BIOL 411 - 2017 Autumn - Exam 2 - Answer Key.pdf

BIOL 411 - 2017 Autumn - Exam 2 - Answer Key.pdf - BIOL 411...

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Unformatted text preview: BIOL​ ​411​ ​-​ ​2017​ ​Autumn Exam​ ​2 Name:​ ​Name​ ​is​ ​written​ ​on​ ​every​ ​page. Date: Write​ ​your​ ​name​ ​on​ ​each​ ​page;​ ​points​ ​will​ ​be​ ​deducted​ ​for​ ​omitted​ ​names.​ ​Write​ ​concise,​ ​precise sentences​ ​or​ ​lists,​ ​as​ ​appropriate.​ ​Do​ ​not​ ​exceed​ ​the​ ​space​ ​provided.​ ​Read​ ​all​ ​instructions​ ​carefully. 1.​ ​To​ ​identify​ ​genes​ ​that​ ​control​ ​development,​ ​Christiane​ ​Nüsslein-Volhard​ ​and​ ​Eric​ ​Wieschaus​ ​screened​ ​for mutants​ ​in​ ​Drosophila​ ​with​ ​body​ ​plan​ ​defects.​ ​They​ ​characterized​ ​the​ ​corresponding​ ​genes,​ ​placing​ ​them​ ​into three​ ​categories.​ ​(Total:​ ​37​ ​points) A. Distinguish​ ​these​ ​three​ ​categories​ ​from​ ​one​ ​another​ ​by​ ​completing​ ​the​ ​following​ ​table.​ E ​ ach​ ​item​ ​is worth​ ​2​ ​points,​ ​for​ ​a​ ​total​ ​of​ ​12​ ​points. What​ ​loss-of-function​ ​mutant phenotype​ ​typifies​ ​the​ ​category?​ ​Be specific,​ ​morphologically. Which​ ​expression​ ​pattern​ ​(i.e.,​ ​A,​ ​B, C,​ ​or​ ​D)​ ​typifies​ ​the​ ​category? Gap​ ​genes lack​ ​several​ ​contiguous​ ​segments (or​ ​large​ ​regions) D Pair-rule​ ​genes lack​ ​portions​ ​of​ ​every​ ​other segment C Segment​ ​polarity​ ​genes show​ ​defects​ ​in​ ​every​ ​segment​ ​(or lack​ ​portions​ ​of​ ​every​ ​segment) A Expression​ ​Pattern​ ​A Expression​ ​Pattern​ ​B Expression​ ​Pattern​ ​C Expression​ ​Pattern​ ​D B. Additional​ ​genetic​ ​experiments,​ ​biochemical​ ​analyses,​ ​and​ ​mathematical​ ​modeling​ ​revealed​ ​a​ ​gap gene​ ​network​ ​that​ ​is​ ​established​ ​by​ ​interactions​ ​among​ ​the​ ​gene​ ​products. i.​ ​Circle​ ​any​ ​gene​ ​products​ ​in​ ​this​ ​model​ ​that​ ​are​ ​not gap​ ​genes.​ ​Bcd​ ​and​ ​Cad​ ​(which​ ​are​ ​maternal effect​ ​genes)​ ​are​ ​circled​ ​(3​ ​points). ii.​ ​Based​ ​on​ ​the​ ​model​ ​on​ ​the​ ​left​ ​(not memorization!),​ ​sketch​ ​the​ ​curve​ ​that​ ​you​ ​would anticipate​ ​for​ ​Giant​ ​(Gt).​ ​The​ ​Gt​ ​curve​ ​has​ ​an anterior​ ​peak​ ​and​ ​a​ ​posterior​ ​peak,​ ​with​ ​the​ ​Kr peak​ ​in​ ​between​ ​these​ ​two​ ​peaks​ ​(3​ ​points). Page​ ​1 BIOL​ ​411​ ​-​ ​2017​ ​Autumn Exam​ ​2 Name:​ ​Name​ ​is​ ​written​ ​on​ ​every​ ​page. Date: C. Pair-rule​ ​gene​ ​products​ ​regulate​ ​segment​ ​polarity​ ​genes,​ ​which​ ​encode​ ​components​ ​of​ ​Hedgehog​ ​and Wnt​ ​signaling​ ​pathways.​ ​Synthesize​ ​your​ ​understanding​ ​of​ ​regulation​ ​of​ ​segment​ ​polarity​ ​genes, Hedgehog​ ​signaling,​ ​and​ ​Wnt​ ​signaling,​ ​by​ ​building​ ​a​ ​map​ ​of​ ​the​ ​interactions​ ​among​ ​the​ ​following components.​ ​Hint:​ ​Eve/Ftz/Prd​ ​and​ ​Odd/Run/Slp​ ​are​ ​pair-rule​ ​genes. Use​ ​arrows​​ ​to​ ​represent​ ​activations​ ​and​ ​blocking-arrows​​ ​to​ ​represent​ ​inhibitions.​ ​Do​ ​not​ ​use​ ​any additional​ ​words​ ​on​ ​your​ ​map.​ ​In​ ​addition,​ ​circle​​ ​any​ ​components​ ​that​ ​are​ ​responsible​ ​for​ ​initiating (rather​ ​than​ ​maintaining)​ ​the​ ​expression​ ​patterns​ ​of​ ​Engrailed​ ​and​ ​Wingless​ ​(Wnt).​ ​Note:​ ​The​ ​pathways may​ ​branch​ ​and​ ​converge.​ ​In​ ​other​ ​words,​ ​the​ ​pathways​ ​may​ ​not​ ​be​ ​completely​ ​linear. β-catenin,​ ​Cell​ ​Fate​ ​Specification​ ​(via​ ​gradients),​ ​Cubitus​ ​Interruptus,​ ​Disheveled,​ ​Engrailed, Eve/Ftz/Prd,​ ​Frizzled,​ ​GSK3,​ ​Hedgehog,​ ​Odd/Run/Slp,​ ​Patched,​ ​Smoothened,​ ​Wingless​ ​(Wnt) Each​ ​of​ ​the​ ​following​ ​functional​ ​interactions​ ​is​ ​worth​ ​1​ ​point,​ ​for​ ​a​ ​total​ ​of​ ​16​ ​points.​ ​Note: Additional​ ​arrows​ ​may​ ​be​ ​possible. ​ ​ ​ ​ ​ ​ ​ ​-------------------------------------→​ ​Cell​ ​Fate​ ​Specification​ ​(via​ ​gradients)​ ​←-----------------​ ​ ​ ​ ​ ​ ​ ​|​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​| ​ ​ ​ ​ ​ ​ ​ ​|​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​Eve/Ftz/Prd​ ​---------------------------------------------------------------------------​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​| ​ ​ ​ ​ ​ ​ ​ ​|​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​↓​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​⊥​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​| Hedgehog​ ​←​ ​Engrailed​ ​←​ ​β-catenin​ ​⊢​ ​GSK3​ ​⊢​ ​Disheveled​ ​←​ ​Frizzled​ ​←​ ​Wingless​ ​(Wnt) ​ ​ ​ ​ ​ ​ ​ ​|​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​⊤​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​↑​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​↑ ​ ​ ​ ​ ​ ​ ​⊥​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​Odd/Run/Slp​ ​---------------------------------------------------------------------------​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​| Patched​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​| ​ ​ ​ ​ ​ ​ ​⊥​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​| Smoothened​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​| ​ ​ ​ ​ ​ ​ ​ ​↓​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​| Cubitus​ ​Interruptus​ ​---------------------------------------------------------------------------------------------In​ ​addition,​ ​Eve/Ftz/Prd​ ​and​ ​Odd/Run/Slp​ ​(which​ ​are​ ​pair-rule​ ​genes)​ ​are​ ​circled​ ​(1​ ​point). D. Gap​ ​genes,​ ​pair-rule​ ​genes,​ ​and​ ​segment​ ​polarity​ ​genes​ ​work​ ​together​ ​to​ ​generate​ ​periodicity​ ​from nonperiodicity​ ​and​ ​to​ ​provide​ ​each​ ​unit​ ​with​ ​a​ ​unique​ ​identity​ ​(e.g.,​ ​activation​ ​of​ ​specific​ ​homeotic genes).​ ​Without​ ​using​ ​gene​ ​names,​ ​explain​ ​what​ ​distinguishes​ ​each​ ​band​ ​of​ ​nuclei​ ​within​ ​a parasegment​ ​from​ ​the​ ​other​ ​bands.​ ​Hint:​ ​Consider​ ​differential​ ​gene​ ​expression. Different​ ​concentrations​ ​and​ ​combinations​ ​of​ ​segment​ ​gene​ ​products​ ​provide​ ​specific “addresses”​ ​for​ ​individual​ ​cells​ ​(and​ ​regulate​ ​expression​ ​of​ ​target​ ​genes​ ​via​ ​enhancers)​ ​(2 points). Page​ ​2 BIOL​ ​411​ ​-​ ​2017​ ​Autumn Exam​ ​2 Name:​ ​Name​ ​is​ ​written​ ​on​ ​every​ ​page. Date: 2.​ ​Consider​ ​how​ ​the​ ​individual​ ​figures​ ​from​ ​“Gradients​ ​of​ K ​ rüppel​ ​and​ ​knirps​ ​Gene​ ​Products​ ​Direct​ ​Pair-Rule Gene​ ​Stripe​ ​Patterning​ ​in​ ​the​ ​Posterior​ ​Region​ ​of​ ​the​ ​Drosophila​ ​Embryo”​ ​by​ ​Michael​ ​J.​ ​Pankratz,​ ​Eveline Seifert,​ ​Nicole​ ​Gerwin,​ ​Bettina​ ​Billi,​ ​Ulrich​ ​Nauber,​ ​and​ ​Herbert​ ​Jäckle​ ​(C ​ ell​ ​1990​ ​61:309-317)​ ​work​ ​together​ ​to “tell​ ​a​ ​story.” (Total:​ ​38​ ​points) A. Developmental​ ​Biology​ ​(Eleventh​ ​Edition)​ ​cites​ ​this​ ​research​ ​paper​ ​as​ ​a​ ​reference.​ ​From​ ​a developmental​ ​biologist’s​ ​perspective,​ ​why​ ​is​ ​this​ ​research​ ​paper​ ​important?​ ​In​ ​other​ ​words,​ ​what important​ ​“story”​ ​does​ ​the ​overall​ ​research​ ​paper​ ​tell?​ ​Hint:​ ​Consider​ ​developmental​ ​biology​ ​themes,​ ​as well​ ​as​ ​underlying​ ​mechanisms. This​ ​research​ ​paper​ ​provides​ ​a​ ​mechanism​ ​for​ ​an​ ​important​ ​developmental​ ​biology​ ​theme:​ ​the conversion​ ​of​ ​(analog)​ ​gradients​ ​(or​ ​non-periodicity)​ ​into​ ​(digital)​ ​segments​ ​(or​ ​periodicity)​ ​(4 points).​ ​Mechanistically,​ ​gap​ ​gene​ ​products​ ​(i.e.,​ ​Krüppel​ ​and​ ​Knirps)​ ​regulate​ ​the​ ​expression​ ​of pair-rule​ ​genes​ ​(i.e.,​ ​hairy​)​ ​via​ ​modular​ ​enhancers​ ​(4​ ​points). B. For​ ​each​ ​figure,​ ​what​ ​are​ ​the​ ​key​ ​q​uestion(s)?​ ​Limit​ ​your​ ​answers​ ​to​ ​one​ ​or​ ​two​ ​questions​ ​per​ ​figure. Hint:​ ​Identify​ ​the​ ​specific​ ​questions​ ​that​ ​are​ ​the​ ​most​ ​important​ ​for​ ​the​ ​overall​ ​research​ ​paper. Note:​ ​For​ ​full​ ​credit,​ ​questions​ ​should​ ​convey​ ​what​ ​researchers​ ​were​ ​attempting​ ​to​ ​learn​ ​(as opposed​ ​to​ ​methods​ ​or​ ​observations). Fig.​ ​1 What​ ​is​ ​the​ ​wild-type​ ​expression​ ​pattern​ ​of​ h ​ airy​ ​(a​ ​pair-rule​ ​gene),​ ​spatially​ ​and temporally​ ​(3​ ​points)? Fig.​ ​2 Are​ ​(separate)​ ​cis-regulatory​ ​elements​ ​(or​ ​enhancers)​ ​sufficient​ ​for​ ​driving​ ​the​ ​expression of​ ​specific​ ​stripes​ ​of​ ​hairy​ ​(3​ ​points)? Fig.​ ​3 Are​ ​(separate)​ ​cis-regulatory​ ​elements​ ​(or​ ​enhancers)​ ​sufficient​ ​for​ ​driving​ ​the​ ​expression of​ ​specific​ ​stripes​ ​of​ ​hairy​ ​(3​ ​points)? Fig.​ ​4 Are​ ​gap​ ​genes​ ​necessary​ ​for​ ​the​ ​expression​ ​of​ ​individual​ ​stripes​ ​of​ h ​ airy​ ​(3​ ​points)? Alternatively,​ ​how​ ​are​ ​individual​ ​stripes​ ​of​ h ​ airy​ ​regulated​ ​by​ ​gap​ ​genes? Fig.​ ​5 Are​ ​gap​ ​gene​ ​products​ ​trans-regulatory​ ​factors​ ​(or​ ​transcription​ ​factors)​ ​for​ ​cis-regulatory elements​ ​(or​ ​enhancers)​ ​of​ ​hairy​ ​(3​ ​points)?​ ​Alternatively,​ ​do​ ​gap​ ​gene​ ​products​ ​bind​ ​to cis-regulatory​ ​elements​ ​of​ ​hairy? ​ How​ ​does​ ​the​ ​strength​ ​of​ ​the​ ​binding​ ​between​ ​a​ ​gap​ ​gene​ ​product​ ​and​ ​an​ ​enhancer​ ​relate to​ ​the​ ​concentration​ ​of​ ​the​ ​gap​ ​gene​ ​product​ ​(3​ ​points)? Page​ ​3 BIOL​ ​411​ ​-​ ​2017​ ​Autumn Exam​ ​2 Name:​ ​Name​ ​is​ ​written​ ​on​ ​every​ ​page. Date: C. This​ ​research​ ​paper​ ​emphasizes​ ​the​ ​roles​ ​of​ ​enhancers.​ ​Your​ ​less​ ​experienced​ ​labmate,​ ​who​ ​has​ ​not taken​ ​BIOL​ ​411,​ ​reads​ ​this​ ​research​ ​paper​ ​and​ ​asks​ ​how​ ​enhancers​ ​and​ ​promoters​ ​are​ ​different. Explain​ ​to​ ​your​ ​labmate​ ​how​ ​one​ ​could​ ​distinguish,​ ​operationally,​ ​between​ ​enhancers​ ​and​ ​promoters, based​ ​on​ ​their​ ​“behaviors”​ ​when​ ​attached​ ​to​ ​a​ ​reporter. For​ ​our​ ​purposes,​ ​a​ ​full-credit​ ​answer​ ​describes​ ​at​ ​least​ ​one​ ​functional​ ​difference​ ​between​ ​an enhancer ​and​ ​a​ ​promoter​ ​(3​ ​points).​ ​For​ ​example,​ ​an​ ​enhancer​ ​is​ ​not​ ​dependent​ ​on​ ​orientation or​ ​distance​ ​from​ ​the​ ​transcription​ ​start​ ​site. D. Based​ ​on​ ​this​ ​research​ ​paper​ ​and​ ​your​ ​knowledge​ ​from​ ​BIOL​ ​411,​ ​explain,​ ​mechanistically,​ ​how​ ​one gene​ ​can​ ​be​ ​expressed​ ​in​ ​multiple,​ ​distinct​ ​stripes.​ ​Hint:​ ​Consider​ ​activators,​ ​repressors,​ ​cis-regulatory elements,​ ​trans-regulatory​ ​factors,​ ​modularity,​ ​and​ ​sensors/switches. Distinct,​ ​modular​ ​cis-regulatory​ ​elements​ ​(or​ ​enhancers)​ ​(3​ ​points)​ ​act​ ​as​ ​sensors/switches​ ​that respond​ ​to​ ​different​ ​combinations​ ​and​ ​concentrations​ ​of​ ​trans-regulatory​ ​factors​ ​(or transcription​ ​factors)​ ​(3​ ​points)​ ​that​ ​activate​ ​or​ ​repress​ ​expression​ ​(3​ ​points). Do​ ​not​ ​write​ ​below​ ​this​ ​line. Page​ ​4 BIOL​ ​411​ ​-​ ​2017​ ​Autumn Exam​ ​2 Name:​ ​Name​ ​is​ ​written​ ​on​ ​every​ ​page. Date: 3.​ ​During​ ​gastrulation,​ ​the​ ​cells​ ​of​ ​the​ ​blastula​ ​are​ ​given​ ​new​ ​positions,​ ​given​ ​new​ ​neighbors,​ ​and​ ​arranged​ ​into multiple​ ​layers. (Total:​ ​37​ ​points) A. Gastrulation​ ​involves​ ​a​ ​complex​ ​set​ ​of​ ​cell​ ​movements.​ ​Your​ ​friend,​ ​who​ ​has​ ​not​ ​taken​ ​BIOL​ ​411, observes​ ​you​ ​watching​ ​a​ ​video​ ​of​ ​amphibian​ ​gastrulation.​ ​Impressed​ ​by​ ​the​ ​beauty​ ​of​ ​epiboly,​ ​she​ ​asks you​ ​to​ ​explain​ ​what​ ​is​ ​occurring.​ ​For​ ​full​ ​credit,​ ​address​ ​at​ ​least​ ​two​ ​distinct​ ​mechanisms​ ​that​ ​contribute to​ ​epiboly. An​ ​epithelial​ ​sheet​ ​(or​ ​ectoderm)​ ​spreads​ ​around​ ​the​ ​embryo​ ​(1​ ​point).​ ​Mechanistically,​ ​cells divide​ ​(1​ ​point)​ ​and​ ​intercalate​ ​into​ ​one​ ​layer​ ​(1​ ​point).​ ​Alternatively,​ ​fibronectin​ ​provides​ ​a substrate​ ​for​ ​migration. B. The​ ​different​ ​germ​ ​layers​ ​originate​ ​in​ ​the​ ​multiple​ ​layers​ ​that​ ​form​ ​during​ ​gastrulation. What​ ​germ​ ​layer​ ​forms​ ​from​ ​the​ ​outer​ ​cells​ ​that converge? ectoderm​ ​(1​ ​point) What​ ​germ​ ​layer​ ​forms​ ​from​ ​the​ ​yolky​ ​cells​ ​that internalize? endoderm​ ​(1​ ​point) What​ ​germ​ ​layer​ ​forms​ ​from​ ​the​ ​cells​ ​that​ ​move between​ ​the​ ​converging​ ​outer​ ​cells​ ​and​ ​the internalizing​ ​yolky​ ​cells? mesoderm​ ​(1​ ​point) Do​ ​not​ ​write​ ​below​ ​this​ ​line. BIOL​ ​411​ ​-​ ​2017​ ​Autumn Exam​ ​2 Name:​ ​Name​ ​is​ ​written​ ​on​ ​every​ ​page. Date: C. Place​ ​the​ ​following​ ​Xenopus​ ​gastrulation-related​ ​events​ ​in​ ​the​ ​correct​ ​order​ ​by​ ​writing​ ​the​ ​appropriate number​ ​(i.e.,​ ​1-11)​ ​in​ ​front​ ​of​ ​the​ ​event.​ ​Each​ ​item​ ​is​ ​worth​ ​2​ ​points,​ ​for​ ​a​ ​total​ ​of​ ​22​ ​points. Order Event 11 Complete​ ​surrounding​ ​of​ ​embryo​ ​by​ ​ectoderm 10 Formation​ ​of​ ​archenteron 8 Formation​ ​of​ ​dorsal​ ​lip​ of​ ​blastopore 2,​ ​3,​ ​or​ ​4 Formation​ ​of​ ​gray​ ​crescent 7 Induction​ ​of​ ​organizer​ ​by​ ​dorsal-most​ ​vegetal​ ​cells 9 Involution​ ​of​ ​mesodermal​ ​precursors​ ​under​ ​roof​ ​of​ ​blastocoel 5 Localization​ ​of​ ​β-catenin​ ​to​ ​side​ ​opposite​ ​sperm​ ​entry 2,​ ​3,​ ​or​ ​4 Movement​ ​GBP,​ ​Dsh,​ ​and​ ​Wnt11​ ​from​ ​vegetal​ ​pole​ ​to​ ​future​ ​dorsal​ ​side 2,​ ​3,​ ​or​ ​4 Reorganization​ ​of​ ​microtubule​ ​cytoskeleton 1 Sperm​ ​entry 6 Synergistic​ ​activation​ ​of​ ​Xenopus​ ​Nodal-related​ ​(Xnr)​ ​genes​ ​by​ ​β-catenin​ ​and​ ​VegT,​ ​Vg1 D. Imagine​ ​that​ ​you​ ​were​ ​to​ ​“break”​ ​molecular​ ​components​ b ​ efore​​ ​the​ ​formation​ ​of​ ​neural​ ​ectoderm. Predict​ ​the​ ​consequences​ ​by​ ​completing​ ​the​ ​following​ ​table.​ E ​ ach​ ​item​ ​is​ ​worth​ ​1​ ​point,​ ​for​ ​a​ ​total​ ​of 9​ ​points. Relative​ ​amount​ ​of BMP​ ​signaling​ ​(i.e., less,​ ​more, unchanged,​ ​as compared​ ​to​ ​wild type) Relative​ ​amount​ ​of SMAD​ ​activation (i.e.,​ ​less,​ ​more, unchanged,​ ​as compared​ ​to​ ​wild type) Relative​ ​amount​ ​of neural​ ​ectoderm (i.e.,​ ​less,​ ​more, unchanged,​ ​as compared​ ​to​ ​wild type) You​ ​add​ ​additional​ ​Chordin,​ ​Noggin,​ ​and Follistatin​ ​to​ ​the​ ​ventral​ ​side​ ​of​ ​an​ ​intact embryo. less less more You​ ​deplete​ ​BMP4​ ​and​ ​related​ ​TGF-β signals​ ​from​ ​an​ ​intact​ ​embryo. less less more You​ ​dissociate​ ​ectodermal​ ​precursor​ ​cells from​ ​an​ ​embryo.​ ​[cells​ ​(or​ ​embryo)] less​ ​(or unchanged) less​ ​(or unchanged) more/less​ ​(or​ ​less) Page​ ​6 BIOL​ ​411​ ​-​ ​2017​ ​Autumn Exam​ ​2 Name:​ ​Name​ ​is​ ​written​ ​on​ ​every​ ​page. Date: 4.​ ​Imagine​ ​that​ ​you​ ​were​ ​one​ ​of​ ​the​ ​co-authors​ ​of​ ​“Injected​ ​Wnt​ ​RNA​ ​Induces​ ​a​ ​Complete​ ​Body​ ​Axis​ ​in Xenopus​ ​Embryos”​ ​by​ ​Sergei​ ​Sokol,​ ​Jan​ ​L.​ ​Christian,​ ​Randall​ ​T.​ ​Moon,​ ​and​ ​Douglas​ ​A.​ ​Melton​ ​(C ​ ell​ ​1991 67:741-752).​ ​Moreover,​ ​imagine​ ​that​ ​you​ ​are​ ​presenting​ ​this​ ​research​ ​at​ ​a​ ​science​ ​conference. (Total:​ ​38​ ​points) A. As​ ​a​ ​developmental​ ​biologist,​ ​you​ ​are​ ​aware​ ​of​ ​the​ ​classic​ ​experiments​ ​of​ ​Hans​ ​Spemann​ ​and​ ​Hilde Mangold.​ ​Revisit​ ​the​ ​following​ ​experiment,​ ​in​ ​which​ ​they​ ​transplanted​ ​newt​ ​dorsal​ ​lip​ ​tissue​ ​into​ ​a differently-pigmented​ ​newt​ ​early​ ​gastrula.​ ​In​ ​terms​ ​of​ ​autonomous​ ​and​ ​conditional​ ​specification,​ ​what can​ ​we​ ​c​onclude​ ​from​ ​the​ ​following​ ​o​bservations? At​ ​this​ ​point,​ ​the​ ​dorsal​ ​lip​ ​is​ ​autonomously​ ​specified​ ​(3​ ​points).​ ​The​ ​tissue​ ​into​ ​which​ ​the dorsal​ ​lip​ ​is​ ​transplanted​ ​is​ ​conditionally​ ​specified​ ​(3​ ​points).​ ​The​ ​dorsal​ ​lip​ ​influences​ ​the tissue​ ​into​ ​which​ ​it​ ​is​ ​transplanted​ ​(3​ ​points). B. Based​ ​on​ ​your​ ​understanding​ ​of​ ​gastrulation​ ​and​ ​organizer​ ​formation,​ ​what​ ​else​ ​could​ ​you​ ​transplant (even​ ​earlier!)​ ​that​ ​could​ ​lead​ ​to​ ​a​ ​second​ ​site​ ​of​ ​gastrulation​ ​and​ ​a​ ​second​ ​axis? Transplanting​ ​the​ ​dorsal-most​ ​vegetal​ ​cells​ ​(3​ ​points)​ ​could​ ​induce​ ​a​ ​second​ ​organizer. C. As​ ​you​ ​are​ ​presenting​ ​your​ ​research,​ ​one​ ​of​ ​the​ ​conference​ ​attendees​ ​suggests​ ​that​ ​your​ ​research​ ​is not​ ​novel.​ ​Indeed,​ ​he​ ​suggests​ ​that​ ​these​ ​results​ ​were​ ​known​ ​in​ ​1924,​ ​referencing​ ​the​ ​work​ ​of​ ​Hans Spemann​ ​and​ ​Hilde​ ​Mangold.​ ​What​ ​is​ ​innovative​ ​about​ ​your​ ​research? Using​ ​relevant​ ​reasoning​ ​(or​ ​clear​ ​explanation)​ ​(3​ ​points),​ ​you​ ​argue​ ​that​ ​your​ ​research​ ​(i.e.,​ ​the research​ ​paper)​ ​contributes​ ​to​ ​our​ ​molecular​​ ​understanding​ ​of​ ​organizer​ ​function​ ​(3​ ​points). D. Another​ ​visitor​ ​astutely​ ​notices​ ​the​ ​word​ ​“complete”​ ​in​ ​the​ ​title​ ​of​ ​your​ ​presentation.​ ​She​ ​asks​ ​you​ ​to elaborate​ ​on​ ​its​ ​significance.​ ​Explain​ ​why​ ​the​ ​word​ ​“complete”​ ​is​ ​important​ ​in​ ​this​ ​title.​ ​Hint:​ ​Consider the​ ​research​ ​that​ ​preceded​ ​your​ ​research,​ ​as​ ​well​ ​as​ ​developmental​ ​biology​ ​themes. Including​ ​the​ ​word​ ​“complete”​ ​could​ ​emphasize​ ​that​ ​Wnt​ ​plays​ ​a​ ​key​ ​“upstream”​ ​role​ ​(rather than​ ​influencing​ ​only​ ​a​ ​subset​ ​of​ ​“downstream”​ ​events)​ ​(3​ ​points)​ ​and​ ​is​ ​more​ ​“capable”​ ​than activin​ ​(3​ ​points). Page​ ​7 BIOL​ ​411​ ​-​ ​2017​ ​Autumn Exam​ ​2 Name:​ ​Name​ ​is​ ​written​ ​on​ ​every​ ​page. Date: E. After​ ​this​ ​work,​ ​you​ ​clone​ ​a​ ​new​ ​gene​ ​(​noggin​)​ ​and​ ​perform​ ​experiments​ ​similar​ ​to​ ​those​ ​described​ ​in “Injected​ ​Wnt​ ​RNA​ ​Induces​ ​a​ ​Complete​ ​Body​ ​Axis​ ​in​ ​Xenopus​ ​Embryos.”​ ​Note:​ ​For​ ​our​ ​purposes, ignore​ ​the​ ​reference​ ​to​ ​Δ5’. i.​ ​Describe​ ​your​ ​m​ethods.​ ​For​ ​full​ ​credit,​ ​explain​ ​the​ ​purpose​ ​of​ ​the​ ​UV​ ​treatment​ ​and​ ​the​ ​use​ ​of Xwnt-8. UV​ ​treatment​ ​eliminates​ ​organizer​ ​function​ ​(3​ ​points).​ ​Use​ ​of​ ​Xwnt-8​ ​provides​ ​a​ ​positive​ ​control and​ ​a​ ​reference​ ​for​ ​comparison​ ​(e.g.,​ ​relative​ ​capability)​ ​(3​ ​points). ii.​ ​Based​ ​on​ ​these​ ​o​bservations,​ ​what​ ​would​ ​you​ ​c​onclude​ ​about​ ​the​ ​role​ ​of​ ​Noggin? Several​ ​answers​ ​are​ ​possible​ ​(4​ ​points).​ ​For​ ​example,​ ​noggin​ ​rescues​ ​dorsal​ ​development. Alternatively,​ ​Noggin​ ​mediates​ ​organizer​ ​function.​ ​Noggin’s​ ​dorsalization​ ​activity​ ​is​ ​comparable to​ ​(or​ ​better​ ​than)​ ​Xwnt-8’s​ ​dorsalization​ ​activity. F. To​ ​follow​ ​up​ ​on​ ​this​ ​experiment,​ ​you​ ​“knock​ ​out”​ ​Noggin,​ ​but​ ​you​ ​do​ ​not​ ​see​ ​a​ ​loss​ ​of​ ​dorsalization. Your​ ​less​ ​experienced​ ​labmate,​ ​who​ ​has​ ​not​ ​taken​ ​BIOL​ ​411,​ ​is​ ​discouraged​ ​and​ ​feels​ ​that​ ​you​ ​should move​ ​onto​ ​the​ ​next​ ​gene.​ ​Your​ ​advisor​ ​encourages​ ​you​ ​to​ ​not​ ​abandon​ ​your​ ​research​ ​path,​ ​however. Why​ ​not? (As​ ​we​ ​now​ ​know​ ​to​ ​be​ ​true,)​ ​Noggin​ ​might​ ​be​ ​one​ ​of​ ​several​ ​(redundant)​ ​factors​ ​contributing​ ​to organizer​ ​function​ ​(or​ ​dorsalization)​ ​(4​ ​points). Page​ ​8 BIOL​ ​411​ ​-​ ​2017​ ​Autumn Exam​ ​2 Name:​ ​Name​ ​is​ ​written​ ​on​ ​every​ ​page. Date: Page​ ​9 ...
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