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"In his Correspondence 'You're the best man for this job, son. What a coincidence!', Albert Ruggi's suspicions about the process by which the offspring of professors are deemed to be the best candidates for new positions may well be justified (Nature 456, 870; 2008). On the other hand, a few rare families just do produce generations of eminent scientists. For example, there are at least seven parent–child pairs of Nobel laureates." via @suryasnair
links for 2009-01-25
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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."
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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."
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"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.
Itching to mutagenize
I’ve been thinking back to my bio-tinkering days. I used to work on protease inhibitors called serpins, serine protease inhibitors. Serine proteases are enzymes that cut up other proteins and have a serine (an amino acid) as the key component of the calalytic chemistry. The two main serpins I studied were practically identical except for the region that acted as bait for the serine protease in the inhibition process. And it turned out, one of the serpins actually inhibited cystein proteases, proteases of a different class, but which use a cystein as the key amino acid in a catalytic process almost identical to serine proteases (see figure to right).
Biochemists will find that cool, in a geeky way.
Site-directed mutagenesis
Furthermore, I showed that changing a few amino acids was enough to change a serine protease inhibitor into a cystein protease inhibitor, and vice versa. I did this by mutagenizing (a fancy word for changing) one amino acid of the protein at a time.
It was a fun process and what really appealed to me was being able to change the function of a protein at the atomic level.
As a grad student, I did similar work with DNA, effectively changing a few atoms to change the function of the DNA with respect to an enzyme that recognized it.
Taking that thought farther, yes, one could change all sorts of DNA and proteins molecules and create new functions. But that’s hard. Small changes, when you’re lucky, are not so hard. But, really crafting whole new types of enzymes or protein functions is the real alchemy of the 21st century as synthetic biology takes off.
Nature trumps all
Fun, though it is to create new functions for molecules, I do think nature has probably experimented with every chemistry possible and created a whole slew of useful enzymes. Will it be necessary to make new types of enzymes? I’m not sure. Nature is interested in a sub-set of chemistries that might be useful for us. We might be able to find an enzyme that suits our needs most of the time, but I think at some point we might need to modify, or even create, an enzyme with a new function.
And it’s already happening on the DNA level (making sequences better at binding proteins or promoting activity). But I haven’t really heard about folks messing with the proteins themselves.
links for 2009-01-24
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"As we develop tools that make it easier for scientists to capture the process of actually doing research, I think that will enable a faster scientific conversation than the current six-month to two-year process."
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"Will synthetic biology improve our lives?
"I think that our cultural understanding of what a machine is will fundamentally change. The machines we build today are completely understandable and predictable. That's why we call them machines. As we get better at engineering biology, maybe that will fall under our understanding of what a machine is. We are biological machines. We might not understand how we work very well yet, but we will. And I think biology is entering a phase in which we can change ourselves for the better."
links for 2009-01-20
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Heh. Didn't I say 2009 is the year of the Netbook. Great time for companies like Jolicloud who will turn Netbooks from mini-computers, that don't do much more than be small computer, to net-savvy service-rich mobile computing devices.
links for 2009-01-20
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Awesome set of photos of urban decay. The sadness of abandonment and the pressing silence of forgotten stories. [via @suryasanir]
links for 2009-01-16
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<sniff> I know this is sure to be interesting. Missing it, of course. (and will miss the one in New York, too). In any case, kudos to the folks from which it sprang!