phylogeny

In my last post, I wrote about insulin and interesting features of the insulin structure.  Some of the things I learned were really surprising.  For example, I was surprised to learn how similar pig and human insulin are.  I hadn't considered this before, but this made me wonder about the human insulin we used to give to one of our cats.  How do cat and human insulin compare? It turns out, that all ... Read more

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 trees

We can get the genome sequences, piece by piece, as I described in earlier, but the NCBI has other tools that are useful, too.

The Influenza Virus Resource will let us pick sequences, align them, and make trees so we can quickly compare the sequences to ... Read more

This afternoon, I was working on educational activities and suddenly realized that the H1N1 strain that caused the California outbreak might be the same strain that caused an outbreak in 2007 at an Ohio country fair. UPDATE: I'm not so certain anymore that the strains are the same. I'm doing some work with nucleic acid sequences to look further at similarity. Here's the data. Once I realized that the genome sequences from the H1N1 swine flu were in the NCBI's virus genome resources database, I had to take a look. And, like eating potato chips, making ... Read more
Ebola virus has impressed me as creepy ever since I read "The Hot Zone: A Terrifying True Story some years back by Richard Preston. (I guess he has a new book, too, ... Read more
I made this video (below the fold) to illustrate the steps involved in making a phylogenetic tree. The basic steps are to:
  1. Build a data set
  2. Align the sequences
  3. Make a tree
In the class that I'm teaching, we're making these trees in order to compare sequences from our metagenomics experiment with the multiple copies of 16S ribosomal RNA (rRNA) genes that we can find in single bacterial genomes. Bacteria contain between 2 to 13 copies of 16S rRNA genes and we' ... Read more
i-8295f915da92d0ca11a67cd144057d90-rhodies.jpgThe first research assignment for our Alaska NSF Chautauqua course has been posted. Your task is to find a wound-inducible plant gene, learn something about it, and post a description in the comment section. We've already had one excellent answer, but I know there are at least 54 wound- ... Read more
If you've ever looked at an evolutionary tree, contemplated phylogeny, cladistics, or the like, you're probably aware that Joe Felsenstein is one of the leaders of the pack. And you will certainly enjoy, this interview that Blind Scientist has posted. I wouldn't advise reading the interview to learn about doing phylogenetics, but you will learn a bit about the social anthropology of the field. Felsenstein does a wonderful job of supplying historical context to phylogenetic arguments and filling in the missing details ... Read more
Five Bulgarian nurses and a Palestinian doctor (dubbed the Tripoli six) may be executed soon by the Libyan government for the crime of deliberately infecting over 400 children with HIV. If they did infect the children, this would be a horrendous crime. If they did not infect the children, it's the Libyan government that will be killing innocent people. The clock is ticking. Some of you might be wondering (I know I was): How exactly is molecular sequence data being used to solve the crime? Why are scientists and science bloggers claiming that the ... Read more

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