Bob Zimmermann

Max F. Perutz Laboratories
Dr. Bohrgasse 9/5
A-1030 Wien
Austria

Hello, I'm Bob. I am a PhD student at Max Perutz Laboratories, with affiliations to Univiersität Wien, for Renée Schroeder (in Group Schoeder) on RNA Biology.

Why exactly are we interested in RNA? What is it in the first place? I'm going to presume that you are not living under a rock, and you have heard of DNA. DNA is a stable carrier of genetic information, purported to completely describe and determine an organism's phenotypic (apparent, visible) traits. RNA is very similar, except for the fact that it is much less stable. One could degrade an RNA molecule simply by touching it.

Why is RNA there? We know a lot of reasons, but we only recently realized that there are a lot more reasons. The (new-ish) running theory is that before DNA and protein (the until-recently de facto cardinal players in cellular activity), there was only RNA. RNA was a transient carrier of genetic information, a catalyst, a be-all for the cell. Although, since the advent of DNA, many other compounds have become essential actors in the cell, evolution has a tendency to retain old and faithful reaction paradigms, adhering to the don't-fix-what's-not-broke ethic, and RNA is no exception. In fact, RNA's role is much more pervasive than we once thought (we had once written it off as simply a part of the long DNA-to-protein pathway). Those demeaningly named "non-coding" RNAs are turning out to be full-fledged genes, performing essential roles in reaction catalysis, among other things, quite interestingly gene regulation.

Countless classes of RNAs are being "discovered" (or perhaps merely dubbed to boost citation numbers) on a regular basis, and the "RNA fever" perhaps overtakes hopes of painting a coherent view of the RNA world. The fact remains that the possibilities for RNA functions are nigh limitless, and finding them is quite useful to the furthering of our understanding of cell dynamics.

"So," you ask, "what, praytell, can you possibly do to help this situation out, Mr. Zimmermann?" Well, that's certainly a good question. I'm still figuring that out. At the moment we're sifting through the possibilities of PhD projects, but as of yet I'm investigating a couple things:

An RNA's function, like protein, is determined in large part by the structure that it forms through folding. There exists an energetically-favorable fold, which may or may not be the so-called "native fold", and there is often also a fold that it can get stuck in, much like one gets their foot stuck in a sufficiently wide crevice in the ground. In order to get the foot back in action, one must exert some energy to pull it out of the rut. Similarly, RNA might need to get "unstuck". How does this happen? Biologists have proposed a model of "chaperones", proteins that give RNA little push to get it along its way. This is a difficult thing to monitor, and so a lot of the discoveries are still hypothetical with respect to the actual cell activity. Currently, I'm working on making a chaperone work in a cell, hopefully proving the in vivo viability of chaperone activity, and further an assay to quickly determine a protein's ability to perform chaperone activity.

Apparently, a whole lot of human non-coding RNA transcripts ("ncRNAs") bind to RNA Polymerase II, the messanger RNA ("mRNA") transcript factory of the cell. RNA Pol II transcribes most of the RNAs which become proteins, making it an essential hub of transfer of genetic information. These ncRNAs could very well act to inhibit the activity of RNA Pol II, making them very important regulators of gene expression. I'm investigating the structure of these RNAs, hoping to elucidate some essential ingredients to realize binding function of these new RNAs.

In another life, I was a research associate/master's student in Brent Lab in the Computer Science Department at Washington University in St. Louis, where I did my Master's degree. Here's a spiel about that.

Previous to that, I worked with Elliot Soloway in the Center for Highly Interactive Computing in Education, where I developed Locker and Chemation, as well as some of the core libraries for Cooties and the Handheld Learning Environment.