20.109(S08):Module 2 Portfolio

Submission notes
Update: In order to split your attention a little less drastically for next week, and reduce the percentage of your assignments due all in one week, the due date for Part 2 of the portfolio will be delayed to Day 1 of Module 3.


 * 1) Parts 1-3 are due on Day 8 of Module 2; Part 4 is due on Day 1 of Module 3.
 * 2) email these as .doc
 * 3) email them to jasanoff, nlerner, and astachow AT mit DOT edu
 * 4) please use the following format to name your files: M2PX_yourfirstname_yourlastname.doc
 * 5) *where X refers to the section number, 1 or 2 or 3 or 4
 * 6) We will return Parts 3 and 4 with comments and you will have one week to re-submit these portions of your portfolio for up to 1 letter grade improvement in your score per section.

Portfolio components
For this module, you will not write a complete lab report. Instead, you will turn in a few independent pieces of written work that provide a summary of and context for your results. The first part of your portfolio is a summary of your design process. It won’t cover precisely the same territory as a traditional Introduction, but should provide a naïve reader with some background necessary for understanding your choices. The second part of your portfolio is essentially a combined Results+Discussion section, but an abbreviated and slightly less formal one, according to the format below. The final sections of the portfolio will be related to your journal club presentation.

Part 1: Description of IPC mutant design
Whether you are writing a grant proposal, seeking venture capital for a new business, or collaborating on almost any project, it’s important to have an awareness of and an ability to describe the key elements of your thought process. Moreover, it is often necessary to address multiple audiences at once. The goal of this writing assignment is to do just that. You should provide enough background (about inverse pericam, mutagenesis, etc.) for a technically adept reader who is not in the field to understand your protein design goals. You should also provide enough technical detail for someone familiar with calmodulin to know exactly what portion of the protein you are modifying and why. Feel free to talk about design choices that you did not ultimately pursue, to give an idea of the breadth of options before you. However, do not let these become a distraction from the more in-depth discussion of your two particular mutants. Please cite references as appropriate. (You are not required to find references besides the ones given to you in class.) This should be a brief, ~2 page summary, and will be worth ~22% of your portfolio grade.

Part 2: Summary of Results
Summarize your results in a series of figures/tables with expanded figure captions. As usual, these captions will include: a concise, meaningful title; only as much Methods as is needed to understand the result; clear labeling and definition of all parts. In contrast to a normal figure caption, you may interpret your data in the caption itself (hence ‘expanded’) rather than in a separate Results and Discussion text. Introduce or conclude the list of figures with a short paragraph summarizing your findings, and describe in a couple of sentences what you would try next if you had another month to spend on this project. Your figures may include but are not limited to:


 * Schematic indicating your design strategy for mutagenesis
 * Table of (or sentence about) colony counts for mutants
 * Table of (or sentence about) cell pellet observations
 * Figure depicting sequence analysis
 * Figure of SDS-PAGE results
 * (Table of purified protein concentrations, if available)
 * Titration curves for WT and mutant proteins, table of KDs

This section will be worth ~44% of your portfolio grade.

Part 3: Mock Submission Letter
This assignment will give you a chance to take a big picture view of the journal article you to present to the class. Normally when a scientific article is submitted for publication, it undergoes a multi-stage review process. The editors of the journal take a quick look over the submission, then decide whether to send it to other scientists in the field for a thorough peer review. Nature alone publishes about a thousand papers per year (including scientific articles, book reviews, editorials, etc.), and receives many more that do not make the cut. Thus, those aspiring to publish their research in a quality journal must catch the editor’s eye – briefly and convincingly – in a cover letter highlighting their work. Consider the researcher who wrote your chosen journal article, and put yourself for a moment in his or her shoes to write such a letter. There is no one accepted format, but keep the following questions in mind, as they will surely be on the mind of the editor: “what is the main question that this paper addresses and why is it important? what are the one or two key findings? what is the significance of these findings to the larger field?” To help you place your paper in a broader context, read the review article(s) associated with your paper category here. This part will be worth ~22% of your portfolio grade. Update: a skeleton letter can be found in the [[Media: 20.109_mock-letter.pdf | linked document]]. Keep in mind that the sample letter is just a guideline, not an exact template to follow.

Part 4: Mock Mini-Review
Now that you have gotten some feedback on the work you presented (during the the question&answer session following your talk), imagine yourself not in the author's shoes, but in the editor's or reviewer's shoes instead. Write a short critique (paragraph or so) in your own voice, addressing the following when relevant: are there alternative explanations for the results seen? are there any experiments or controls that you think would be useful additions to the paper? did the paper have (or is it likely to have) the impact that the authors anticipated? This part will be worth ~11% of your portfolio grade.