genetics
razib | August 13, 200825-Hydroxyvitamin D Levels and the Risk of Mortality in the General Population:
In cross-sectional multivariate analyses, increasing age, female sex, nonwhite race/ethnicity, diabetes, current smoking, and higher body mass index were all independently associated with higher odds of 25(OH)D deficiency...while greater physical activity, vitamin D supplementation, and nonwinter season were inversely associated. During a median 8.7 years of follow-up, there were 1806 deaths, including 777 from CVD. In multivariate models (adjusted for baseline demographics, season, and traditional and novel CVD…
mikethemadbiologist | August 11, 2008I realize science is hard and stuff, but there are serious problems with the evidence in the anthrax investigation. I'm not the only who thinks so: ScienceBloglings Tara and Revere think so too, along with most of the commentors. Thankfully, these problems are finally starting to enter the discussion. First, from Glenn Greenwald:
The NYT today has an excellent Op-Ed from a microbiologist (the former Chief of Fort Detrick's bacteriology division) pointing out the numerous deficiencies in the FBI's scientific assertions. Critically, that Op-Ed describes the properties of the high-grade…
clock | August 7, 2008On Tuesday night, when I posted my personal picks from this week's crop of articles published in PLoS ONE, I omitted (due to a technical glitch on the site), to point out that a blog-friend of mine John Logsdon published his first PLoS ONE paper on that day:
It's a updated and detailed report on the ongoing work in my lab to generate and curate an "inventory" of genes involved in meiosis that are present across major eukaryotic lineages. This paper focuses on the protist, Trichomonas vaginalis, an organism not known to have a sexual phase in its life cycle.
Here is the paper (and check John's…
mikethemadbiologist | August 7, 2008Yesterday, I mentioned my doubts about there being two anthrax strains used in the 2001 attacks. Thanks to an article identified by reader TomJoe, I'm convinced that there was only one anthrax strain involved, if the only evidence for the existence of two strains is that there is a DNA inversion.
Just to remind everyone, this is what I mean by a DNA inversion:
In many bacteria, inversions are used as regulatory mechanisms--when the DNA is in one direction, nearby genes are turned on, and when in the other, they're turned off. Like so (this is a made up example for illustrative purposes only…
edyong | August 6, 2008Viruses may cause disease but some can fall ill themselves. For the first time, a group of scientists have discovered a virus that targets other viruses. This new virus-of-viruses was discovered by Bernard La Scola and Christelle Desnues at the University of the Mediterranean, who have playfully named it Sputnik, after the Russian for "fellow traveller". It is so unique that they have classified it in an entirely new family - the "virophages" - in honour of the similarities it shares with the bacteriophage viruses that use bacteria as hosts.
The story of Sputnik started in 1992 with some…
clock | August 6, 2008Since this article came out in The American Scientist (the only pop-sci magazine that IMHO has not gone downhill in quality over the past decade) in early 1999 (you can read the entire thing here (pdf)) I have read it many times, I used it in teaching, I discussed it in Journal Clubs, and it is a never-ending fascination for me. Now Andrew and Greg point out there is YouTube video about the fox domestication project:
Back in the 1950s, Dmitri Konstantinovich Belyaev started an experiment in which he selectively bred Silver Foxes, very carefully, ONLY for their tameness (and "tameness" was…
grrlscientist | August 6, 2008tags: researchblogging.org, premature hair graying, autosomal dominant trait, genetics, horses, hair color, syntaxin-17, melanocortin-1 receptor, cis-acting regulatory mutation, melanoma, evolution
This horse is in the process of losing its pigment.
It will end up being all white by the time it is eight years old.
Image: Horse Wallpaper [larger view].
Even though I have always been a fan of black horses, my heart did leap at the sight of the noble Shadowfax racing towards Gandalf in response to his call in the Lord of the Rings. White horses have symbolized purity throughout most ages…
mikethemadbiologist | August 6, 2008In reading this NY Times story about the anthrax investigation, this statement about how the presence of an inversion (a region of flipped DNA) puzzled me (italics mine):
The genome of various stocks of the Ames strain of anthrax used in the attacks were almost identical in all the 5 million chemical letters of their DNA. But researchers found enough differences in the attack strain to provide a reasonable chance of identifying its source.
The chief difference was that a stretch of DNA was flipped head to tail in some bacteria in the attack strain, but not in any other samples.
Further, the…
edyong | August 4, 2008For the first time, scientists have developed drugs that mimics the effects of endurance exercise. With the aid of two chemicals, Vihang Narkar, Ronald Evans and colleagues from the Salk Institute managed to turn regular lab rodents into furry Paula Radcliffes - mighty mice that were capable of running further and for longer than their peers. One of the drugs only worked in combination with exercise, but the other managed to boost stamina without it.
Using drugs to boost performance isn't a new development. Steroids can help body-builders to build their bodies, while giving athletes an extra…
razib | August 2, 2008My post from a few weeks ago, Why does race matter for women?, elicited a lot of response (made it to the front page of Digg). Most of the open public discourse on race is bracketed in a few coarse frameworks; it is a social construction, and no one cares who is truly enlightened anymore, white racism keeps people of color down, etc. Though of utility in sloganeering I think most of these generalizations are such half-approximations that they mislead a great deal of time. So for example the interesting repeated finding that women in the United States are consistently more race conscious in…
razib | July 29, 2008Indo-European and Asian origins for Chilean and Pacific chickens revealed by mtDNA:
European chickens were introduced into the American continents by the Spanish after their arrival in the 15th century. However, there is ongoing debate as to the presence of pre-Columbian chickens among Amerindians in South America, particularly in relation to Chilean breeds such as the Araucana and Passion Fowl...The modern Chilean sequences cluster closely with haplotypes predominantly distributed among European, Indian subcontinental, and Southeast Asian chickens, consistent with a European genetic origin.…
clock | July 25, 2008PLoS Genetics is celebrating its third birthday this month! Let's see what's new this week, among else...
PLoS Genetics Turns Three: Looking Back, Looking Ahead:
PLoS Genetics is three years old this month--a milestone worth celebrating! As we do, and as we recognize all who have helped us reach this point in time, we thought this would be a good opportunity to share with you a summary of our brief history and a look ahead.
Our original intent was to provide an open-access journal for the community that would "reflect the full breadth and interdisciplinary nature of genetics and genomics…
razib | July 24, 2008I've posted a fair amount about the new field of historical population genetics. Some of the most popular mass-market books in genetics deal with this field, for example Spencer Wells' Journey of Man. On the other hand, there's a lot of sloppy overreach on the part of some practitioners, especially due to the excessive reliance on uniparental lineages; the unbroken female and male lineages (mtDNA and NRY). Nevertheless, in specific narrow cases where hypotheses are being tested they can be very illuminating.
For example, here is a question: do the mixed-race populations of the Caribbean…
gregladen | July 23, 2008The phrase "genomic imprinting" has come to refer the turning off of a gene (a particular instance of a gene on a particular chromosome duplicated across the cells in a body) so that the gene is not expressed at all, with the turning off of the gene not caused in the body in question, but rather, during the previous generation by a process happening in the soma of one of the parents. A maternally imprinted gene is passed on to junior, but will not be expressed in junior. a paternally imprinted gene is passed on to junior, but will not be expressed in junior. Typically (as far as we know) a…
pharyngula | July 22, 2008
Epigenetics is the study of heritable traits that are not dependent on the primary sequence of DNA. That's a short, simple definition, and it's also largely unsatisfactory. For one, the inclusion of the word "heritable" excludes some significant players — the differentiation of neurons requires major epigenetic shaping, but these cells have undergone a terminal division and will never divide again — but at the same time, the heritability of traits that aren't defined by the primary sequence is probably the first thing that comes to mind in any discussion of epigenetics. Another problem is…
evolgen | July 21, 2008We all know that Drosophila are the gayest bunch of gays that ever gayed up genetics. This is especially true when you create mutations in fruitless (nee fruity), "the gay gene". Male flies with mutations in fruitless will try to get it on with other males (e.g., doi:10.1016/S0092-8674(00)81802-4). That's gay!
But fruitless is an old school gene that needs to be fucked up to turn the flies gay (doi:10.1093/molbev/msj070; the first author on that paper is, I shit you not, named Gailey). Drosophila really aren't as gay as they are made to appear in the articles describing fruitless mutants.…
razib | July 19, 2008Over the past few days I've blogged a bit about the story about an HIV susceptibility allele; Evolution, a reason for the African HIV epidemic?, Overplaying "AIDS genes" and HIV susceptibility, a "black" thing, not a Duffy thing?. But there's an important post Genetic Future, Duffy-HIV association: an odd choice of ancestry markers:
In the Duffy study the authors attempt to perform this type of correction using a set of just 11 markers they describe as "differentially distributed between European and African populations". p-ter notes that several of these markers are not particularly ancestry…
razib | July 19, 2008Just a quick follow up to my post about genetic screening of embryos and subsequent implantation. The spontaneous abortion rate for humans is very high. Probably on the order of 50% of fertilized ova implant and complete to term. I've seen numbers all over the place. In any case, I assume many of these are chromosomal abnormalities. But I've also posted to data which strongly suggests that immunological incompatibilities between mother & fetus also play a role in spontaneous abortions and may result in natural selection which we're not too well aware of. In The Cooperative Gene the…
razib | July 19, 2008DARC and HIV: a false positive due to population structure?:
The authors are aware of this potential confounder, and develop a measure of admixture based on 11 SNPs to include as a covariate in their regression. However, this measure is kind of weak, which I imagine in the sticking point for the skeptics in the Times article. If you have access to the supplemental information, take a look at it--several of these 11 SNPs are in the same gene, which means they're not independent, and several don't even have big frequency differences between African and European samples (if you're trying to…
razib | July 18, 2008Genetic Future points me to a Nature News story, Making babies: the next 30 years. He highlights this section:
There's speculation that people will have designer babies, but I don't think the data are there to support that. The spectre of people wanting the perfect child is based on a false premise. No single gene predicts blondness or thinness or height or whatever the 'perfect baby' looks like. You might find genetic contributors but there are so many environmental factors too.
The details are important here. Height is a tough cookie; it seems like there are going to at least hundreds of…