September 17, 2010 § 1 Comment
So this week seems to be turning out to be cooperation week. We talked about cooperative behavior of the proteins that make up the cytoskeleton on Monday, cooperation in breeding behavior in birds on Wednesday, and now it’s time to talk about cooperative behavior in bacteria. If only I’d planned it in advance. Ah well; can’t have everything.
You know, of course, that in the wild bacteria do not typically live in monocultures: different varieties of bacteria both compete and collaborate, and the complex interactions that result are not easy to study. A number of labs have been working on developing well-defined synthetic communities to ask questions about how communities evolve. The Silver lab has now taken a rather different approach (Wintermute and Silver 2010, Emergent cooperation in microbial metabolism. Molecular Systems Biology 6: 407 PMID: 20823845), by exploring the interactions among 46 different metabolically impaired strains of E. coli and rationalizing the results in terms of a flux-balance-analysis model of interacting strains.
What interested Wintermute and Silver was the fact that bacterial communities can perform all kinds of important metabolic tricks that individual species can’t manage. This is not hard to understand, or at least to imagine that you understand: one species finds an efficient way to produce rare metabolite A, another species develops an efficient way to produce rare metabolite B, when you mix the two together they both have the advantages of a supply of both A and B, but they’ve effectively halved the cost of production (making all those enzymes) by sharing. But is that really how it works?
July 5, 2010 § 1 Comment
The first entry in the “cite the oldest paper” competition is in, a suggestion from Pam Silver. Ever the student’s friend, Pam also wanted to offer a clue: there is at least one paper written in French, published in 1959, that has a very clear relationship with systems biology. Can you find it? [Remember, it is the difference between your age and the age of the publication that matters, not the absolute age of the paper. Anyone under 38 would spring into the lead with a paper published in 1959.]
Pam’s entry is older (Srb, AM and Horowitz, NH, 1944. The ornithine cycle in Neurospora and its genetic control. J. Biol. Chem 154 129-139), but also perhaps more controversial. Published only three years after Beadle and Tatum used Neurospora to demonstrate the connection between genes and enzymes, and at a time when the nature of genes was uncertain — it was suspected that they consisted of nucleoprotein complexes, or at least contained such complexes as essential elements — this paper describes the existence of a network of genes whose products perform a complex set of biochemical reactions, producing arginine.
Now one of the less fashionable model organisms, but once a supremely important one, Neurospora first came to scientific notice as a major pest in bakeries, growing as large salmon-colored clouds on the bread loaves. The menace was later reduced somewhat by the routine use of mold inhibitors, but by that time scientists were hooked. In the ’20s it was discovered that what makes Neurospora so good at thriving in bakeries is that the spores survive high heat (indeed, require heat to germinate). It also turns out to be the first organism that colonizes areas that have been semi-sterilized by volcanic eruptions — “producing great masses of brilliant conidia of bizarre appearance”. [Google Images has failed me on this one, if anyone can find some “brilliant conidia” please send me a picture or a link]. Early scientists who collected Neurospora species in the tropics ran in to some difficulty: it had a tendency to grow straight through the cotton wool they were using to close the tops of their tubes. But once they got it into a cool, dry climate, it became more manageable.