genomics
evolgen | December 18, 2006Since my last report on Nature's copy number polymorphism (CNP) papers, a couple other journals have published studies of human structural polymorphisms:
Genome Research has two papers on detecting CNPs using oligonucleotide microarrays. The strategy here is to develop a microarray that contains all the unique regions of the genome (divided into ~20 nucleotide pieces). You can quantify the amount of DNA hybridized to the array. So, when you test genomic DNA, regions of single copy DNA will have a certain intensity, whereas regions that are present at multiple copies will have higher…
evolgen | December 5, 2006A few weeks ago PNAS published a paper on the evolution of snake sex chromosomes. The authors compare snake sex chromosome evolution with that of mammals and birds. Given my passing interest in sex chromosome evolution, I decided to check it out.
Snakes use sex chromosomes to determine the sex of their progeny. Sex in other reptiles, such as crocodiles, is determined by the temperature at which the eggs are incubated. There are two main types of sex chromosome systems in vertebrates: XY and ZW. Most mammals, some fish, some reptiles, and some amphibians use the XY system -- males are…
evolgen | December 3, 2006Sandy has declared her love for all things "-omics". She even came up with a nifty table to define a bunch of omes. It's like she's created a list-o-omes-eome.
Snark aside, here's why she likes omes:
I like "ome" [see, I told you she would tell us why she likes omes] because it simultaneously gives us more precise definitions for fields of study, while making a distinction between the reductionist view of biology, that was so popular when I was in graduate school, and the more global-omic-view that's been emerging of late. When I grew up, we were mired in the one gene - one enzyme rut.
As a…
sporte | December 1, 2006In which I present a quick guide for the omically challenged and a defense of 'arth and "ome."
Other SciBloggers have shared their thoughts on the use of ome here and here.
Sometimes I get frustrated too, with the way language is abused and tweaked by those around me. So many word pairs that once made phrases—;log in, data set, file name, set up, and pick up—;have been condensed into single words, that I've had to start using Google to double-check my editing. Perhaps it's surprising then, that I like "ome," "omics," and even Sydney Brenner's chief phrase-to-hate, "systems biology."
I…
evolgen | November 30, 2006Dr. Joan Bushwell (not her real name) has hurled some poo at the -omicists. You know, those people who attach -omics to everything and act like they've come up with a brand new research discipline. I imagine them making the "guitar player changing chords" face (go to 1:09 in this video) when they coin a new "ome".
As one last hurrah for omeomics, Doc Bushwell coined the meme-ome. That would be a collection of all the memes floating around the blogosphere. Or is it all memes everywhere? Who knows? But it is the perfect congruence of two terms that have worn out there welcome.
And systems…
evolgen | November 23, 2006Happy Turkey Day!! As a special gift, I give you yet another -ome to spread on your Thanksgiving bird. You see, I'm fascinated by -omics, the idea that you can affix "-ome" to your favorite biological system to prime the hype machine. And what I have for you this time makes me think of the juices of a turkey that's been cooked just right.
With that in mind, I give you the secretome. From what I can gather, these are the proteins secreted by an organism. The authors of the article linked above are interested in the evolution of the mollusk shell, but mice, humans, pufferfish, and pigs all have…
evolgen | November 23, 2006There's an old paradigm in human population genetics that we each differ from each other by less than one percent at the DNA sequence level. While that may be true for our DNA sequences, recent work indicates that there's also quite a bit of variation amongst individuals in the actual content of their genomes. Such variation is known as copy number variation (CNV) or copy number polymorphism (CNP). What it means is that some people may have one copy of a genomic region, other may have two, and even others may have none.
Nature thinks this research on CNV is quite important, as there are five…
evolgen | November 18, 2006Most of the DNA sequenced from the Neanderthal genome projects came from the microbes that decomposed the dead fella'. This poses a problem for the human geneticists who are only interested in the Neanderthal DNA. But you could probably do some interesting things with the non-Neanderthal DNA. John Hawks says:
I suppose if you were interested in the long-term microbial decomposition of fossil bone, you could do your dissertation on those. For the rest of us, the final step is to let the computer spit out the humanlike sequences, which are assumed to be the Neandertal DNA plus some proportion…
evolgen | November 15, 2006Razib and John Hawks have been all over the Neanderthal introgression story, but they hinted that there was more. And they thought that more would come from Svante Paabo. And it has, in the form of one million base pairs of Neanderthal DNA sequence published in this week's issue of Nature (here is Nature's Neanderthal page).
Not to be outdone, Science has published a paper described 65,250 base pairs of Neanderthal DNA (here is a link to the pdf and here is some coverage from Science). It looks like Science got the short end of the stick, with over an order of magnitude less DNA than the…
evolgen | November 10, 2006Neil Saunders goes searching for the MCPH1 gene in the Neanderthal sequences available in Genbank. You'll have to go over to his site to see what he found.
evolgen | November 10, 2006In case you didn't hear, a sea urchin genome has been sequenced, analyzed, and the results published (Science has a page dedicated to it here). I say a sea urchin genome because there are many species of sea urchins. This paper reports the sequence of one species, Strongylocentrotus purpuratus, a model organism in developmental biology.
Despite the fact they are quite common-place, genome sequencing projects still draw some attention in the popular science press (see the honeybee as an example). And, as usual, the articles written about this scientific study are fraught with errors and…
evolgen | October 26, 2006There will be a ton of papers coming out over the next couple of weeks on the recently sequenced honeybee (Apis mellifera) genome. Carl Zimmer has a review of some of the topics that will be addressed in the upcoming publications. The NHGRI also has some information.
evolgen | October 17, 2006Science has published THE genome of breast and colorectal cancers. Not the whole genome, mind you, but just 13,023 protein coding genes. The researchers identified mutations associated with cancers, but I'm not sure if they looked outside of the protein coding sequences (I have yet to read the paper, and I'm not sure when I'll get around to it). Nobel Intent has a review of the paper.
When I first heard about this project I wondered what exactly they'd be doing. The fact that this study only looked at 11 cancers for each tissue is somewhat surprising. What I'd really like to see is a study…
evolgen | October 16, 2006I've said it before. I'll say it again:
The best way to get your paper into a high profile journal like Science or Nature is to find the biggest of something, the smallest of something, or something that fucks funny.
This paper further supports my point.
evolgen | October 12, 2006Ralf Neumann has interpreted my fascination with -omics as distaste for neologisms:
A blogger named "RPM" reacted even more drastically to the methylome-paper on his weblog "evolgen" (http://scienceblogs.com/evolgen) in a post entitled "Yet Another '-ome'". "We can thank Andrew Feinberg for introducing the term methylome, which he defines as 'a neologism that describes the complete set of DNA methylation modifications of a cell'. Check out this definition of neologism: 'A meaningless word used by a psychotic.' Exactly. Enough with the -ome already." It seems as if more and more researchers…
evolgen | October 5, 2006Nick Wade thinks there's a race to decode genomes. CNN thinks there's a race to map the human genome:
$10 million prize for mapping human genomes
Sturtevant mapped genomes. The contest is to sequence and assemble a genome. Well, that's what we think the contest is. And it's pretty unclear how they will measure accuracy.
evolgen | October 5, 2006Nicholas Wade is up to his old antics, blabbering about a contest to award $10 million to the first person to decode 100 genomes in 10 days. Only he means 'sequencing' rather than 'decoding'. But he still thinks they're synonyms:
"The announcement of the prize brought together two former rivals, Drs. J. Craig Venter of the Venter Institute and Francis S. Collins, head of the National Human Genome Research Institute, which financed the government project to sequence, or decode, the genome."
The 100 genomes in 10 days contest is brought to you buy the people who gave away $10 million to the…
sporte | September 26, 2006Razib inspired me to share some of the story behind why white people are considered derivatives.
Reposted from the Classic Digital Bio.
No red herrings, here! Lamason et. al. found a single gene that controls human skin color while studying pigmentation in zebra fish (1).
These zebra fish had an unusual golden color that turned out to be an important clue. Lamason and collaborators found that the golden zebra fish lost their normal color because of a mutation in the slc24a5 gene. When the zebra fish have the mutant form, they produce fewer melanosomes.
A short language lesson
Fewer…
evolgen | September 18, 2006Adam Eyre-Walker has published a review of adaptive evolution in a few well studied systems: Drosophila, humans, viruses, Arabidopsis, etc. These organisms have been the subject of many studies that used DNA polymorphism, DNA divergence, or a combination of the two to detect natural selection in both protein coding and non-coding regions of the genomes. Now that we have whole genome sequences for multiple closely related species from a few different taxa, many researchers are interested in determining the role of natural selection in the evolution of DNA sequences.
Eyre-Walker claims that the…
evolgen | September 15, 2006I've told you before that I once dreamt of becoming a conservation geneticist. I major turning point for me occurred after I had completed rotations during my first year of grad school. I had to decide between two different labs: in one I would use molecular markers to study the demography of a species of tree and in the other I would study the evolution of Drosophila genomes. I chose the Drosophila lab (for reasons I won't get into here or now), and the rest was history.
It turns out I could have been a coauthor on a Science paper if I had chosen the tree lab. My potential advisor in that…