links for 2009-01-25

Cool use of our own bacterial flora to chart population migration.

"Over the many thousands of years, H. pylori evolved into distinct strains found in distinct geographic regions. For example, one strain is only found in Europe, another only in Africa, and a third only in East Asia. So, just as genetic anthropologists use differences in our DNA to trace ancient human migrations, so too have scientists used H. pylori to reveal how humans first colonized some of the most remote parts of the world."

One thing that is always hard is understanding the interaction networks between proteins in an organism. Most work is done pair by pair, which really does not scale.

This paper is about a team that created a highly-parallel in vitro system for measuring interactions. Barring the usual caveats, this is really interesting. And one can see this developing quickly to be able to measure hundreds of thousands of protein-protein interactions.

Hm, could they also throw in some DNA-protein interactions?

"We developed an in vitro protein expression and interaction analysis platform based on a highly parallel and sensitive microfluidic affinity assay, and used it for 14,792 on-chip experiments, which exhaustively measured the protein-protein interactions of 43 Streptococcus pneumoniae proteins in quadruplicate."

[Another interesting paper behind a pay-wall. I gotta see if my wife has access.]

Tick-tock. I wonder if they could do one cycle with one fluorescent protein and a quicker one with another, kinda like minutes and seconds. [of course, because this paper is not open access, I need to go to a library to find out the time-scale of the oscillations.]

"After detailed systems design with experimental analyses and mathematical modelling, we monitored oscillating concentrations of green fluorescent protein with tunable frequency and amplitude by time-lapse microscopy in real time in individual Chinese hamster ovary cells."

"Here, we used FRET to systematically map all protein interactions in the chemotaxis signaling pathway in Escherichia coli, one of the most studied models of signal transduction, and to determine stimulation-induced changes in the pathway."

Cool method for (painstakingly) mapping interactions between proteins in a network.