We've been fans of the Molecule of the Month series by David Goodsell, for many years. Not only is Dr. Goodsell a talented artist but he writes very clear descriptions of the ways molecules like proteins, RNA, and DNA work together and function inside a cell. To learn about proteins ...
In the class that I'm teaching, we found that several PCR products, amplified from the 16S ribosomal RNA genes from bacterial isolates, contain a mixed base in one or more positions. We picked samples where the mixed bases were located in high quality regions of the sequence (Q >40), and ...
DNA sequence traces are often used in cases where: We want to identify the source of the nucleic acid. We want to detect drug-resistant variants of human immune deficiency virus. We want to know which base is located at which position, especially where we might be able to diagnose a ...
The simple fact is this: some DNA sequences are more believable than others. The problem is, that many students and researchers never see any of the metrics that we use for evaluating whether a sequence is "good" and whether a sequence is "bad." All they see are the base calls ...
What tells us that this new form of H1N1 is swine flu and not regular old human flu or avian flu? If we had a lab, we might use antibodies, but when you're a digital biologist, you use a computer. Activity 4. Picking influenza sequences and comparing them with phylogenetic ...
We had a great discussion in the comments yesterday after I published my NJ trees from some of the flu sequences. If I list all the wonderful pieces of advice that readers shared, I wouldn't have any time to do the searches, but there are a few that I want ...
We have lots of DNA samples from bacteria that were isolated from dirt. Now it's time to our own metagenomics project and figure out what they are. Our class project is on a much smaller scale than the honeybee metagenomics project that I wrote about yesterday, but we're using many ...
" By night all cats are gray" - Miguel Cervantes in Don Quixote I've always liked Siamese cats. Students do, too. "Why Siamese cats wear masks" is always a favorite story in genetics class. So, when I opened my January copy of The Science Teacher, I was thrilled to see ...
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 have an effect, a molecule must bind to a receptor and trigger a signal. Studying a receptor's structure can give us insights about the way this triggering process works. Capsaicin is a fascinating molecule that puts the "pep" into peppers. Curiously, the amount of capsaicin in a pepper is ...
ScienceBlogs and science bloggers, in general, have enthusiastically supported fund-raising efforts by DonorsChoose for the past two years, and we're doing it once again for 2008. DonorsChoose works like this: teachers write descriptions of what they want and how they'll use it for teaching, and submit their proposals to DonorsChoose ...
BLAST is a collection of programs that are used to compare sequences (DNA, RNA, or protein) to larger collections of sequences that are stored in databases. I've used BLAST as a teaching tool for many years, partly because it's become a standard tool for biological work and partly because it's ...
This quarter, I'm using a wiki with my bioinformatics class and posting sometimes about the things that I learn. Two things I've been experimenting with are: Setting up pages for individual students so they can take notes while they're working. Embedding a Google form into one of my wiki pages ...
Reposted from Halloween 2006. Since Ben shared his family's taxonomy of candy types, and it's Friday, after all, I thought I'd share some of things that we do with candy around our house and describe some fun things that you can do with candy at home. Materials and methods. First ...
Okay OpenOffice fans, show me what you can do. Earlier this week, I wrote about my challenges with a bug in Microsoft Excel that only appears on Windows computers. Since I use a Mac, I didn't know about the bug when I wrote the assignment and I only found out ...
By now, many of you have probably seen the the new BLAST web interface at the NCBI. There are many good things that I can say about it, but there are a few others that caught me by surprise during my last couple of classes. tags: Because of these changes ...
I just love this title! It's nerdy and cute, all at the same time. I read about this in www.researchblogging.org and had to check out the paper and blog write up from The Beagle Project (BTW: some of you may be interested in knowing that The Beagle Project is not ...
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 ...
When can a really bad virus be used to do something good? When we can use it to learn. The human immunodeficiency virus, cause of AIDS, scourge of countries, and recent focus of ScienceBlogs; like humans, evolves. As one of my fellow ScienceBloggers noted, few biological systems demonstrate evolution as ...
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 ...
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 ...
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 ...
In which we identify unknown human proteins. Yesterday, I wrote about using the BLOSUM 62 matrix to calculate a score for matches between two proteins. Those scores give us a good start on understanding how blastp determines whether two sequences are matching by chance or because they're more likely to ...
In which we search for Elvis, using blastp, and find out how old we would have to be to see Elvis in a Las Vegas club. Introduction Once you're acquainted with proteins, amino acids, and the kinds of bonds that hold proteins together, we can talk about using this information ...
There's no question that the ability to work with information is one that will be required and valued for a long time to come. I think it's imperative for teachers to have students practice this skill whenever an opportunity comes about. The problem for many teachers is finding the time ...
Want to learn more about Parkinson's disease? See why a single nucleotide mutation messes up the function of a protein? I have a short activity that uses Cn3D (a molecular viewing program from the NCBI) to look at a protein that seems to be involved in a rare form of ...
If you're going to create a new life form ( even if it's only digital), Sunday Saturday seems like the best day to give it a try. Reposted from an earlier year. Build-A-Virus is a quick, fun, and simple game that was created and put on-line by Bioreliance, now owned ...
Experimenting with on-line worksheets I know some people who always teach their classes the same way, semester after semester, year after year.. Not me. I always want to experiment and try new things. This fall, I'm experimenting with using a wiki in the classroom, in addition to my blog. This ...
We'll have a blast, I promise! But there's one little thing we need to discuss first... I want to explain why I'm going to use nucleotide sequences for the blast search. (I used protein the other day). It's not just because someone told me too, there is a solid rational ...
Dave Robinson and Joann Lau from Bellarmine College in Kentucky are going to be describing their student project in a free webinar next Friday, May 16th. Their students clone GAPDH (Glyceraldehyde 3-Phosphate Dehydrogenase) genes from new plants, assemble the DNA sequences, and submit them to the NCBI. Here's an example ...
