gene
sporte | September 25, 2008Lots of bloggers in the DNA network have been busy these past few days writing about Google's co-founder Sergey Brin, his blog, his wife's company (23andme), and his mutation in the LRRK2 gene.
I was a little surprised to see that while other bloggers (here, here, here, and here) have been arguing about whether or not the mutation really increases the risk to the degree (20-80%) mentioned by Brin, no one has really looked into the structure and biochemistry of the LRRK2 protein to see if there's a biochemical explanation for Parkinson's risk. I guess that task is up to me.
Let's begin at…
sporte | September 23, 2008Part III. Serendipity strikes when we Blink
In which we find an unexpected result when we Blink while looking at the mumps polymerase.
This is the third in a five part series on an unexpected discovery of a paramyxovirus in mosquitoes. And yes, this is where the discovery happens.
I. The back story from the genome record
II. What do the mumps proteins do? And how do we find out?
III. Serendipity strikes when we Blink.
IV. Assembling the details of the case for a mosquito paramyxovirus
V. A general method for finding interesting things in GenBank
To paraphrase Louis Pasteur,…
sporte | September 21, 2008Part I. The back story from the genome record
Together, these five posts describe the discovery of a novel paramyxovirus in the Aedes aegyptii genome and a new method for finding interesting anomalies in GenBank.
I. The back story from the genome record
II. What do the mumps proteins do? And how do we find out?
III. Serendipity strikes when we Blink.
IV. Assembling the details of the case for a mosquito paramyxovirus
V. A general method for finding interesting things in GenBank
I began this series on mumps intending to write about immunology and how vaccines work to stimulate the immune…
sporte | August 21, 2008One of the things that drives me crazy on occasion is nomenclature. Well, maybe not just nomenclature, it's really the continual changes in the nomenclature, and the time it takes for those changes to ripple through various databases and get reconciled with other kinds of information. And the realization that sometimes this reconciliation may never happen.
One of the projects that I've been working on during the past couple of years has involved developing educational materials that use bioinformatics tools to look at the isozymes that metabolize alcohol. As part of this project, I've been…
sporte | August 8, 2008A few weeks ago, I wrote about a paper in Science(1) that I read on a connection between a mutation in the dopamine D2 receptor and the genetics of learning.
Only, it turned out that when I looked at the gene map...
the mutation mapped in a completely different gene.
I presented the data here and wrote a bit about my surprise at finding this mistake and even greater surprise at seeing this same mistake perpetuated by others.
Now, I have some updates to the story.
The folks at the NCBI responded quickly and added annotations to both the DRD2 and the ANKK1 citations in the Gene database.
Now…
sporte | June 24, 2008or is it just an idea that's ahead of the curve?
Last week, I was stunned to discover at least 31 papers in an NCBI Gene database entry that were in the entry for the wrong gene. I wrote about this here, here, here, and here.
Now, an oversight like this is a little understandable. The titles of the entries do include the name of the wrong gene (DRD2 - the dopamine D2 receptor). And it was only four years ago that people figured out that the marker in the title of the articles mapped somewhere else.
If computers were responsible for the annotation, well, this would be understandable.…
sporte | June 19, 2008Right or wrong, the word "dopamine" always conjures up images in my head of rats pushing levers over and over again, working desperately hard to send shots of dopamine into their tiny little rodent brains.
Dopamine, like many other neurotransmitters (chemicals that send signals in the brain), works by binding to proteins on the surface of brain cells and sending a signal to the cell. There are five different subtypes of receptors for dopamine (D1-D5) with somewhat different activities (1) and drugs that bind to these receptors are known to have potent effects on brain activity and behavior (…
sporte | June 18, 2008In a recent post, I wrote about an article that I read in Science magazine on the genetics of learning.
One of things about the article that surprised me quite a bit was a mistake the authors made in placing the polymorphism in the wrong gene. I wrote about that yesterday. The other thing that surprised me was something that I found at the NCBI.
The article that I wrote about definitely made a mistake and I don't understand why it wasn't caught by the reviewers. I found it pretty quickly by searching OMIM and I was only trying to find information about dopamine, not verify results.…