Module 2 Assignment: Protein Engineering Research Article

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.

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

Writing a "Research Article" versus a "Lab Report"

A quick but unscientific survey of several journal's "instructions for authors" shows some common themes that are worth considering here. For instance, the instructions from The Journal of Cell Biology (JCB) say:

"To warrant publication in the JCB, a manuscript must provide novel and significant mechanistic insight into a cellular function that will be of interest to a general readership. Manuscripts containing purely descriptive observations will not be published."

Similarly, the instructions from Molecular Cell Biology (MCB) state:

"MCB is devoted to the advancement and dissemination of fundamental knowledge concerning the molecular biology of eukaryotic cells, of both microbial and higher organisms. In most cases, reports that emphasize methods and nucleotide sequence data alone (without experimental documentation of the functional significance of the sequence) will not be considered."

Clearly the goal of published research is not merely to catalog or describe observations but to collect the information into some coherent story that advances general understanding and provides insights that others can use. This is the critical difference between a "lab report" which primarily describes your observations and the "research article" you'll write which invites you to share the insights your data gives. Here you must frame your results to address a larger question that's of general interest to the community. Many of the format instructions that applied to a lab report also apply to your research article, but keep in mind how the intention of the two written assignments differs.

Logistics

First Draft Submission

The first draft of your research article is due by 11 am on Day 1 of Module 3.

Revised Article Submission

Your first draft, with feedback from both the writing and the technical faculty, will be returned 9 days later on Day 4 of Module 3. You will then have the opportunity to revise your report for up to a one letter grade improvement. The final draft is due on Day 6 of Module 3. Please highlight any substantial revisions to your text, for example, by using a different colored 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 writing up your research. 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, consider what 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 for writing up your research. The weighting for Module 2, which is different than that for Module 1, is as follows: