Sunday, May 27, 2007 - 03:34
An introduction to our Alaskan NSF Chautauqua course and a pre-course assignment. I don't know how well this will work, but I thought it might be interesting this year to experiment with blogging about our course and sharing some of our experiences with the rest of the world. Here's your chance readers, if you'd like to do some of the assignments, you are very welcome to follow along and give it a try.
tags:I'm not likely to get all the assignments or course info posted on-line, but since we have some constraints with photocopying, we also have incentives for posting rather than printing. You can find the first assignment farther down the page. Introduction Those of you who've attended our courses in past years know that every year we use bioinformatics to investigate a different subject. This year is no exception. In fact, we went beyond changing subjects and changed our location, too; from Austin, Texas to Anchorage, Alaska. (This was Linnea's idea.) Trust, me on this, Anchorage won't be quite as hot. One of the things that I like the most about bioinformatics is the ability to apply many of the same tools to studying any kind of biological question. In this respect, bioinformatics is a lot like molecular biology. A basic tool set for molecular biology includes cell and microbial culture techniques, recombinant DNA, PCR, DNA sequencing, protein purification, antibodies, microarrays, and all kinds of gels. Bioinformatics covers the computing side of molecular biology. Our basic tools include searching databases, comparing sequences, designing and testing primers, analyzing and graphing data, and working with molecular structures. Of course there are more methods, but techniques can get us pretty far. Last year, we used bioinformatics techniques to look at the evolution of viruses, especially influenza. This year, we're going to look at co-evolution. Since we'll be in Alaska, our evolutionary partners will be two Alaskan icons: moose and willows. It looks like we may even be doing a bit of wet lab stuff, too, with some PCR and perhaps a bit of sequencing. Why would we think that moose and willows might influence each other's evolution? It's pretty clear that Alaskan moose eat willows, and in fact, that moose only eat willows. It's also clear that willows can't run away from the moose. The first question, we'll look at is to see if willows do anything to protect themselves. Other plants respond and send out warnings when they're wounded. Presumably, willows are wounded when they get chomped on by moose. So we can begin by looking for wound-inducible genes. Your first assignment will be to find some examples. Before the course begins, I would like you to see if you can find a plant gene that's expressed in response to wounding and do some research on your own to learn about the function. (We often determine if a gene is expressed by looking for RNA transcripts that match that gene.) Assignment #1. Find and describe the function of wound-inducible plant gene. Instructions: 1.Work on this before class begins in June. 2.Go to the NCBI gene database. 3.Search for plant genes that are induced by wounding. In class, we will talk about different methods for searching with Entrez. In the example below, I used the query: wound NOT hypothetical to eliminate hypothetical proteins. I also limited the search to plants and to current records by selecting the Limits tab, and clicking the check box for "Plants" under Limit by Taxonomy (not shown) and the check box for Current records under the Include Only heading.
4.When you've finished your search, pick one of the genes and investigate it on your own to find out what it does. 5.You may wish to look up some articles in PubMed and PubMed Central. If your access to journals is limited, I posted a four part tutorial on this topic (part I, part II, part III, and part IV). Look at part III for instructions on searching PubMed. 6.Post the name of your gene and very short description in the comments section. We'll talk about these on the first day of class. (Readers: you're all welcome to join in on step 6, even if you aren't coming to Anchorage.)