20.109(S14):Microbiome summary

Overview

The primary assignment for Module 1 will consist of two elements: an abstract that succinctly describes your bird microbiota 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 submit your completed summary on Stellar, with filename TeamColor _LabSection_Mod1.doc (for example, Rainbow_TR_Mod1.doc).

Be sure to review the class late policy (link) as well as the further clarification below.

First Draft Submission: March 11th/12th

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

Professor Runstadler will comment on your submissions and assign them a draft grade. Additionally, a writing instructor will give feedback about abstract structure and comprehensibility.

Revised Article Submission: April 3rd/4th

Your commented first draft will be returned on March 20th (Thursday) or 21st (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 3rd (Thursday) or April 4th (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.

OR

Please re-submit your marked up report (with Prof. Engelward’s comments) so she can compare the old and new versions side by side. Please also 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.)

Late Policy Clarification

Penalties for a late draft are direct. A late draft that is not revised will have the penalized grade recorded. For example, a B paper that is one day late and not revised will be recorded as a B-. If submitted on time, the B paper could go up to an A+, while the penalized B- paper can go up "only" to an A.

Penalties for a late revision affect the maximum possible grade. A revision that is one day late can only go up one full letter grade, one that is two days late can only increase by two-thirds of a letter grade, etc. For example, a B paper that is not late can earn up to an A+, that is one day late can earn an A, that is two days late can earn an A-, that is three days late can earn a B+, and that is four days late cannot improve on the B.

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.

Core document length should be about xx pages, and certainly not exceed yy pages. Though somewhat variable, typical section lengths (including both text and figures) might be:

Figure out!

• Background and motivation: ~2 pages
• Data presentation and interpretation: ~x-y pages
• Implications and future work: ~1-2 pages

The first page of the document should include an informative title and author information (section/color/names); the second page should include just an abstract. These two pages will not count toward the suggested xx-yy pages. A typical context page will be enhanced by a supporting figure, though some might include only text. A typical data page should include a figure or two, each with associated caption, and a few bullet points/short blocks of text interpreting that piece of data. (Reminder: Your figure captions themselves should avoid interpretation.) More detailed suggestions for content (as opposed to style) are below.

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: guiding questions

• 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?

• 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?
• AWK FINAL CLAUSE As you bring the reader closer to your specific study, can you clearly and succinctly 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?

CF BPE:

• 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 assay depiction 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 and audience. What elements might be cut or added? How can you modify the figure to best highlight key takeaways?
• Topic: What kinds of questions can the HR assay address?

Data: potential topics and figures

USEFUL CLAUSE FOR M2 MAYBE, LESS SO HERE Figures and topics are listed below according to the 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 we will hold off on practicing a proper methods section until the second module. In this assignment, figure captions and/or supporting text should include only the most relevant aspects of the methods, such as the XYZ REVISE names of the diagnostic enzymes, a clear description of any normalization or statistics done on the flow cytometry data, etc.

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!

NEWER THOUGHTS ABOUT GUIDING Q:

• Revise Day 7 intro and/or protocol to emphasize a few key points about the analysis, particulary the alignment phase in MEGA. Prompt students to consider why “identical” species might show up on different leaves. Also add mean/max bp differences a la W/F Green report? Helps overcome differing tree scales. • Improve guidance in content and approach for discussion section and figures. Successful discussion content and figure styles that we might pose as questions: - How might you highlight differences and similarities between species identities found in MA and AK? Consider a Venn diagram. - How might you highlight differencess and similarities between species frequencies found in MA and AK? Consider a color-coded bar chart that depicts species frequency found in each location. Pie charts that show percent abundance could also be useful. - For the each composite (multi-gull) tree representing a single location, consider whether individual gull samples are evenly distributed among species and/or higher-level branches or not. - How do the topologies of the trees differ, both intra-state and inter-state? Consider how many major clusters each tree has and how far apart they are. - If you create one comprehensive tree for both MA and AK gulls, do you gain any further insights about the relatedness of bacteria in the two locations? - What hypotheses can you present for why certain bacteria are shared among locations and why certain bacteria are unique to a specific location? What further experiments can you propose to test these hypotheses? Are the primary functions of any of these bacteria in the gut already known? - Given the limitations of defining to the species level, what patterns (if any) do you see at higher order levels such as family or phyla? Can you think of possible specific reasons for these patterns related to the disparate environmental conditions in the two locations? - What aspects of your data/findings might you expect to be different, and which the same, if the sample size was increased?

CF BPE EXCERPT:

System construction: making and verifying plasmid

• 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

Hypothesis testing: DNA repair assay

Implications and future work: guiding questions

• MOVE HERE? 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.

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