BIOL 411 - 2017 Autumn - Exam 1 - Answer Key.pdf

BIOL 411 - 2017 Autumn - Exam 1 - Answer Key.pdf - BIOL 411...

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Unformatted text preview: BIOL​ ​411​ ​-​ ​2017​ ​Autumn Exam​ ​1 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.​ ​From​ ​Developmental​ ​Biology​ ​(Eleventh​ ​Edition):​ ​“We​ ​now​ ​know​ ​that​ ​sea​ ​urchins​ ​and​ ​frogs​ ​alike​ ​use​ ​both autonomous​ ​and​ ​conditional​ ​specification​ ​of​ ​their​ ​early​ ​embryonic​ ​cells.”​ ​Nonetheless,​ ​examining​ ​the​ ​different strategies​ ​for​ ​specification​ ​can​ ​shine​ ​light​ ​on​ ​the​ ​different​ ​mechanisms​ ​that​ ​influence​ ​cell​ ​fate​ ​determination. (Total:​ ​30​ ​points) A. In​ ​general​ ​terms,​ ​what​ ​molecular​ ​mechanisms​ ​underlie​ ​the​ ​different​ ​strategies​ ​for​ ​specification? Autonomous​ ​specification cytoplasmic​ ​determinants​ ​(4​ ​points) Conditional​ ​specification signals​ ​from​ ​neighboring​ ​cells​​ ​(or​ ​extracellular​ ​signals)​ ​(4​ ​points) Syncytial​ ​specification cytoplasmic​ ​determinants​ ​(2​ ​points)​ ​and​ ​signals​ ​from​ ​neighboring​ n ​ uclei (or​ ​extranuclear​ ​signals)​ ​(2​ ​points) B. Based​ ​on​ ​the​ ​existence​ ​of​ ​identical​ ​twins,​ ​would​ ​you​ ​classify​ ​early​ ​human​ ​embryos​ ​as​ ​displaying autonomous​ ​or​ ​conditional​ ​specification?​ ​Explain​ ​your​ ​reasoning. Conditional​ ​specification​ ​(5​ ​points).​ ​If​ ​specified​ ​autonomously,​ ​the​ ​two​ ​halves​ ​of​ ​a​ ​split​ ​embryo would​ ​form​ ​two​ ​half-embryos​ ​(5​ ​points).​ ​Alternatively,​ ​if​ ​specified​ ​conditionally,​ ​the​ ​cells​ ​could influence​ ​one​ ​another’s​ ​development,​ ​resulting​ ​in​ ​two​ ​complete​ ​embryos. C. In​ ​terms​ ​of​ ​commitment,​ ​what​ ​do​ ​the​ ​following​ ​manipulations​ ​tell​ ​you​ ​about​ ​your​ ​favorite​ ​embryonic​ ​cell at​ ​the​ ​time​ ​of​ ​its​ ​removal?​ ​Be​ ​as​ ​precise​ ​as​ ​possible. When​ ​placed​ ​in​ ​a​ ​neutral​ ​environment,​ ​it differentiates​ ​into​ ​its​ ​normal​ ​cell​ ​type. specified​ ​(4​ ​points) When​ ​transplanted​ ​into​ ​another​ ​region​ ​of​ ​the embryo,​ ​it​ ​differentiates​ ​into​ ​an​ ​alternative​ ​cell​ ​type. not​ ​determined​ ​(or​ ​specified​ ​but​ ​not​ ​determined) (4​ ​points) Do​ ​not​ ​write​ ​below​ ​this​ ​line. Page​ ​1 BIOL​ ​411​ ​-​ ​2017​ ​Autumn Exam​ ​1 Name:​ ​Name​ ​is​ ​written​ ​on​ ​every​ ​page. Date: 2.​ ​Polyspermy​ ​can​ ​be​ ​prevented​ ​by​ ​a​ ​fast​ ​block​ ​(e.g.,​ ​sea​ ​urchins)​ ​and/or​ ​a​ ​slow​ ​block​ ​(e.g.,​ ​sea​ ​urchins, mammals). (Total:​ ​30​ ​points) A. Compare​ ​and​ ​contrast​ ​the​ ​fast​ ​block​ ​and​ ​the​ ​slow​ ​block​ ​by​ ​completing​ ​the​ ​following​ ​table. Fast​ ​block Slow​ ​block Is​ ​the​ ​block electrical​ ​or mechanical​ ​in nature? electrical​ ​(2​ ​points) mechanical​ (2​ ​points) Which​ ​ions,​ ​if any,​ ​are important​ ​for propagating​ ​the block? Na​+​​ ​(2​ ​points) Ca​2+​​ ​(2​ ​points) How​ ​does​ ​the block​ ​prevent polyspermy? The​ ​more​ ​positive​ ​membrane​ ​potential​ ​(2 The​ ​hardened,​ ​raised​ ​membrane​ ​(2 points)​ ​prevents​ ​fusion​ ​(2​ ​points). points)​ ​provides​ ​barrier​ ​(1​ ​point)​ ​and displaces​ ​sperm​ ​(1​ ​point). B. Your​ ​acquaintance​ ​makes​ ​the​ ​following​ ​assertions.​ ​For​ ​each​ ​assertion,​ ​provide​ t​ wo​​ ​counterexamples​ ​to challenge​ ​the​ ​myth. ● “The​ ​egg​ ​is​ ​the​ ​passive​ ​recipient​ ​of​ ​the​ ​active​ ​sperm.” Several​ ​answers​ ​are​ ​possible.​ ​For​ ​example,​ ​the​ ​egg​ ​actively​ ​attracts​ ​(2​ ​points)​ ​and​ ​recognizes​ ​(2 points)​ ​sperm. ● “The​ ​female​ ​reproductive​ ​tract​ ​is​ ​a​ ​passive​ ​conduit.” Several​ ​answers​ ​are​ ​possible.​ ​For​ ​example,​ ​the​ ​female​ ​reproductive​ ​tract​ ​actively​ ​regulates capacitation​ ​(2​ ​points)​ ​and​ ​transportation​ ​(2​ ​points)​ ​of​ ​sperm. Do​ ​not​ ​write​ ​below​ ​this​ ​line. Page​ ​2 BIOL​ ​411​ ​-​ ​2017​ ​Autumn Exam​ ​1 Name:​ ​Name​ ​is​ ​written​ ​on​ ​every​ ​page. Date: C. Revisit​ ​the​ ​capacitation​ ​pathway,​ ​as​ ​presented​ ​in​ D ​ evelopmental​ ​Biology​ ​(Eleventh​ ​Edition). ● Why​ ​is​ ​mammalian​ ​capacitation​ ​difficult​ ​to​ ​study​ ​in​ ​vivo? Several​ ​answers​ ​are​ ​possible.​ ​For​ ​example,​ ​in​ ​mammals,​ ​fertilization​ ​occurs​ ​inside​ ​the​ ​female​ ​(3 points).​ ​Alternatively,​ ​in​ ​mammals,​ ​the​ ​population​ ​of​ ​sperm​ ​that​ ​is​ ​ejaculated​ ​is​ ​heterogenous. ● Based​ ​on​ ​this​ ​proposed​ ​pathway,​ ​how​ ​might​ ​medical​ ​scientists​ ​treat​ ​sperm​ ​to​ ​increase​ ​their​ ​utility​ ​for​ ​in vitro​ ​fertilization?​ ​Explain​ ​your​ ​reasoning. Treatments​ ​that​ ​promote​ ​signaling​ ​through​ ​the​ ​pathway​ ​(1​ ​point)​ ​might​ ​be​ ​useful.​ ​Several examples​ ​are​ ​possible.​ ​For​ ​example,​ ​medical​ ​scientists​ ​might​ ​add​ ​HCO​3​-​​ ​to​ ​buffers​ ​(2​ ​points). Alternatively,​ ​they​ ​might​ ​add​ ​Ca​2+​​ ​ionophores​ ​to​ ​increase​ ​intracellular​ ​Ca​2+​​ ​concentrations. Do​ ​not​ ​write​ ​below​ ​this​ ​line. Page​ ​3 BIOL​ ​411​ ​-​ ​2017​ ​Autumn Exam​ ​1 Name:​ ​Name​ ​is​ ​written​ ​on​ ​every​ ​page. Date: 3.​ ​In​ ​this​ ​course,​ ​we​ ​have​ ​examined​ ​specification​ ​of​ ​the​ ​anterior-posterior​ ​axis​ ​in​ D ​ rosophila​ ​in​ ​detail,​ ​in​ ​part​ ​to provide​ ​examples​ ​of​ ​developmental​ ​organization​ ​and​ ​patterning,​ ​morphogen​ ​gradients,​ ​and​ ​genetic​ ​analysis​ ​of regulation​ ​of​ ​development. (Total:​ ​30​ ​points) A. In​ ​“Seeing​ ​Is​ ​Believing:​ ​The​ ​Bicoid​ ​Morphogen​ ​Gradient​ ​Matures”​ ​(​Cell​ ​2004​ ​116:143-152),​ ​Anne Ephrussi​ ​and​ ​Daniel​ ​St.​ ​Johnston​ ​wrote: “Although​ ​Cell​ ​has​ ​a​ ​long​ ​history​ ​of​ ​publishing ​some​ ​of​ ​the​ ​most​ ​significant​ ​advances​ ​in​ ​developmental biology,​ ​the​ ​back​ ​to​ ​back​ ​papers​ ​by​ ​Driever​ ​and​ ​Nüsslein-Volhard​ ​on​ ​the​ ​role​ ​of​ ​the​ ​Bicoid​ ​gradient​ ​in patterning​ ​the​ ​Drosophila​ ​embryo​ ​stand​ ​out​ ​as​ ​the​ ​first​ ​molecular​ ​demonstration​ ​of​ ​two​ ​of​ ​the​ ​longest standing​ ​concepts​ ​of​ ​the​ ​field,​ ​namely​ ​localized​ ​cytoplasmic​ ​determinants​ ​and​ ​morphogen​ ​gradients.” What​ ​distinguishes​ ​“morphogen​ ​gradients”​ ​(e.g.,​ ​Bicoid,​ ​Nanos)​ ​from​ ​“localized​ ​cytoplasmic determinants”​ ​(e.g.,​ ​Macho-1)?​ ​For​ ​full​ ​credit,​ ​address​ ​both​ ​localization​ ​and​ ​function. Both​ ​“localized​ ​cytoplasmic​ ​determinants”​ ​and​ ​“morphogen​ ​gradients”​ ​involve​ ​asymmetrical localizations​ ​(2​ ​points).​ ​For​ ​morphogen​ ​gradients,​ ​however,​ ​concentration​ ​gradients​ ​(2​ ​points) are​ ​of​ ​critical​ ​importance,​ ​leading​ ​to​ ​activation​ ​or​ ​inhibition​ ​of​ ​different​ ​genes​ ​at​ ​different thresholds​ ​(as​ ​opposed​ ​to​ ​binary​ ​responses)​ ​(2​ ​points). B. Build​ ​a​ ​map​ ​of​ ​the​ ​interactions​ ​among​ ​the​ ​following​ ​components.​ ​Use​ ​arrows​ ​to​ ​represent​ ​activations and​ ​blocking-arrows​ ​to​ ​represent​ ​inhibitions.​ ​Do​ ​not​ ​use​ ​any​ ​additional​ ​words​ ​on​ ​your​ ​map.​ ​Note:​ ​The pathways​ ​may​ ​branch​ ​and​ ​converge.​ ​In​ ​other​ ​words,​ ​the​ ​pathways​ ​may​ ​not​ ​be​ ​completely​ ​linear. anterior​ ​development,​ ​anterior-to-posterior​ ​microtubule​ ​orientation,​ ​Bicoid,​ ​CUP,​ ​Hunchback,​ ​Nanos, Oskar,​ ​Par-1,​ ​posterior​ ​development,​ ​Smaug Each​ ​of​ ​the​ ​following​ ​functional​ ​interactions​ ​is​ ​worth​ ​1​ ​point,​ ​for​ ​a​ ​total​ ​of​ ​12​ ​points.​ ​Note: Additional​ ​arrows​ ​(e.g.,​ ​from​ ​Hunchback)​ ​may​ ​be​ ​possible. ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​posterior​ ​development​ ​⊢-------------------------------------------​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​↑​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​| Smaug​ ​→​ ​CUP​ ​⊣​ ​Nanos​ ​----------------------------------------------------------|---------------------​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​⊤​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​⊥​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​|​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​| ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​Oskar​ ​ ​Hunchback​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​|​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​| ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​↓​ ​ ​ ​ ​ ​ ​ ​↑​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​|​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​⊥ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​Par-1​ ​→​ ​anterior-to-posterior​ ​microtubule​ ​orientation​ ​→​ ​Bicoid​ ​→​ ​anterior​ ​development Page​ ​4 BIOL​ ​411​ ​-​ ​2017​ ​Autumn Exam​ ​1 Name:​ ​Name​ ​is​ ​written​ ​on​ ​every​ ​page. Date: C. In​ ​class,​ ​we​ ​discussed​ ​how​ ​the​ ​range​ ​and​ ​shape​ ​of​ ​a​ ​morphogen​ ​gradient​ ​quantitation​ ​curve​ ​can​ ​be influenced​ ​by​ ​synthesis,​ ​movement,​ ​and​ ​stability.​ ​Provide​ o ​ ne​​ ​example,​ ​if​ ​applicable​,​ ​that​ ​illustrates how​ ​each​ ​factor​ ​influences​ ​the​ ​localization​ ​of​ ​each​ ​morphogen.​ ​Be​ ​precise​ ​and​ ​concise. bicoid​/Bicoid nanos​/Nanos Synthesis Synthesis​ ​of​ ​Bicoid​ ​protein​ ​is​ ​restricted to​ ​posterior​ ​(because​ ​of​ ​bicoid localization)​ ​(2​ ​points). Synthesis​ ​of​ ​Nanos​ ​protein​ ​is​ ​restricted to​ ​posterior​ ​(because​ ​of​ ​nanos localization)​ ​(2​ ​points). Movement Microtubule​ ​motors​ ​(i.e.,​ ​dyneins)​ ​move biocoid​ ​mRNA​ ​anteriorly​ ​(2​ ​points). nanos​ ​mRNA​ ​diffuses​ ​but​ ​is​ ​anchored​ ​in posterior​ ​(2​ ​points). Alternatively,​ ​microtubule​ ​motors​ ​(i.e., kinesins)​ ​move​ ​oskar​ ​mRNA​ ​posteriorly. Alternatively,​ ​Nanos​ ​protein​ ​diffuses from​ ​sites​ ​of​ ​synthesis. Alternatively,​ ​Bicoid​ ​protein​ ​diffuses from​ ​sites​ ​of​ ​synthesis. Stability n/a​ ​(2​ ​points) Oskar​ ​stabilizes​ ​nanos​ ​(2​ ​points). Alternatively,​ ​CUP​ ​destabilizes​ ​nanos​. Do​ ​not​ ​write​ ​below​ ​this​ ​line. Page​ ​5 BIOL​ ​411​ ​-​ ​2017​ ​Autumn Exam​ ​1 Name:​ ​Name​ ​is​ ​written​ ​on​ ​every​ ​page. Date: 4.​ ​Based​ ​on​ ​their​ ​investigations​ ​of​ ​anterior-posterior​ ​specification​ ​in​ D ​ rosophila​,​ ​Ruth​ ​Lehmann​ ​and​ ​Christiane Nüsslein-Volhard​ ​co-authored​ ​“The​ ​Maternal​ ​Gene​ ​Nanos​ ​Has​ ​a​ ​Central​ ​Role​ ​in​ ​Posterior​ ​Pattern​ ​Formation​ ​of the​ ​Drosophila​ ​Embryo”​ ​by​ ​Ruth​ ​Lehmann​ ​and​ ​Christiane​ ​Nüsslein-Volhard​ ​(D ​ evelopment​ ​1991​ ​112:679-691). (Total:​ ​30​ ​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? For​ ​full​ ​credit,​ ​the​ ​answer​ ​must​ ​address:​ ​(1)​ ​developmental​ ​biology​ ​themes​ ​(e.g.,​ ​axis specification,​ ​determinants,​ ​much​ of​ ​Tuesday’s​ ​lecture!)​ ​(2​ ​points),​ ​(2)​ ​characterization​ ​of posterior​ ​group​ ​genes​ ​(e.g.,​ ​nanos)​ ​ ​(2​ ​points),​ ​and​ ​(3)​ ​ordering​ ​of​ ​those​ ​genes​ ​into​ ​a​ ​functional pathway​ ​(2​ ​points). B. During​ ​her​ ​investigations​ ​of​ ​Drosophila​,​ ​Christiane​ ​Nüsslein-Volhard​ ​chose​ ​to​ ​examine​ ​maternal​ ​effect mutations​ ​that​ ​resulted​ ​in​ ​defects​ ​in​ ​the​ ​establishment​ ​of​ ​the​ ​anterior-posterior​ ​axis.​ ​Why​ ​might​ ​she have​ ​chosen​ ​to​ ​examine​ ​(1)​ ​maternal​ ​effect​ ​mutations​​ ​in​ ​(2)​ ​Drosophila​? Because​ ​Drosophila​ ​establishes​ ​the​ ​anterior-posterior​ ​axis​ ​early​ ​in​ ​development​ ​(i.e.,​ ​during oogenesis),​ ​this​ ​process​ ​likely​ ​depends​ ​on​ ​maternal​ ​contributions​ ​(3​ ​points).​ ​Alternatively, genetic​ ​screens​ ​readily​ ​link​ ​defects​ ​in​ ​axis​ ​formation​ ​with​ ​maternal​ ​effect​ ​mutations.​ ​Drosophila is​ ​amenable​ ​to​ ​genetic​ ​screens​ ​(3​ ​points). C. Your​ ​less​ ​experienced​ ​labmate,​ ​who​ ​has​ ​not​ ​taken​ ​BIOL​ ​411,​ ​concludes​ ​from​ ​Figure​ ​2​ ​that​ ​Nanos​ ​is sufficient​ ​for​ ​posterior​ ​development.​ ​What​ ​constructive​ ​criticism​ ​could​ ​you​ ​offer,​ ​and​ ​what​ o ​ ​bservations would​ ​you​ ​like​ ​to​ ​see​ ​to​ ​support​ ​that​ ​c​onclusion? Because​ ​the​ ​experiments​ ​in​ ​Figure​ ​2​ ​are​ ​“lose​ ​it”​ ​experiments,​ ​they​ ​test​ ​whether​ n ​ anos​ ​is necessary​ ​for​ ​posterior​ ​development​ ​(3​ ​points).​ ​To​ ​test​ ​for​ ​sufficiency,​ ​we​ ​should​ ​use​ ​“move​ ​it” experiments,​ ​such​ ​as​ ​injections​ ​of​ ​exogenous​ n ​ anos​ ​(3​ ​points). D. From​ ​your​ ​research​ ​mentor,​ ​you​ ​learn​ ​that​ ​you​ ​can​ ​prick​ ​a​ ​Drosophila​ ​egg​ ​and​ ​allow​ ​about​ ​5%​ ​of​ ​its cytoplasm​ ​to​ ​leak​ ​out.​ ​How​ ​could​ ​you​ ​use​ ​this​ ​technique​ ​to​ ​complement​ ​the​ ​experiments​ ​in​ ​Table​ ​2​ ​and Figure​ ​2?​ ​In​ ​other​ ​words,​ ​what​ ​relevant​ ​q​uestion​ ​could​ ​you​ ​address​ ​with​ ​this​ ​m​ethod? “Losing”​ ​localized​ ​cytoplasm​ ​(3​ ​points)​ ​allows​ ​us​ ​to​ ​test​ ​whether​ ​localized​ ​activities​ ​are necessary​ ​(or​ ​whether​ ​activities​ ​are​ ​distributed​ ​asymmetrically)​ ​(3​ ​points). E. In​ ​class,​ ​we​ ​grouped​ ​genes​ ​that​ ​establish​ ​anterior-posterior​ ​polarity​ ​in​ D ​ rosophila​ ​into​ ​three​ ​groups:​ ​(1) anterior​ ​group,​ ​(2)​ ​posterior​ ​group,​ ​and​ ​(3)​ ​terminal​ ​group.​ ​Based​ ​on​ ​the​ o ​ ​bservations​ ​presented​ ​in Figure​ ​2A,​ ​what​ ​can​ ​you​ ​c​onclude​ ​about​ ​interactions​ ​between​ ​the​ ​terminal​ ​group​ ​and​ ​one​ ​of​ ​the​ ​other groups?​ ​For​ ​full​ ​credit,​ ​explain​ ​your​ ​reasoning. The​ ​extra​ ​telson​ ​in​ ​the​ ​absence​ ​of​ ​bicoid​ ​(3​ ​points)​ ​suggests​ ​that​ ​the​ ​anterior​ ​group​ ​inhibits (directly​ ​or​ ​indirectly)​ ​the​ ​terminal​ ​group​ ​(3​ ​points). Page​ ​6 BIOL​ ​411​ ​-​ ​2017​ ​Autumn Exam​ ​1 Name:​ ​Name​ ​is​ ​written​ ​on​ ​every​ ​page. Date: 5.​ ​Imagine​ ​that​ ​you​ ​were​ ​one​ ​of​ ​the​ ​co-authors​ ​of​ ​the​ ​research​ ​paper​ ​that​ ​we​ ​discussed​ ​during​ ​our​ ​“Specifying Muscle​ ​Fate​ ​in​ ​Ascidians”​ ​journal​ ​club.​ ​Moreover,​ ​imagine​ ​that​ ​you​ ​will​ ​present​ ​this​ ​research​ ​at​ ​a​ ​science conference. (Total:​ ​30​ ​points) A. Scott​ ​Gilbert,​ ​one​ ​of​ ​the​ ​co-authors​ ​of​ ​Developmental​ ​Biology​ ​(Eleventh​ ​Edition),​ ​describes​ ​the​ ​formula for​ ​success​ ​in​ ​developmental​ ​biology​ ​as​ ​“Find​ ​it,​ ​lose​ ​it,​ ​move​ ​it.”​ ​For​ ​each​ ​figure,​ ​does​ ​the​ ​figure include​ ​find​ ​it,​ ​lose​ ​it,​ ​and/or​ ​move​ ​it​ ​experiments?​ ​Limit​ ​your​ ​answers​ ​to​ ​“yes”​ ​or​ ​“no.” Find​ ​it? Lose​ ​it? Move​ ​it? Fig.​ ​1 yes​ ​(1​ ​point) no​ ​(1​ ​point) no​ ​(1​ ​point) Fig.​ ​2 yes​ ​or​ ​no​ ​(0​ ​points) yes​ ​(1​ ​point) no​ ​(1​ ​point) Fig.​ ​3 no​ ​(1​ ​point) yes​ ​(1​ ​point) yes​ ​(1​ ​point) Fig.​ ​4 no​ ​(1​ ​point) yes​ ​or​ ​no​ ​(0​ ​points) yes​ ​or​ ​no​ ​(0​ ​points) Fig.​ ​5 no​ ​(1​ ​point) no​ ​(1​ ​point) yes​ ​(1​ ​point) Note:​ ​Understanding​ ​the​ ​q​uestion​ ​(i.e.,​ ​what​ ​the​ ​researchers​ ​are​ ​attempting​ ​to​ ​learn)​ ​is​ ​key​ ​to understanding​ ​the​ ​purpose​ ​of​ ​an​ ​experiment. B. For​ ​the​ ​b​ackground​ ​of​ ​your​ ​presentation,​ ​explain​ ​what​ ​was​ ​known​ ​about​ ​development​ ​in​ ​the​ ​ascidian Halocynthia​ ​roretzi​ ​before​ ​the​ ​research​ ​paper​ ​was​ ​published.​ ​For​ ​full​ ​credit,​ ​address​ ​both​ ​mode​ ​and mechanism​ ​of​ ​specification. Before​ ​this​ ​research​ ​paper​ ​was​ ​published,​ ​researchers​ ​knew​ ​that​ H ​ .​ ​roretzi​ ​displayed autonomous​ ​development​ ​(2​ ​points)​ ​and​ ​that​ H ​ .​ ​roretzi​ ​myoplasm​ ​includes​ ​a​ ​cytoplasmic determinant​ ​(2​ ​points). C. You​ ​and​ ​your​ ​co-authors​ ​wrote​ ​“Interest​ ​has​ ​been​ ​concentrated​ ​on​ ​the​ ​mechanisms​ ​underlying​ ​the formation​ ​of​ ​muscle​ ​cells​ ​in​ ​the​ ​tail,​ ​as​ ​yellow-coloured​ ​myoplasm​ ​in​ ​eggs​ ​is​ ​preferentially​ ​segregated into​ ​muscle-lineage​ ​blastomeres.”​ ​Rephrase​ ​this​ ​statement​ ​as​ ​an​ ​important​ q ​ ​uestion​ ​that​ ​your​ ​research attempts​ ​to​ ​answer. Several​ ​answers​ ​are​ ​possible.​ ​For​ ​example,​ ​how​ ​does​ ​myoplasm​ ​specify​ ​muscle​ ​fate​ ​(2​ ​points)? Alternatively,​ ​what​ ​is​ ​the​ ​cytoplasmic​ ​determinant​ ​in​ ​myoplasm? Page​ ​7 BIOL​ ​411​ ​-​ ​2017​ ​Autumn Exam​ ​1 Name:​ ​Name​ ​is​ ​written​ ​on​ ​every​ ​page. Date: D. Your​ ​presentation​ ​will​ ​be​ ​limited​ ​to​ ​ten​ ​minutes.​ ​What​ ​are​ ​the​ ​three​ ​most​ ​important​ ​c​onclusions​ ​to include​ ​in​ ​your​ ​presentation?​ ​Which​ ​figure(s)​ ​directly​ ​support​ ​these​ ​conclusions? Conclusion Figure(s) (1)​ ​The​ ​macho-1​ ​mRNA​ ​is​ ​localized​ ​to​ ​myoplasm​ ​(2​ ​points). 1​ ​(1​ ​point) (2)​ ​The​ ​macho-1​ ​mRNA​ ​is​ ​necessary​ ​for​ ​specification​ ​of​ ​muscle​ ​fate​ ​(2​ ​points). 3​ ​(1​ ​point) (3)​ ​The​ ​macho-1​ ​mRNA​ ​is​ ​sufficient​ ​for​ ​specification​ ​of​ ​muscle​ ​fate​ ​(2​ ​points). 3​ ​&​ ​5​ ​(1 point) Alternatively: Conclusion Figure(s) (1)​ ​The​ ​macho-1​ ​mRNA​ ​is​ ​localized​ ​to​ ​myoplasm. 1 (2)​ ​The​ ​macho-1​ ​mRNA​ ​can​ ​be​ ​depleted​ ​effectively​ ​and​ ​specifically. 2​ ​(or​ ​2​ ​&​ ​4) (3)​ ​The​ ​macho-1​ ​mRNA​ ​is​ ​necessary​ ​and​ ​sufficient​ ​for​ ​specification​ ​of​ ​muscle​ ​fate. 3​ ​&​ ​5 E. Following​ ​your​ ​presentation,​ ​a​ ​researcher​ ​from​ ​another​ ​lab​ ​asks​ ​about​ ​your​ ​confidence​ ​in​ ​your “antisense”​ ​experiments.​ ​Using​ ​evidence​,​ ​explain​ ​why​ ​you​ ​are​ ​confident​ ​that​ ​your​ ​m​ethods​ ​were​ ​both effective​ ​and​ ​specific. Based​ ​on​ ​Figure​ ​2,​ ​the​ ​methods​ ​deplete​ ​macho-1​ ​mRNA​ ​(1​ ​point)​ ​without​ ​depleting​ ​control mRNA​ ​(i.e.,​ ​HrWnt-5)​ ​(1​ ​point).​ ​Based​ ​on​ ​Figure​ ​4,​ ​injected​ ​macho-1​ ​mRNA​ ​rescues​ ​depletion effects,​ ​further​ ​demonstrating​ ​specificity​ ​(1​ ​point). Do​ ​not​ ​write​ ​below​ ​this​ ​line. BIOL​ ​411​ ​-​ ​2017​ ​Autumn Exam​ ​1 Name:​ ​Name​ ​is​ ​written​ ​on​ ​every​ ​page. Date: Fig.​ ​2 Fig.​ ​1 Fig.​ ​3 Fig.​ ​4 Fig.​ ​5 Page​ ​9 BIOL​ ​411​ ​-​ ​2017​ ​Autumn Exam​ ​1 Name:​ ​Name​ ​is​ ​written​ ​on​ ​every​ ​page. Date: Fig.​ ​1:​ ​c–e,​ ​Localization​ ​of​ ​muscle​ ​determinants​ ​in​ ​unfertilized​ ​egg​ ​(c),​ ​and​ ​eggs​ ​after​ ​the​ ​first​ ​(d)​ ​and​ ​second (e)​ ​phase​ ​of​ ​ooplasmic​ ​segregation​7​.​ ​Animal​ ​pole​ ​is​ ​top,​ ​and​ ​posterior​ ​is​ ​to​ ​the​ ​right.​ ​f–h,​ ​Distribution​ ​of maternal​ ​macho-1​ ​mRNA​ ​shown​ ​by​ ​in​ ​situ​ ​hybridization​ ​in​ ​eggs​ ​at​ ​stages​ ​corresponding​ ​to​ ​c–e.​ ​A,​ ​anterior;​ ​P, posterior.​ ​i–m,​ ​Localization​ ​of​ ​macho-1​ ​mRNA​ ​during​ ​embryogenesis.​ ​Anterior​ ​is​ ​to​ ​the​ ​left.​ ​i,​ ​Eight-cell​ ​stage, lateral​ ​view.​ ​In​ ​situ​ ​hybridization​ ​signal​ ​is​ ​localized​ ​to​ ​tiny​ ​spots​ ​in​ ​B4.1​ ​blastomeres.​ ​Sixteen-cell​ ​stage​ ​(j)​ ​and 110-cell​ ​stage​ ​(k)​ ​embryos​ ​shown​ ​in​ ​vegetal​ ​view.​ ​Staining​ ​is​ ​restricted​ ​to​ ​the​ ​B7.6​ ​blastomeres​ ​that​ ​do​ ​not divide​ ​further​ ​during​ ​embryogenesis.​ ​l,​ ​m,​ ​Late​ ​gastrula​ ​and​ ​early​ ​tailbud​ ​stage.​ ​mRNA​ ​is​ ​observed​ ​in​ ​two​ ​cells in​ ​the​ ​endodermal​ ​strand​ ​derived​ ​from​ ​the​ ​B7.6​ ​blastomeres​ ​in​ ​k.​ ​No​ ​zygotic​ ​expression​ ​of​ ​macho-1​ ​is observed. Fig.​ ​2:​ ​a–c,​ ​Antisense​ ​oligonucleotide-injected​ ​unfertilized​ ​eggs​ ​(a),​ ​eggs​ ​after​ ​the​ ​second​ ​phase​ ​of​ ​ooplasmic segregation​ ​(b)​ ​and​ ​eight-cell​ ​embryos​ ​(c)​ ​probed​ ​for​ ​macho-1​ ​mRNA.​ ​d,​ ​e,​ ​Sense​ ​oligonucleotide-injected controls​ ​at​ ​the​ ​second​ ​phase​ ​(d)​ ​and​ ​the​ ​eight-cell​ ​stage​ ​(e).​ ​f,​ ​g,...
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