20.109(S17): M1 Data Summary

Overview

The culminating assignment for Module 1 will consist of two elements: an abstract that succinctly describes your ligand screening investigation, and 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 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 Gradebook Module with filename TeamColor_LabSection_Mod1.ppt, (for example, Fuchsia_TR_Mod1.ppt). The document must be submitted as a powerpoint!

Draft submission: March 13th

Your Data Summary is due by 10 pm on Monday, March 13th.

Prof. Koehler and Dr. Lyell will comment on your submission and assign it a grade. The BE Communication Instructor, Dr. Chien, will provide feedback about abstract structure and comprehensibility -- she will also assign the grade for the Abstract portion of the assignment. You will receive all comments on Monday, March 20th.

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: March 27th

Your Data Summary revision is due by 10 pm on Monday, March 27th.

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, April 3rd.

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 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 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 chemical probes in biology and / or research.
• Topic: Introduce and discuss the utility of small-molecule microarrays (SMMs).
• Figure: Simplified schematic of SMM slide printing.
• Topic: Introduce and discuss the role of FKBP12.
• Topic: Discuss your experimental goal.
• 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?

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 important reagents, experimental techniques, or assays.

Protein purification

• Schematic: Experimental design.
  • Do not include minor technical details that are not necessary to understand your experimental conditions.
• Topic: FKBP12 purification.
• Figure: Image of polyacrylamide gel.
• Figure: Graph or table displaying cell protein concentration.

Ligand screening

• Schematic: Experimental approach.
  • Do not include minor technical details that are not necessary to understand the goal of the experiment.
• Topic: Identification of positive hits.
• Figure: Image from representative scan.
• Figure: Graph or table comparing z-scores and p-values.
• Topic: Chemical structure comparison.
• Figure: Images of positive hits.

Implications and Future Work: potential topics

• Topic: What is the positive hit rate? Is this consistent with similar research?
• Topic: Do your hits share any common chemical structures?
  • If no, provide a putative explanation. If yes, how can you further test if this structure is important in binding?
• Topic: How can you use your FKBP12 binders to further research focused on this protein?
• Topic: How might this method be improved?
• Topic: How might this assay be used in the clinic? in industry?