Friday, October 26, 2007

Open Access

Here's an interesting article about open access journals. Basically, Senator Inhofe (R, Oklahoma) tried with all of his might to prevent a bill from being passed which called for open access to government (NIH) funded research. The bill called for all research to be made public no more than 12 months after publication. Seems pretty reasonable, right? If the government (and taxpayers) are paying for something, they should have the right to read it. So why would this guy put so much effort into putting the kibosh on it? Turns out one of his largest campaign donors is Elsevier, which in turn is one of the largest scientific publishers in the world. It's amazing how these things work. Inhofe is one of the most deplorable characters in politics today, and has been for a while. But now I think I'll be boycotting Elsevier journals due to their underhanded ways.

Tuesday, October 9, 2007

Still No Comments... But Nobel Prizes to Discuss!!!

I'm ok with the lack of activity, even though it probably means that nobody has read my first post. Maybe I'll put a little more effort into spreading the word. I guess I should write more as well, but I've been a bit busy for the past week. Anyway, I'm thinkin' I'll post a long one describing one of the winners of the Nobel this year. If you don't know (I'm speaking to the void right now since I have yet to attract any readers) the prize for medicine was awarded yesterday, physics was today, and chemistry will be out tomorrow. If anyone is out there reading, waiting, observing... I'll be happy to parentify* any of the work that lead to one of the prizes. Maybe I'll take a poll. Send comments if you have a preference!

*Parentification is the tentative term that I will use for explaining science in everyday terms. I think it fits because a) I have to do it all the time with my parents b) I don't think my parents are dumb, so it is very different from 'dumbing things down', and c) a famous scientist once said that all scientists should know their material well enough to explain it to their parents (actually he said grandmother, but in this context I take them to be interchangeable), so practicing this will be good for me.

Tuesday, October 2, 2007

A Flip-Book Animation of Translation Initiation

The dynamics of proteins while they go through biological processes fascinates me. Most of biochemistry and related fields involves measuring things indirectly and, after going to great lengths to validate hypotheses, scientists are able to make useful statements about the process at hand. It can however, be difficult to say things definitively about dynamics. Let me explain a little further.

An enzyme is a biological macromolecule that performs a specific chemical reaction within a cell. There are millions of different types of enzymes within each cell, whether we're talking about an individual cell within a human body or a single-celled bacterium. Each of these enzymes is a series of amino acids strung together, and each have evolved a specific amino acid sequence over the millennia which conveys a specific function to each enzyme. Now, typically the activity of (or the chemical reaction specific to) a particular enzyme involves the following: 1) the enzyme binds a substrate (the compound being chemically altered by the specific reaction of the enzyme) 2) the enzyme modifies the substrate 3) the enzyme releases the substrate. Hopefully you can see how this would be important for a cell or an organism. If you have ever wondered how we metabolize food into energy, it's through this process. Frequently there are many enzymes involved, like people working at different steps on an assembly line. Each enzyme binds to the substrate, modifies it into something more useful, and shoves it down the conveyor belt to the next enzyme which follows the same process, and so forth until the substrate is no longer a substrate, but a product which our bodies can utilize (e.g. an amino acid for making new proteins). So, biochemical analysis of a particular enzyme typically gives us the following information about it; we can find out what substrate it binds to, how strongly it binds to it, and what the product is. We can even learn about the specific mechanism the enzyme employs to perform its chemical reaction. This is all extremely important information, but there is something missing. What does the enzyme look like when it is undergoing it's process? Does it change the way it looks, allowing the substrate to bind? Does it change shape again when the product is ready to be released? These are the dynamics of the enzyme. To be fair, biochemistry (with it's long and powerful reach) can tell us a little about these problems and has in the past. The information learned has tended to be hard-fought and (dare I say it?) inferred from indirect evidence.

Now a recent article published in Cell called 'Structured mRNAs Regulate Translation Initiation by Binding to the Platform of the Ribosome' (Marzi et. al. Cell 130, 1019-1031, 2007) shows that this information can be determined directly. The work was a collaborative effort between groups from France and the US, and it visualizes the discrete stages of translation. Translation is the process whereby a message RNA (mRNA) is relayed into a protein. This is how genetic information is carried out within a cell. DNA is "transcribed" into mRNA, which is "translated into a protein. Proteins carry out a bulk of the processes within a cell (they make up enzymes as well as structural molecules that give cells their shape). Anyway, the ribosome is the enzyme that converts mRNA into protein. Follow? I hope so. In this paper, they literally take pictures of the ribosome while it is binding to mRNA. The cool thing that they show is that there can be structural features in the mRNA which prevent it from being translated (think of a tangled ribbon on a cassette tape which will not go into the tape). The ribosome binds to this knotted mRNA, but temporarily shoves it off to the side because it is not in the correct state to be translated. When the mRNA is in the correct state (i.e. unknotted), it moves to the correct region of the ribosome and is translated as normal. The great thing about this paper is that it shows a series of pictures that essentially describes the steps leading up to the translation of a "knotted" mRNA. So we know, with pretty great resolution where the mRNA molecule binds at each stage. It's like watching a movie of a biological process, or more accurately, a flip-book style animation. It's great. They used a technique called cryoEM which I won't get into today (maybe another time, or ask if you're interested), but it's basically the use of a very powerful microscope to look at things that are much, much smaller than the size of a bacterial cell (I'm talking millionths of a millimeter here). They use a clever trick to trap the various stages of the process so they can take these snapshots.

Ok, so why is this important? I guess one can argue for the general utility of a system that shows where substrates are bound to enzymes when they are going through their functional cycle. Drug companies like this kind of information because the drugs that they design are often inhibitors of these processes. Additionally though, translation of mRNA is a fundamental process in all organisms. If we want to ask ourselves "where did we come from?' we need to understand the biological processes that make us who we are. Some processes are specific to humans. Some are specific to vertebrates, and many still are present in all organisms from the simplest bacterium to us. Translation is one of these, and this means that it was probably one of the first processes to evolve and one that is critical to life, as we know it. Therefore understanding the details of such a process is critical to understanding ourselves. Being able to watch a critically important process take place is a major goal of biology. We aren't yet even near a stage where we can point a camera at a region of a cell and watch what happens, but this was a step in that direction.

Monday, October 1, 2007

First... Blog Post... Ever

OK. I'm new to this game, so I'll start small. My goals are simple. I just want to talk about my opinions on various scientific/societal issues that may catch my fancy. As a graduate student I do a pretty hefty amount of reading, and I'm always trying to think of how best to pass this information to the general public in a not-dumbed-down but easy to understand way. Hopefully I can use this as a forum for trying out various styles and techniques for disseminating these all too important and sometimes hard to comprehend issues. And if anybody reads it they can let me know if I'm supplying anything useful. If so, maybe it will evolve into something interesting. If not, I'll kill it, and finish my PhD. Wish me luck!