Difference between revisions of "20.109(F08): Protein engineering research article"
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+ | ==Schedule for Module 2 research article== | ||
+ | ===November 4th or 5th, 2008=== | ||
+ | *First draft is due by 11:00 a.m. on the day you have lab. Please turn in your research articles electronically by emailing them to nkuldell, nlerner, myapoe AT mit DOT edu. It is important that you name your files according to this convention: <font color = red> Firstinitial_Lastname_LabSection_Mod2.doc</font color>, for example: S_Hockfield_TR_Mod2.doc | ||
+ | ===November 20th or 21st, 2008=== | ||
+ | *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 [http://www.jcb.org/misc/ifora.shtml#Manuscript_organization JCB] say:<center> | |
+ | "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 Manuscripts containing purely descriptive observations will not be published."</center> | ||
+ | Similarly, the instructions from [http://mcb.asm.org/cgi/content/full/28/1/1 ''MCB'']state:<br><center> | ||
+ | "''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."</center> | ||
+ | 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 [[20.109(F08):Guidelines for writing up your research| format instructions]] that applied to the lab report also apply to your research article, but keep in mind how the intention of the two written assignments differs. | ||
− | * | + | ==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 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. | ||
+ | ===<center>Abstract</center>=== | ||
+ | *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. | ||
− | + | ===<center>Introduction</center>=== | |
− | + | The homework you wrote after the first day of this new module will serve at the heart of your introduction. You should add (at least) one final paragraph to narrow the information funnel, ending your introduction with a clear description of the problem you re studying and the method 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. | |
− | + | ||
− | + | ===<center>Materials and Methods</center>=== | |
− | * | + | Cite the class wiki as follows: "Protocols were according to "20.109 F'08 lab wiki: URL accessed on January 1, 2020." unless otherwise noted" then subdivide the M&M section into the following |
+ | #Yeast strains and plasmids | ||
+ | #*list genotypes and plasmid names when known | ||
+ | #PCR | ||
+ | #*include primer design info here | ||
+ | #*include primer sequences, for tagging and for candidate verification | ||
+ | #*include PCR cycling conditions | ||
+ | #Yeast transformation | ||
+ | #* include how you selected for transformants | ||
+ | #* include what you did to verify that TAP tag was integrated where you thought. | ||
+ | #Western Analysis | ||
+ | #*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 | ||
+ | #Yeast Microarray | ||
+ | #*mention kits as relevant, including deviations from the wiki/published protocol if any | ||
+ | #*mention how many yeast and how much RNA was used | ||
+ | #*describe array analytical methods in results section rather than in Materials and Methods | ||
+ | General note for M&M: If you used any kits for any of the manipulations, it is sufficient to cite the manufacturer s directions, e.g. |