genetics
razib | November 3, 2008FuturePundit points me to new work on a genetic mutation which might predispose one to Season Affective Disorder, A missense variant (P10L) of the melanopsin (OPN4) gene in seasonal affective disorder:
SAD participants had a higher frequency of the homozygous minor genotype (T/T) for the missense variant rs2675703 (P10L) than controls, compared to the combined frequencies of C/C and C/T. Individuals with the T/T genotype were 5.6 times more likely to be in the SAD group than the control group, and all 7 (5%) of individuals with the T/T genotype at P10L were in the SAD group.
It looks like…
razib | November 3, 2008Geneic Future has a review & mulling over of implications of a new paper, High-Resolution Mapping of Expression-QTLs Yields Insight into Human Gene Regulation. Well worth the read.
edyong | November 3, 2008Mammals like ourselves pass our genes 'vertically' from parent to child. But bacteria aren't quite so limited; they have mastered the art of gene-swapping and regularly transfer DNA 'horizontally' from one cell to another. This "horizontal gene transfer" has been largely viewed as a trademark of single-celled organisms, with few examples among animals and plants. That is, until now.
A group of American researchers have discovered a group of genetic sequences that have clearly jumped around the genomes of several mammals, one reptile and one amphibian. It's the most dramatic example yet that…
razib | November 2, 2008Photo: Zhou Xun
I've mentioned EDAR before. If you've ever wondered why East Asians tend to have rather thick hair, it is likely due to genetic variation at this locus, in particular the SNP rs3827760. Yann reminded me that a new paper has come out which replicates and clarifies some earlier findings, A replication study confirmed the EDAR gene to be a major contributor to population differentiation regarding head hair thickness in Asia. Below the fold is an important figure from the paper.
JPN obviously means "Japanese," and 1540T/C is the same SNP I pointed to above. The concluding…
evolgen | November 2, 2008After a few months off, here's the return of Mendel's Garden.
Blast from the past: rENNISance woman gives us a post on viral genetics.
Figuring out DNA looping with unbelievably advanced technology: Greg Laden reviews a paper on the structure of nucleic acids.
In the fly, delayed reproduction also delays aging: Ouroboros describes research on senescence in Drosophila.
Balancer Chromosomes: Larry Moran describes this marked chromosomal inversions (see also Hermann Muller Invented the Balancer Chromosome).
The Genetics of Voting: From Bayblab, a post on the heritability of filling the…
razib | November 1, 2008My discussion with Jim Manzi on epistasis generated a lot commentary. It's a complex topic, as I said there are different ways to define epistasis, and evolutionarily its effect on trait value might be different from its effect on fitness. Finally, I think it is important that epistatic and additive genetic variation can convert from one to the other; and over the long term it is this heritable variation which is the "stuff of evolution," so to speak. But a friend recommended that I post a figure from Genome-wide association analysis identifies 20 loci that influence adult height.
One…
razib | October 30, 2008Dienekes and Kambiz both hit a new paper which claims to find the Y chromosomal (direct male descent lines) signatures of the ancient Phoenician colonization of the Mediterranean. I tend to see a lot of merit in Dienekes' criticisms, the net here is thrown so wide that it's almost one of those models where it explains everything so that it explains nothing. Compare this to the recent work on the genetics of the Etruscans and modern populations of Tuscany, which strongly lend credence to ancient myths of their origin in Anatolia The historical data I've seen suggests that both the Phoenician…
razib | October 30, 2008Jim Manzi has a long post up on epistasis, that is, gene-gene interactions:
We could call this process of competing algorithms struggling to find the best solution as fast as possible "meta-evolution". That is, each potential search method must compete for survival. The fact that the algorithm that has won this (idealized) competition in the real world has the form of a GA seems to indicate that there is some structure to the relationship between gene vectors and physical outcomes, but that it is much more complex that simple linear combinations without interaction terms, otherwise nature…
mikethemadbiologist | October 30, 2008ScienceBlogling Revere links to a news article about high levels of VRE, vancomycin resistant enterococci in beach sand. While Revere and the article both describe how this indicates that VRE are established in the community, I think a far more chilling problem isn't mentioned at all: VMRSA.
What's VMRSA? Vancomycin resistant MRSA (methicillin resistant Staphylococcus aureus).
Every instance of VMRSA has involved an MRSA strain acquiring a plasmid (mini-chromosome) from a VRE strain. So far, most of these cases have occurred in Michigan. Apparently, the VRE strain that carries this…
grrlscientist | October 28, 2008tags: blue tit, Cyanistes caeruleus, extrapair fertilization, genetic benefit hypothesis, genetic similarity, plumage color, birdsong, ornithology, behavioral ecology
Blue tit, Cyanistes caeruleus.
Image: Paul Hillion, 26 April 2008.
Even though most bird species form social bonds with their mates, they are not always faithful partners to each other. It's easy to figure out why male birds engage in extrapair copulations: this increases the total number of their offspring -- and this increases their reproductive fitness. But since female birds are physically capable of producing only…
evolgen | October 28, 2008
I will be hosting the next edition of Mendel's Garden on Sunday, November 2. If you have written any blog posts about genetics in the past few months, send me a link (evolgen[at]yahoo[dot]com). Also, if you've seen any good genetics posts on other people's blogs, let me know.
For those not in the know, Mendel's Garden is the original genetics blog carnival. On the first Sunday of every month, the carnival plays host to the best genetics blogging of the past month. After a hiatus of a few months, the carnival is back.
edyong | October 27, 2008Most of the planet's ecosystems are made of a multitude of different species, rich tangles of living things all interacting, competing and cooperating in order to eke out an existence. But not always - in South Africa, within the darkness of a gold mine, there is an ecosystem that consists of a single species, a type of bacteria that is the only thing alive in the hot, oxygen-less depths. It is an ecosystem of one, living in complete isolation from the Sun's energy.
This incredible and unique habitat was discovered by Dylan Chivian from the Lawrence Berkeley National Laboratory, leading a…
clock | October 26, 2008As a follow-up to the yesterday's press release, Dr. Manzoor Bhat and Joseph Piven, M.D., researchers at the University of North Carolina in Chapel Hill who use the Drosophila model system to study neurexin and its implications in the development of autism, have now released the video response - well worth watching:
razib | October 24, 2008Dienekes points to another paper on European population substructure, Genome-Wide Analysis of Single Nucleotide Polymorphisms Uncovers Population Structure in Northern Europe:
In this study, we analysed almost 250,000 SNPs from a total of 945 samples from Eastern and Western Finland, Sweden, Northern Germany and Great Britain complemented with HapMap data. Small but statistically significant differences were observed between the European populations...The latter indicated the existence of a relatively strong autosomal substructure within the country, similar to that observed earlier with…
gregladen | October 24, 2008There is a new paper, just coming out in Proceedings of the National Academy of Sciences, that explores the idea that humans have undergone an increased rate of evolution over the last several tens of thousands of years.
By an increased rate of evolution, the authors mean an increased rate of adaptive change in the genome. By recent times, the authors mean various things, depending on which part of the analysis you examine, and depending on what is meant by "increased." ... In other words, the timing of an event that is not really an event (but rather a change in rate of something) is hard…
razib | October 21, 2008If you are interested in the Personal Genome Project, you can get the all the down-low over at Genetic Future. Really, just go read Genetic Future.
edyong | October 21, 2008
Fighting malaria with mosquitoes seems like an bizarrely ironic strategy but it's exactly what many scientists are trying to do. Malaria kills one to three million people every year, most of whom are children. Many strategies for controlling it naturally focus on ways of killing the mosquitoes that spread it, stopping them from biting humans, or getting rid of their breeding grounds.
But the mosquitoes themselves are not the real problem. They are merely carriers for the true cause of malaria - a parasite called Plasmodium. It suits neither mosquitoes nor humans to be infected with…
razib | October 21, 2008Finding Hidden Tomb Of Genghis Khan Using Non-Invasive Technologies. Cool right? My first thought was Serpentor:
...He was created through a breakthrough in cloning research by Dr. Mindbender from the DNA extracted from the unearthed remains of the most ruthless and effective military leaders in history, including Julius Caesar, Napoleon Bonaparte, Attila the Hun, Philip II of Macedon and his son Alexander the Great, Ivan the Terrible, Vlad the Impaler, Hannibal, Genghis Khan, and Grigori Rasputin....
With ancient DNA extraction techniques if there's genetic material perhaps we could actually…
gregladen | October 13, 2008 A very good day of grunting worms. Credit: Ken Catania So-called Gene-Culture Co-Evolution can be very obvious and direct or it can be very subtle and complex. In almost all cases, the details defy the usual presumptions people make about the utility of culture, the nature of human-managed knowledge, race, and technology. I would like to examine two cases of gene-culture interaction: One of the earliest post-Darwinian Synthesis examples addressing malaria and sickle-cell disease, and the most recently published example, the worm-grunters of Florida, which it turns out is best…
razib | October 11, 2008John Hawks succinctly responds to Steve Jones' argument that evolution is ending. Nothing surprising, but a very tight and accessible exposition.
Related: Evolution, why it still happens (in pictures) and No Virginia, evolution isn't ending.