Tag Archives: genetics

Patagonian tree fungus is the secret ingredient in beer

The new issue of PNAS shows some evidence for the origins of my other favorite beverage.  “The draft genome sequence of S. eubayanus [Patagonian tree fungus] revealed that this long-sought partner of ale-yeast gave rise to a domesticated, hybrid species used to brew lager beer.”

It’s worth a quick look at the picture on the cover. Who would guess something so ugly could yield such a tasty product. Beer is, in the apocryphal words of Ben Franklin, “proof that God loves us and wants us to be happy.”

Are our fates determined by our genes? I doubt it. It’s not that simple even for worms.

I have done some work with the C. Elegans model organism. They are fun little bugs, and the PETA doesn’t get all up-in-arms when you shoot their brain with a laser. Here are some fun C. Elegans Facts:

wikimedia commons: adult caenorhabditis elegans

They are about 1 mm long at maturity
They are transparent
They have about 300 nerves
Their genome was sequenced in 1998
They can hunt down food on a plate
They have forms of memory and learning

Here are some things I have noticed: When illuminated with a blue laser, they panic and squirm all over the place. When you use a UV laser to blow up a portion of their outer cuitcle, they practically turn inside-out due to internal pressure. Some of the strains available through the WormBank have single nerve cells that express fluorescent protein, so that not only do their brains glow, but only the part you might be interested in glows.

Why are these critters cool? Well, despite being really small, they share a lot of biochemistry with humans. Their neurons function in the same way and the cellular processes that allow the worm to grow from an egg into a larva and from a larva into an adult are all analogous on a cellular level to changes in human development. But if you do an experiment on a worm, you can see what happens in a few days instead of months (rats) years (monkeys) or decades (humans). Also, there are some ethical constraints with humans that don’t apply to worms.

Here’s a new fact just released in Nature: they seem to have a sleep-like state. “Lethargus is a Caenorhabditis elegans sleep-like state” by Raizen et. al. “Conserved effects on sleep-like behaviour of homologous genes in C. elegans and Drosophila suggest a common genetic regulation of sleep-like states in arthropods and nematodes. Our results indicate that C. elegans is a suitable model system for the study of sleep regulation.”

They sleep, they eat, they learn (sort-of), they have lots of sex with themselves (they are hermaphrodites) and they make eggs. And they do it all in 3 days. And despite the fact that we know the fate of every cell in its body from birth to death – where it comes from, what it becomes and where it goes – we still don’t know how it manages most of its behavior.

I’d like to point out that this leaves very little hope for a reductionist perspective on psychology.  We know every connection of every nerve in this worm’s body and the thing is still a mystery. I wrote a post recently about how foolish it is to make sweeping assertions about genetic differences. Just to reiterate the big upshot: even in the simplest case, our understanding of the causes-and-effects that make up psychology is limited.  To think that a human being is perfectly predictable is… well… just plain dumb.


spider silk proteins, microfluidics, and cool stuff that is small

A pair of German groups collaborated to produce an artificial spinarette. They made very small tubes (called Microfluidics by those in the business) into which they injected engineered spider silk proteins produced in bacteria. The obvious cool tings aside (e.g. arachnoweave armor) there are several interesting scientific oddities. The first is in the aggregation of protein eADF3. According to the article, at low concentrations it forms aggregates. But if you add shear flow (like forcing it through a small channel or a spinarette) it makes fibers instead of particles. That’s pretty strange.
Here’s something else. The protein aggregates in salt water under static conditions into tiny particles. These particles unfold and dissolve in pure water. The the fibers made of the same stuff in the same conditions stable in pure water. Something pretty drastic has changed about how those proteins are structured when they assemble under the shear conditions in the flow of that microfluidically confined stream. Indeed, spectroscopy shows a high beta-sheet content of the fibers, although I didn’t see anything about the beta-sheet content of the particles.
But these authors go one step further. A two part mixture of two silk proteins, both found in spiders (the above mentioned eADF3 and another, eADF4) produce a twisted fiber of higher strength and similarity to the natural product of a spider. If you’ve ever watched a nature show and seen a spider at work, you’ll know that they have to pull the silk tightly when they are spinning in order to make it strong; this explains why. The shear forces of the fluid moving through the spider’s little orifice are really important. Maybe that’s another step toward that arachnoweave armor. That and that d3o stuff (like a d3o Hat to protect your head) would make a product fit for Batman.

It’s not recombinant spider silk, but the D3O videos are worth looking at, if you have not already.