BIMM101 Winter 2021 CRISPR Write-up

BIMM101 Winter 2021 CRISPR Write-up
• Complete first draft due Monday March 1st, 11:59pm, to Turnitin via Canvas
• After submitting your complete draft, you will be assigned to do peer-reviews of two papers (on
Canvas)
• Peer-reviews are due by Wednesday March 3rd, 11:59pm (estimated time to complete peer
reviews is about 1 hour)
• Final version due Friday March 12th, 11:59pm, to Turnitin via Canvas
• Do not put your name and student ID on the submitted drafts to ensure peer-reviewing is
anonymous.
PLEASE read the guidelines and rubric carefully
Notes: All text must be typed. Use spell check. You are required to work independently. Identical or
very similar reports (or sections of reports) will result in zero for the entire lab report.
Remember:
• The purpose of an introduction is to acquaint the reader with the rationale behind the work, and
enough background to enable the reader to understand and appreciate your objectives.
• The purpose of a results section is to present and illustrate your findings. Make this section a
completely objective report of the results, and save all interpretation for the conclusions.
• The objective of the discussion/conclusion section is to provide an interpretation of your results
and support for all of your conclusions, using evidence from your experiment and generally accepted
knowledge, if appropriate.
• This write-up should be thought of as a short journal article, to summarize the results of yeast
ADE2 editing (as they relate to the research questions).
o 1. What is the frequency of loss-of-function mutations in ADE2 when specific (HDR) and
non-specific (NHEJ) mutations are introduced after Cas9-induced cutting in the coding
sequence (gRNA1 target)?
o 2. How often are all the HDR mutations incorporated?
o 3. What types of NHEJ mutations are found that caused loss-of-function of ADE2?
• The intended audience is someone with BIMM 101-level knowledge, but who has not completed
these experiments or analysis. Your write-up should have the following sections:
Title (no more than 15 words) describes the purpose of the project
Background & Goals
Please summarize the goal of our CRIPSR experiment, and in your own words describe what
questions you will be answering in the report. (detailed above) Include brief descriptions of what we
did to answer our experimental questions. (Ie. In order to answer our question about how often all the
HDR mutations were incorporated, we examined sequencing results and….etc.)
What is your hypothesis on which treatment(s) should show the highest amount of ADE2 disruption?
(Or do you think they will all be about the same?) What about your thoughts about how often the HDR
template will be used versus NHEJ when template is given during the treatment? Briefly explain your
rationale for your predictions.
Methods
A short paragraph to summarize, in your own words, what we did to get these results. This is NOT a
methods section in enough detail so someone could repeat the experiment. This is an overview of
what was done. You need to provide enough of an overview so the reader can understand how the
experiment was done and how the results were generated. It is up to you to decide what information
is important to include. If you aren’t sure, talk to your IA and instructor about your ideas. Also be sure
to include how you analyzed the data to address each research question.
Results
You need to have analysis of all the yeast transformation results and all of the sequencing
results. You do not need to include any prior results (e.g. plasmid digests, etc.). You decide what is
the best way to show the results. Figures have to clearly communicate the results in a logical way.
There has to be enough information provided so the reader can draw their own conclusions. All
figures/tables should have proper and complete captions: (see here for tips:
https://blog.bioturing.com/2018/05/10/how-to-craft-a-figure-legend-for-scientific-papers/)
The results section should have a written part where you describe the overall trends, make relevant
comparisons and quantify relevant differences.
Summarize the results in writing by describing the data. Refer to the figures as you interpret your
results.
Discussion/Conclusions
State your conclusions in the form of scientific arguments: Claim (what can you conclude); Evidence
(what data supports your claim – summarize the data); and Explanation (what is the reason – whether
it be biological or procedural, or both – for these results). Explanations can be hypotheses, and you
can also include future experiments that would help identify any unknowns.
Peer review questions and instructions
1. On your draft, 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: 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? Is there anything missing?”
Try to avoid questions that can be answered with just a “yes” or “no”.
These are needed only on your first draft.
2. 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.
Rubric
120 possible points Expected (points can be lost for not
fulfilling the expected criteria):
Percent of total
Introduction/Background
24 points
Experiment purpose clear & correct
Big picture is clear & correct
Questions posed in guidelines
sufficiently answered
Predictions reasonable
20%
Methods
12 points
Brief overview of what was done is clear
and correct
How data was analyzed
No unnecessary details
10%
Results:
30 points
Organized & clear
Figures/tables fully and clearly labeled
Figure/table caption explains what the
figure contains and includes enough info
for reader to interpret.
Results described in words, with
relevant reference to figures
Results presented are appropriate for
addressing the research questions, and
are presented in a way such that the
reader can draw their own conclusions
No unnecessary results presented
25%
Conclusions and future
directions
30 points
Claims are accurate, complete &
precise
Evidence is accurate, complete &
precise – results/data are summarized
Explanation is clear and logical
Future directions are reasonable and
sufficient
25%
Overall clarity of writing
10 points
Clear, easy to follow, logical flow of ideas,
little to no grammar, notation, or spelling
errors
Uses appropriate scientific language
8.3%
Draft
8 points
Complete, high-quality draft submitted on
time with questions for reviewers
6.7%
Peer-review
6 points
Thoughtful peer-review completed on time
*you are not permitted to do the peerreview if you do not submit a d