influenza

Nick's post on Amantadine resistance in swine flu was so interesting, I had to look at the protein structures myself.

I couldn't find any structures with the S31N mutation that Nick discussed, but I did find some structures with the M2 protein and Amantadine. Not only are these structures beautiful, but you can look at them and see how the protein works and how the drug prevents the protein from functioning.

As Nick mentions, the M2 protein from influenza makes a ... Read more

Last night, the phone rang at 9:22 pm. I quickly glanced at the caller ID. Hmmm. Why is the Seattle School district calling us at this time of night?

Apparently the swine flu has come to Seattle and the school district thought we should know.

Those messages are helpful if you're a parent, but they don't tell much about the rest of the world.

Health Map is a really wonderful, user-friendly, resource for following the epidemic.

... Read more

I'm teaching an on-line bioinformatics course this semester for Austin Community College. They are in Texas of course, but I am in Seattle. This presents a few interesting challenges and some minor moments of amusement.

Today, the school sent all the faculty emails telling us to stay home if we're sick.

Got it. If I think I have flu, I will not fly to Texas.

Instead, I'll stay home and watch videos on coughing without contaminating others.

Watch "Why don't we do it in our sleeves?" and find out how you rank on the safe coughing scale.

... 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 ... Read more

Genome sequences from California and Texas isolates of the H1N1 swine flu are already available for exploration at the NCBI. Let's do a bit of digital biology and see what we can learn.

Activity 1. What kinds of animals get the flu?

For the past few years we've been worrying about avian (bird). Now, we're hearing about swine (pig) flu.

All of this news might you wonder just who gets the flu besides pigs, birds, and humans. We can find out by looking at the data.

Over the past few years, researchers have been sequencing ... Read more