Genome
awild | April 29, 2009
Atta cephalotes, in the fungus garden
Big ant news today! Roche Applied Sciences is apparently funding the sequencing of a series of genomes- three ant and an array of fungal and microbial genomes- in an ambitious project to better understand the relationships among the players in the celebrated ant-fungus relationship. The sequencing project is headed by Nicole Gerardo of Emory University and Cameron Currie of the University of Wisconsin.
This trend in genomics away from sequencing isolated organisms in favor of comparative projects is a welcome one. With multiple attine species- in…
razib | April 23, 2009There are some papers out on the genome of the domestic cow out right now. ScienceNews has an overview:
Two competing research teams have cataloged the "essence of bovinity" found in the DNA of cattle, but not without disagreement on some essential points.
Reporting online April 23 in Science and April 24 in Genome Biology, the two groups compiled drafts of the bovine genome, identifying genes important for fighting disease, digesting food and producing milk.
I don't see the Genome Biology paper on the site yet, but there are two in Science. First, The Genome Sequence of Taurine Cattle: A…
razib | April 11, 2009Science News has an interesting piece up, Shared Differences: The architecture of our genomes is anything but basic. The main focus is on genetic variation, the possibility that there might be important information in copy number variance, and that the common disease-common variant hypothesis is dead. At least for complex traits that we're interested in like schizophrenia. If any of this is unfamiliar or confusing, I recommend the article, it even has references to the primary literature that you can follow up on.
amillikan | March 25, 2009A new paper published in Genome Research provides the most comprehensive scan to date of the genetic signatures of natural selection resulting from the last 10-40,000 years of human evolution, with some intriguing results. The results show strikingly different patterns of selection in distantly related human populations, suggesting that different human groups have adapted to their environments in different ways. Many of the regions seen to be most subject to selection contain genes of unknown function—or no genes at all—but regions linked to increased risk of type 2 diabetes showed a…
edyong | February 12, 2009This is the eighth of eight posts on evolutionary research to celebrate Darwin's bicentennial.
In Virginia, USA, sits a facility called the American Type Culture Collection. Within its four walls lie hundreds of freezers containing a variety of frozen biological samples and among these, are 99 strains of the common cold. These 99 samples represent all the known strains of the human rhinoviruses that cause colds. And all of their genomes have just been laid bare.
Ann Palmenberg from the University of Wisconsin and David Spiro from the J. Craig Venter Institute have cracked the genomes of all…
sporte | October 21, 2008Maybe you did it for the extra cash. Maybe you wanted to be part of the sperm cube public art project. Whatever the reason, it's possible, just possible, your sperm took on a life of it's own, once you left it.
And now that a genome is no longer an entirely personal bit of information, you may be in for a surprise meeting someday, with the end result.
That's right.
Male adoptees are getting their DNA tested and getting information about their possible surnames.
According to the BBC news:
At least 30 men registered with US consumer genetic testing firm Family Tree DNA have found their…
sporte | September 26, 2008Let's play anomaly!
Most of this week, I've written about the fun time I had playing around with NCBI's Blink database and finding evidence that at least one mosquito, Aedes aegypti, seems to have been infected at some point with a plant paramyxovirus and that the paramyxovirus left one of its genes behind, stuck in the mosquito genome.
During this process, I realized that the method I used works with other viruses, too. I tried it with a few random viruses and sure enough, I found some interesting things.
You've got a week to give it a try. Let's see what you find! The method is…
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 25, 2008Do mosquitoes get the mumps? Part V. A general method for finding interesting things in GenBank
This is the last in a five part series on an unexpected discovery of a paramyxovirus in mosquitoes and a general method for finding other interesting things.
In this last part, I discuss a general method for finding novel things in GenBank and how this kind of project could be a good sort of discovery, inquiry-based project for biology, microbiology, or bioinformatics students.
I. The back story from the genome record
II. What do the mumps proteins do? And how do we find out?
III.…
sporte | September 24, 2008Part IV. Assembling the details and making the case for a novel paramyxovirus
This is the fourth in a five part series on an unexpected discovery of a paramyxovirus in a mosquito. In this part, we take a look at all the evidence we can find and try to figure out how a gene from a virus came to be part of the Aedes aegypti genome.
image from the Public Health Library
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 novel mosquito paramyxovirus
V. A…
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 22, 2008Part II. What do mumps proteins do? And how do we find out?
This is the second in a five part series on an unexpected discovery of a paramyxovirus in mosquitoes, and a general method for finding interesting things.
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
In Part I, we looked at the NCBI SeqViewer, and found a new way to check out a genome map, and learn more…
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 | May 29, 2008I got my copy of "A short guide to the human genome" by Stewart Scherer today from Cold Spring Harbor Laboratory Press (2008, ISBN 978-087969791-4). Usually, I would wait until after I've read a book to write a review, but this book doesn't require that kind of study. As soon I skimmed through it and read some of the questions and answers, I knew this would be the kind of quick reference that I would like to have sitting above my desk.
Scherer has compiled a wonderful text that not only answers many of the kinds of questions that I can think to ask about the human genome, but the kinds of…
sporte | April 4, 2008This morning I had a banana genome, an orange genome, two chicken genomes (haploid, of course), and some fried pig genome, on the side. Later today, I will consume genomes from different kinds of green plants and perhaps even a cow or fish genome. I probably drank a bit of coffee DNA too, but didn't consume a complete coffee genome since my grinder isn't that powerful and much of the DNA would be trapped inside the ground up beans.
Of course, microbes have genomes, too. But I do my best to cook those first.
So, what is a genome? Is it a chromosome? Is it one of those DNA fragments or…
awild | March 24, 2008
Tribolium castaneum - Red Flour Beetle
The genome of the red flour beetle Tribolium castaneum was published today in Nature. This latest insect genome is interesting not for what it says about beetles but for what it says about another model species, the venerable fruit fly. The more we learn about other insect genomes- the honeybee, the mosquito, and now the flour beetle- the more we see that the famed Drosophila fruit fly is an odd little beast. The bee and now the beetle, it turns out, are both rather normal. They share a lot of proteins with mammals, and fish, and other animals we…
awild | February 27, 2008
Meet Ectatomma tuberculatum. This tropical insect has the largest genome of 40 species of ants measured in a study by Neil Tsutsui et al in BioMed Central. Weighing in at 690 megabases, E. tuberculatum has nearly twice as much DNA as most other ant species, leading the authors to suggest that a whole genome duplication occurred somewhere in the line of Ectatommine ancestry.
Tsutsui et al's study, released today, is the first comprehensive genomic survey across ants. What's more, it is open access. You can read the whole thing here:
Evolution of Genome Size in Ants
Summary: Here, we…
grrlscientist | December 10, 2007tags: James Watson, racism, African ancestry, genetics, genome, deCODE Genetics
James Watson, 1962 Nobel Prize winner
for co-discovering the structure of DNA along with
Francis Crick and Maurice Wilkins.
This is one of the funnier things I've read recently. It turns out that 1962 Nobel laureate, James Watson, who recently made some disparaging comments about the intelligence of Africans, probably is of African descent himself.
Watson, whose genome was completely sequenced, is the second person whose entire genome was published on the internet. As a result, it is freely accessible to the…
sporte | September 4, 2007
"Come quickly, Watson," said Sherlock Holmes, "I've been asked to review a mysterious sequence, whose importance I'm only now beginning to comprehend."
The unidentified stranger handed Holmes a piece of paper inscribed with symbols and said it was a map of unparalleled value.
Holmes gazed thoughtfully at the map, then slowly lifted his eyes and coldly surveyed his subject's beaming countenance. "You have an affinity for the ocean," said Holmes, "that you indulged to excess as a reckless youth. An experience as a medic in the military changed your life and gave you a reason to do more than…