20.109(S14):NHEJ system research article

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20.109(S14): Laboratory Fundamentals of Biological Engineering

Home        Schedule Spring 2014        Assignments       
Module 1        Module 2        Module 3              



The culminating assignment for Module 2 will be a research article in which you describe your systems engineering investigation. The term research article (as opposed to laboratory report) is meant to indicate your growing maturity as scientific writers, and our growing expectations of you. While your Module 1 assignments contained many of the same elements that you'll include here, the research article will be a more complete, cohesive, and formal document. Your Module 2 paper should approach the quality of the primary scientific literature (excepting its lack of experiment repetition), especially with respect to explaining rather than merely documenting your observations. For more information about research articles vs. laboratory reports see here.


Method of Submission

Please submit your completed report on Stellar, with filename FirstName_LastInitial_LabSection_Mod2.doc (for example, Raphael_R_TR_Mod2.doc). Late assignments should be submitted on Stellar as well.

You will complete this assignment individually. Please review the 20.109 statement on collaboration and integrity as you proceed.

Date of Submission: April 23rd

The final draft of your research article is due by 5 pm on April 23rd (Wednesday) for everyone.

Note that there is no lab Tuesday or Wednesday that week.

Formatting Expectations

  • Your main document (excluding figures) should be/have
    • .docx (preferred) or .pdf
    • 12-pt font
    • with 1-inch margins
    • double-spaced (excepting the abstract)
  • Figures can be made in a separate drawing program (such as powerpoint), and should be submitted as .pdf

Guidelines on Length

Not counting figures, report length should not exceed 13 pages. The following rough division is recommended:

Please take the following guidelines with a grain of salt. Because we are teaching a brand-new module, we necessarily can only estimate the requisite section lengths. You will not be penalized for going modestly over a section limit if you are being thorough yet concise. Conversely, you might technically stay within a section limit yet use more space than your content warrants, which would lower your evaluation.

  • Introduction: 2-2.5 pages
  • Methods: 3ish pages
  • Results: 2.5-3 pages
  • Discussion: 3-4 pages

Concise writing is appreciated and rewarded! In other words, longer is not always better.

Content Guidelines

Begin by reading the general guidelines for scientific writing. A few notes specific to Module 2 are below:


Recall from the scientific writing guidelines the funnel structure for the introduction, and also review the specific guiding questions in the M2D6 FNT.


The methods section will be evaluated by your lab section instructor (Shannon or Agi) and be worth approximately 10% of the report grade. Please take full advantage of the feedback that you receive on the FNTs.

Results and Figures

Individual versus class-wide data

You may take an approach similar to what you did in Module 1. More explicitly, you should present just your individual results for all of the validation experiments. You may briefly comment on class-wide consistency if you wish. For the investigative flow cytometry experiment, you should take a class-wide view.

Suggested figures

The suggested list of figures below should be suitable for most of your write-ups (not necessarily in this order!), but you are welcome to make additions/deletions/modifications as you see fit. Be sure to present the data in whatever progression you feel tells the most logical story. Remember that the order of our experiments does not necessarily correspond to the best way to tell the story of this investigation.

  • Schematics/diagrams
    • Overall approach (not every single method to get there!) and question being asked
    • Often the overview schematic is designed to support the first/overview paragraph of the Results section
  • Figures
    • Ku80 immunoblot
    • C401 dose response curve
    • Post-digest DNA gel
    • Select raw flow cytometry images
      • Not all 12 of yours!
      • Ideally show how gating was determined, followed by one or two experimental plots
  • Figures and possibly also Tables
    • Class-wide flow cytometry results
    • Ultimately interested in NHEJ repair values for different conditions
      • Vertical bar plot with 95% confidence interval error bars is one good representation
    • Perform statistical comparisons where possible
      • We're fine with t-tests for 20.109 purposes, but you can use ANOVA or other multiple-comparison approaches if you wish
    • Some comment on interim results (e.g., typical B/G ratio and its consistency in intact case) is fine
    • Remember that some data may be excluded for clear and consistently applied reasons

Discussion and Citations

This section should realize all the good practices described in the Module 1 assignment in regards to concisely stating conclusions about your research, but do so at a more advanced level. You will be expected to cite the broader scientific literature more thoroughly than before, both to set up your investigative question in the introduction and to inform your analysis in the discussion. You should also propose specific future experiments and otherwise show that you deeply understand the meaning and significance of your results; for example, if you have a hypothesis about why a DNA topology had the relative repair frequency that it did, consider what follow-up experiments you might try. Also, make sure to do a bit of literature digging to determine if your results have any precedent or if your experiments are contrary to what has been reported. Modest speculation as to why that it the case is highly encouraged. The best scientific writers are creative in their discussion sections – convincing their readers that whatever the results, the study was interesting and contributes to forward movement of the field.

You will need to include a References section in your report. Follow the guidelines here.


The full descriptive rubric for lab reports can be found on the guidelines page. Methods will be graded by Dr. Stachowiak or Dr. Hughes and the rest of the report will be graded by Professor Samson.
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