20.109(F17): M1 Data Summary
Contents
Overview
The culminating assignment for Module 1 will consist of two elements: an abstract that succinctly describes your genome instability investigation, and a thorough summary of your data in figures and supporting text – including context for understanding the work’s broader implications.
The figure format is similar to that of a scientific journal article, but the traditional Results and Discussion sections found in journal articles are to be condensed into succinct bullet point form accompanying each figure. The purpose of this assignment is to prepare you to write a full journal article at the end of Module 2 by encouraging you to practice writing concisely using bullet points.
The target audience for this report is a scientifically literate reader who is unfamiliar with your specific field. Thus, you can assume rapid comprehension – but not a priori knowledge – of technical information, and consequently should strive to present your work in a logical, step-by-step fashion.
Logistics
- You will complete this assignment with your partner. Please review the 20.109 statement on collaboration and integrity as you proceed.
- Be sure to review the class late policy as well as the further clarification below.
Method of submission
Please submit your completed summary via Stellar with filename TeamColor_LabSection_Mod1.ppt, (for example, Fuchsia_TR_Mod1.ppt). The document must be submitted as a powerpoint!
Draft submission: October 11th
Your Data Summary is due by 10 pm on Wednesday, October 11th.
Prof. Engelward will comment on your submission and assign it a grade. The BE Communication Instructors, Dr. Clarke and/or Dr. Bhargava, will provide feedback about abstract structure and comprehensibility -- they will also assign the grade for the Abstract portion of the assignment. You will receive all comments on Monday, October 16th.
You will then have the opportunity to revise your report for up to a one and one-third letter grade improvement. In other words, a C can be revised up to a B+, a C+ to an A-, a B- to an A, etc.
Revision submission: October 22nd
Your Data Summary revision is due by 10 pm on Sunday, October 22nd.
For your final report, all changes need to be in a different colored font so the improvements you made are clear. You should also include a cover letter with your final draft that explains how you addressed the concerns raised (e.g. "paragraph x was completely rewritten to better explain….” or “Results for the agarose gel analysis were clarified by …."). You will receive additional comments and your final grade on the assignment by Monday, October 30th.
Guidelines on formatting and length
See example of appropriate format here.
Create your report as a series of PowerPoint slides. This will allow you to create figures that are representative of those found in the literature (i.e. sized appropriately with sub-panels if necessary).
Format details
- Layout: Portrait, not landscape.
- Font: Arial 14pt for text; Arial 12pt for figure captions.
- Text should be written as bullet points, not full sentences and paragraphs.
Content details
- First page: Title and Author information (section/color/names)
- Second page: Abstract
- Body: 8-12 pages (not including Title and Abstract pages). Recommended section lengths (including both text and figures):
- Background and Motivation: 2 slides
- Contents of Background and Motivation: The majority of this section will be bulleted text. Include schematic figures when appropriate.
- Results and Interpretation: 5-8 slides
- Contents of a Results and Interpretation slide: Top half: figure(s) with caption(s). Bottom half: bullet points that present and interpret the data. (Remember that captions should not contain interpretation.)
- Figure presentation: In published research figures are rarely a full page in size; rather each plot is usually only 3 inches x 3 inches.
- Present your Results and Interpretation such that the figure, caption, and interpretation bullet points all fit on a single slide. Remember that when you shrink a figure, you must make sure it remains legible.
- Implications and Future Work: 1-2 slides
- Contents of Implications and Future Work: This section will be bulleted text.
- Background and Motivation: 2 slides
Content guidelines
Begin by reading the general guidelines for scientific writing. In particular, the sections on Title, Abstract, Figures, and Holistic View of Data are particularly applicable to this assignment.
A few prompts to get you started are below, but note that this list is not exhaustive and also that several elements could reasonably be included in more than one section. In addition, this is not a checklist of what should be in your summary. Think about which elements are most appropriate in answering your research question.
Title and Abstract
Please review the Title and Abstract worksheet and rubric from the BE Communication Lab workshop.
Background and Motivation: potential topics and figures
- Topic: Introduce and discuss the importance of maintaining genomic stability.
- Topic: Introduce and discuss the importance of measuring genomic instability.
- Figure: Simplified schematic of BER pathway.
- Topic: Impact of chemical drug treatments on DNA stability.
- Figure: Types of DNA damage induced by chemical drug treatments.
- Topic: Discuss the utility and importance of the CometChip assay as a scientific tool.
- Topic: What is your experimental question? How will you answer this question?
- Schematic: Experimental approach.
- Be sure your schematic is tailored specifically to this assignment and audience. What steps can be cut or added? How can you highlight the key steps?
- Topic: Why is it useful to measure DNA damage and repair?
Results and Interpretation: potential topics and figures
Figures and topics are listed below according to the three major phases of your experiment. Within each phase, you should look for sub-groupings of interest, rather than treat each piece of data in isolation. In other words, try to both interpret and communicate outcomes holistically.
Keep in mind that you described the detailed methods in a separate homework assignment and it does not need to be included in this report. Therefore, figure captions and/or supporting text should include only the most relevant aspects of the methods, such as the names of the diagnostic enzymes, experimental techniques, or assays.
System optimization: testing cell loading and measuring cell growth
- Schematic: Experimental design.
- Do not include minor technical details that are not necessary to understand your experimental conditions.
- Topic: Testing cell loading number.
- Figure: Image of CometChip after cell loading.
- Figure: Graph or table displaying cell loading data.
Examining the mechanism of DNA damage using chemical drug treatments
- Schematic: Experimental approach.
- Do not include minor technical details that are not necessary to understand the goal of the experiment.
- Topic: Level of DNA damage as a function of treatment concentration.
- Figure: Images from CometChip with different concentrations of treatment.
- Figure: Images from CometChip comparing wild type and mutant.
- Figure: Graph or table comparing DNA damage levels across different treatment concentrations for wild type and mutant cells.
- Topic: DNA damage observed with and without enzyme treatment.
- Figure: Images from CometChip comparing wild type and mutant with and without enzyme treatment
- Figure: Graph comparing relative DNA damage levels (damage level with enzyme minus damage level without enzyme) for wild type and mutant cells.
- Figure: Graph or table comparing DNA damage levels with and without enzyme treatment for wild type cells
- Figure: Graph or table comparing DNA damage levels with and without enzyme treatment for mutant cells
- Topic: DNA damage observed following H2O2 and MMS exposure.
- Figure: Images from CometChip with H2O2 and MMS treated cells.
- Figure: Graph or table comparing DNA damage levels in H2O2 and MMS treated cells.
Measuring foci abundance using sub-nuclear visualization assay
- Schematic: Experimental approach.
- Do not include minor technical details that are not necessary to understand the goal of the experiment.
- Topic: DNA damage (foci) abundance as a function of treatment concentration.
- Figure: Images from γH2AX assay with different concentrations of treatment.
- Figure: Images from γH2AX assay comparing wild type to mutant.
- Figure: Graph or table quantifying percentage of wild type and mutant cells with high amounts of double strand breaks given various treatment conditions
- Topic: Comparison of CometChip results and γH2AX results.
- Topic: Recovery time required to repair DNA damage.
- Figure: Images from γH2AX assay throughout timecourse.
- Figure: Graph or table quantifying percentage of wild type and mutant cells with high amounts of double strand breaks given various recovery times
Implications and Future Work: potential topics
- Topic: Did your results match your expectations?
- If no, provide a putative explanation. If yes, how can you further test if your hypothesis is correct?
- Topic: Based on the results, whether they matched your expectations or not, what experiments might you recommend next?
- Follow-up experiments could distinguish between competing explanations of a given outcome or broaden the sample set for a question you already asked, to give just two examples.
- Topic: How might this assay be improved?
- Topic: How might this assay be used as a research tool? in the clinic? in industry?
