What type of mutation to the PAM is best for reducing recutting?
The research question is which Mustion is best to Edite the PAM to reduce rutting?
Page limit info:
Each figure/table with its caption goes on a separate page at the end (after your reference section) **that’s one page per figure or table**
Writing for sections 1-3 + references (section 4) needs to be no longer than 3 pages, 12 point font, normal margins (single spaced is OK).
OVERVIEW OF WRITE-UP
This write-up should be thought of as a portion of a scientific article, with a focus on the results and discussion sections. You will summarize your findings with respect to the research question you chose to address (RQ2 or 3): What type of mutation to the PAM is best for reducing recutting?
The intended audience is someone with a CRISPR editing background but who has NOT done our experiment (so avoid using experiment-specific jargon and terms, but clear and specific).
Your write-up should have the sections below. Each section should have a clear heading (e.g., bold or underlined). You are welcome to use additional sub-headings if you feel that helps keep the writing organized!
SECTIONS OF THE WRITE-UP:
1. OUR WORK IN THE CONTEXT OF EXISTING LITERATURE:
This section will likely be a paragraph or two.
What has been done previously that very closely relates to our work? You need to choose at least one prior study (published research) that is relevant to our area of study. Describe the results of the study, specifically explain how their results relate to our work, and describe how our research questions expand upon prior work.
How do you find relevant papers?
2. RESULTS:
The results section should contain your analysis of the yeast phenotype/colony count data (e.g. mean total colonies and mean % red that was analyzed on Aug 30) and sequencing analysis (all the sequencing analysis we do that is relevant to your question, e.g., multiple sequencing alignments and frequency of mutations analysis)
You do not need to include a report of your individual results, only analysis of pooled data.
You do not need to include any results about how we made the plasmid and HDR templates (e.g., plasmid digests, etc.).
Results sections include presentations of the analysis (Figures and/or Tables) AND a written results description. Figures and Tables have to clearly communicate the results in a logical way. There has to be enough information provided so the reader can interpret the results and draw their own conclusions. All figures/tables should have proper and complete captions.
The written results portion is where trends are described and relevant comparisons are made. Save extensive interpretations/conclusions for the discussion section. The results should be divided into subsections, with a heading for each sub-section. For example, a results section on colony analysis, a result section on sequence analysis. IF YOU AREN’T SURE what is meant by a “written results” please ask. This is not the same as a figure caption.
Written results structure:
Goal (one sentence)
What was done (one, maybe two sentences)
Describe overall trends
Describe/quantify some important results and differences between samples
3. Discussion:
The discussion is centered around presenting scientific arguments. Arguments consist of claims (what can you conclude); Evidence (what data supports your claim); and Explanations (what is the reason – whether it be biological or procedural, or both – for these results). Arguments can and should also include qualifiers or limitations – e.g., assumptions one must make when interpreting the results, or limitations of our claims. Explanations can be hypotheses. You should include comparisons (either in the form of support or contradictions) to existing, peer-reviewed, published research. There should also be an indication of possible future directions – what additional work would you want to do and the questions this would address. These future directions should help clarify things that our work could not. Consider using subheadings in the discussion section, e.g., one for each research question.
4. REFERENCES:
You should have at least four relevant citations/references from peer-reviewed articles. At least three must be cited and relevant to something in your discussion section. You can use any format you like for citations and references as long as it is clear. For the full references you can use any format but you must include a link to the paper.
5. PEER-REVIEW QUESTIONS & INSTRUCTIONS
A. At the end of your full draft (for peer reviewing), include 3 questions for your peer-reviewers to address. These should be focused specifically on things you want feedback on. Questions need to be specific. For example, asking “is this logical” is too vague. A better type of question could be “in what ways does my molecular explanation for the yeast transformation results help connect the evidence and claim?” or “are there any claims I made that aren’t not supported by the data? Please explain”
TRY TO AVOID QUESTIONS THAT CAN BE ANSWERED WITH “YES” or “NO”.
B. When you conduct the peer-review, answer the reviewers three questions, as well as the following:
A. What do you feel works well in this paper? Why? List at least two things.
B. What doesn’t work in this paper/needs improvement? Why? List at least two things.
Please work to ensure your write up is as concise as possible. Cut our redundant statements, ensure only the essential information related to your research questions is presented.
OUTLINE TEMPLATE (OPTIONAL, BUT PLEASE KEEP IT ORGANIZED WITH HEADINGS AND SUBHEADINGS)
Our work in the context of existing literature:
What has been done previously that very closely relates work?
Describe the results of these prior studies, how they relate to our work, and describe how our research questions expand upon prior work.
Results
Use sub-sections
Figure/table + written results
Written results structure:
Goal (one sentence)
What was done (one, maybe two sentences)
Describe overall trends
Describe/quantify some important results and differences between samples
Results Section 1
Results Section 2
Results Section 3
Results Section 4
……
Discussion
Also use sub-sections here, could be based on research questions (headers could be “answers” or claims)
**if you only have one claim to make, you may only have one discussion section vs. sub-sections. Think about separating based on distinct claims and explanations
Claims (significance of results/take home messages)
Evidence to support claim
Biological explanations/mechanisms
Placing your work in the context of existing literature – this can be literature that supports what you observed, or contradicts
Follow-up/future directions – what might you do next to better understand what is happening?
References
At least four peer-reviewed journal articles, at least three in the discussion section.
Any format is fine, as long as it is consistent and contains enough info to find the article.
Requirements: | .doc file
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