classroom activities

I was frantically getting ready for class when I happened to glance out the window. What did I see? Big fluffy white flakes rapidly falling from above. You can't say we weren't warned. The newspapers have been predicting snow since Monday. It's just, well, unusual. And Seattle is never prepared to deal with it. Even the kids aren't looking too happy about it, though. By this time of the school year, they've caught on that every snowday has a price. And, they will pay ... 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
Why is an eye, an eye and a nose, a nose? Why do different cells create different kinds of tissues when all the cells in a single organism start out with the same set of instructions (aka DNA)? Head, Shoulders, Knees, and Toes is a learning activity that helps students discover, for themselves, that certain genes are expressed in some tissues but not in others. My goal here, as part of our NSF-funded project, is to show how students can learn biology by doing science with bioinformatics tools. If ... 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
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
No biology course is complete these days without learning how to do a BLAST search. Herein, I describe an assignment and an animated tutorial that teachers can readily adopt and use, and give teachers a hint for obtaining the password-protected answer key. Development of the tutorial and the activity were supported by funding from the National Science Foundation. This is reposted from the the original DigitalBio blog. This popular activity, designed to accompany the BLAST for beginners tutorial, has been updated to ... Read more
Did HIV become resistant to Atazanavir because of a genetic change? Was that genetic change inherited? Did HIV evolve? Can we explain why genetic changes at specific sites might help HIV escape the effects of the drug? Let's find out. All of the sequences in the image below (except for the first) come from HIV strains that were isolated from patients who took Atazanavir and no other protease inhibitors. All of the strains of HIV from patients were resistant to the drug. If an amino acid is different from other strains, the color at that position is changed. ... Read more
In which we see the results and come to our own conclusions. If you want to let other people tell you what's right and what's wrong, they will surely do so. Turn on the TV and hordes of happy actors bounce around, only too happy to help you purchase the right deodorant. Open your e-mail and everyone wants to share the best on-line pharmacy and investment guide. Ugh. I prefer making my own decisions, thank you very much. So, I want to give you a chance to look at the data and decide for yourself, if the data show HIV protease sequences changing over ... Read more
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 ... Read more

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