20.109(F15): Protein engineering report

Link back to Module 2.

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.

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 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 Manuscripts containing purely descriptive observations will not be published."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 MCBstate:
"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.

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

Logistics

You will complete this assignment individually.

Method of submission

Please submit your completed summary on Stellar, with filename Name_LabSection_Mod2.doc (for example, NoreenLyell_TR_Mod2.doc).

Date of submission: ,font color = red>Nov 14th

Your Protein engineering report is due by 5 pm on Saturday, Nov 14th. The final version of your research article is due by 5 pm on November 27th (Friday) for everyone.

Formatting expectations

• Your main document (excluding figures) should be/have
  • .docx (preferred) or .pdf
  • 12-point 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: 2-3 pages
• Materials and methods: 3-3.5 pages
• Results: 2-2.5 pages
• Discussion: 3-4 pages

Concise writing is appreciated and rewarded! In other words, longer is not always better.

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 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. (Include the mutants most relevant to your own results rather than every mutant in the class.)

Suggested figures

In most research endeavors, 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 mutants
• Figures
  • Sequencing
  • SDS-PAGE
  • Titration curves for wild-type and mutant proteins
• Tables or just text
  • Cell pellet observations – color and relative growth rates
  • Purified protein concentration
  • K_D and/or Hill values for relevant model(s)

Evaluation

The full descriptive rubric for lab reports can be found on the guidelines page. The report will be graded by Dr. Noreen Lyell.