20.109(S10): Protein engineering report

Overview
The culminating assignment for Module 2 will be a research article in which you describe your protein engineering investigation. The term research article (as opposed to laboratory report) is meant to indicate your growing maturity as scientific writers, and our growing expectations of you. Your Module 2 paper should approach the quality of the primary scientific literature (excepting its lack of experiment repetition), especially with respect to explaining rather than merely documenting your observations. For more information about research articles vs. laboratory reports see here.

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 Firstinitial_Lastname_LabSection_Mod2.doc (for example, S_Hockfield_TR_Mod2.doc).

First Draft Submission: April 13th/14th
The first draft of your research article is due by 11 am on April 13th (Tuesday) or April 14th (Wednesday), according to which day you have lab.

Revised Article Submission: May 4th/5th
Your first draft, with feedback from both the writing and the technical faculty, will be returned on April 27th (Tuesday) or 28th (Wednesday). You will then have the opportunity to revise your report for up to a one letter grade improvement. The final draft is due on May 4th (Tuesday) or 5th (Wednesday), according to which day you have lab. Please highlight any substantial revisions to your text, for example, by using a different coloured font.

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 not exceed 13 pages. The following rough division is recommended:


 * Introduction: 2-2.5 pages
 * Methods: 3-3.5 pages
 * Results: 2-2.5 pages
 * Discussion: 3-4 pages

Concise writing is appreciated and rewarded!

Content Guidelines
Begin by reading the general guidelines for scientific writing. A few notes specific to Module 2 are below:

Discussion and Citations
This section should realize all the good practices described in the Module 1 assignment, but do so at a more advanced level. You will be expected to cite the broader scientific literature more thoroughly than before, both to set up your investigative question in the introduction and to inform your analysis in the discussion. You should also propose specific future experiments and to otherwise show that you deeply understand the meaning and significance of your results; for example, if you have a hypothesis about why a mutation had the effect that it did, considerwhat follow-up experiments you might try. In addition to drawing conclusions from your own data, you are expected to spend some time considering your classmates’ data.

Suggested Figures
In most research endeavours, you will collect more data than you ultimately publish. In the spirit of writing a research article, in this assignment you should present only essential data. For example, if your sequencing reactions worked, there is no need to present the redundant diagnostic digest that you used to quickly check your construct. The suggested list of figures below should be suitable for most of your write-ups, but you are welcome to make changes with good reason.


 * Schematics/diagrams
 * Depiction of your design strategy for mutagenesis
 * Figures
 * SDS-PAGE
 * Titration curves for WT and mutant protein
 * Tables or just text
 * Sequence analysis
 * Cell pellet observations – colour and relative growth
 * Purified protein concentration
 * Table of KD and/or Hill values for competing models

Evaluation
The full descriptive rubric for lab reports can be found on the guidelines page. The weighting for Module 2, which is different than that for Module 1, is shown below: