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Q1: In the Tree Building Challenge exercise, please use the following steps to build a tree. Identify which tree of the options below is the one that you constructed. 1. Start on Peak 1. Reset the simulation until you get to this starting point. 2. Let some time pass. 3. Move a flower from Peak 1 to Peak 3 4. Let some time pass. 5. Move a flower from Peak 3 to Peak 4 6. Let some time pass. 7. Move a flower from Peak 1 to Peak 2. 8. Let some time pass. See Answer
Q2: Consider the three trees below. One of them has different evolutionary relationships among the four peaks than the other two. Which one is it? Tree A Tree BC' Tree CSee Answer
Q3: Question 1.4 in this exercise asks about whether the timing of a trait change (in this case dark petals) differs when you rotate the tree around the nodes (your answer to this should be NO!). What would alter the timing of a trait change? If the simulation was run again and I allowed the columbines to evolve for different numbers of generations before I made the mutation happen If I rotated around the node that joins the columbines on all four peaks If I rotated around the node that joins Peaks 1, 3 and 4 There is no way this can changeSee Answer
Q4: Consider the tree that you are working with (shown here again so you don't have to scroll around!). What is the order that trait change occurred in the group of columbines, starting at the one that happened earliest? anthers petal tips spur colour petal colourSee Answer
Q5: Advanced Cell Biology 2022-23: Coursework 3 Topic: Genome Editing Aim: To demonstrate an ability to explain scientific research to a non-specialist audience. This is a key skill for all scientists and helps clarify our thinking about what is most important about a particular piece of work. Most funding applications for research require a lay summary, and this is considered an essential part of public engagement and scientific accountability. Similarly, many jobs in science involve communication of complex data to non-specialist audiences such as the general public, shareholders, or politicians. For a wider context, see also: https://www.nature.com/articles/d41586-020-00580-w The Task: Write a lay summary of not more than 250 words explaining the research described in the technical abstract below from a controversial scientific paper about genome editing in human embryos. Use the example from class to guide you in structuring the summary. You will be introduced to the scientific concepts described in the abstract in the Genome Editing lectures on the ACB course. For this coursework, your target reader is an engaged year 11 school student (~age 16). This coursework should be submitted in electronic format using Moodle by midnight on 27th January 2023. You must express the summary in your own words - text transcribed from other sources will be excluded from marking. Please include your student number at the start of your document. Correction of a pathogenic gene mutation in human embryos ABSTRACT Genome editing has potential for the targeted correction of germline mutations. Here we describe the correction of the heterozygous MYBPC3 mutation in human preimplantation embryos with precise CRISPR-Cas9-based targeting accuracy and high homology-directed repair efficiency by activating an endogenous, germline-specific DNA repair response. Induced double-strand breaks (DSBs) at the mutant paternal allele were predominantly repaired using the homologous wild-type maternal gene instead of a synthetic DNA template. By modulating the cell cycle stage at which the DSB was induced, we were able to avoid mosaicism in cleaving embryos and achieve a high yield of homozygous embryos carrying the wild-type MYBPC3 gene without evidence of off-target mutations. The efficiency, accuracy and safety of the approach presented suggest that it has potential to be used for the correction of heritable mutations in human embryos by complementing preimplantation genetic diagnosis. However, much remains to be considered before clinical applications, including the reproducibility of the technique with other heterozygous mutations. Nature. 2017 Aug 24;548(7668):413-419. https://www.nature.com/articles/nature23305 Further reading Some of the interpretations in this paper have been questioned by other researchers. Their views are published as Brief Communications Arising in the same journal: https://www.nature.com/articles/s41586-018-0380-z https://www.nature.com/articles/s41586-018-0379-5 The authors of the original study then had the chance to reply: https://www.nature.com/articles/s41586-018-0381-y Reading these associated articles will give a broader perspective on the original study. Plagiarism statement Digital submission of your answer file is equivalent to your explicit declaration that you have adhered to our community expectations of academic integrity and that the work submitted is entirely your own. Answer files will be checked with software designed to detect plagiarism. Answers comprised mainly of text simply copied directly from learning materials will reveal little understanding by the student and hence cannot score highly. Further: markers will be looking for unseemly degrees of similarity in the answers of multiple students; such answers will attract no marks. Assessment Criteria See next page. Grade (Degree Class) A+ (1) D (1) A- (1) B+ B B- (21) C+ tu (2ii) D- (3) F (Fail) Numerical Scale 98 95 92 88 85 82 78 75 72 68 65 62 58 55 52 48 45 40 Pass-Fail Boundary 38 30 20 10 Level 6 Assessment Criteria: ACB Coursework 3 O CRITERIA Exceptional. All the attributes of an A, plus: A highly sophisticated grasp of the topic, with sufficient clarity and originality that the submission could be used without editing for effective communication with non-scientists.. Outstanding. All the positive attributes of an A-, plus: further/deeper outside reading, marshalled effectively in the submission. Minor defects in synthesis may be compensated for by originality and clarity of presentation. Excellent. Clear, complete and logical description of the topic. Appreciation of the wider context underlying key concepts is evident, some of which may have been gained from outside reading. Lucid and original communication of the topic is clearly demonstrated. Very Good. The answer displays a very sound understanding of the main issues and concepts, is generally well-organised, and the quality of writing and the language used is overall very good. Lucid and original communication will be evident, but will be less sophisticated than in a First Class answer. Some errors, minor omissions and/or partial understanding of some aspects of the topic may be tolerated, so long as these do not detract from an otherwise sound answer. Good, but limited. The answer displays a reasonable understanding of the key issues and concepts relevant to the topic, but may go little further than to reword, with little evidence of insight or synthesis, information in the source material. Organisation of the information is adequate for most of the answer. Errors, omissions, poorly expressed ideas, and/or use of technical language -although none too serious-detract from the overall quality. Weak, but passable. The answer demonstrates a partial understanding of at least some of the topic. Writing quality is adequate for at least part of the answer. However, the answer is likely to be poorly organised and some of the basic requirements of the question may not have been met. Errors, omissions, poorly expressed ideas using highly technical language, and/or partial understanding will be too frequent/serious to merit a higher grade. Just passing. The answer must demonstrate a minimal understanding of the topic, but coverage is only partial and superficial. The topic is covered by only the bare minimum of required information, primarily in the form of minimal rephrasing of source material. The minimum mark for a pass is 40%. Borderline Fail. A serious attempt, but of insufficient quality to pass. A structured answer is attempted, but it fails to demonstrate an adequate depth of knowledge and understanding of the topic. This deficiency may be compounded by a disorganised explanation and/or very poor or very technical language. Minimum serious attempt. An attempt has been made to engage with the question, and parts of the answer may have some merit, but there are major errors and/or omissions. May also apply to an answer that is reasonably competent in parts, but for the most part does not address the question set. Clear Fail. A few relevant points show some engagement with the question, but these are outweighed by severe errors and/or omissions. An extremely brief answer, probably with only one or two key words or phrases of any relevance to the subject addressed by the question. Answer given has no merit, or answer is absent.See Answer
Q6:Advanced Cell Biology Topic: Genome Editing Aim: To demonstrate an ability to explain scientific research to a non-specialist audience. This is a key skill for all scientists and helps clarify our thinking about what is most important about a particular piece of work. Most funding applications for research require a lay summary, and this is considered an essential part of public engagement and scientific accountability. Similarly, many jobs in science involve communication of complex data to non-specialist audiences such as the general public, shareholders, or politicians. For a wider context, see also: https://www.nature.com/articles/d41586-020-00580-w The Task: Write a lay summary of not more than 250 words explaining the research described in the technical abstract below from a controversial scientific paper about genome editing in human embryos. Use the example from class to guide you in structuring the summary. You will be introduced to the scientific concepts described in the abstract in the Genome Editing lectures on the ACB course.See Answer
Q7: Imagine you started the Tree Building Challenge with columbines starting on Peak 2 (HINT - you can actually do this by resetting the simulation until they start there!). Which of the following steps could be involved in making the tree below (the same one from the workbook)? Select all that apply- they might not be in order, but that's okay. Just pick the ones that you would actually have to do to build the correct tree.THERE MAY BE MORE THAN ONE WAY TO BUILD THIS TREE!!That's okay. Just choose from the steps that would work to make this happen. \Gamma \quad \text { peak } 2->\text { peak } 1 \text { peak 2 -> peak } 3 \square \quad \text { peak 1 -> peak 4 } \text { peak 3 ->peak } 4 peak 3-> peak 1 peak 1-> peak 2See Answer
Q8: Consider the tree below that was obtained by doing the Growing Tree exercise. Which traits do you expect to differ between the flowers on Peak 4 and those of the common ancestor of all populations? Select all that apply. stripes spur length petal tips spur colour anthers blade colour stigmas petal colourSee Answer
Q9: Given your experience with playing around building trees,evaluate the statement below: The structure of the phylogenetic trees tell us something about the order in which the peaks were colonized.See Answer
Q10: In the columbine populations, how to new traits arise? by moving seeds to different mountains by mating flowers with one anotherC' by mutationSee Answer
Q11: In the columbine tree, what do branch lengths represent? the branch lengths arbitrary (they do not represent anything)are the branch lengths correspond to the number of mutations that have occurred the branch lengths correspond to time the branch lengths correspond to the number of seeds that established a new populationSee Answer
Q12: As time passes, when and where do new traits arise in the columbine populations? randomlyon different peaks, but at regular intervals through time randomly through time, but always when a population appears on apreviously uninhabited peak at the same time as they establish a population on a new peak randomly through time and randomly on different peaksSee Answer
Q13: The tree below is the one that you are looking at (or should be!) for this exercise. Your classmate says that if you rotate around the node that joins Peaks 1 and 4, the flowers on Peak1 will have blue spurs. What would you say about this? "If you do this, then both Peak 1 and Peak 4 columbines will have blue spurs" "Rotating nodes does not change the evolution of the traits on the tree" If I rotated around the node that joins Peaks 1, 3 and 4 There is no way this can changeSee Answer
Q14: Your classmate says that when they ran their simulation,anthers were the first trait to mutate (from white to yellow).When you tell your classmate that in your tree the anthers did not mutate after 800 years, they indicate that they think you did something wrong. What would you tell your classmate?Choose the answer that best fits this situation. "You are right. All of the mutations should show up within 800 years." "Hmmm. I guess I did do something wrong. My tree should be the same as yours." "Every simulation is different, and the mutations arise at random. It is completely possible that another colour might not mutate at all."See Answer
Q15: Consider the tree of columbines below. Given what you see here, which peak had columbines on it first? Peak 1 Peak 2 Peak 3 Peak 4See Answer
Q16: Imagine that you wanted to build a tree where columbines onPeak 2 were most closely related to only columbines on Peak3. What would you do when building your tree to accomplish this? Make sure your simulation starts on Peak 3 and then immediately move columbines to Peak 2 Move columbines between the two peaks at the last step Make sure your simulation starts on Peak 2 and then immediately move columbines to Peak 3 Move columbines between the two peaks at the first stepSee Answer
Q17: TRUE OR FALSE: Rotating branches around nodes is the same thing as cutting them off and then putting them in different places on the tree. True FalseSee Answer

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