genetics
clock | June 30, 2007
Lots of new papers just got published in PLoS-Genetics and PLoS-Computational Biology. Here are a couple of papers that caught my eye:
From Morphology to Neural Information: The Electric Sense of the Skate:
The electric sense appears in a variety of animals, from the shark to the platypus, and it facilitates short-range prey detection where environments limit sight. Typically, hundreds or thousands of sensors work in concert. In skates, rays, and sharks, each electrosensor includes a small, innervated bulb, with a thin, gel-filled canal leading to a surface pore. While experiments have…
pharyngula | June 28, 2007She's fired up the The Sixth International again, and she threatens promises to be at it for a long, long, long time—she bears a longevity mutation, a single nucleotide substitution in the mitochondrial genome associated with some long-lived people. And some people claim there is no such thing as a beneficial mutation…
Anyway, it's personally interesting that it's mitochondrial—that means it is passed down through the maternal line. Since my father's side of the family is grievously short-lived, but my mother's side keeps going for nearly forever, that's good news, if the maternal secret is…
razib | June 28, 2007There's a paper to be published on domestic cat phylogenetics in Science tomorrow. National Geographic has a summary, but Forbes has a more thorough treatment. The short of it is that the maternal lineages (mtDNA) of domestic cats seem derived from the Near Eastern varieties . The acculturation of humanity toward domestic cats seems to have taken place gradually between 12,000 and 3,600 years ago, the presence of five distinct maternal lineages suggests that it wasn't one event, but several simultaneous parallel ones. Sedentary populations rooted around agriculture were the likely…
razib | June 27, 2007John Hawks has the details on a new paper (DOI might not work yet) coming out in PNAS. The researchers trying to reconstruct the Neandertal genome are reporting biases in degradation which is aiding their task. Scientific American has a summary.
razib | June 25, 2007Humans Have Spread Globally, and Evolved Locally (The New York Times):
No one yet knows to what extent natural selection for local conditions may have forced the populations on each continent down different evolutionary tracks. But those tracks could turn out to be somewhat parallel. At least some of the evolutionary changes now emerging have clearly been convergent, meaning that natural selection has made use of the different mutations available in each population to accomplish the same adaptation.
This is the case with lactose tolerance in European and African peoples and with pale skin in…
razib | June 25, 2007On occasion I've decided I'll quickly review some population genetic concepts. These are really "background assumptions," but sometimes comments make it clear that they're not in the "common" background. So to the left you see two normal distributions, assume these are quantitative traits. The x-axis is the trait value, while the y-axis is the frequency of that value within a population. As you might note I've labeled the two populations "generation 1" (g1) and "generation 100" (g100). The implication is that the two distributions represent the "same" population shifted in time.…
razib | June 24, 2007Agnostic translates an Italian interview with mathematical biologist Martin Nowak. Here are my posts read relating to Nowak's work. His book Evolutionary Dynamics is one of the best coffee table books for nerds out there (nice sturdy hard cover and glossy pages with helpful charts to navigate the formalism).
razib | June 24, 2007By now you've probably heard/read about the relationship of HIV resistance and hominoid evolutionary genetics. The original paper in Science that started it off is titled Restriction of an Extinct Retrovirus by the Human TRIM5α Antiviral Protein; quite a mouthful. Lucky for us Carl Zimmer has an excellent exposition as well as a background primer, while John Hawks offers further thoughts looking at the various hypotheses through the lens of someone with a deep grasp of paleoanthropology.
pharyngula | June 23, 2007
The general pattern of developing positional information in Drosophila starts out relatively simply and gets increasingly complicated as time goes by. Initially, there is a very broad distribution of a gradient of a maternal morphogen. That morphogen then triggers the expression of narrower (but still fairly broad) bands of aperiodic gap genes. The next step in this process is to turn on sets of genes in narrow, periodic bands that correspond to body segments. This next set of genes are called the pair-rule genes, because they do something surprising and rather neat: they are turned on in…
clock | June 22, 2007Remember when we discussed the mammal vs. bird survival at Chernobyl the other day? Well, I learned today that someone is about to go and study the humans there as well. I am not exactly sure what kind of reserch it will be, but it will have something to do with the mutations in genomes of the surrounding population.
Sarah Wallace, a senior at Duke University, will be part of the team. And you will be able to follow her adventures and her science on her blog: Notes from Ukraine (MT will not render Cyrillics well so I translated the name of the country)
purepedantry | June 21, 2007Two big studies on genetics came out in the past couple weeks, and I want to talk about both. One of them -- the ENCODE study -- was well covered by the media. The other seems to have slipped through.
Paper #1:
In the ENCODE study, the authors compiled data using a variety of experimental techniques focusing on a small portion (about 1%) of the human genome. There purpose here was to go deep; they wanted to thoroughly catalog in their target area all the transcriptional elements, all the resulting RNA sequences, all the histone and chromatin modifications, and all of the intronic and…
razib | June 19, 2007Go read RPM's post On the Causes of Variation in the Rate of Molecular Evolution.
razib | June 18, 2007Update: John Hawks has more.
Male twins reduce fitness of female co-twins in humans:
Here we investigate the effects of being gestated with a male co-twin for daughter lifetime reproductive success, and the fitness consequences for mothers of producing mixed-sex twins in preindustrial (1734-1888) Finns. We show that daughters born with a male co-twin have reduced lifetime reproductive success compared to those born with a female co-twin. This reduction arises because such daughters have decreased probabilities of marrying as well as reduced fecundity. Mothers who produce opposite-sex twins…
grrlscientist | June 18, 2007tags: blog carnival, genetics
The 9th edition of the new blog carnival, Gene Genie is now available for your reading pleasure. They included a story that I wrote, along with a very nice introduction to it. But there are a lot of other stories that you also will enjoy, so be sure to go there to give them some support!
pharyngula | June 18, 2007There are a couple of small towns on the border between Utah and Arizona that are basically feudal theocracies, ruled by a particularly nasty splinter sect of polygamist Mormons. It's got some truly ugly social consequences — daughters are prizes given away to church leaders, while sons are competitors who are driven away — but now it turns out that there also some biological consequences. The community is deeply inbred, and their prize is the possession of the highest rate of fumarase deficiency in the world, with at least 20 afflicted children in the last 15 years. Fumarase is an enzyme in…
razib | June 18, 2007Nature Reviews Genetics has a short article titled Sociogenetics: Cheating gets you nowhere (free registration). I was intrigued by the title, "Sociogenetics." The Chomskysists always talk about how infinitely flexible language is, and in science the proliferation of fields like "biophysical chemistry" are examples of that range. But a close reading this article shows that "sociogenetics" is just a new sticker on an old field within genetics & evolution:
When food is scarce, solitary D. discoideum cells aggregate into a fruiting body that distributes spores. However, only 75% of the…
razib | June 17, 2007Update: On my other blog I have a post up addressing skeptics in the archaeological community.
A few months ago I posted several times about the Etruscans, the ancient non-Indo-European people of north-central Italy whose provenance has always been a matter of debate. To make it short, genetic data suggests that the ancient Etruscans and some inhabitants of modern Tuscany share a relatively close ancestry with the peoples of the near east, in particular, Turkey. Additionally, an independent line of data from cattle suggests a congruent phylogenetic relationship between the herds of Tuscany…
grrlscientist | June 17, 2007tags: Junkin's warbler, birds, ornithology, DNA technology
An ornithologist prepares to band a mysterious Junkin's warbler.
Image: Sandy Junkin.
With all the skilled birders and ornithologists in North America, it is truly remarkable to find a bird that cannot be identified, especially when that bird was captured in a mist net. After all, when you have a bird in your hand, you have the opportunity to examine its field marks closely.
Enter Dave Junkin. Junkin was the director of Buffalo Audubon's Beaver Meadow Wildlife Sanctuary in Java, and even after his retirement, he is an expert bird…
clock | June 15, 2007
Microarrays have been used in the study of circadian expression of mammalian genes since 2002 and the consensus was built from those studies that approximately 15% of all the genes expressed in a cell are expressed in a circadian manner. I always felt it was more, much more.
I am no molecular biologist, but I have run a few gels in my life. The biggest problem was to find a control gene - one that does not cycle - to make the comparisons to. Actin, which is often used in such studies as control, cycled in our samples. In the end, we settled on one of the subunits of the ribosome as we…
grrlscientist | June 14, 2007tags: human genome, DNA, ENCODE
New research shows that the human genome is much more complex than once thought.
Image: ABC News.
A study was published this week in the journal Nature, revealing that genomes are more complex than previously thought. These studies, which analyzed just 1% of human genome, or DNA code, challenges the view that genes are the primary players in biochemistry. Instead, so-called "junk DNA" and other regions appear to collaborate with each other to form a network that controls gene expression and cell physiology.
ENCODE, short for The Encyclopedia of DNA Elements…