Genetics & Molecular Biology

Our genome is a patchwork of neighborhoods that couldn't be more different: Some areas are hustling and bustling with gene activity, while others are sparsely populated and in perpetual lock-down. Breaking down just a few of the molecular fences that separate them blurs the lines and leads to the inactivation of at least two tumor suppressor genes, according to researchers at the Salk Institute for Biological Studies. 

Their findings published in the May 15, 2009 issue of Molecular Cell explain how a single event can put a cell well ahead on the road to becoming a tumor cell.
A new report published in Cell says that a heart beat and blood circulation are critical signals for the production of blood-forming, or hematopoietic, stem cells in the developing embryo.
Can fundamental genes acquire new functions?  A new study in the Proceedings of the National Academy of Sciences by Indiana University Bloomington biologist Armin Moczek and research associate Debra Rose reports that two ancient genes were "co-opted" to help build a new trait in beetles -- the fancy antlers that give horned beetles their name. The genes, Distal-less and homothorax, touch most aspects of insect larval development, and have therefore been considered off-limits to the evolution of new traits.
As Feynman told the story in late 1959:

We have friends in other fields---in biology, for instance. We physicists often look at them and say, "You know the reason you fellows are making so little progress?" (Actually I don't know any field where they are making more rapid progress than they are in biology today.) ``You should use more mathematics, like we do." They could answer us---but they're polite, so I'll answer for them: "What you should do in order
for us to make more rapid progress is to make the electron microscope 100 times better."

There's a line that politicians opposed to embryonic stem cell research have been peddling lately: recent breakthroughs in stem cell technology have now made ethically questionable embryonic stem cell research obsolete and unnecessary. This isn't a new line - for years, opponents of embryonic stem cell research have always claimed that the latest research (whatever it happens to be) has obviated the need for embryonic stem cells.
On the Road

On the Road

May 05 2009 | 3 comment(s)

The Rugbyology show has gone at the road.  I'll be at the Biology of Genomes meeting at scenic and currently drizzly Cold Spring Harbor Laboratory all week.  Will I live blog the conference?  No.  I value my carpel tunnels too much.  If you happen to also be at Cold Spring Harbor and would like to buy me a beer, however, my liver comes cheap.
Will we ever have a set of standardized biochemical devices that synthetic biologists can snap together to make more complex systems? I'm skeptical that any single standardized biological device will hold up well under very different cellular contexts, without a lot of trial-and error modifications. We may successfully end up with a few really useful parts, but I'm betting that ultimately the catalog of useful and widely functional parts is going to be limited.

Engineering A Biological Pulse Generator

I've got my issues with synthetic biology. Either synthetic biologists do something trivial dressed up in elaborate engineering language, or they achieve something impressive and complex the old fashioned way (the way molecular biologists have been doing it for decades) - genetic engineering through trial and error, with very little principles-based engineering involved.

What I want to see is a result that falls somewhere in between these two extremes: genetic engineering that's non-trivial, but not so complex that it's impossible to use simulation and the rudimentary quantitative design principles that are useful in biology.
With hot, new technologies, biologists are taking higher-resolution snapshots of what's going on inside the cell, but the results are stirring up controversy. One of the most interesting recent discoveries is that transcription is everywhere: DNA is transcribed into RNA all over the genome, even DNA that has long been thought to have a non-functional role. What is all of this transcription for? Does the 'dark matter' of the genome have some cryptic, undiscovered function?
As you know, when different species directly compete for the same finite resource, only the fitter will survive.  A new study in Proceedings of the National Academy of Sciences (PNAS) says they have demonstrated that in a laboratory environment, along with how, when given a variety of resources, the different species will evolve to become increasingly specialized, each filling different niches within their common ecosystem.