Sigma factors

In a new study appearing in PNAS this week, Brandeis Molecular and Cell Biology graduate student Houra Merrikh and co-workers from the Lovett lab identified the E.coli gene iraD as a regulator of the response to oxidative DNA damage in exponentially growing bacteria. Interestingly, the mechanism seems to involve the alternative RNA polymerase sigma factor RpoS, previously characterized as a regulator of expression during the “stationary phase”. Merrikh et al. argue that this response works in parallel with the previously characterized SOS response in protecting growing bacteria from DNA damage.

BLAST (2): Computational Biology Course

If you don’t really know what BLAST is, but think you might need to, maybe COSI 178A (Computational Biology) would be a good course for you to take. Prof. Pengyu Hong will be teaching the course in the spring semester.

BLAST (1): New versions

NCBI has released new versions of their web and standalone BLAST+ programs. This appears to me significant mostly if you BLAST lots of sequences. I used to have a computer with the standalone programs installed, but no one was using it. If someone needs BLAST+ installed on a local computer, let me know.

Microscopy (2): studying molecular motors

An article in Cell by recent Molecular and Cell Biology Ph.D. graduate Susan Tran and coworkers demonstrates the power of single particle microscopy in combination with Drosophila genetics in studying molecular motors. Studying lipid droplet movement in embryos, they show that multiple motors are attached to droplets in vivo. Surprisingly, having multiple motors per droplet in vivo doesn’t result in higher velocities or distances traveled.

Microscopy (1): Quant Bio Instrumentation Lab

Want to learn the principles of microscopy? Jeff Gelles writes:

Dear Life Sciences Ph.D. students,

This semester we will again be teaching the Quantitative Biology Instrumentation Lab course, QBIO 120b.  This course, now in its third year, was developed with funding from HHMI.  The course aims to give Ph.D. students who use (or will use) optical instruments in their research practical, hands-on training in the principles and practice of light microscopy (both phase and fluorescence), absorbance spectroscopy, and fluorescence spectroscopy.  A syllabus is attached.

The course is open to all students whether or not they participate in the Quantitative Biology program.  However, space in the course is limited, so it would be a good idea for students who want to enroll to email me prior to the first meeting, which is Wed. January 14 at 2:00 in Abelson 335.  Please feel free to contact me with any questions.

Jeff Gelles

Also, don’t forget about the Quantitative Biology Bootcamp next weekend.

Justice Brandeis will be on a US postage stamp

It’s been a slow news week, not much to report.

In random, almost sort-of-relevant news, Justice Brandeis (for whom our university is named) will be on a USPS postage stamp in September.

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