Blog of Bermanism

A great many people have asked me over the years to repeatedly explain to them what it is that I study for my research. It seems that every time I tell someone, they forget inside of 10 minutes and need to be told again. This is all very understandable and I appreciate that people care enough to want to know what I do, even if they can’t remember long enough to tell someone else. So, for my second ever post to this blog, I will describe what I have been up to during graduate school for the past few years in a simple form so that everyone can understand it. Please note that I am intentionally leaving out a lot of the details of how things are done and why you’d want to do them from a biological standpoint. This explanation is for the general person who is interested in being able to amaze their friends with the fact that they know this guy who is doing this thing that is cool.

Basically, I am studying how long-term intoxication by alcohol affects brain gene expression. Ok, what does that mean? Well, for all you alcoholics out there, it turns out that addiction is genetic and you probably inherited the predisposition for alcoholism from your parents! Weird right? Between 40-60% of one’s risk for becoming an alcoholic is genetic, and the rest is usually influenced by the environment you grew up in and how it affected you. So, even if you have inherited as much of a risk for alcoholism as you can, if you don’t ever drink alcohol, you won’t become an alcoholic.

So, when most people think of something as being genetic, they think that there is a gene for the trait. Thus, based on my statement above, one would conclude that there is an alcoholism gene. Sorry, but it turns out that alcoholism is an incredibly complex behavior, and there isn’t a single alcoholic gene that will make you an alcoholic. The disease is likely caused by the combination of hundreds of genes that contribute to your risk for alcoholism. Up until now, researchers have been trying to discover which genes to study out of the ~40,000 genes in the human genome. A lot of research has already been done on certain genes and we know that they react in some small or large way to the presence of alcohol in the system, but the research has been limited to a few obvious targets for alcohol. So, we needed a way to find as many of these candidate genes as possible in order to begin to crack the code of inherited addiction.

So, some really brilliant scientists at Stanford University decided to design a method of research that takes advantage of what we know about how genes work. Genes are stored in every cell in your body as deoxyribonucleic acid, or DNA. DNA is stored in the nucleus of the cell. When the cell needs to make more of what a gene encodes, it transcribes the appropriate DNA sequence into ribonucleic acid, or RNA. This particular type of RNA is called messenger RNA (mRNA), and it is exported out of the nucleus into the cell. The cell then reads the new message with tiny organelles called ribosomes which translate the mRNA into a sequence of polypeptides which ultimately become a protein or enzyme. These proteins or enzymes are then taken to whatever part of the cell that their function is needed. The compliment of proteins that are active in your body at any time make you who and what you are. Proteins are the primary functional molecular machinery that drive all of the actions in your body. These actions include everything from getting salt into or out of your cells to muscles contracting or relaxing. With this in mind, you can imagine that any change that happens in your body is likely going to be the result of a change in the amounts or types of proteins that are active in your body at that time. Since the presence of alcohol in your system can ultimately cause a disease like alcoholism, it is likely that alcohol can change some aspect of the way your body functions, which means changing the protein complement that your body has. If your body, for instance, needs to make more of a protein that helps break down sugar into energy that your body can use, it tells the cell machinery to make more of it. The immediate response is for the cell to make more mRNA for that protein. The amount of mRNA in the cell at any time is called the gene expression level. The gene expression level can go up or down, or even turn off completely if necessary. The scientists at Stanford took all of this into account and developed a research tool called the microarray. This innovative tool allows researchers to scan tens of thousands of mRNA sequences simultaneously from a complex sample like a mouse brain. Individual genes are “printed” onto a microscope slide and the samples are washed over the slide in a manner that allows the same gene in the mouse sample to bind to the gene printed on the microarray. This process is called hybridization. At UT, we have a microarray facility that allows us to put up to 50,000 genes on a single microarray slide. Ultimately, we would like to be able to represent the entire genome at once on the arrays, but that is a little ways off.

So, in order for me to discover new genes that are being affected by alcohol, I needed to use microarrays. I also needed a model system to work with, since humans don’t generally like having their brains cut out at the end of an experiment. Plus, they take so damn long to grow! So, I used mice. Cute little gray buggers that are called DBA/2J mice. These particular mice have a strong aversion to drinking alcohol and go through a severe withdrawal when they are forced to take it. Since withdrawal only occurs once a subject is dependent upon a substance, it is an important part of an addiction of any kind. We chose this mouse and a study of withdrawal as our model system. So, this study is looking for the effects of long-term exposure to alcohol. We chose a long-term (chronic) exposure so that we could more accurately approximate the condition of alcoholism.

Well, now we were stuck with a mouse strain that didn’t drink alcohol, so we had to find another way to give them all alcohol in a controlled and predictible fashion. So, we made them breathe alcohol. We built this nice chamber that vaporizes alcohol holds it at a certain level. The mice were all put in the chamber and made quite drunk for three days. Oh, they were having fun in there, let me tell you! Once the three days were up, we took their brains, pulled out the mRNA, and put the extracted samples onto the microarrays. The result was 1.5 million data points!! This is a lot of data. We had gene expression data for 17,000 genes in six different brain regions, at three different time points beginning after we stopped giving them alcohol, and there were five mice in each group!! Now we had to make sense of it. So, we put the data through very rigorous statistical tests, mathematical routines, and visualization algorithms. The end result was a subset of the original data that we are confident represent the major portion of the effects that alcohol has on brain gene expression. This is where we are now. The trick now is to take all this data and find some sort of meaning to it all. It is great that we have 3,000+ new candidate genes to study for alcoholism, but there is more there. The data contains some biological insight into the development of dependence on alcohol. Now, we must find that story and tell it. Once I’ve written the story up into a paper, I’ll be able to graduate. (*cheer*)

Well campers, that, in a nutshell, is what I’ve been doing for five years. I am very near to the end of my long journey and have only to write it all up and I’ll be finished. I hope this post is useful to you and that you feel like you learned something from it. Please feel free to post comments on what I’ve written if you have questions or find anything confusing and I’ll answer them for you.

Ok, Ok! Back to work!!

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