genetics
pharyngula | September 17, 2007
The Hox genes are a set of transcription factors that exhibit an unusual property: they provide a glimpse of one way that gene expression is translated into metazoan morphology. For the most part, the genome seems to be a welter of various genes scattered about almost randomly, with no order present in their arrangement on a chromosome — the order only becomes apparent in their expression through the process of development. The Hox genes, on the other hand, seem like an island of comprehensible structure. These are all genes that specify segment identity — whether a segment of the embryo…
grrlscientist | September 17, 2007tags: researchblogging.org, salmon, trout, spawning, molecular biology, cloning, conservation, endangered species
A trout germ cell is transplanted into the body cavity of a newly hatched salmon embryo. This is part of the process that allowed adult salmon to successfully spawn trout offspring.
Image: Science magazine
Have you ever heard of a trout with salmon for parents? Since when has one species given birth to another species? Well, ever since scientists began experimenting with salmon in the hope that they could genetically alter these fish by injecting sex cells from trout so the…
razib | September 17, 2007A genome-wide association study of global gene expression:
We found that 15,084 transcripts (28%) representing 6,660 genes had narrow-sense heritabilities (H2) > 0.3. We executed genome-wide association scans for these traits and found peak lod scores between 3.68 and 59.1. The most highly heritable traits were markedly enriched in Gene Ontology descriptors for response to unfolded protein (chaperonins and heat shock proteins), regulation of progression through the cell cycle, RNA processing, DNA repair, immune responses and apoptosis. SNPs that regulate expression of these genes are…
razib | September 16, 2007Over at my other blog p-ter has a nice post with a few links to databases where you can do your own querying for SNPs & sniffing for selection.
razib | September 16, 2007Do you smell what I smell? Perhaps not, and it might not be due to a cold...Genetic variation in a human odorant receptor alters odour perception (Nature):
Human olfactory perception differs enormously between individuals, with large reported perceptual variations in the intensity and pleasantness of a given odour...A common variant of this receptor (OR7D4 WM) contains two non-synonymous single nucleotide polymorphisms (SNPs), resulting in two amino acid substitutions (R88W, T133M; hence 'RT') that severely impair function in vitro. Human subjects with RT/WM or WM/WM genotypes as a group…
pharyngula | September 16, 2007Greg Laden has an excellent article on the genetics and evolution of race — basically, it's an irrelevant pairing of concepts.
"Eat your heart out, Philip Rushton," indeed.
razib | September 15, 2007Olivia Judson's piece The Selfless Gene in The Atlantic is a pretty good survey of the various theories of the evolution of altruism. If you read Narrow Roads of Gene Land or Natural Selection and Social Theory, nothing new, but if you aren't familiar with the lay of the land it's worth checking out. But you can't find it free online, so you'll have to get a subscription to The Atlantic or run out to the book store and sneak a peak.
razib | September 14, 2007About a week ago I posted on a new paper about worldwide variation on a gene which results in differences in muscle fiber. The author left a comment, which I'll reproduce below:
We thought about selection for cold tolerance, but our latest data on global distribution of the null allele don't really fit with that. Most likely it's something to do with famine resistance, although we're not ruling out the idea that it's selection for some sort of muscle performance phenotype (it's surprising how many muscle genes are popping up in recent genome-wide scans for selection).
We haven't got genotype…
razib | September 11, 2007Foetal testosterone linked to autistic traits:
This latest update on their progress, presented by Simon Baron-Cohen and Bonnie Auyeung at the British Association's Festival of Science in York today, shows that the correlation between foetal hormone levels and autistic-trait behaviour continues as the children grow up.
...Baby boys produce more testosterone in the womb, which means they can also expose a non-identical female twin to higher levels of the hormone. But other genetic and environmental factors are thought to also play a role.
This is of course part of Simon Baron-Cohen's research…
razib | September 10, 2007Loss of ACTN3 gene function alters mouse muscle metabolism and shows evidence of positive selection in humans:
More than a billion humans worldwide are predicted to be completely deficient in the fast skeletal muscle fiber protein α-actinin-3 owing to homozygosity for a premature stop codon polymorphism, R577X, in the ACTN3 gene. The R577X polymorphism is associated with elite athlete status and human muscle performance, suggesting that α-actinin-3 deficiency influences the function of fast muscle fibers. Here we show that loss of α-actinin-3 expression in a knockout mouse model results in a…
razib | September 10, 2007I've been bandying a particular hypothesis about lately in terms of human evolution: strong recent selection for adaptive alleles will result in a fitness drag due to pleiotropic effects. In short, I'm working with the assumption that a new mutant which has significant positive benefits because of a phenotypic change is also liable to foul up other functional pathways. Sickle cell as an adaptation to malaria is a classic case of this; the fitness benefits of heterozygosity are great enough to outweigh the drag of a proportion of anemic homozygotes (this is a case of balancing selection via…
grrlscientist | September 10, 2007tags: genetics, blog carnivals
The 18th edition of Mendel's Garden is now available for your reading pleasure. This blog carnival devoted to genetics, featuring some of the best science blogging focused on genetics, from the past month. They included a story that I wrote, so be sure to check it out.
evolgen | September 10, 2007Mendel's Garden is the original blog carnival devoted to genetics. A new carnival is traditionally posted on the first Sunday of the month (although the date is somewhat flexible). The newest edition of Mendel's Garden has been posted at balancing life.
Sandy at Discovering Biology in a Digital World will be hosting the next edition. If you would like to submit a post, visit the blog carnival submission page. If you would like to host a future edition, email me (evolgen--at--yahoo--dot--com) or leave on a comment on this post.
sporte | September 9, 2007If you haven't, then hustle over to Mendel's Garden for a wonderful story about the monk and his life as a scientist, check out Gene Genie for best drawing of Craig Venter that I've ever seen; and if you're into computers, take a good long look at the lightning edition of Bio::blogs. I've visited them all out myself and I assure you, they're all a good time and chock full of fun links.
razib | September 9, 2007Diet and the evolution of human amylase gene copy number variation:
...We found that copy number of the salivary amylase gene (AMY1) is correlated positively with salivary amylase protein level and that individuals from populations with high-starch diets have, on average, more AMY1 copies than those with traditionally low-starch diets. Comparisons with other loci in a subset of these populations suggest that the extent of AMY1 copy number differentiation is highly unusual. This example of positive selection on a copy number-variable gene is, to our knowledge, one of the first discovered in…
pharyngula | September 8, 2007I got some email today with lots of constructive suggestions (See? Not all my email is evil!) for how we ought to change the education of biology students — such as by giving them a foundation in the history and philosophy of our science, using creationist arguments as bad examples so the students can see the errors for themselves, etc. — and it was absolutely brilliant, even the parts where he disagreed with some things I'd written before. Best email ever!
Of course, what helped is that I spent my summer "vacation" putting together a new freshman first semester course for biology majors that…
razib | September 7, 2007Over at my other blog I reaffirm Richard Dawkins' criticism of Freeman Dyson's off the cuff opinions about evolutionary genetics. Dyson is basically asserting that the rate of evolution is inversely proportional to the square root of population size. In short, small populations evolve fast in his mind because of stochastic fluctuations, clearly drift. I've posted a fair amount about stochastic dynamics...and it's complicated. Science is complicated. That's just life.
Now, Dyson is pretty much wrong. But his intuition is conventional; I've met many people who believe that somehow…
razib | September 7, 2007Over at my other blog I have an exposition of a set of ideas which have crystallized in my mind in regards to the patterns of human physical variation that we see around us in the world today. A reconsideration of some concepts was triggered in large part by the material I covered in the post about South Asian skin color. Over the next few months I hope to flesh out a precise and clear verbal outline of what I believe to be the general trends in human evolution over the past 50,000 years. In terms of formal/mathematical representations I know of what I speak, but translating the ideas into…
razib | September 6, 2007Why are brown people so many shades of brown? If you were raised in a South Asian family I'm sure that you've had to deal with the "color" issue somehow. This isn't a cultural blog, so I'm not going to go there, but I do think that the salience of complexion in South Asian culture makes this new paper, A genome-wide association study of skin pigmentation in a South Asian population (PDF), of more than passing interest. If you plotted a frequency distribution of skin reflectances of South Asians within 2 standard deviations from the median you would see a range from brunette white from…
razib | September 6, 2007A few days ago I posted on a gene, HMGA2, which seems to be implicated in a small proportion of the normal human variation in height. There seems to be an SNP which comes in two flavors which results in a different in height in an additive & independent manner. A friend of mine pointed out that this SNP exhibits different frequencies in different populations. The "short" allele, which tends to have an average effect of decreasing the expectation in height, is the derived form. That is, it is a newer mutant in relation to the ancestral "tall" allele. Second, it seems that it is extant…