7.89/CSB.100  Topics in Comp & Sys Biology

Hi CSB.100 students,

I have decided that you've all done enough writing this semester, so
there will be no writing assignment due Dec 5.
I hope that none of you are too disappointed. 

We will be doing evaluations in class next Friday (Dec 5) during class.
For this purpose it would be very helpful if you could review your memory
(or notes) from the semester and perhaps jot down what your favorite
papers and topics were during the semester, and also your least favorite,
and mention these in your evaluations for use in planning next year's course.

Also, for those who are interested in understanding more about how proteomics
and phosphoproteomics works, I have posted two reviews on the course web site
which provide background on methods used in next week's papers.
These reviews are optional.

Enjoy your Thanksgiving!

See you all next week.

Cheers,

Chris

See course web site under Homework or below:


CSB.100/7.89 Writing Assignment due 11am Friday Nov 14

News Release
The press represents a vital link between science and the public. It is important that the public, who after all fund most scientific research, hear about the discoveries that their support makes possible.  From time to time in your scientific careers, your work may attract the attention of the press, and you may be asked to conduct an interview with a reporter who is affiliated with a university news office, or with a magazine or newspaper or online periodical.  The role of the news office reporter is to identify those aspects of recently- or soon-to-be-published research that may be of interest to the press and to the public and to summarize the work in a way that will be generally accessible (i.e. minimizing scientific jargon).  University news releases are then distributed to the media and are often picked up by the specialty press (e.g., "RNAi News") or by the mainstream press (e.g., "The Boston Globe").  It takes a bit of practice to conduct or give a good interview that presents the research in an interesting, accessible and accurate light. For this exercise, your task is to play the role of a university news office reporter and to write a news release about your assigned paper.  You should first request a copy of the paper from the author.  You should read the paper and also ask the graduate student author for a short interview about the paper.  At the interview, be sure to have a list of questions prepared in advance.  The purpose of your questions can be to clarify things about the paper that were unclear to you, to help establish which aspects of the paper are likely to be of most general interest, and to obtain quotes that you may wish to use in your story (try to include at least one quote if possible).  Be sure to take notes.  I expect that most student authors will be willing to grant interviews (many have confirmed to me that they are happy to participate), but if your author does not want to be interviewed, just write the story without the interview (in this case, you can quote directly from the paper if you wish).  Your news release should be no longer than 2 pages, double-spaced, with 1" margins.  Your name and a catchy title for your story should be at the top.  The paper citation (journal name, title of paper, vol, pages, year, etc.) should be listed at the end of your story. If printed on separate sheets, please staple the two pages together. Your news release should understandable and interesting to someone who has a bachelor's degree (but not necessarily in a biology-related field). For examples of style, see the following recent releases by MIT news office staff:

Computer model reveals cells' inner workings
http://web.mit.edu/newsoffice/2008/cell-signal-1016.html

Too much of a good thing: cells with extra chromosomes share detrimental traits
http://web.mit.edu/newsoffice/2008/chromosome-1030.html

Immunity, from the cell's point of view
http://web.mit.edu/newsoffice/2008/vaccination-1103.html

Untangling DNA regulation
http://web.mit.edu/newsoffice/2008/stemcell-1106.html

For reference, the students and paper titles for this assignment are listed below.
All are current MIT CSB graduate students (except one who is in HST).

Author             Title of paper

Lawrence David    Resource Partitioning and Sympatric Differentiation Among
            Closely Related Bacterioplankton

Robin Friedman    Most mammalian mRNAs are conserved targets of microRNAs

Charles Lin        Global control of cell-cycle transcription by coupled CDK and
            network oscillators

Ramon Salsas-Escat    The molecular mechanics of collagen degradation:
                implications for human disease

Jesse Shapiro    Comparing patterns of natural selection across species using
            selective signatures

Sabrina Spencer    Origins of cell-to-cell variability in apoptosis induced by TRAIL
            (under revision)

Chandni Valiathan    Genomic predictors of interindividual differences in response to
            DNA damaging agents

Eric Wang        Alternative isoform regulation in human tissue transcriptomes

Grace Zheng        Dynamic regulation of miRNA expression in ordered stages of
            cellular development

Hi CSB.100/7.89ers,

I wanted to let you all know that I have posted 1 page of notes (under >Materials>General) listing some questions you may want to ask yourself when reading a paper or preparing to lead a discussion.  Also, there will be NO written assignment due this Friday 9/12, but there will be an assignment due the following week. Please read this week's papers and supplementary readings (posted under >Materials>Week 2...) carefully.

Best,

Chris