Discovering Biology in a Digital World

Let the experiment begin.

We're experimenting with HIV in this series. And yes, you can try this at home!

If you want to see where we've been and get an idea where we're going, here are the links.

Part I. Meet HIV and learn how we're going to use it look at evolution. An introduction to the experiment and a link to a short flash movie on HIV.
Part II. Instructions for doing the experiment.
Part III. Look at the sequence results.
Part IV. Look at protein structures and see if we can explain why the experiment worked the way it did.

Let's move onward.

1. I made a data set of amino acids sequences from HIV protease. This set contains a sequence from a wild type HIV protease along with amino acid sequences from the Colonno paper (2004) (I'll give a link to the reference in part IV).

Your first task is to copy the data.

Open the Geospiza Education teaching materials page, in a new browser window.

Look for the word "Colonno" in the Data Set section and open that link in new window, too. Copy all the text on that page.

2. Scroll to the very bottom of the Geospiza Education teaching materials page, to the Web Site section and click the link to the Embl-EBI ClustalW server.

3. Paste all the sequences in the medium sized empty box in the middle of the page and click the button that says "Run."

You are now using ClustalW to align all those amino acid sequences.

We could use other alignment programs, like BLAST or Cross_Match, or Muscle, or Multi-Align, to do this, but ClustalW, in combination with JalView, gives us some nice coloring options that help us interpret the results.

4. Eventually, a table will appear, like this one, with a button that says "Start Jalview." Click the button on the Embl server page when you see it apear.

At last, the results.

5. A window will open that has all of the HIV protease sequences lined up so you can see were they match each other.

I've intentionally set this up so that the wild-type protease sequence is at the top. All the other sequences have been obtained from HIV-infected AIDS patients who were taking Atazanavir. Atazanavir is an anti-HIV drug that inhibits the HIV protease.

Each row in the sequence alignment corresponds to a single protein sequence. All the letters that you see represent amino acids. I made a key to amino acid abbreviations, and structures, that you can download, if you want a guide to the names.

The really cool thing about JalView, is that we can change the color to reflect the percent identity (they spell "color" strangely in the JalView menu, but it works just fine. ; ).

6. Open up the JalView color menu and change the color choice to Percentage Identity. This option highlights every amino acid that's differs between any of the sequences. All the identical amino acids are purple. I like this because it makes it easy to spot changes.

Now that you have results, what do you do with them?

Remember, we were asking questions about evolution. This is your chance to answer those questions, on your own, from real data.

I said that natural selection can occur because populations are diverse.

Is that true? Do your results support that?

I also said that, some individuals reproduce and their traits are inherited. The sequence at the top comes from a virus that wasn't exposed to the drug.

Can you see if the other viruses inherited a change that might have helped them survive and reproduce, even in the presence of the drug?

Give it a try, or if you're more patient wait a few days and we'll go through the data together.

technorati tags: digital biology,
AIDs, bioinformatics, evolution, HIV,
protease,
genetics