20.109(S21):Data Summary

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20.109(S21): Laboratory Fundamentals of Biological Engineering

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Spring 2021 schedule        FYI        Assignments        Homework        Communication |        Accessibility

       M1: Antibody engineering        M2: Drug discovery        M3: Protein engineering       


Overview

The major writing assignment for Module 1 will consist of a thorough summary of your data in figures and supporting text – including context for understanding the work and insight into the 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 laboratory partner.

As you prepare your assignment be sure to review the resources provided on the Communication tab.

Please submit your completed Data summary draft and revision on Stellar, with filename TeamColor_LabSection_DS.pptx (for example, Rainbow_TR_DS.pptx. The file should be submitted as a powerpoint!

Data summary draft is due by Wednesday, March 24th at 10 pm

Dr. McClain will comment on your submission and assign it a grade. The BE Communication Instructors will provide feedback concerning the Title and Abstract and also assign the grade for this portion of the assignment. You will receive all comments on Monday March 29th.

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.

Data summary revision is due by Sunday, April 4th at 10 pm

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 ….").

Formatting and length guidelines

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). See example of appropriate format here.

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: 4-6 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 you 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.

Content considerations

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, these are SUGGESTIONS and are 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 presentation from the BE Communication Lab workshop.

Background and Motivation: potential topics and figures

  • Topic:Motivate antibody engineering
  • Topic:Background of the experimental approach: yeast surface display of a scFV followed by quantitative screening via FACS and flow cytometry
  • 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: What is your research question? What specific variables are you testing to answer this question?
  • Topic: What are the implications of this experiment?

Results and Interpretation: potential topics and figures

Figures and topics are listed below according to the 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.

Generating scFv library and FACS

  • Schematic: Library generation.
    • Do not include minor technical details that are not necessary to understand your experimental conditions.
  • Topic: Details important to creation of scFv library diversity and expression.
  • Figure: FACS plot.
  • Topic: Expression of scFv in yeast and incubation with lysozyme
  • Topic: Staining in preparation for analysis and cell sorting

Characterization of individual clone

  • Schematic: Experimental approach to clone characterization.
    • Do not include minor technical details that are not necessary to understand the goal of the experiment.
  • Figure:DNA and Protein Alignment of mutagenized clone to parental clone.
  • Topic: What can we predict about scFv-antigen binding based off amino acid mutation?
  • Figure: Representative flow cytometry plots from titration with lysozyme
  • Topic: What do we expect to see in the control plots vs. experimental plots?
  • Figure:Plot of titration with lysozyme and calculation of mutagenized clone Kd
  • Topic: Did the mutation increase or decrease Kd compared to the parental clone?

Implications and Future Work: potential topics

  • Topic: Did this experimental approach result in a scFv clone with an increased or decreased Kd?
    • If no, provide a putative explanation. If yes, how can you further test this approach?
  • Topic: Did the characterization of the scFv clones add new knowledge to what's known about the antibody-antigen interaction?
  • 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 approach be improved?
  • Topic: Discuss a novel way this approach can be used in research, medicine or industry.
  • Topic: What are the broader implications of this experiment and approach?
    • Don't overreach. Suggest impact within the field of antibody engineering.

References

References are generally used in the Introduction and Discussion sections to support any claims that are not common knowledge. Include only those references that pertain to the question at hand. Journals vary considerably in their preferred format for the reference list. For this class, you should list the references alphabetically by the first author's last name. Include all the authors, the title, the name of the journal in which it was published, the year of publication, the volume number, and page numbers. Please carefully follow the punctuation and format requirements.

Your references should be provided at the end of your Research article in the following format:

Pavletich NP, Pabo CO. Zinc finger-DNA recognition: crystal structure of a Zif268-DNA complex at 2.1 Å. Science 1991; 252:809-817.

In the body of your report, this article would be cited as follows:

"The crystal structure of the Zif268-DNA complex has been solved (Pavletich 1991)."

If two or more articles can be cited for this finding, then they are listed alphabetically, separated by a comma.

See also the MIT libraries information on citing sources, here.