20.109(F13): DNA engineering summary

Overview

The culminating assignment for Module 1 will consist of two elements: an abstract that succinctly describes your DNA engineering investigation, and a thorough summary of your data in figures and supporting text – including context for understanding the work’s broader implications.

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 in pairs. Be sure to review the 20.109 statement on collaboration and integrity as you proceed.

Method of Submission

Please email your completed report to 20109 DOT submit AT gmail DOT com, with filename TeamColor _LabSection_Mod1.doc (for example, Rainbow_TR_Mod1.doc).

First Draft Submission: Oct 10th/11th

The first draft of your abstract and summary is due by 11 am on October 10th (Thursday) or 11th (Friday), according to which day you have lab.

Professor Engelward will comment on your submissions and assign them a draft grade. Additionally, your section-specific writing instructor will give feedback about abstract strucure and comprehensibility.

Revised Document Submission: October 29th/30th

Your commented first draft will be returned on October 22nd (Tuesday) or 23nd (Wednesday). You will then have the opportunity to revise your work for up to a one and one-third letter grade improvement. In other words, a C can be revised up to an B+, a C+ to an A-, a B- to an A, etc. ) The final draft is due by 11 am on October 29th (Tuesday) or 30th (Wednesday), according to which day you have lab.

Please re-submit your marked up report (with Prof. Engelward’s comments) so she can compare the old and new versions side by side. AND MAYBE? Please briefly highlight any substantial revisions to your text in the “notes” section of the slide. (For example, “this slide was substantially revised to clarify the figure and deepen the analysis.)

Guidelines on Formatting and Length

We recommend that you prepare your document in a drawing program such as PowerPoint, using a portrait rather than landscape layout. This approach will allow you to create your figures with minimal hassle but maintain the look of a document rather than a presentation. A typical data page should include a figure or two and its caption on the top half, and a few bullet points/short blocks of text interpreting that piece of data below. (Reminder: Your figure captions themselves should avoid interpretation.) A typical context page might include only text, or may also include a supporting figure. More detailed suggestions for content (as opposed to style) are below.

The first page of the document should include an informative title, your section/color/names etc.; the second page should include just an abstract.

Document length should be about X pages, and certainly not exceed Y pages.

Though somewhat variable, typical section lengths might be:

• Background and motivation: ~x pages
• Data presentation and interpretation: ~y pages
• Implications and future work: ~z pages

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.

Background and motivation: potential topics and figures

• Topic: Why is measuring HR interesting and/or useful?
• Topic: How does HR work?
• Figure: Depiction of HR
• Topic: How does the HR assay work?
• Schematic: HR assay approach
  • • You may prepare something similar to the depiction of the assay from Bevin’s lecture notes, but should NOT copy and insert it directly. Your goal should be to make a figure tailored specifically to this assignment. What elements might be cut or added? Think about ways that you can modify the figure to better express your specific experiment.
• Topic: What kinds of questions can the HR assay address?

Data: potential topics and figures

Figures and topics are listed below according to two 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 are describing the detailed methods in a separate assignment. The figure captions and/or supporting text should include only the most relevant aspects of the methods, such as the names of the diagnostic enzymes, a clear description of any normalization or statistics done on the flow cytometry data, etc.

• Plasmid construction and verification
  • Schematic: overall approach
    • You may prepare something similar to the M1D1 intro figure, but should not copy and insert it directly.
  • Figure: gel of digested DNA prior to cloning
  • Figure: recovery gel of purified, digested DNA
  • Topic: apparent success of PCR, digestion, and recovery, including role of controls when applicable
  • Table: colony counts after ligation and transformation
  • Topic: apparent success of ligation and transformation, including role of controls when applicable
  • Schematic and/or Table: diagnostic digest plan, for example in marked up plasmid map form
  • Figure: diagnostic digest gel
  • Topic: apparent success of cloning, explicitly including predicted versus observed sizes, extraneous bands, and role of controls when applicable
• DNA repair assay
  • Schematic: overall approach and question(s) being asked
    • if not in background section, or further modified to emphasize specific samples
  • Figure: sample raw flow cytometry data from own experiment (at a minimum, a negative control, positive control, and one sample)
  • Topic: reliability of flow cytometry data and gating choices
  • Figure: processed individual flow cytometry data (e.g., bar chart)
  • Topic: Did the relative amounts of HR match your expectations/hypotheses…? How might you explain discrepancies?
  • Topic: comparing to class-wide data (for repeated samples), are any results likely to be in error?
  • Figure: processed class-wide flow cytometry data (e.g., bar chart and error bars)
  • Topic: Did the relative amounts of HR match your expectations/hypotheses…? How might you explain discrepancies?

Implications and future work: potential topics and figures

• • Topic: Based on the results, whether they matched your expectations or not, what experiments might you recommend next?
  • Topic: Will the HR assay tend to over-estimate or under-estimate HR, and why?
  • Topic: What other DNA repair assays exist, and what are the pros/cons compared to this one? How might this one be improved?
  • Topic: What future applications might be best-suited to this or other DNA repair assays?