BIOL 411 - 2022 Autumn - Exam 1 - Answer Key

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Apr 3, 2024

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BIOL 411 - 2022 Autumn Exam 1 - Part 1 Begin by making a copy of this document, via “File - Make a copy.” Use UW Google Docs to write your answers. Write precisely and concisely, and use your own words. Paraphrase; do not quote. Do not exceed the sentence limits. Remember to complete both parts of the exam. As an individual, submit your document via our Canvas assignment. Please format your written answers (bold, colored blue) to make exam grading easier. You may consult your notes, research articles, slides, and textbook. In addition, you optionally may consult up to two of your classmates. Although you may consult your classmates, you must write your own answers. Sharing your written answers with a peer is strictly prohibited. Failure to comply with these guidelines may result in our being unable to accept or grade your exam or initiating disciplinary actions. 1. With whom, if anyone, did you work? Limit: 1 sentence. 2. Do you agree or disagree with each of the following statements? Explain your reasoning using an example from Unit 1. Limit: 2 sentences. [5 pts each: 2pts for agree/disagree; 1.5pts for reasoning; 1.5pts for example] a. _ Disagree _ It is necessary to perform a “find it” experiment before a “lose it” experiment. Reasoning: Find it, lose it, move it experiments can be performed in any order. Several possible examples: any of the Drosophila or C. elegans mutants that we discussed in class that were discovered by forward genetics - in this case a “lose it” was performed before a “find it”. b. _ Disagree _ In their Nobel Prize-winning genetic screen, Eric Weischaus and Christiane Nüsslein-Volhard used a chemical mutagen to target mutations to specific genes. Reasoning: The researchers had no a priori knowledge of which genes to target and the chemical mutagen they used randomly generated mutations in the genome. Several possible examples: any of the Drosophila mutants that we discussed in class that were discovered by forward genetics. c. _ Agree _ Nurse cells contribute to A/P axis specification by synthesizing cytoplasmic determinants prior to fertilization. Reasoning: The nurse cells contribute numerous factors to the oocyte including cytoplasmic determinants. Several possible examples: any of the maternal effect Drosophila genes. Page 1

BIOL 411 - 2022 Autumn Exam 1 - Part 1 3. In quiz section, you analyzed the paper “ macho-1 encodes a localized mRNA in ascidian eggs that specifies muscle fate during embryogenesis” by Hiroki Nishida and Kaichiro Sawada ( Nature 2001 409:724-729). a. You are on an interview for medical school and you meet with a physician who has not read the paper. They ask you why anyone would be interested in mechanisms involved in establishing the ascidian body plan. What do you say? Limit: 2 sentences. [5 pts] Ascidians are close relatives of vertebrates and share a similar embryonic body plan and similar cell types. b. As part of a summer undergraduate research project at Friday Harbor Labs, you revisit experiments from this paper. You treat one-cell zygotes with Actinomycin D immediately after fertilization to prevent RNA transcription. You repeat the in situ hybridization experiment shown in Fig. 1h on your treated embryos. ● Do you expect the staining of macho-1 to: increase, decrease, or remain unchanged [2pts] (choose one). ● Explain your reasoning for your prediction above. Limit: 1 sentence. Because macho-1 is maternally contributed, the RNA transcript is already present in the oocyte thus inhibiting transcription will have no effect. (alternatively, there is no transcription happening at these early stages) [3pts] c. Based solely on the results shown in Fig. 5, mark each of these statements as true or false. Explain your reasoning below each statement. Limit: 1 sentence each. [5 pts each: 2pts for true/false; 3pts for reasoning] _ True _ At the eight-cell stage, the B4.1 blastomere is specified to become muscle. In this experiment, when the B4.1 blastomere is isolated and put in a neutral environment, it is capable of producing muscle. _ False _ At the eight-cell stage, the B4.1 blastomere is determined to become muscle. This experiment does not test whether the B4.1 blastomere is determined to produce muscle; to do so would require putting B4.1 in a non-neutral environment. _ False _ Overexpression of macho-1 is necessary to induce ectopic muscle in the a4.2 blastomere. This “move it” experiment tests for sufficiency, not necessity; to do so would require performing a “lose it” experiment. 4. Browsing through the stacks at Suzzallo library, you stumble across an old (and quite dusty) edition of the journal Genes & Development . The following set of experiments on nanos catch your attention. Page 2

BIOL 411 - 2022 Autumn Exam 1 - Part 1 Background: Researchers generated flies transgenic for a lacZ-nanos3’UTR construct. Legend: A) Structure of the hybrid RNA produced by the lacZ-nanos3'UTR transgene. This RNA contains the lacZ coding region fused to the nanos 3'UTR . The construct is driven by a promoter that is active during oogenesis (not diagrammed). B-E) Whole-mount in situ hybridization of early Drosophila embryos derived either from a wild-type (B,C) or an oskar ー / ー female. Embryos are oriented with anterior to the left and dorsal up. Probes used were antisense RNA against either the nanos coding region (B,D) or the lacZ coding region (C,E). a. A peer in your 411 class happens to walk by and has their interest piqued. Describe to your colleague the question that the authors are addressing with these experiments. Limit: 1 sentence. [4pts] What cis and trans elements promote nanos localization to the posterior pole in the early Drosophila embryo? [½ credit example] Is oskar necessary for nanos localization? (oskar is trans element, half credit for asking about trans element effect but not cis element) b. What do you conclude based on the results presented in panels B and C? Explain your reasoning. Limit: 2 sentences. [5pts total] We have “moved” the nanos 3’UTR to a new location (attached to lacZ in a transgene) [2pts]. Thus, based on the observation in panel C that lacZ-nanos3’UTR localizes to the posterior pole, we can conclude that the nanos 3’UTR is sufficient to localize an RNA transcript to the posterior of the early embryo [3pts]. c. What do you conclude based on the results presented in panels D and E? Explain your reasoning. Limit: 2 sentences. [5pts total] This is a “lose it” since we are now looking at an oskar mutant. Thus, we conclude that oskar is necessary to localize the lacZ-nanos3’UTR transcript to the posterior pole of the early embryo. d. Mark each of the following statements as true or false. For any that you mark as “true”, list the corresponding element/factor below the statement. [6pts total; 1pt for each true/false; 1.5pt for listing correct factor] if student offers additional explanation, and it is incorrect, 0.5pt deducted _ True _ This experiment investigates a cis -regulatory element. nanos 3’UTR _ True _ This experiment investigates a trans -regulatory factor. oskar _ False _ This experiment investigates a transcription factor. Page 3

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