Digital Biology Fridays

I've had some requests for some more molecular puzzles since the last one that I posted (see A DNA puzzle ). One person liked it so much he even blogged about it. So, here's one for you to chew on over the weekend. This puzzle is a variation of an activity in Exploring DNA Structure, a CD/lab book that I made (with funding from the NSF) ... Read more
How does grass grow in the extremely hot soils of Yellowstone National Park? Could a protein from a virus help plants handle global warming? Okay, that second sentence is wild speculation, but we will try to find the answer to our mystery by aligning our protein sequence to a sequence from a related structure.

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Read part I, part II, ... Read more

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How does grass grow in the extremely hot soils of Yellowstone National Park? The quest continues. Read part I, part II, part III, and part IV to see how we got here. And read onward ... Read more
I found it in the MeSH database. Really! Looking for a quick answer? Don't ask a scientist It doesn't take long to realize that scientists can spend countless hours debating the meaning of words. Our very own ScienceBlogs is a great example, just look at the many ways we can define (and debate) the meaning of a small, four-letter word like "gene". We also like to qualify our answers with a thousand conditions "usually, it's like this, but...." This ... Read more
In last week's episode, your assignment was to think of an interesting plant trait and find a description about a gene, related to that trait, by searching PubMed. Since coming up with an interesting trait might be a challenge for some people, let's think about how to approach this step. Picking your trait. ... Read more
Many of you might take this for granted, and I know it seems amazing today, but I when first started teaching, our access to scientific literature was pretty limited. I could go to the UW and use Grateful Med to search Medline, but we didn't have anything like it at my college and web browsers, like Mosaic, had yet to be invented. So, when I first started giving workshops for teachers on biotechnology and the world of the web, many were quite surprised to find out about the PubMed database. Since PubMed is (to me) one of the best resources to ever come along, I think we ... Read more
and what is the volume of the sea? This sounds a bit like the beginning of a poem but it's really the answer to the question we posed last week on a Digital Biology Friday. i-3faa77de2c8e6cc50b5fa2cbca9c38b0-rainbow_direction.pngWe can see, in the sequence window, that two strands are both labeled 5' on the left ... Read more
Today, we're going to look for rainbows in double-stranded DNA and see what they can tell us about DNA structure. First, we're going to get a structure for a double-stranded molecule of DNA and open it in Cn3D. 1K9L If you want to do this at home and you haven't already downloaded a copy of Cn3D, you may want to read these instructions and get a copy. These directions ... Read more
Why do I love Cn3D? Let me count the ways. What does Cn3D do? (Hint: say "Cn3D" out loud). Seriously, Cn3D is a program that draws lovely pictures of molecular structures by using experimental data from techniques like X-ray crystallography and nuclear magnetic resonance spectroscopy. Surprisingly (to some), and in contrast to many bioinformatics programs, Cn3D is really easy and fun to use. Have you ever used programs like MS Office? Using Cn3D is at least 10 times easier. An added benefit is that you don't have to try and find old copies ... Read more
If we compare sections 1, 2, and 3, we see that section 2 matches very well in a number of different samples, and that there are differences between the sequences in sections 1 and 3. i-bed5846063bbebc59fa0a4516d917562-small_mito_mut.gif We also learn something about the ... Read more

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