20.109(S13): DNA engineering report

Link back to Module 1.

Overview

The culminating assignment for Module 1 will be a laboratory report in which you describe your investigation of bacteria in different bird populations. It is essential that you relate not merely what you did but why you did it, and not only what your data presently shows but what it means for the future. 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.

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

Logistics

Method of Submission

Please email your completed report to 20109 DOT submit AT gmail DOT com, with filename Firstinitial_Lastname_LabSection_Mod1.doc (for example, S_Hockfield_TR_Mod2.doc).

First Draft Submission: March 12th/13th

The first draft of your research article is due by 11 am on March 12th (Tuesday) or March 13th (Wednesday), according to which day you have lab.

Professor Runstadler will comment on all reports. Additionally, you may request written feedback from your section-specific writing instructor at the time you submit your report.

Revised Article Submission: April 4th/5th

Your commented first draft will be returned on March 21st (Thursday) or 22nd (Friday). 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 an B+, a C+ to an A-, a B- to an A, etc. ) The final draft is due by 11 am on April 4th (Thursday) or April 5th (Friday), according to which day you have lab. Please highlight any substantial revisions to your text, for example, by using a different colored font or a track changes function.

Formatting Expectations

• Your main document (excluding figures) should be/have
  • .doc (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 be about 7-10 pages, and certainly not exceed 12 pages.

Though somewhat variable, typical section lengths might be:

• Introduction: ~1.5-2.5 pages
• Methods: ~1.5-2 pages
• Results: ~1.5-2.5 pages
• Discussion: ~2-3 pages

Content Guidelines

Begin by reading the general guidelines for scientific writing, which describe the expectations for every section of the report, from Abstract to References. A few notes specific to Module 1 are below:

Introduction

You are welcome to use your own creativity and judgment as to what a good introduction should look like for your paper; however, you may find the suggested structure (see general guidelines) and the following guiding questions useful:

• What is the context of the study that you are presenting? Can you convince your reader that your specific study relates to broader questions or a bigger picture that this research might help clarify? In other words, why is this research interesting?
• Is there a context for biological engineering that is not too far fetched? You may wish to think about how you can connect some of your discussion to topics you bring up in your introduction.
• For module 1, you may wish to focus on the microbiome, the host/microbe relationship, ecology and host interaction with the environment, another aspect, or some combination of these topics that you think will intrigue your reader. Keep in mind, you have little space to motivate your work and you need to catch the reader’s attention.
• Are there some unanswered questions a step below the big picture that this type of work could help answer? What sort of result would be a clear step forward in understanding how microbial communities vary between species or geography? Are there some types of changes that have been tested experimentally or examined in natural populations in prior studies that shed light on your expectations? Are human studies relevant to this work? Studies in poultry?
• As you bring the reader closer to your specific study, can you clearly describe what aspects of the microbiota you have examined, and how you have applied this to examine the variables in your experiment/analysis?
• What were your expectations at the outset of the experiment? (Be sure you’ve clearly explained your hypothesis.) Would your introduction benefit from a brief summary of your (and the class’s as a whole) results? Do these contrast with your expectations?

Suggested Figures

UPDATED:

Your report is expected to contain more or less the following figures. Of course you are welcome to make modifications and additions as you see fit. Recall that figures should generally be described in the Results section.

Throughout the Results section, you may focus on your two individual samples (up to 16 per lab pair) first, and then branch out to discussing the contributions of “[my] colleagues.” In the construction/experimental phase (PCR gel, cloning), you may focus mostly on your own samples and treat the class-wide samples briefly. In the evaluation/analysis phase (and continuing into the Discussion section), you should most thoroughly assess your own samples but also treat the class-wide samples in detail. More guidance is provided below.

• Schematics/diagrams
  • Schematic showing overall experimental plan and main steps involved
• Figures and Tables
  • Gel from initial PCR
  • Species summary table for your personal samples and your partner’s, up to 8 each (similar to Excel table that you made but more simple/just the key elements)
  • MEGA phylogenetic tree for each of seven gulls (up to 32 samples each)
    • two of these you have contributed to, and five are taken from the wiki as is
  • Composite phylogenetic trees for MA (three gulls) and AK (four gulls) samples (2 trees total)
  • Possibly other table(s) or figures that summarize interesting individual or class-wide findings, such as:
    • excerpt of your MEGA sequence alignment, such as an area with many substitutions
    • class-wide species table in some high-level form
    • UniFrac comparison of MA vs AK treees – unfortunately, this analysis requires re-doing the trees in MEGA to be rooted rather than unrooted, as only the former format is accepted by UniFrac
    • Your brilliant idea here!

Keep in mind that some minor pieces of data might not require a figure but could be mentioned in passing (e.g., DNA concentration and purity).

OLD VERSION FOR COMPARISON PURPOSES ONLY:

Your report is expected to contain more or less the following figures. Of course you are welcome to make modifications and additions as you see fit. Recall that figures should generally be described in the Results section.

• Schematics/diagrams
  • Schematic showing overall experimental plan and main steps involved
• Figures
  • Gel from initial PCR
  • Sequencing snapshots for your own set of data
  • Tree analysis for class-wide data
• Table and/or Figure
  • Summary findings for class-wide data

Keep in mind that some minor pieces of data might not require a figure but could be mentioned in passing (e.g., DNA concentration and purity).

References

You are not expected to do a thorough survey of the relevant primary literature for this first report. However, your introduction (and potentially discussion) should contain a total of at least three references.

Evaluation

The full descriptive rubric for lab reports can be found on the guidelines page.