20.109(F09): System engineering research article

November 12th or 13th, 2009

 * First draft is due by 11:00 a.m. on the day you have lab. Please turn in your research articles electronically by submitting them to the | Stellar drop box for our class. It is important that you name your files according to this convention: Firstinitial_Lastname_LabSection_Mod2.doc, for example: S_Hockfield_TR_Mod2.doc

November Nov 24th or 25th, 2009

 * Your first draft will be returned. You will have one week from the time your report is returned to address any comments and resubmit your report if you choose. Improvements can increase your grade up to one full letter grade (e.g. a B- on the first draft could become an A-). The grades on the draft and final version are *NOT* averaged.

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 Manuscripts containing purely descriptive observations will not be published."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

Originality

 * This report must be written by you, and thus should not be written with your lab partner, though we encourage you to discuss your results with eachother.

Format
General format requirements are:
 * 12 pt font
 * double spaced text except for the abstract which is single spaced
 * 1” margins

Required content
Several of these elements will have been drafted as homework assignments but the instructions are repeated here.

Abstract

 * Please keep the number of words under 250.
 * Do not include references in the abstract.
 * Try drafting this section after you’ve written the rest of the report.
 * If you’re truly stuck, start by modifying one crystallizing sentence from each of the sections of your report.
 * Please do not plagiarize (accidentally or other) the class wiki. This applies to your entire report.

Introduction
Be sure to end your introduction with a clear description of the problem you’re studying and the method(s) you are using. If you would like to preview for the reader your key results and conclusions in the last sentence of your introduction, you may.

Materials and Methods
Cite the class wiki as follows: "Protocols were according to "20.109 F'09 lab wiki: URL accessed on January 1, 2020." unless otherwise noted" then subdivide the M&M section into the following
 * 1) Bacterial strains and plasmids
 * 2) *list genotypes and plasmid names when known
 * 3) Taking photographs
 * 4) b-gal assay
 * 5) Library screen
 * 6) *include the way the library was built (even though you didn't do this part)
 * 7) *include sequencing information here
 * 8) Western Analysis (if and only if the blot gave results worth including in the research article)
 * 9) *include how cells were grown and how they were lysed
 * 10) *include details about gel and antibodies used
 * 11) *you do not have to include information about how to blot the gel, which you can assume most folks already know

Results
You are welcome to add more figures than those listed here. These are what we consider minimally necessary.

figures
Your figures should be appended to the end of your article. If the files are large, the figures can be sent together as a file, separate from the article. ''*Table 1 (this is now suggested as part of your discussion and is not required as a table in the results): Data from other groups can be included in your discussion section. You might, for instance, talk about the groups with data similar or notably different from what you've spotlighted in the results''
 * Figure 1: Starting conditions for Bacterial Photography System. This figure will have at least 2 panels, namely the "light" petri dish and the "dark" petri dish and, if it looked OK, the photograph you took at the start of the module, as well as the b-gal data you measured for the original system
 * Figure 2: Results for mutant. This figure will include several panels, including but not limited to your sequence alignments, your Western results (if they worked well), and your b-gal data

text

 * In paragraph form, describe each figure and the observations you made.
 * Divide your results section into subsections to help the reader parse the information.
 * As much as possible, reserve conclusions about your data for the discussion section. Clearly an exception to this will be which of your library candidates you chose to pursue, as this information is critical for the next steps in the experiments.

Discussion
You should include but are not limited to
 * conclusions you can draw from your work, including any uncertainties
 * other data (published or personal communications) that support or contradict your conclusions
 * limitations of your work, e.g. what kinds of experiments/controls/samples would have been great to include
 * next experiments you would like to try to extend your findings and strengthen your conclusions