genetics
razib | September 17, 2008Lactase persistence-related genetic variant: population substructure and health outcomes:
Lactase persistence is an autosomal-dominant trait that is common in European-derived populations. A basic tendency for lactase persistence to increase from the southeast to the northwest across European populations has been noted, but such trends within countries have not been extensively studied. We genotyped the C/T-13910 variant (rs4988235) that constitutes the putatively causal allele for lactase persistence (T allele representing persistence) in a general population sample of 3344 women aged 60-79…
razib | September 15, 2008A few months ago I reviewed David Goldstein's Jacob's Legacy, a geneticists look at the history of the Jewish people. Today The New York Times has a piece, A Dissenting Voice as the Genome Is Sifted to Fight Disease, which profiles Goldstein and uses his own positions and opinions as a jumping off point into many diverse topics. First, he suggests that the common disease-common variant hypothesis has been falsified. Or, more pragmatically it has not returned great results which may be applied by medical researchers in the quest for treatments and diagnoses of susceptibilities. Goldstein…
edyong | September 15, 2008We like to idolise fearlessness and we equate it to bravery but there is a fine line between that and stupidity. Immunity to the pangs of fear would leave someone unable to assess threats to themselves and to other people, which means that fear not only has consequences for an individual but for their entire social circle. Guillaume Martel and colleagues from Rutgers University demonstrated these far-reaching consequences by examining a special group of mice which had been genetically engineered to be fearless.
Martel's team focused their attention on the amygdalae, a pair of almond-shaped…
razib | September 14, 2008Population substructure in Finland and Sweden revealed by the use of spatial coordinates and a small number of unlinked autosomal SNPs:
We genotyped 34 unlinked autosomal single nucleotide polymorphisms (SNPs), originally designed for zygosity testing, from 2044 samples from Sweden and 657 samples from Finland, and 30 short tandem repeats (STRs) from 465 Finnish samples. We saw significant population structure within Finland but not between the countries or within Sweden, and isolation by distance within Finland and between the countries. In Sweden, we found a deficit of heterozygotes that we…
razib | September 13, 2008I've mentioned MHC before; they're interesting from an evolutionary perspective because they're one of the most polymorphic loci in humans, likely due to their role in disease resistance and the "diversified portfolio" strategy which seems optimal over the long term (kind of like sex). The logic is pretty simple, pathogens are good at adapting because there are so many who replicate so fast so they figure out ways to get around common defensive strategies before a few host generations have come to pass. This increases the fitness of the rare alleles in the hosts, until they become not-so-…
grrlscientist | September 12, 2008tags: Bovine spongiform encephalopathy, BSE, mad cow disease, Creutzfeldt-Jakob Disease, CJD, pathogenic mutation, prion protein gene
Image: Orphaned.
Mad Cow Disease, technically known as Bovine Spongiform Encephalopathy (BSE), is one of a group of transmissible diseases that destroy brain tissue, collectively known as Transmissible Spongiform Encephalopathies (TSEs). TSEs are an unknown agent(s) that act by damaging the structure of brain proteins known as "prions" (PREE ons). In turn, these damaged prion proteins damage other normal prions and together, they build up to collectively…
mikethemadbiologist | September 12, 2008New data show that antibiotic resistance genes travel together, at least in E. coli isolated from farms. Lookee, a picture:
(click to embiggen)
These are the major types of antibiotics. Anytime you see a "+", that means that a gene that provides resistance to some or all of the antibiotic in that class*. For example, the second "+" in the first column means that E. coli with a tetracycline resistance gene are more likely than those without a tetracycline resistance gene to also have an aminoglycoside resistance gene. And by more likely, it's usually five to fifty times more likely.
When…
razib | September 8, 2008The 90% rate of abortion upon prenatal discovery that a fetus likely has Down Syndrome is being quoted a lot today. Is it true? Seems like it. Termination rates after prenatal diagnosis of Down syndrome, spina bifida, anencephaly, and Turner and Klinefelter syndromes: a systematic literature review:
...Termination rates varied across conditions. They were highest following a prenatal diagnosis of Down syndrome (92 per cent; CI: 91 per cent to 93 per cent) and lowest following diagnosis of Klinefelter syndrome (58 per cent; CI: 50 per cent to 66 per cent). Where comparisons could be made,…
razib | September 8, 2008Is a personal genome sequence worth $350,000?:
Basically, we're currently at a stage where costs are dropping much faster than the rate at which the value of genetic information is increasing - in other words, you and I will be able to afford a genome sequence long before science will be able to tell us much about what it really means. However, the beauty of a genome sequence is that (unlike 23andMe-style chips, which are constantly being replaced by higher-resolution models) it never becomes obsolete. Once you have your entire sequence sitting on your hard drive you can simply sit back and…
razib | September 6, 2008Earlier this week I posted a link to new research on the genomics of Mexican populations and the impact of selective evolutionary pressures within the last 500 years. I also pointed to the fact that despite Argentina's self-conception as a European settler nation, a non-trivial Amerindian ancestral proportion remains detectable. Puerto Rico is another interesting case; new research strongly suggests that Taino ancestry exists among the modern peoples of the island, contrary to the assumption by many scholars that they disappeared within the first generation of European settlement.
Today I…
clock | September 6, 2008Jonathan describes, step by step.
I wonder if there are any palindromic sequences to be found?
razib | September 5, 2008Language Log has an excellent critique of the media stories around AVPR1a and its effect on male behavior. This sort of media criticism is warranted, but I don't know exactly how headline writing will clearly communicate that a given dependent variable might have myriad independent variables. Huntington's disease was easy to write a headline for; trying to juice up a story about genes which explain 0.3% of the variation in height is going to be a taller order....
razib | September 4, 2008Genome-wide distribution of ancestry in Mexican Americans:
Migrations to the new world brought together individuals from Europe, Africa and the Americans. Inter-mating between these migrant and indigenous populations led to the subsequent formation of new admixed populations, such as African and Latino Americans. These unprecedented events brought together genomes that had evolved independently on different continents for tens of thousands of years and presented new environmental challenges for the indigenous and migrant populations, as well as their offspring. These circumstances provided…
edyong | September 4, 2008The image on the right is both beautiful and exciting. Let me explain why. It's the paw of an embryonic mouse and a team of geneticists have inserted a fragment of human DNA into its cells. The fragment contains an "enhancer" element, a short span of DNA that switches other genes on and off; in this case, they put the enhancer in control of a gene whose activity creates a blue chemical.
This particular enhancer is called HACNS1. Throughout the course of animal evolution, its sequence has gone relatively unchanged in almost all back-boned animals, but it has evolved rapidly in the human…
mikethemadbiologist | September 4, 2008A recent paper examined if use of the antibiotic cotrimoxazole was correlated with resistance in three different bacterial pathogens, Streptococcus pneumoniae, Haemophilus influenzae, and Moraxella catarrhalis. To quickly summarize, in one species, S. pneumoniae, resistance was correlated with use, whereas it was not for the other two species. While the study is fine for what it is, it inadvertently highlights a problem most surveillance systems have:
they don't incorporate genetic information.
Without genotypic information, we don't really know what happened. Is the correlation spurious,…
razib | September 3, 2008Years before Genetic Future, there was Future Pundit. If you haven't checked out, I think you should. Yes, the title is cheesy, but so what?
razib | September 3, 2008Since I pointed to a blog geared toward reviewing technologies which serve to benefit the perpetuation of the white European hegemony yesterday, I thought I should make it known that you should check out Not Exactly Rocket Science. Dawg has been bringing his game.
razib | September 2, 2008The post below on AVPR1A and fidelity alluded to the fact that this locus has been implicated in many other behavioral traits. I spent some of today digging through the literature. So check it....
AVPR1a and SLC6A4 Gene Polymorphisms Are Associated with Creative Dance Performance
AVPR1A and OXTR polymorphisms are associated with sexual and reproductive behavioral phenotypes in humans
Link Between Vasopressin Receptor AVPR1A Promoter Region Microsatellites and Measures of Social Behavior in Humans
Association between a vasopressin receptor AVPR1A promoter region microsatellite and eating…
razib | September 2, 2008Commentary has a long piece, Jews and Their DNA, which covers the recent findings coming out of genetics in regards to the "Who is a Jew" question. It's a fair summary of the field, though I would note that the author relied heavily on uniparental lineages passed purely through males and females, and that autosomal studies which look at total genome content are now coming to the fore and fleshing out the picture. I suspect that the main result that will come out of these findings is that many, many, groups are going to be unhappy. Some will find that Jewish ancestry is admixed and that…
razib | September 2, 2008Over the years I've blogged a fair amount on the AVPR1A gene. Variation on this locus has been associated with differences altruism in humans and mating preferences in voles. Now a new paper is out in PNAS, at some point in the near future (not online, but will be here), which shows differences in martial behavior based on AVPR1A. From Study Links Gene Variant in Men to Marital Discord:
About 40 percent of men have one or two copies of the allele. Walum, a PhD student, said that men with two copies of the allele had a greater risk of marital discord than men with one copy, and that men with…