Anthropology.net

Razib found this really fascinating paper which compares differences in gene expression between populations. The results of the study has been published in an open access paper in the American Journal of Human Genetics. The paper is titled, “Evaluation of Genetic Variation Contributing to Differences in Gene Expression between Populations,” and comes from researchers in the University of Chicago and the gene expression company, Affymetrix.

The authors sampled blood from 180 individuals (actually samples were collected from closely related three individuals from 60 different families) and created cell lines from lymphoblastoid cells. The families were either white people from Utah or Yorubans from Nigeria. The cells were lysed and the transcripts were hybridized to microarray chips, which show the expression pattern for lots of genes at once.

How do microarrays work? Well, each chip has microscopic spots loaded with single stranded fragments of one gene. There’s so many spots on each chip that almost all the known genes from the organism of the interest are there. Transcripts, genes that are transcribed and expressed, are single stranded and when they are isolated from cells and washed over microarrays with the little fragments they hybridize or latch onto their complement. The fragments act like anchors since they are bound to the chip. Every time a hybridization event occurs, a florescence reaction also occurs and is picked up by a computerized eye. The amount of transcripts that hybridize can tell us the relative expression level of the gene. The image to your right is an actual scan of a microarray that I’ve put up just so you can see what it looks like. Microarrays aren’t always the best way to compare gene expression differences between populations because SNPs and other allelic differences between genes could affect the hybridization and ultimately the quantification — but there’s really no other high throughput method out there that’s better than this.

Since they were dealing with somewhat differentiated immune system stem cells, the authors limited their results of differences in gene expression they observed. So, it’s not too surprising that they saw big differences between the populations among genes involved in producing antibodies to potential microbial invaders. The unexpected differences were,

“significant differences in expression levels among genes involved in fundamental cellular processes such as ribosomal biogenesis, transfer RNA processing, and Notch-signaling–part of a complex system of communication that governs basic cellular activities and coordinates cell actions.”

Last year we saw the first population comparison of gene expression in the American Journal of Human Genetics paper, “Gene-Expression Variation Within and Among Human Populations,” which found a 17% difference in gene expression between European and African populations. I appreciate this sort of research because our phenotypic differences are not just due to the little differences we harbor in the actual sequence of our DNA but also into the patterns in which genes are expressed or regulated. I’ve said this time and time again, and am happy to see people are continuing to investigate the differences in gene expression between human populations.

STOREY, J. (2007). Gene-Expression Variation Within and Among Human Populations. The American Journal of Human Genetics, 80(3), 502-509. DOI: 10.1086/512017

So there’s this hypotheses that Neandertal extinction was due to cannibalism. This is an alternative but complementary hypothesis to the climate change one. In an upcoming paper in Medical Hypotheses, Simon Underdown investigates this hypotheses by looking at Transmissible Spongiform Encephalopathies (TSEs). The paper is titled, “A potential role for Transmissible Spongiform Encephalopathies in Neanderthal extinction.”

TSEs are also known as prion diseases, a communicable disease where the infectious agent is a malformed protein that replicates by imprinting and transforming other proteins. Most TSEs manifest in the host’s neurological tissues because he or she ate infected nervous tissue. Ultimately, the host’s tissues degenerate and lead to serious problems, most often death. In anthropology, one form of TSEs has been well documented, the spread and eradication of kuru in the Fore from Papua New Guinea.

Before I read the abstract, I assumed Simon looked at Neandertal fossils for paleopathological evidence of spongiform encephalopathies…. at least to some degree. However, the abstract doesn’t definitively indicate whether or not Simon looked into the Neandertal fossil record. Instead, the abstract tells us,

“A modern human hunter-gatherer proxy has been developed and applied as a hypothetical model to the Neanderthals. This hypothesis suggests that the impact of TSEs on the Neanderthals could have been dramatic and have played a large part in contributing to the processes of Neanderthal extinction.”

For those that are curious if there’s evidence of Neandertal cannibalism, you’re in luck. Neandertal cannibalism has been previously documented from remains from sites like Moula-Guercy caves in Ardèche, France, and El Sidrón, Asturias, Spain, so it is totally probable that some got prion diseases. But they were eating each other for 100,000 or so years before the faded out of the picture. You’d think that if they died of prion dieases it wouldn’t take so damn long. Anyways, I just really wonder how Simon went about figuring out if Neandertals really got TSEs.

UNDERDOWN, S. (2008). A potential role for Transmissible Spongiform Encephalopathies in Neanderthal extinction. Medical Hypotheses DOI: 10.1016/j.mehy.2007.12.014