Using Bioinformatics to Study Evolution, intro

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.

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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.

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? i-56f53305abb47927da992d86f6a37f23-465310490_8c1b5b5c72.jpg
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.

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.)

Copyright Geospiza, Inc.

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I'd like to join in on step 6. My gene is proteinase inhibitor I prepropeptide. The protein it codes for is the only proteinase inhibitor to be found in both plant and animal kingdoms. It's known to be released in tomato leaves in response to stress, in an effort to disrupt the metabolism of attacking insects.

This gene has two advantages for me. Firstly, tomatoes are in the same class (Magnoliopsida) as willow, so the gene is likely to be more recognisable if present. Secondly, there are two open-access papers discussing it. As a bonus, there's a a corresponding inhibitor II gene, which could provide us with an extra data point.

May I ask how often you expect to post on this series, so that I know when to check scienceblogs?

Good work!

May I ask how often you expect to post on this series, so that I know when to check scienceblogs?

You may ask, but I don't know the answer. I think you can subscribe to the RSS feed, there should be a link in the side bar. There are other services, too, that notify people about new posts.

Readers- do you have any you recommend?


I am interested about your works. As a professional bioinformatics is my work of everyday. i like see your work in progress, I dont know if I can help you anyway or not, but it will be very kind of you if you post me your advancements.

By kaushik chatterjee (not verified) on 29 May 2007 #permalink

The tobacco plant genome contains a wound-inducible peroxidase gene with the designation tpoxN1. The tpoxN1 gene and its promoter, the GUS fusion gene, are rapidly expressed within an hour of wounding in the vascular tissues of stems and petioles. Chemical inducers which stimulate expression in other tobacco wound-responsive genes have no effect on tpoxN1, however. The wound-signaling pathway for tpoxN1, therefore, is currently unknown.

I do not know if the tpoxN1 is species-specific or found in all types of tobacco plants. Hopefully the full text paper will provide additional information.

K. Sasaki, S. Hiraga, H. Ito, S. Seo, H. Matsui, and Y. Ohashi. �A Wound-Inducible Tobacco Peroxidase Gene Expresses Preferentially in the Vascular System.� Plant and Cell Physiology, 2002, Vol. 43, No. 1, pp.108-117.

By Marjorie Larkin (not verified) on 31 May 2007 #permalink

Evolution does not exists, there is NO proof.

If evolutionists want to end the arguments all they have to do is, get their brilliant heads together and assemble a 'simple' living cell. This should be possible, since they certainly have a very great amount of knowledge about what is inside the 'simple' cell.

After all, shouldn't all the combined Intelligence of all the worlds scientist be able the do what chance encounters with random chemicals, without a set of instructions, accomplished about 4 billion years ago,according to the evolutionists, having no intelligence at all available to help them along in their quest to become a living entity. Surely then the evolutionists scientists today should be able to make us a 'simple' cell.

If it weren't so pitiful it would be humorous, that intelligent people have swallowed the evolution mythology.

Beyond doubt, the main reason people believe in evolution is that sources they admire, say it is so. It would pay for these people to do a thorough examination of all the evidence CONTRARY to evolution that is readily available: Try The evolutionists should honestly examine the SUPPOSED evidence 'FOR' evolution for THEMSELVES.

Build us a cell, from scratch, with the required raw material, that is with NO cell material, just the 'raw' stuff, and the argument is over. But if the scientists are unsuccessful, perhaps they should try Mother Earth's recipe, you know, the one they claim worked the first time about 4 billion years ago, so they say. All they need to do is to gather all the chemicals that we know are essential for life, pour them into a large clay pot and stir vigorously for a few billion years, and Walla, LIFE!

Oh, you don't believe the 'original' Mother Earth recipe will work? You are NOT alone, Neither do I, and MILLIONS of others!

By James Collins (not verified) on 01 Jun 2007 #permalink

Uh, James, I think you're looking for a different blog. Perhaps, Pharyngula?

Debating evolution here is like going to the Boeing web site and telling them that airplanes don't fly.

My gene of choice is wun1. As far as I know it is the first member described (1) of what turned out to be an entire family of wound-induced genes. It was described in a series of papers in 1989 that in addition to (1) also included (2) and (3). The mRNA levels of wun1 increased rapidly upon mechanical wounding of potato. The increase in wun1 mRNA levels is inhibited by osmotically active agents (like sugar; 1). Fusions of parts of the wun1 5' region to a GUS reporter gene verified the inducibility and strength of the wun1 promoter by wounding and also showed that the promoter is most active in epidermal cells of leaves and stems (2, 3).

The wun1 gene has family members described in potato (Solanum tuberosum), tobacco (Nicotiana tabacum), Arabidopsis thaliana, Mesembryanthemum crystallinum, Medicago truncatula, and rice (Orzya sativa). This is significant, because it shows that the gene is conserved between dicots and monocots (rice). The proteins belonging to this family are small, about 100 amino acids in length. They have a theoretical pI of about 6.8, a molecular weight of about 11.5 k (based on wun1), analysis done at ExPasy server . I could not detect any coiled coils. No transmembrane regions are predicted.

The WUN1 protein is predicted to be secreted (48%) by pSORT for plants, with a 16% score for cytoplasmic localization.

1. Logemann, J. and Schell, J. (1989) Nucleotide sequence and regulated expression of a wound-inducible potato gene (wun1). Mol. Gen. Genet. 219:81-88

2. Siebertz, B., Logemann, J., Willmitzer, L., and Schell, J. (1989) cis-analysis of the wound-inducible poromoter wun1 in transgenic tobacco plants and histochemical localization of its expression. Plant Cell 1:961-968

3. Logemann, J., Lipphardt, S., Lorz, H., Hauser, I, Willmitzer, L, and Schell, J. (1989) 5' upstream sequences from the wun1 gene are responsible for gene activation by wounding in transgenic plants. Plant Cell 1:151-158


Oh, by the way, regarding wun1, I forgot to add that according to pfam07107.3, the members of this family indeed do accumulate in the cell wall, and that a role has been suggested in reinforcement of the cell wall after wounding.


A new bioinformatics based application, CHROMHOME ( has been lauched for comparing genomes among mammalian species.The homology maps indicate the rearrangement of chromosomes that have taken place among various species. This would probably tell us more about the ancestral chromosomes.

Assignment 1: WIP1 (second attempt)

WIP1 codes for wound induced protein in corn Zea mays. WIP1 is homologous to Bowman-Birk proteinase inhibitor. It is a serpin-like protein. Serpin1 of Arabidopsis thaliana is a suicide inhibitor for metacaspase 9.

References:Eckelkamp C, Ehmann B, Schopfer P. 1993. Wound-induced systemic accumulation of a transcript coding for a Bowman-Birk trypsin inhibitor-related protein in maize (Zea mays L.) seedlings. FEBS Lett. 1993 May 24;323(1-2):73-6.Rohrmeier T, Lehle L. 1993. WIP1, a wound-inducible gene from maize with homology to Bowman-Birk proteinase inhibitors. Plant Mol Biol. 1993 Aug;22(5):783-92.Vercammen D, Belenghi B, van de Cotte B, Beunens T, Gavigan JA, De Rycke R, Brackenier A, Inz� D, Harris JL, Van Breusegem F. 2006. Serpin1 of Arabidopsis thaliana is a suicide inhibitor for metacaspase 9. J Mol Biol. 2006 Dec 8;364(4):625-36.

By Antonieto Tan (not verified) on 24 Jun 2007 #permalink

I am interested about your works. As a professional bioinformatics is my work of everyday. i like see your work in progress, I dont know if I can help you anyway or not, but it will be very kind of you if you post me your advancements.

By Arun kumar N (not verified) on 25 Jun 2007 #permalink

Another good search phrase could be "innate immunity plants"; moose eating on willow must induce its innate immune system--trees, plants ---they possess an innate immune system and just like our system--have an inflammatory response

By Linnea Fletcherr (not verified) on 26 Jun 2007 #permalink

I have chosen wound induced protein (win). No strong reason at this point, it just sounded interesting.

By burton webb (not verified) on 27 Jun 2007 #permalink