
| cd5=
| cd56=
| cd57=
| cd68=
| cd7=
| cd79a=
| cd8=
| cd99=
| cdx2=
| cea=
| chromo=
| chromo=
| ck17=
| ck19=
| ck20= -ve
| ck34be12=
| ck5_6=
| ck7= +ve
| cmv=
| cmyc=
| cyclin_d1=
| d2_40=
| desmin=
| dog1=
| ebv=
| ema=
| erpr=
| f_viii=
| f_xiiia=
| fascin=
| fsh=
| gastrin=
| gcdfp=
| gfap=
| gh=
| glucagon=
| glypican3=
| hbme1=
| hbv_core=
| hbv_surf=
| hcaldesmon=
| hcg=
| helicobacter=
| hepatocyte=
| her2=
| hhv8=
| hmb45=
| hnf1beta=
| hpv=
| hsv1=
| hsv2=
| Idh-1=
| inhibin=
| insulin=
| kappa=
| ki67=
| lambda=
| leu7=
| lga=
| lgg=
| lgm=
| lh=
| lysozyme=
| mammogl=
| mcv=
| melanin_a=
| mitf=
| mum1=
| myleoperox=
| myo_d1=
| myog=
| myog=
| nf=
| nse=
| oct3_4=
| p16=
| p53=
| p57=
| p63=
| panker=
| pax2=
| pax5=
| pax8=
| pcna=
| pdgfr=
| plap=
| pnl-2c=
| prolactin=
| psa=
| psap=
| rcc=
| s100=
| sma=
| somatsatin=
| synapto=
| tdt=
| tfe3=
| thyrogl=
| toxopl=
| tsh=
| ttf1=
| ubiquitin=
| uchl1=
| ulex_europe=
| vim=
| vip=
| vzv=
| wt1=
}}
====Chromosomal translocations====
{{Case Translocations
| blank=Dr Torres would ask why!
| t1_13=
| t2_13=
| t8_14=
| t9_22bcr_abl=
| t9_22chn_ews=
| t11_14=
| t11_22dsrct=
| t11_22ews=
| t12_15=
| t12_16afh=
| t12_16liposar=
| t12_22=
| t14_18=
| t15_17=
| t16_21=
| t17_22=
| t21_22=
| tx_1=
| tx_17=
| tx_18=
}}

===Diagnosis===
{{hidden|Diagnosis|<center>DIAGNOSIS GOES HERE</center>}}
 
===Other cases===
{{Cases navigation}}

__NOTOC__

[[Category:Cases]]



[[Category:Cases difficulty 4]]

Case 74

2014-07-06T00:12:16Z

Yuanny: /* Ask a colleague */

===Provided clinical history===
46 year old man/woman, asymptomatic, incidental finding

===Site===
Ovary

===Primary image===
[[Image: Brenner tumour intermed mag.jpg |500px|link=|center|]]
<center>Low magnification. [[H&E stain]].</center>

{{hidden|Intermediate magnification|[[Image: Brenner tumour high mag.jpg |500px|link=|center|]]
<center>Intermediate magnification. [[H&E stain]].</center>}}

{{hidden|High magnification|[[Image: Brenner tumour high mag cropped.jpg |500px|link=|center|]]
<center>High magnification. [[H&E stain]].</center>}}

===Differential diagnosis===
{{hidden|Differential diagnosis|<center>[[Ovarian fibroma]], [[Thecoma]], [[Brenner tumour]]</center>}}

===Additional tests===
====More history====
{{hidden|More history|<center>Patient has an unremarkable history</center>}}

====Ask a colleague====
{{hidden|Ask a colleague|<center>This is a very Benign lesion</center>}}

====Stains====
{{Case Stains
| blank=Dr Torres would ask why!
| alcpas=
| alc1=
| alc25=
| aur=
| biel=
| bili=
| iron=
| congored=
| cresylv=
| dieterle=
| diffquik=
| fontana=
| gallyas=
| giemsa=
| gms=
| gomori=
| gram=
| gremelius=
| jms=
| jones=
| kinyoun=
| luxol=
| masson=
| mmas=
| movat=
| mucicar=
| oilredo=
| orecein=
| pas=
| pasd=
| pasf=
| ptah=
| prussian=
| reticulin=
| sudanblackb=
| toluidine=
| verhoeff=
| vonkossa=
| warthinstarry=
| zn=
}}
====IHC====
{{Case IHC
| blank=Dr Torres would ask why!
| a1at=
| acth=
| ae1ae3=
| afp=
| alk1=
| amacr=
| ar=
| b2microglobulin=
| b72_3=
| bcatenin=
| bcl2=
| bcl6=
| bclxl=
| c3=
| calcitonin=
| calponin=
| calretinin=
| cam5p2=
| cd10=
| cd117=
| cd138=
| cd15=
| cd1a=
| cd20=
| cd21=
| cd23=
| cd3=
| cd30=
| cd31=
| cd34=
| cd35=
| cd4=
| cd43=
| cd45=
| cd45=
| cd5=
| cd56=
| cd57=
| cd68=
| cd7=
| cd79a=
| cd8=
| cd99=
| cdx2=
| cea=
| chromo=
| chromo=
| ck17=
| ck19=
| ck20=
| ck34be12=
| ck5_6=
| ck7=
| cmv=
| cmyc=
| cyclin_d1=
| d2_40=
| desmin=
| dog1=
| ebv=
| ema=
| erpr=
| f_viii=
| f_xiiia=
| fascin=
| fsh=
| gastrin=
| gcdfp=
| gfap=
| gh=
| glucagon=
| glypican3=
| hbme1=
| hbv_core=
| hbv_surf=
| hcaldesmon=
| hcg=
| helicobacter=
| hepatocyte=
| her2=
| hhv8=
| hmb45=
| hnf1beta=
| hpv=
| hsv1=
| hsv2=
| Idh-1=
| inhibin=
| insulin=
| kappa=
| ki67=
| lambda=
| leu7=
| lga=
| lgg=
| lgm=
| lh=
| lysozyme=
| mammogl=
| mcv=
| melanin_a=
| mitf=
| mum1=
| myleoperox=
| myo_d1=
| myog=
| myog=
| nf=
| nse=
| oct3_4=
| p16=
| p53=
| p57=
| p63=
| panker=
| pax2=
| pax5=
| pax8=
| pcna=
| pdgfr=
| plap=
| pnl-2c=
| prolactin=
| psa=
| psap=
| rcc=
| s100=
| sma=
| somatsatin=
| synapto=
| tdt=
| tfe3=
| thyrogl=
| toxopl=
| tsh=
| ttf1=
| ubiquitin=
| uchl1=
| ulex_europe=
| vim=
| vip=
| vzv=
| wt1=
}}
====Chromosomal translocations====
{{Case Translocations
| blank=Dr Torres would ask why!
| t1_13=
| t2_13=
| t8_14=
| t9_22bcr_abl=
| t9_22chn_ews=
| t11_14=
| t11_22dsrct=
| t11_22ews=
| t12_15=
| t12_16afh=
| t12_16liposar=
| t12_22=
| t14_18=
| t15_17=
| t16_21=
| t17_22=
| t21_22=
| tx_1=
| tx_17=
| tx_18=
}}

===Diagnosis===
{{hidden|Diagnosis|<center>DIAGNOSIS GOES HERE</center>}}
 
===Other cases===
{{Cases navigation}}

__NOTOC__

[[Category:Cases]]



[[Category:Cases difficulty 4]]

Case 74

2014-07-06T00:11:52Z

Yuanny: /* More history */

===Provided clinical history===
46 year old man/woman, asymptomatic, incidental finding

===Site===
Ovary

===Primary image===
[[Image: Brenner tumour intermed mag.jpg |500px|link=|center|]]
<center>Low magnification. [[H&E stain]].</center>

{{hidden|Intermediate magnification|[[Image: Brenner tumour high mag.jpg |500px|link=|center|]]
<center>Intermediate magnification. [[H&E stain]].</center>}}

{{hidden|High magnification|[[Image: Brenner tumour high mag cropped.jpg |500px|link=|center|]]
<center>High magnification. [[H&E stain]].</center>}}

===Differential diagnosis===
{{hidden|Differential diagnosis|<center>[[Ovarian fibroma]], [[Thecoma]], [[Brenner tumour]]</center>}}

===Additional tests===
====More history====
{{hidden|More history|<center>Patient has an unremarkable history</center>}}

====Ask a colleague====
{{hidden|Ask a colleague|<center>COLLEAGUE'S ADVICE HERE</center>}}

====Stains====
{{Case Stains
| blank=Dr Torres would ask why!
| alcpas=
| alc1=
| alc25=
| aur=
| biel=
| bili=
| iron=
| congored=
| cresylv=
| dieterle=
| diffquik=
| fontana=
| gallyas=
| giemsa=
| gms=
| gomori=
| gram=
| gremelius=
| jms=
| jones=
| kinyoun=
| luxol=
| masson=
| mmas=
| movat=
| mucicar=
| oilredo=
| orecein=
| pas=
| pasd=
| pasf=
| ptah=
| prussian=
| reticulin=
| sudanblackb=
| toluidine=
| verhoeff=
| vonkossa=
| warthinstarry=
| zn=
}}
====IHC====
{{Case IHC
| blank=Dr Torres would ask why!
| a1at=
| acth=
| ae1ae3=
| afp=
| alk1=
| amacr=
| ar=
| b2microglobulin=
| b72_3=
| bcatenin=
| bcl2=
| bcl6=
| bclxl=
| c3=
| calcitonin=
| calponin=
| calretinin=
| cam5p2=
| cd10=
| cd117=
| cd138=
| cd15=
| cd1a=
| cd20=
| cd21=
| cd23=
| cd3=
| cd30=
| cd31=
| cd34=
| cd35=
| cd4=
| cd43=
| cd45=
| cd45=
| cd5=
| cd56=
| cd57=
| cd68=
| cd7=
| cd79a=
| cd8=
| cd99=
| cdx2=
| cea=
| chromo=
| chromo=
| ck17=
| ck19=
| ck20=
| ck34be12=
| ck5_6=
| ck7=
| cmv=
| cmyc=
| cyclin_d1=
| d2_40=
| desmin=
| dog1=
| ebv=
| ema=
| erpr=
| f_viii=
| f_xiiia=
| fascin=
| fsh=
| gastrin=
| gcdfp=
| gfap=
| gh=
| glucagon=
| glypican3=
| hbme1=
| hbv_core=
| hbv_surf=
| hcaldesmon=
| hcg=
| helicobacter=
| hepatocyte=
| her2=
| hhv8=
| hmb45=
| hnf1beta=
| hpv=
| hsv1=
| hsv2=
| Idh-1=
| inhibin=
| insulin=
| kappa=
| ki67=
| lambda=
| leu7=
| lga=
| lgg=
| lgm=
| lh=
| lysozyme=
| mammogl=
| mcv=
| melanin_a=
| mitf=
| mum1=
| myleoperox=
| myo_d1=
| myog=
| myog=
| nf=
| nse=
| oct3_4=
| p16=
| p53=
| p57=
| p63=
| panker=
| pax2=
| pax5=
| pax8=
| pcna=
| pdgfr=
| plap=
| pnl-2c=
| prolactin=
| psa=
| psap=
| rcc=
| s100=
| sma=
| somatsatin=
| synapto=
| tdt=
| tfe3=
| thyrogl=
| toxopl=
| tsh=
| ttf1=
| ubiquitin=
| uchl1=
| ulex_europe=
| vim=
| vip=
| vzv=
| wt1=
}}
====Chromosomal translocations====
{{Case Translocations
| blank=Dr Torres would ask why!
| t1_13=
| t2_13=
| t8_14=
| t9_22bcr_abl=
| t9_22chn_ews=
| t11_14=
| t11_22dsrct=
| t11_22ews=
| t12_15=
| t12_16afh=
| t12_16liposar=
| t12_22=
| t14_18=
| t15_17=
| t16_21=
| t17_22=
| t21_22=
| tx_1=
| tx_17=
| tx_18=
}}

===Diagnosis===
{{hidden|Diagnosis|<center>DIAGNOSIS GOES HERE</center>}}
 
===Other cases===
{{Cases navigation}}

__NOTOC__

[[Category:Cases]]



[[Category:Cases difficulty 4]]

Case 74

2014-07-06T00:11:05Z

Yuanny: /* Differential diagnosis */

===Provided clinical history===
46 year old man/woman, asymptomatic, incidental finding

===Site===
Ovary

===Primary image===
[[Image: Brenner tumour intermed mag.jpg |500px|link=|center|]]
<center>Low magnification. [[H&E stain]].</center>

{{hidden|Intermediate magnification|[[Image: Brenner tumour high mag.jpg |500px|link=|center|]]
<center>Intermediate magnification. [[H&E stain]].</center>}}

{{hidden|High magnification|[[Image: Brenner tumour high mag cropped.jpg |500px|link=|center|]]
<center>High magnification. [[H&E stain]].</center>}}

===Differential diagnosis===
{{hidden|Differential diagnosis|<center>[[Ovarian fibroma]], [[Thecoma]], [[Brenner tumour]]</center>}}

===Additional tests===
====More history====
{{hidden|More history|<center>MORE HISTORY HERE</center>}}

====Ask a colleague====
{{hidden|Ask a colleague|<center>COLLEAGUE'S ADVICE HERE</center>}}

====Stains====
{{Case Stains
| blank=Dr Torres would ask why!
| alcpas=
| alc1=
| alc25=
| aur=
| biel=
| bili=
| iron=
| congored=
| cresylv=
| dieterle=
| diffquik=
| fontana=
| gallyas=
| giemsa=
| gms=
| gomori=
| gram=
| gremelius=
| jms=
| jones=
| kinyoun=
| luxol=
| masson=
| mmas=
| movat=
| mucicar=
| oilredo=
| orecein=
| pas=
| pasd=
| pasf=
| ptah=
| prussian=
| reticulin=
| sudanblackb=
| toluidine=
| verhoeff=
| vonkossa=
| warthinstarry=
| zn=
}}
====IHC====
{{Case IHC
| blank=Dr Torres would ask why!
| a1at=
| acth=
| ae1ae3=
| afp=
| alk1=
| amacr=
| ar=
| b2microglobulin=
| b72_3=
| bcatenin=
| bcl2=
| bcl6=
| bclxl=
| c3=
| calcitonin=
| calponin=
| calretinin=
| cam5p2=
| cd10=
| cd117=
| cd138=
| cd15=
| cd1a=
| cd20=
| cd21=
| cd23=
| cd3=
| cd30=
| cd31=
| cd34=
| cd35=
| cd4=
| cd43=
| cd45=
| cd45=
| cd5=
| cd56=
| cd57=
| cd68=
| cd7=
| cd79a=
| cd8=
| cd99=
| cdx2=
| cea=
| chromo=
| chromo=
| ck17=
| ck19=
| ck20=
| ck34be12=
| ck5_6=
| ck7=
| cmv=
| cmyc=
| cyclin_d1=
| d2_40=
| desmin=
| dog1=
| ebv=
| ema=
| erpr=
| f_viii=
| f_xiiia=
| fascin=
| fsh=
| gastrin=
| gcdfp=
| gfap=
| gh=
| glucagon=
| glypican3=
| hbme1=
| hbv_core=
| hbv_surf=
| hcaldesmon=
| hcg=
| helicobacter=
| hepatocyte=
| her2=
| hhv8=
| hmb45=
| hnf1beta=
| hpv=
| hsv1=
| hsv2=
| Idh-1=
| inhibin=
| insulin=
| kappa=
| ki67=
| lambda=
| leu7=
| lga=
| lgg=
| lgm=
| lh=
| lysozyme=
| mammogl=
| mcv=
| melanin_a=
| mitf=
| mum1=
| myleoperox=
| myo_d1=
| myog=
| myog=
| nf=
| nse=
| oct3_4=
| p16=
| p53=
| p57=
| p63=
| panker=
| pax2=
| pax5=
| pax8=
| pcna=
| pdgfr=
| plap=
| pnl-2c=
| prolactin=
| psa=
| psap=
| rcc=
| s100=
| sma=
| somatsatin=
| synapto=
| tdt=
| tfe3=
| thyrogl=
| toxopl=
| tsh=
| ttf1=
| ubiquitin=
| uchl1=
| ulex_europe=
| vim=
| vip=
| vzv=
| wt1=
}}
====Chromosomal translocations====
{{Case Translocations
| blank=Dr Torres would ask why!
| t1_13=
| t2_13=
| t8_14=
| t9_22bcr_abl=
| t9_22chn_ews=
| t11_14=
| t11_22dsrct=
| t11_22ews=
| t12_15=
| t12_16afh=
| t12_16liposar=
| t12_22=
| t14_18=
| t15_17=
| t16_21=
| t17_22=
| t21_22=
| tx_1=
| tx_17=
| tx_18=
}}

===Diagnosis===
{{hidden|Diagnosis|<center>DIAGNOSIS GOES HERE</center>}}
 
===Other cases===
{{Cases navigation}}

__NOTOC__

[[Category:Cases]]



[[Category:Cases difficulty 4]]

Case 74

2014-07-06T00:09:27Z

Yuanny:

===Provided clinical history===
46 year old man/woman, asymptomatic, incidental finding

===Site===
Ovary

===Primary image===
[[Image: Brenner tumour intermed mag.jpg |500px|link=|center|]]
<center>Low magnification. [[H&E stain]].</center>

{{hidden|Intermediate magnification|[[Image: Brenner tumour high mag.jpg |500px|link=|center|]]
<center>Intermediate magnification. [[H&E stain]].</center>}}

{{hidden|High magnification|[[Image: Brenner tumour high mag cropped.jpg |500px|link=|center|]]
<center>High magnification. [[H&E stain]].</center>}}

===Differential diagnosis===
{{hidden|Differential diagnosis|<center>THE DDx GOES HERE</center>}}

===Additional tests===
====More history====
{{hidden|More history|<center>MORE HISTORY HERE</center>}}

====Ask a colleague====
{{hidden|Ask a colleague|<center>COLLEAGUE'S ADVICE HERE</center>}}

====Stains====
{{Case Stains
| blank=Dr Torres would ask why!
| alcpas=
| alc1=
| alc25=
| aur=
| biel=
| bili=
| iron=
| congored=
| cresylv=
| dieterle=
| diffquik=
| fontana=
| gallyas=
| giemsa=
| gms=
| gomori=
| gram=
| gremelius=
| jms=
| jones=
| kinyoun=
| luxol=
| masson=
| mmas=
| movat=
| mucicar=
| oilredo=
| orecein=
| pas=
| pasd=
| pasf=
| ptah=
| prussian=
| reticulin=
| sudanblackb=
| toluidine=
| verhoeff=
| vonkossa=
| warthinstarry=
| zn=
}}
====IHC====
{{Case IHC
| blank=Dr Torres would ask why!
| a1at=
| acth=
| ae1ae3=
| afp=
| alk1=
| amacr=
| ar=
| b2microglobulin=
| b72_3=
| bcatenin=
| bcl2=
| bcl6=
| bclxl=
| c3=
| calcitonin=
| calponin=
| calretinin=
| cam5p2=
| cd10=
| cd117=
| cd138=
| cd15=
| cd1a=
| cd20=
| cd21=
| cd23=
| cd3=
| cd30=
| cd31=
| cd34=
| cd35=
| cd4=
| cd43=
| cd45=
| cd45=
| cd5=
| cd56=
| cd57=
| cd68=
| cd7=
| cd79a=
| cd8=
| cd99=
| cdx2=
| cea=
| chromo=
| chromo=
| ck17=
| ck19=
| ck20=
| ck34be12=
| ck5_6=
| ck7=
| cmv=
| cmyc=
| cyclin_d1=
| d2_40=
| desmin=
| dog1=
| ebv=
| ema=
| erpr=
| f_viii=
| f_xiiia=
| fascin=
| fsh=
| gastrin=
| gcdfp=
| gfap=
| gh=
| glucagon=
| glypican3=
| hbme1=
| hbv_core=
| hbv_surf=
| hcaldesmon=
| hcg=
| helicobacter=
| hepatocyte=
| her2=
| hhv8=
| hmb45=
| hnf1beta=
| hpv=
| hsv1=
| hsv2=
| Idh-1=
| inhibin=
| insulin=
| kappa=
| ki67=
| lambda=
| leu7=
| lga=
| lgg=
| lgm=
| lh=
| lysozyme=
| mammogl=
| mcv=
| melanin_a=
| mitf=
| mum1=
| myleoperox=
| myo_d1=
| myog=
| myog=
| nf=
| nse=
| oct3_4=
| p16=
| p53=
| p57=
| p63=
| panker=
| pax2=
| pax5=
| pax8=
| pcna=
| pdgfr=
| plap=
| pnl-2c=
| prolactin=
| psa=
| psap=
| rcc=
| s100=
| sma=
| somatsatin=
| synapto=
| tdt=
| tfe3=
| thyrogl=
| toxopl=
| tsh=
| ttf1=
| ubiquitin=
| uchl1=
| ulex_europe=
| vim=
| vip=
| vzv=
| wt1=
}}
====Chromosomal translocations====
{{Case Translocations
| blank=Dr Torres would ask why!
| t1_13=
| t2_13=
| t8_14=
| t9_22bcr_abl=
| t9_22chn_ews=
| t11_14=
| t11_22dsrct=
| t11_22ews=
| t12_15=
| t12_16afh=
| t12_16liposar=
| t12_22=
| t14_18=
| t15_17=
| t16_21=
| t17_22=
| t21_22=
| tx_1=
| tx_17=
| tx_18=
}}

===Diagnosis===
{{hidden|Diagnosis|<center>DIAGNOSIS GOES HERE</center>}}
 
===Other cases===
{{Cases navigation}}

__NOTOC__

[[Category:Cases]]



[[Category:Cases difficulty 4]]

Cases

2014-07-06T00:04:37Z

Yuanny: /* Cases */

'''Cases''', also '''learning with simulated cases''' and '''interactive cases''', is a part of [[onlinepathology]] that is focused on individual specimens.

The cases presented usually do not exactly mirror the details behind the pictures. The reason they aren't exactly like real life is: real life often isn't a good test, e.g. if the requisition say ''Peutz-Jeghers syndrome'' and the specimen is ''polyps''... it isn't hard to diagnose the Peutz-Jeghers polyps.

==Objective==
The objective here is to simulate the decision making in pathology practise.

There are opportunities to look for more history, order [[special stains]], order [[immunostains]], order molecular testing for translocations, and ask a colleague -- before clicking on ''diagnosis'' to see if one is correct.

==Cases==
{| class="wikitable sortable"
! Case #
! Tease
! Subspecialty
! Difficulty
|-
| [[Case 1]]
| enlarged inguinal lymph node
| [[:Category:Cases in lymph node pathology|Lymph node pathology]]
| {{Hide |header=|content=[[:Category:Cases in lymph node pathology - fellow and expert|Fellow and expert]] }}
|-
| [[Case 2]]
| duodenal mass
| [[:Category:Cases in gastrointestinal pathology|Gastrointestinal pathology]]
| {{Hide |header=|content=[[:Category:Cases in gastrointestinal pathology - senior|Senior]] }}
|-
| [[Case 3]]
| renal mass
| [[:Category:Cases in genitourinary pathology|Genitourinary pathology]]
| {{Hide |header=|content=[[:Category:Cases in genitourinary pathology - senior|Senior]] }}
|-
| [[Case 4]]
| renal mass
| [[:Category:Cases in genitourinary pathology|Genitourinary pathology]]
| {{Hide |header=|content=[[:Category:Cases in genitourinary pathology - senior|Senior]] }}
|-
| [[Case 5]]
| cerebellar mass
| [[:Category:Cases in neuropathology|Neuropathology]]
| {{Hide |header=|content=[[:Category:Cases in neuropathology - junior|Junior]] }}
|-
| [[Case 6]]
| testicular mass
| [[:Category:Cases in genitourinary pathology|Genitourinary pathology]]
| {{Hide |header=|content=[[:Category:Cases in genitourinary pathology - junior|Junior]] }}
|-
| [[Case 7]]
| cervical lymphadenopathy
| [[:Category:Cases in lymph node pathology|Lymph node pathology]]
| {{Hide |header=|content=[[:Category:Cases in lymph node pathology - senior|Senior]] }}
|-
| [[Case 8]]
| cervical mass
| [[:Category:Cases in gynecologic pathology|Gynecologic pathology]]
| {{Hide |header=|content=[[:Category:Cases in gynecologic pathology - senior|Senior]] }}
|-
| [[Case 9]]
| brown esophageal ulcers
| [[:Category:Cases in gastrointestinal pathology|Gastrointestinal pathology]]
| {{Hide |header=|content=[[:Category:Cases in gastrointestinal pathology - senior|Senior]] }}
|-
| [[Case 10]]
| colon biopsy - diarrhea
| [[:Category:Cases in gastrointestinal pathology|Gastrointestinal pathology]]
| {{Hide |header=|content=[[:Category:Cases in gastrointestinal pathology - junior|Junior]] }}
|-
| [[Case 11]]
| pons - multi-organ dysfunction and stroke
| [[:Category:Cases in neuropathology|Neuropathology]]
| {{Hide |header=|content=[[:Category:Cases in neuropathology - senior|Senior]] }}
|-
| [[Case 12]]
| colon biopsy - diarrhea
| [[:Category:Cases in gastrointestinal pathology|Gastrointestinal pathology]]
| {{Hide |header=|content=[[:Category:Cases in gastrointestinal pathology - junior|Junior]] }}
|-
| [[Case 13]]
| renal mass
| [[:Category:Cases in genitourinary pathology|Genitourinary pathology]]
| {{Hide |header=|content=[[:Category:Cases in genitourinary pathology - senior|Senior]] }}
|-
| [[Case 14]]
| terminal ileum - hematochezia & diarrhea
| [[:Category:Cases in gastrointestinal pathology|Gastrointestinal pathology]]
| {{Hide |header=|content=[[:Category:Cases in gastrointestinal pathology - senior|Senior]] }}
|-
| [[Case 15]]
| duodenum - older man, weight loss
| [[:Category:Cases in gastrointestinal pathology|Gastrointestinal pathology]]
| {{Hide |header=|content=[[:Category:Cases in gastrointestinal pathology - junior|Junior]] }}
|-
| [[Case 16]]
| elbow lesion
| [[:Category:Cases in dermatopathology|Dermatopathology]]
| {{Hide |header=|content=[[:Category:Cases in dermatopathology - junior|Junior]] }}
|-
| [[Case 17]]
| colonic polyp
| [[:Category:Cases in gastrointestinal pathology|Gastrointestinal pathology]]
| {{Hide |header=|content=[[:Category:Cases in gastrointestinal pathology - senior|Senior]] }}
|-
| [[Case 18]]
| dome-shaped papules
| [[:Category:Cases in dermatopathology|Dermatopathology]]
| {{Hide |header=|content=[[:Category:Cases in dermatopathology - junior|Junior]] }}
|-
| [[Case 19]]
| vas deferens
| [[:Category:Cases in genitourinary pathology|Genitourinary pathology]]
| {{Hide |header=|content=[[:Category:Cases in genitourinary pathology - senior|Senior]] }}
|-
| [[Case 20]]
| failure to progress
| [[:Category:Cases in placental pathology|Placental pathology]]
| {{Hide |header=|content=[[:Category:Cases in placental pathology - junior|Junior]] }}
|-
| [[Case 21]]
| thyroid mass in young woman
| [[:Category:Cases in endocrine pathology|Endocrine pathology]]
| {{Hide |header=|content=[[:Category:Cases in endocrine pathology - junior|Junior]] }}
|-
| [[Case 22]]
| parotid mass
| [[:Category:Cases in head and neck pathology|Head and neck pathology]]
| {{Hide |header=|content=[[:Category:Cases in head and neck pathology - senior|Senior]] }}
|-
| [[Case 23]]
| 6 month old with chronic diarrhea
| [[:Category:Cases in pediatric pathology|Pediatric pathology]]
| {{Hide |header=|content=[[:Category:Cases in pediatric pathology - fellow and expert|Fellow and expert]] }}
|-
| [[Case 24]]
| breast of a young man
| [[:Category:Cases in breast pathology|Breast pathology]]
| {{Hide |header=|content=[[:Category:Cases in breast pathology - junior|Junior]] }}
|-
| [[Case 25]]
| breast mass
| [[:Category:Cases in breast pathology|Breast pathology]]
| {{Hide |header=|content=[[:Category:Cases in breast pathology - junior|Junior]] }}
|-
| [[Case 26]]
| bladder mass
| [[:Category:Cases in genitourinary pathology|Genitourinary pathology]]
| {{Hide |header=|content=[[:Category:Cases in genitourinary pathology - senior|Senior]] }}
|-
| [[Case 27]]
| skin with brown patches
| [[:Category:Cases in dermatopathology|Dermatopathology]]
| {{Hide |header=|content=[[:Category:Cases in dermatopathology - senior|Senior]] }}
|-
| [[Case 28]]
| woman with dyspnea
| [[:Category:Cases in pulmonary pathology|Pulmonary pathology]]
| {{Hide |header=|content=[[:Category:Cases in pulmonary pathology - senior|Senior]] }}
|-
| [[Case 29]]
| atrial mass
| [[:Category:Cases in cardiovascular pathology|Cardiovascular pathology]]
| {{Hide |header=|content=[[:Category:Cases in cardiovascular pathology - junior|Junior]] }}
|-
| [[Case 30]]
| anasarca and renal failure
| [[:Category:Cases in medical kidney pathology|Medical kidney pathology]]
| {{Hide |header=|content=[[:Category:Cases in medical kidney pathology - senior|Senior]] }}
|-
| [[Case 31]]
| scalp lesion
| [[:Category:Cases in dermatopathology|Dermatopathology]]
| {{Hide |header=|content=[[:Category:Cases in dermatopathology - senior|Senior]] }}
|-
| [[Case 32]]
| sudden death
| [[:Category:Cases in cardiovascular pathology|Cardiovascular pathology]]
| {{Hide |header=|content=[[:Category:Cases in cardiovascular pathology - senior|Senior]] }}
|-
| [[Case 33]]
| aortic valve mass
| [[:Category:Cases in cardiovascular pathology|Cardiovascular pathology]]
| {{Hide |header=|content=[[:Category:Cases in cardiovascular pathology - junior|Junior]] }}
|-
| [[Case 34]]
| "appendicitis"
| [[:Category:Cases in gastrointestinal pathology|Gastrointestinal pathology]]
| {{Hide |header=|content=[[:Category:Cases in gastrointestinal pathology - junior|Junior]] }}
|-
| [[Case 35]]
| RLQ abdominal pain with nausea & vomiting
| [[:Category:Cases in gastrointestinal pathology|Gastrointestinal pathology]]
| {{Hide |header=|content=[[:Category:Cases in gastrointestinal pathology - senior|Senior]] }}
|-
| [[Case 36]]
| routine pap test
| [[:Category:Cases in cytopathology|Cytopathology]]
| {{Hide |header=|content=[[:Category:Cases in cytopathology - junior|Junior]] }}
|-
| [[Case 37]]
| left arm lesion
| [[:Category:Cases in dermatopathology|Dermatopathology]]
| {{Hide |header=|content=[[:Category:Cases in dermatopathology - senior|Senior]] }}
|-
| [[Case 38]]
| screening colon
| [[:Category:Cases in gastrointestinal pathology|Gastrointestinal pathology]]
| {{Hide |header=|content=[[:Category:Cases in gastrointestinal pathology - junior|Junior]] }}
|-
| [[Case 39]]
| colonic polyp
| [[:Category:Cases in gastrointestinal pathology|Gastrointestinal pathology]]
| {{Hide |header=|content=[[:Category:Cases in gastrointestinal pathology - junior|Junior]] }}
|-
| [[Case 40]]
| stomach with large polyp
| [[:Category:Cases in gastrointestinal pathology|Gastrointestinal pathology]]
| {{Hide |header=|content=[[:Category:Cases in gastrointestinal pathology - senior|Senior]] }}
|-
| [[Case 41]]
| parotid mass
| [[:Category:Cases in head and neck pathology|Head and neck pathology]]
| {{Hide |header=|content=[[:Category:Cases in head and neck pathology - junior|Junior]] }}
|-
| [[Case 42]]
| parotid mass
| [[:Category:Cases in head and neck pathology|Head and neck pathology]]
| {{Hide |header=|content=[[:Category:Cases in head and neck pathology - junior|Junior]] }}
|-
| [[Case 43]]
| parotid mass
| [[:Category:Cases in head and neck pathology|Head and neck pathology]]
| {{Hide |header=|content=[[:Category:Cases in head and neck pathology - junior|Junior]] }}
|-
| [[Case 44]]
| placental lesion - white
| [[:Category:Cases in placental pathology|Placental pathology]]
| {{Hide |header=|content=[[:Category:Cases in placental pathology - junior|Junior]] }}
|-
| [[Case 45]]
| large ovarian mass
| [[:Category:Cases in gynecologic pathology|Gynecologic pathology]]
| {{Hide |header=|content=[[:Category:Cases in gynecologic pathology - senior|Senior]] }}
|-
| [[Case 46]]
| painful lesion, buttock
| [[:Category:Cases in soft tissue pathology|Soft tissue pathology]]
| {{Hide |header=|content=[[:Category:Cases in soft tissue pathology - senior|Senior]] }}
|-
| [[Case 47]]
| face lesion
| [[:Category:Cases in dermatopathology|Dermatopathology]]
| {{Hide |header=|content=[[:Category:Cases in dermatopathology - junior|Junior]] }}
|-
| [[Case 48]]
| colon lesion
| [[:Category:Cases in gastrointestinal pathology|Gastrointestinal pathology]]
| {{Hide |header=|content=[[:Category:Cases in gastrointestinal pathology - junior|Junior]] }}
|-
| [[Case 49]]
| eroded GI lesion
| [[:Category:Cases in gastrointestinal pathology|Gastrointestinal pathology]]
| {{Hide |header=|content=[[:Category:Cases in gastrointestinal pathology - junior|Junior]] }}
|-
| [[Case 50]]
| acute appendicitis
| [[:Category:Cases in gastrointestinal pathology|Gastrointestinal pathology]]
| {{Hide |header=|content=[[:Category:Cases in gastrointestinal pathology - junior|Junior]] }}
|-
| [[Case 51]]
| thyroid mass
| [[:Category:Cases in head and neck pathology|Head and neck pathology]]
| {{Hide |header=|content=[[:Category:Cases in head and neck pathology - senior|Senior]] }}
|-
| [[Case 52]]
| left lung mass
| [[:Category:Cases in pulmonary pathology|Pulmonary pathology]]
| {{Hide |header=|content=[[:Category:Cases in pulmonary pathology - junior|Junior]] }}
|-
| [[Case 53]]
| right lung biopsy
| [[:Category:Cases in pulmonary pathology|Pulmonary pathology]]
| {{Hide |header=|content=[[:Category:Cases in pulmonary pathology - junior|Junior]] }}
|-
| [[Case 54]]
| airspace disease unresponsive to antimicrobials
| [[:Category:Cases in pulmonary pathology|Pulmonary pathology]]
| {{Hide |header=|content=[[:Category:Cases in pulmonary pathology - senior|Senior]] }}
|-
| [[Case 55]]
| skin lesion
| [[:Category:Cases in dermatopathology|Dermatopathology]]
| {{Hide |header=|content=[[:Category:Cases in dermatopathology - junior|Junior]] }}
|-
| [[Case 56]]
| swelling at the angle of the jaw
| [[:Category:Cases in head and neck pathology|Head and neck pathology]]
| {{Hide |header=|content=[[:Category:Cases in head and neck pathology - junior|Junior]] }}
|-
| [[Case 57]]
| cervical biopsy
| [[:Category:Cases in gynecologic pathology|Gynecologic pathology]]
| {{Hide |header=|content=[[:Category:Cases in gynecologic pathology - junior|Junior]] }}
|-
| [[Case 58]]
| testicular mass
| [[:Category:Cases in genitourinary pathology|Genitourinary pathology]]
| {{Hide |header=|content=[[:Category:Cases in genitourinary pathology - junior|Junior]] }}
|-
| [[Case 59]]
| lymph node from a sigmoidectomy
| [[:Category:Cases in lymph node pathology|Lymph node pathology]]
| {{Hide |header=|content=[[:Category:Cases in lymph node pathology - junior|Junior]] }}
|-
| [[Case 60]]
| sigmoid polyp
| [[:Category:Cases in gastrointestinal pathology|Gastrointestinal pathology]]
| {{Hide |header=|content=[[:Category:Cases in gastrointestinal pathology - junior|Junior]] }}
|-
| [[Case 61]]
| rectal polyp
| [[:Category:Cases in gastrointestinal pathology|Gastrointestinal pathology]]
| {{Hide |header=|content=[[:Category:Cases in gastrointestinal pathology - junior|Junior]] }}
|-
| [[Case 62]]
| rectal polyp
| [[:Category:Cases in gastrointestinal pathology|Gastrointestinal pathology]]
| {{Hide |header=|content=[[:Category:Cases in gastrointestinal pathology - senior|Senior]] }}
|-
| [[Case 63]]
| urinary bladder lesion
| [[:Category:Cases in genitourinary pathology|Genitourinary pathology]]
| {{Hide |header=|content=[[:Category:Cases in genitourinary pathology - junior|Junior]] }}
|-
| [[Case 64]]
| kidney mass
| [[:Category:Cases in genitourinary pathology|Genitourinary pathology]]
| {{Hide |header=|content=[[:Category:Cases in genitourinary pathology - junior|Junior]] }}
|-
| [[Case 65]]
| dyspepsia in a young man
| [[:Category:Cases in gastrointestinal pathology|Gastrointestinal pathology]]
| {{Hide |header=|content=[[:Category:Cases in genitourinary pathology - junior|Junior]] }}
|-
| [[Case 66]]
| Uterine mass
| [[:Category:Cases in gynecologic pathology|Gynecologic pathology]]
| {{Hide |header=|content=[[:Category:Cases in Gynecologic pathology - junior|Junior]] }}
|-
| [[Case 67]]
| Lymph node/Colon Cancer
| [[:Category:Cases in lymph node pathology|Lymph node pathology]]
| {{Hide |header=|content=[[:Category:Cases in Lymph node pathology - junior|Junior]] }}
|-
| [[Case 68]]
| Lung Bx
| [[:Category:Cases in pulmonary pathology|Pulmonary pathology]]
| {{Hide |header=|content=[[:Category:Cases in pulmonary pathology - junior|Junior]] }}
|-
| [[Case 69]]
| Back lesion
| [[:Category:Cases in dermatopathology|Dermatopathology]]
| {{Hide |header=|content=[[:Category:Cases in dermatopathology - junior|Junior]] }}
|-
| [[Case 70]]
| Stomach biopsy
| [[:Category:Cases in gastrointestinal pathology|Gastrointestinal pathology]]
| {{Hide |header=|content=[[:Category:Cases in gastrointestinal pathology - junior|Junior]] }}
|-
| [[Case 71]]
| Lung Bx
| [[:Category:Cases in pulmonary pathology|Pulmonary pathology]]
| {{Hide |header=|content=[[:Category:Cases in pulmonary pathology - junior|Junior]] }}
|-
| [[Case 72]]
| Ureteral mass
| [[:Category:Cases in genitourinary pathology|Genitourinary pathology]]
| {{Hide |header=|content=[[:Category:Cases in genitourinary pathology - junior|Junior]] }}
|-
| [[Case 73]]
| Ovarian mass
| [[:Category:Cases in gynecologic pathology|Gynecologic pathology]]
| {{Hide |header=|content=[[:Category:Cases in gynecologic pathology - senior|Senior]] }}
|-
| [[Case 74]]
| Ovarian mass
| [[:Category:Cases in gynecologic pathology|Gynecologic pathology]]
| {{Hide |header=|content=[[:Category:Cases in gynecologic pathology - senior|Senior]] }}
|-
| [[Case 75]]
|
| [[:Category:Cases in placeholder|placeholder]]
| {{Hide |header=|content=[[:Category:Cases in pulmonary pathology - junior|Junior]] }}

|}

==See also==
*[[Case how-to]].
*[[Case:Notes]]

[[Category:Cases]]

Cases

2014-07-06T00:02:06Z

Yuanny:

'''Cases''', also '''learning with simulated cases''' and '''interactive cases''', is a part of [[onlinepathology]] that is focused on individual specimens.

The cases presented usually do not exactly mirror the details behind the pictures. The reason they aren't exactly like real life is: real life often isn't a good test, e.g. if the requisition say ''Peutz-Jeghers syndrome'' and the specimen is ''polyps''... it isn't hard to diagnose the Peutz-Jeghers polyps.

==Objective==
The objective here is to simulate the decision making in pathology practise.

There are opportunities to look for more history, order [[special stains]], order [[immunostains]], order molecular testing for translocations, and ask a colleague -- before clicking on ''diagnosis'' to see if one is correct.

==Cases==
{| class="wikitable sortable"
! Case #
! Tease
! Subspecialty
! Difficulty
|-
| [[Case 1]]
| enlarged inguinal lymph node
| [[:Category:Cases in lymph node pathology|Lymph node pathology]]
| {{Hide |header=|content=[[:Category:Cases in lymph node pathology - fellow and expert|Fellow and expert]] }}
|-
| [[Case 2]]
| duodenal mass
| [[:Category:Cases in gastrointestinal pathology|Gastrointestinal pathology]]
| {{Hide |header=|content=[[:Category:Cases in gastrointestinal pathology - senior|Senior]] }}
|-
| [[Case 3]]
| renal mass
| [[:Category:Cases in genitourinary pathology|Genitourinary pathology]]
| {{Hide |header=|content=[[:Category:Cases in genitourinary pathology - senior|Senior]] }}
|-
| [[Case 4]]
| renal mass
| [[:Category:Cases in genitourinary pathology|Genitourinary pathology]]
| {{Hide |header=|content=[[:Category:Cases in genitourinary pathology - senior|Senior]] }}
|-
| [[Case 5]]
| cerebellar mass
| [[:Category:Cases in neuropathology|Neuropathology]]
| {{Hide |header=|content=[[:Category:Cases in neuropathology - junior|Junior]] }}
|-
| [[Case 6]]
| testicular mass
| [[:Category:Cases in genitourinary pathology|Genitourinary pathology]]
| {{Hide |header=|content=[[:Category:Cases in genitourinary pathology - junior|Junior]] }}
|-
| [[Case 7]]
| cervical lymphadenopathy
| [[:Category:Cases in lymph node pathology|Lymph node pathology]]
| {{Hide |header=|content=[[:Category:Cases in lymph node pathology - senior|Senior]] }}
|-
| [[Case 8]]
| cervical mass
| [[:Category:Cases in gynecologic pathology|Gynecologic pathology]]
| {{Hide |header=|content=[[:Category:Cases in gynecologic pathology - senior|Senior]] }}
|-
| [[Case 9]]
| brown esophageal ulcers
| [[:Category:Cases in gastrointestinal pathology|Gastrointestinal pathology]]
| {{Hide |header=|content=[[:Category:Cases in gastrointestinal pathology - senior|Senior]] }}
|-
| [[Case 10]]
| colon biopsy - diarrhea
| [[:Category:Cases in gastrointestinal pathology|Gastrointestinal pathology]]
| {{Hide |header=|content=[[:Category:Cases in gastrointestinal pathology - junior|Junior]] }}
|-
| [[Case 11]]
| pons - multi-organ dysfunction and stroke
| [[:Category:Cases in neuropathology|Neuropathology]]
| {{Hide |header=|content=[[:Category:Cases in neuropathology - senior|Senior]] }}
|-
| [[Case 12]]
| colon biopsy - diarrhea
| [[:Category:Cases in gastrointestinal pathology|Gastrointestinal pathology]]
| {{Hide |header=|content=[[:Category:Cases in gastrointestinal pathology - junior|Junior]] }}
|-
| [[Case 13]]
| renal mass
| [[:Category:Cases in genitourinary pathology|Genitourinary pathology]]
| {{Hide |header=|content=[[:Category:Cases in genitourinary pathology - senior|Senior]] }}
|-
| [[Case 14]]
| terminal ileum - hematochezia & diarrhea
| [[:Category:Cases in gastrointestinal pathology|Gastrointestinal pathology]]
| {{Hide |header=|content=[[:Category:Cases in gastrointestinal pathology - senior|Senior]] }}
|-
| [[Case 15]]
| duodenum - older man, weight loss
| [[:Category:Cases in gastrointestinal pathology|Gastrointestinal pathology]]
| {{Hide |header=|content=[[:Category:Cases in gastrointestinal pathology - junior|Junior]] }}
|-
| [[Case 16]]
| elbow lesion
| [[:Category:Cases in dermatopathology|Dermatopathology]]
| {{Hide |header=|content=[[:Category:Cases in dermatopathology - junior|Junior]] }}
|-
| [[Case 17]]
| colonic polyp
| [[:Category:Cases in gastrointestinal pathology|Gastrointestinal pathology]]
| {{Hide |header=|content=[[:Category:Cases in gastrointestinal pathology - senior|Senior]] }}
|-
| [[Case 18]]
| dome-shaped papules
| [[:Category:Cases in dermatopathology|Dermatopathology]]
| {{Hide |header=|content=[[:Category:Cases in dermatopathology - junior|Junior]] }}
|-
| [[Case 19]]
| vas deferens
| [[:Category:Cases in genitourinary pathology|Genitourinary pathology]]
| {{Hide |header=|content=[[:Category:Cases in genitourinary pathology - senior|Senior]] }}
|-
| [[Case 20]]
| failure to progress
| [[:Category:Cases in placental pathology|Placental pathology]]
| {{Hide |header=|content=[[:Category:Cases in placental pathology - junior|Junior]] }}
|-
| [[Case 21]]
| thyroid mass in young woman
| [[:Category:Cases in endocrine pathology|Endocrine pathology]]
| {{Hide |header=|content=[[:Category:Cases in endocrine pathology - junior|Junior]] }}
|-
| [[Case 22]]
| parotid mass
| [[:Category:Cases in head and neck pathology|Head and neck pathology]]
| {{Hide |header=|content=[[:Category:Cases in head and neck pathology - senior|Senior]] }}
|-
| [[Case 23]]
| 6 month old with chronic diarrhea
| [[:Category:Cases in pediatric pathology|Pediatric pathology]]
| {{Hide |header=|content=[[:Category:Cases in pediatric pathology - fellow and expert|Fellow and expert]] }}
|-
| [[Case 24]]
| breast of a young man
| [[:Category:Cases in breast pathology|Breast pathology]]
| {{Hide |header=|content=[[:Category:Cases in breast pathology - junior|Junior]] }}
|-
| [[Case 25]]
| breast mass
| [[:Category:Cases in breast pathology|Breast pathology]]
| {{Hide |header=|content=[[:Category:Cases in breast pathology - junior|Junior]] }}
|-
| [[Case 26]]
| bladder mass
| [[:Category:Cases in genitourinary pathology|Genitourinary pathology]]
| {{Hide |header=|content=[[:Category:Cases in genitourinary pathology - senior|Senior]] }}
|-
| [[Case 27]]
| skin with brown patches
| [[:Category:Cases in dermatopathology|Dermatopathology]]
| {{Hide |header=|content=[[:Category:Cases in dermatopathology - senior|Senior]] }}
|-
| [[Case 28]]
| woman with dyspnea
| [[:Category:Cases in pulmonary pathology|Pulmonary pathology]]
| {{Hide |header=|content=[[:Category:Cases in pulmonary pathology - senior|Senior]] }}
|-
| [[Case 29]]
| atrial mass
| [[:Category:Cases in cardiovascular pathology|Cardiovascular pathology]]
| {{Hide |header=|content=[[:Category:Cases in cardiovascular pathology - junior|Junior]] }}
|-
| [[Case 30]]
| anasarca and renal failure
| [[:Category:Cases in medical kidney pathology|Medical kidney pathology]]
| {{Hide |header=|content=[[:Category:Cases in medical kidney pathology - senior|Senior]] }}
|-
| [[Case 31]]
| scalp lesion
| [[:Category:Cases in dermatopathology|Dermatopathology]]
| {{Hide |header=|content=[[:Category:Cases in dermatopathology - senior|Senior]] }}
|-
| [[Case 32]]
| sudden death
| [[:Category:Cases in cardiovascular pathology|Cardiovascular pathology]]
| {{Hide |header=|content=[[:Category:Cases in cardiovascular pathology - senior|Senior]] }}
|-
| [[Case 33]]
| aortic valve mass
| [[:Category:Cases in cardiovascular pathology|Cardiovascular pathology]]
| {{Hide |header=|content=[[:Category:Cases in cardiovascular pathology - junior|Junior]] }}
|-
| [[Case 34]]
| "appendicitis"
| [[:Category:Cases in gastrointestinal pathology|Gastrointestinal pathology]]
| {{Hide |header=|content=[[:Category:Cases in gastrointestinal pathology - junior|Junior]] }}
|-
| [[Case 35]]
| RLQ abdominal pain with nausea & vomiting
| [[:Category:Cases in gastrointestinal pathology|Gastrointestinal pathology]]
| {{Hide |header=|content=[[:Category:Cases in gastrointestinal pathology - senior|Senior]] }}
|-
| [[Case 36]]
| routine pap test
| [[:Category:Cases in cytopathology|Cytopathology]]
| {{Hide |header=|content=[[:Category:Cases in cytopathology - junior|Junior]] }}
|-
| [[Case 37]]
| left arm lesion
| [[:Category:Cases in dermatopathology|Dermatopathology]]
| {{Hide |header=|content=[[:Category:Cases in dermatopathology - senior|Senior]] }}
|-
| [[Case 38]]
| screening colon
| [[:Category:Cases in gastrointestinal pathology|Gastrointestinal pathology]]
| {{Hide |header=|content=[[:Category:Cases in gastrointestinal pathology - junior|Junior]] }}
|-
| [[Case 39]]
| colonic polyp
| [[:Category:Cases in gastrointestinal pathology|Gastrointestinal pathology]]
| {{Hide |header=|content=[[:Category:Cases in gastrointestinal pathology - junior|Junior]] }}
|-
| [[Case 40]]
| stomach with large polyp
| [[:Category:Cases in gastrointestinal pathology|Gastrointestinal pathology]]
| {{Hide |header=|content=[[:Category:Cases in gastrointestinal pathology - senior|Senior]] }}
|-
| [[Case 41]]
| parotid mass
| [[:Category:Cases in head and neck pathology|Head and neck pathology]]
| {{Hide |header=|content=[[:Category:Cases in head and neck pathology - junior|Junior]] }}
|-
| [[Case 42]]
| parotid mass
| [[:Category:Cases in head and neck pathology|Head and neck pathology]]
| {{Hide |header=|content=[[:Category:Cases in head and neck pathology - junior|Junior]] }}
|-
| [[Case 43]]
| parotid mass
| [[:Category:Cases in head and neck pathology|Head and neck pathology]]
| {{Hide |header=|content=[[:Category:Cases in head and neck pathology - junior|Junior]] }}
|-
| [[Case 44]]
| placental lesion - white
| [[:Category:Cases in placental pathology|Placental pathology]]
| {{Hide |header=|content=[[:Category:Cases in placental pathology - junior|Junior]] }}
|-
| [[Case 45]]
| large ovarian mass
| [[:Category:Cases in gynecologic pathology|Gynecologic pathology]]
| {{Hide |header=|content=[[:Category:Cases in gynecologic pathology - senior|Senior]] }}
|-
| [[Case 46]]
| painful lesion, buttock
| [[:Category:Cases in soft tissue pathology|Soft tissue pathology]]
| {{Hide |header=|content=[[:Category:Cases in soft tissue pathology - senior|Senior]] }}
|-
| [[Case 47]]
| face lesion
| [[:Category:Cases in dermatopathology|Dermatopathology]]
| {{Hide |header=|content=[[:Category:Cases in dermatopathology - junior|Junior]] }}
|-
| [[Case 48]]
| colon lesion
| [[:Category:Cases in gastrointestinal pathology|Gastrointestinal pathology]]
| {{Hide |header=|content=[[:Category:Cases in gastrointestinal pathology - junior|Junior]] }}
|-
| [[Case 49]]
| eroded GI lesion
| [[:Category:Cases in gastrointestinal pathology|Gastrointestinal pathology]]
| {{Hide |header=|content=[[:Category:Cases in gastrointestinal pathology - junior|Junior]] }}
|-
| [[Case 50]]
| acute appendicitis
| [[:Category:Cases in gastrointestinal pathology|Gastrointestinal pathology]]
| {{Hide |header=|content=[[:Category:Cases in gastrointestinal pathology - junior|Junior]] }}
|-
| [[Case 51]]
| thyroid mass
| [[:Category:Cases in head and neck pathology|Head and neck pathology]]
| {{Hide |header=|content=[[:Category:Cases in head and neck pathology - senior|Senior]] }}
|-
| [[Case 52]]
| left lung mass
| [[:Category:Cases in pulmonary pathology|Pulmonary pathology]]
| {{Hide |header=|content=[[:Category:Cases in pulmonary pathology - junior|Junior]] }}
|-
| [[Case 53]]
| right lung biopsy
| [[:Category:Cases in pulmonary pathology|Pulmonary pathology]]
| {{Hide |header=|content=[[:Category:Cases in pulmonary pathology - junior|Junior]] }}
|-
| [[Case 54]]
| airspace disease unresponsive to antimicrobials
| [[:Category:Cases in pulmonary pathology|Pulmonary pathology]]
| {{Hide |header=|content=[[:Category:Cases in pulmonary pathology - senior|Senior]] }}
|-
| [[Case 55]]
| skin lesion
| [[:Category:Cases in dermatopathology|Dermatopathology]]
| {{Hide |header=|content=[[:Category:Cases in dermatopathology - junior|Junior]] }}
|-
| [[Case 56]]
| swelling at the angle of the jaw
| [[:Category:Cases in head and neck pathology|Head and neck pathology]]
| {{Hide |header=|content=[[:Category:Cases in head and neck pathology - junior|Junior]] }}
|-
| [[Case 57]]
| cervical biopsy
| [[:Category:Cases in gynecologic pathology|Gynecologic pathology]]
| {{Hide |header=|content=[[:Category:Cases in gynecologic pathology - junior|Junior]] }}
|-
| [[Case 58]]
| testicular mass
| [[:Category:Cases in genitourinary pathology|Genitourinary pathology]]
| {{Hide |header=|content=[[:Category:Cases in genitourinary pathology - junior|Junior]] }}
|-
| [[Case 59]]
| lymph node from a sigmoidectomy
| [[:Category:Cases in lymph node pathology|Lymph node pathology]]
| {{Hide |header=|content=[[:Category:Cases in lymph node pathology - junior|Junior]] }}
|-
| [[Case 60]]
| sigmoid polyp
| [[:Category:Cases in gastrointestinal pathology|Gastrointestinal pathology]]
| {{Hide |header=|content=[[:Category:Cases in gastrointestinal pathology - junior|Junior]] }}
|-
| [[Case 61]]
| rectal polyp
| [[:Category:Cases in gastrointestinal pathology|Gastrointestinal pathology]]
| {{Hide |header=|content=[[:Category:Cases in gastrointestinal pathology - junior|Junior]] }}
|-
| [[Case 62]]
| rectal polyp
| [[:Category:Cases in gastrointestinal pathology|Gastrointestinal pathology]]
| {{Hide |header=|content=[[:Category:Cases in gastrointestinal pathology - senior|Senior]] }}
|-
| [[Case 63]]
| urinary bladder lesion
| [[:Category:Cases in genitourinary pathology|Genitourinary pathology]]
| {{Hide |header=|content=[[:Category:Cases in genitourinary pathology - junior|Junior]] }}
|-
| [[Case 64]]
| kidney mass
| [[:Category:Cases in genitourinary pathology|Genitourinary pathology]]
| {{Hide |header=|content=[[:Category:Cases in genitourinary pathology - junior|Junior]] }}
|-
| [[Case 65]]
| dyspepsia in a young man
| [[:Category:Cases in gastrointestinal pathology|Gastrointestinal pathology]]
| {{Hide |header=|content=[[:Category:Cases in genitourinary pathology - junior|Junior]] }}
|-
| [[Case 66]]
| Uterine mass
| [[:Category:Cases in gynecologic pathology|Gynecologic pathology]]
| {{Hide |header=|content=[[:Category:Cases in Gynecologic pathology - junior|Junior]] }}
|-
| [[Case 67]]
| Lymph node/Colon Cancer
| [[:Category:Cases in lymph node pathology|Lymph node pathology]]
| {{Hide |header=|content=[[:Category:Cases in Lymph node pathology - junior|Junior]] }}
|-
| [[Case 68]]
| Lung Bx
| [[:Category:Cases in pulmonary pathology|Pulmonary pathology]]
| {{Hide |header=|content=[[:Category:Cases in pulmonary pathology - junior|Junior]] }}
|-
| [[Case 69]]
| Back lesion
| [[:Category:Cases in dermatopathology|Dermatopathology]]
| {{Hide |header=|content=[[:Category:Cases in dermatopathology - junior|Junior]] }}
|-
| [[Case 70]]
| Stomach biopsy
| [[:Category:Cases in gastrointestinal pathology|Gastrointestinal pathology]]
| {{Hide |header=|content=[[:Category:Cases in gastrointestinal pathology - junior|Junior]] }}
|-
| [[Case 71]]
| Lung Bx
| [[:Category:Cases in pulmonary pathology|Pulmonary pathology]]
| {{Hide |header=|content=[[:Category:Cases in pulmonary pathology - junior|Junior]] }}
|-
| [[Case 72]]
| Ureteral mass
| [[:Category:Cases in genitourinary pathology|Genitourinary pathology]]
| {{Hide |header=|content=[[:Category:Cases in genitourinary pathology - junior|Junior]] }}
|-
| [[Case 73]]
| Ovarian mass
| [[:Category:Cases in gynecologic pathology|Gynecologic pathology]]
| {{Hide |header=|content=[[:Category:Cases in gynecologic pathology - senior|Senior]] }}
|-
| [[Case 74]]
|
| [[:Category:Cases in gynecologic pathology|Gynecologic pathology]]
| {{Hide |header=|content=[[:Category:Cases in gynecologic pathology - senior|Senior]] }}
|-
| [[Case 75]]
|
| [[:Category:Cases in placeholder|placeholder]]
| {{Hide |header=|content=[[:Category:Cases in pulmonary pathology - junior|Junior]] }}

|}

==See also==
*[[Case how-to]].
*[[Case:Notes]]

[[Category:Cases]]

Case 73

2014-07-05T23:53:56Z

Yuanny: /* Other cases */

===Provided clinical history===
22 year old woman, Ovarian mass

===Site===
Left Ovary Bx

===Primary image===
[[Image: Sertoli-Leydig cell tumour - intermed mag.jpg |500px|link=|center|]]
<center>Low magnification. [[H&E stain]].</center>

{{hidden|Intermediate magnification|[[Image: Sertoli-Leydig cell tumour - high mag.jpg |500px|link=|center|]]
<center>Intermediate magnification. [[H&E stain]].</center>}}

{{hidden|High magnification|[[Image: Sertoli-Leydig cell tumour - very high mag.jpg |500px|link=|center|]]
<center>High magnification. [[H&E stain]].</center>}}

===Differential diagnosis===
{{hidden|Differential diagnosis|<center>[[Endometrioid carcinoma of the ovary]], Luteinized adult granulosa cell tumour, [[Sertoli-Leydig cell tumour]]</center>}}

===Additional tests===
====More history====
{{hidden|More history|<center>6 months history of Anovulation, recent history of progressive masculinization. </center>}}

====Ask a colleague====
{{hidden|Ask a colleague|<center>When these cells are found in testes, they may be normal</center>}}

====Stains====
{{Case Stains
| blank=Dr Torres would ask why!
| alcpas=
| alc1=
| alc25=
| aur=
| biel=
| bili=
| iron=
| congored=
| cresylv=
| dieterle=
| diffquik=
| fontana=
| gallyas=
| giemsa=
| gms=
| gomori=
| gram=
| gremelius=
| jms=
| jones=
| kinyoun=
| luxol=
| masson=
| mmas=
| movat=
| mucicar=
| oilredo=
| orecein=
| pas=
| pasd=
| pasf=
| ptah=
| prussian=
| reticulin=
| sudanblackb=
| toluidine=
| verhoeff=
| vonkossa=
| warthinstarry=
| zn=
}}
====IHC====
{{Case IHC
| blank=Dr Torres would ask why!
| a1at=
| acth=
| ae1ae3=
| afp= +ve
| alk1=
| amacr=
| ar=
| b2microglobulin=
| b72_3=
| bcatenin=
| bcl2=
| bcl6=
| bclxl=
| c3=
| calcitonin=
| calponin=
| calretinin= +ve
| cam5p2=
| cd10=
| cd117=
| cd138=
| cd15=
| cd1a=
| cd20=
| cd21=
| cd23=
| cd3=
| cd30=
| cd31=
| cd34= -ve
| cd35=
| cd4=
| cd43=
| cd45=
| cd45=
| cd5=
| cd56=
| cd57=
| cd68=
| cd7=
| cd79a=
| cd8=
| cd99= +ve
| cdx2=
| cea= -ve
| chromo=
| chromo=
| ck17=
| ck19=
| ck20=
| ck34be12=
| ck5_6=
| ck7=
| cmv=
| cmyc=
| cyclin_d1=
| d2_40=
| desmin=
| dog1=
| ebv=
| ema= -ve
| erpr=
| f_viii=
| f_xiiia=
| fascin=
| fsh=
| gastrin=
| gcdfp=
| gfap=
| gh=
| glucagon=
| glypican3=
| hbme1=
| hbv_core=
| hbv_surf=
| hcaldesmon=
| hcg=
| helicobacter=
| hepatocyte=
| her2=
| hhv8=
| hmb45=
| hnf1beta=
| hpv=
| hsv1=
| hsv2=
| Idh-1=
| inhibin=
| insulin=
| kappa=
| ki67=
| lambda=
| leu7=
| lga=
| lgg=
| lgm=
| lh=
| lysozyme=
| mammogl=
| mcv=
| melanin_a=
| Melan A = +ve
| mitf=
| mum1=
| myleoperox=
| myo_d1=
| myog=
| myog=
| nf=
| nse=
| oct3_4=
| p16=
| p53=
| p57=
| p63=
| panker=
| pax2=
| pax5=
| pax8=
| pcna=
| pdgfr=
| plap= -ve
| pnl-2c=
| prolactin=
| psa=
| psap=
| rcc=
| s100= -ve
| sma=
| somatsatin=
| synapto=
| tdt=
| tfe3=
| thyrogl=
| toxopl=
| tsh=
| ttf1=
| ubiquitin=
| uchl1=
| ulex_europe=
| vim= +ve
| vip=
| vzv=
| wt1= +ve
}}
====Chromosomal translocations====
{{Case Translocations
| blank=Dr Torres would ask why!
| t1_13=
| t2_13=
| t8_14=
| t9_22bcr_abl=
| t9_22chn_ews=
| t11_14=
| t11_22dsrct=
| t11_22ews=
| t12_15=
| t12_16afh=
| t12_16liposar=
| t12_22=
| t14_18=
| t15_17=
| t16_21=
| t17_22=
| t21_22=
| tx_1=
| tx_17=
| tx_18=
}}

===Diagnosis===
{{hidden|Diagnosis|<center>[[Sertoli-Leydig cell tumour]]</center>}}
 

===Other cases===
{{Cases navigation}}

__NOTOC__

[[Category:Cases]]
[[Category:Cases in gynecologic pathology]]
[[Category:Cases difficulty 4]]
[[Category:Cases in gynecologic pathology - senior]]