20.109(F12): System engineering research article

General requirements

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 each other.
• This report should not be based on previous versions of this teaching module--which differ in critical ways so you wouldn't want to use them anyway!

Format

General format requirements are:

• 12 pt font
• double spaced text except for the abstract which is single spaced
• 1” margins

Specific requirements

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

Please keep this section to one page, double spaced.

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

Please keep this section to two pages, double spaced.

Cite the class wiki as follows: "Protocols were according to "20.109 F'12 lab wiki: URL accessed on Month Day, 20xx." unless otherwise noted" then subdivide the M&M section into the following

1. Bacterial strains and plasmids
   • list genotypes and plasmid names when known
2. Taking photographs
3. β-gal assay
4. Library screen
   • include the way the library was made (even though you didn't do this part)
   • include the way you looked for mutants
   • include sequencing information here
5. Western Analysis (if and only if the blot gave results worth including in the research article)
   • include how cells were grown and how they were lysed
   • include details about gel and antibodies used
   • 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 & legends

Your figures should be appended to the end of your article. Do not waste time trying to fit the figures into the text of your report. If the figure files are large, they can be collected and sent together, as a document that is separate from the text of the article.

• 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 β-gal data
  

Please remember to carefully craft the figure legends...this will often be carefully examined by readers and editors as they decide whether or not to read the rest of your article!

text

• Please keep this section between one and two pages, double spaced.
• Begin this section with a short review/overview.
• 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

Please keep this section between two and three pages, double spaced.

You should include but are not limited to

• a short sentence overview/review to begin this section
• 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

Annotated References

• Please follow instructions that are here
• Carefully format these, including a wiki citation like: "20.109 F'12 lab wiki: URL accessed on Month Day, 20xx."
• Do not include encyclopedias (including Wikipedia) in your reference list since these sources are insufficiently scholarly. You should find the primary references that support those summaries.
• You should have read the articles you cite in your reference list. Please be careful about using "google scholar" and other information retrieval options since it can be difficult to glean their relevance by the titles and abstracts, but they are dead giveaways of a "padded" reference list.
• For half of your references, please follow the citation with 10-15 word description of the key aspect of the paper you're citing. A nice example of such an annotated reference list is shown here.