Circular scanning fluorescence correlation spectroscopy on membranes

We discuss circular scanning Fluorescence Correlation Spectroscopy (sFCS) as a simple extension of standard FCS for accurate, robust and fast diffusion measurements on membranes. The implementation is based on a straightforward conversion of a conventional FCS instrument to a sFCS device by mounting a mirror onto a two-axis piezo scanner. The measurement volume is scanned in a circle with sub-micron radius, allowing the determination of diffusion coefficients and concentrations without any a priori knowledge of the size of the detection volume. This is highly important in measurements on two-dimensional surfaces, where the volume size, and therefore the quantitative outcome of the experiment, is determined by the relative position of the surface and the objective focus, a parameter difficult to control in practice. The technique is applied to diffusion measurements on model membrane systems: supported lipid bilayers and giant unilamellar vesicles. We show that the method is insensitive to membrane positioning and to disturbing processes on faster or slower time scales than diffusion, and yields accurate results even for fluctuating or drifting membranes. Its robustness, short measurement times, and small size of the probed area makes this technique particularly attractive for analyzing the properties of membranes and molecules diffusing and interacting within them. (C) 2011 Optical Society of Americ

The Y-chromosome C3* star-cluster attributed to Genghis Khan\u27s descendants is present at high frequency in the Kerey clan from Kazakhstan

In order to verify the possibility that the Y-chromosome C3* star-cluster attributed to Genghis Khan and his patrilineal descendants is relatively frequent in the Kereys, who are the dominant clan in Kazakhstan and in Central Asia as a whole, polymorphism of the Y-chromosome was studied in Kazakhs, represented mostly by members of the Kerey clan. The Kereys showed the highest frequency (76.5%) of individuals carrying the Y-chromosome variant known as C3* star-cluster ascribed to the descendants of Genghis Khan. C3* star-cluster haplotypes were found in two sub-clans, Abakh-Kereys and Ashmaily-Kereys, diverged about 20-22 generations ago according to the historical data. Median network of the Kerey star-cluster haplotypes at 17 STR loci displays a bipartite structure, with two subclusters defined by the only difference at DYS448 locus. It is noteworthy that there is a strong correspondence of these subclusters with the Kerey sub-clans affiliation. The data obtained suggest that the Kerey clan appears to be the largest known clan in the world descending from a common Y-chromosome ancestor. Possible ways of Genghis Khan‟s relation to the Kereys are discussed

Polymorphism of the cold receptor gene TRPM8 in native populations of Siberia: putative selective role of rs11563208 polymorphism in Northeast Asia

The TRPM8 gene encodes the cold-activated receptor TRPM8, which has an important role in cold adaptation as well as in metabolic and immune responses. Previously, it has been found that polymorphic variants of the TRPM8 gene, which are present in human populations, are associated with different cold sensitivity. In the present study we have investigated variability of all exons and adjacent intronic sequences of this gene in samples of native populations of Siberia, including regional groups from Northeastern, Central, Southern and Western parts of Siberia. In 9 out of 21 variable loci revealed, the frequency of the derived alleles accounts for more than 10 % (loci rs28901637, rs11562975, rs10929319, rs28901644, rs7593557, rs12185590, rs10171428, rs11563208, and rs11563071). Different variants of these polymorphic loci, which are most frequent in native Siberians, generate 26 haplotypes. In addition to 7 haplotypes shared by all regional groups and present there at frequencies of 2–28 %, unique haplotypes were found in all regional samples. One of them characterized by derived allele T at rs11563208 locus is very interesting because it is spread at the frequency of 14 % only in Northeast Asia (in Koryaks and Chukchi). A synonymous substitution at rs11563208 locus may have a functional role because the amino acid residue (isoleucine at position 1016 of TRPM8 protein) corresponding to this locus is located in functionally important TRP-domain and, hence, it can influence thermoreception processes. It is assumed that the appearance of the haplotype carrying the rs11563208-T allele may be due to the necessity to counteract the inhibition of TRPM8 receptors by polyunsaturated fatty acids, which are typical of the traditional diet of native people of Northeast Asia (Siberian Eskimo, Chukchi and Koryaks)

Evaluating the role of selection in the evolution of mitochondrial genomes of aboriginal peoples of Siberia

Studies of the nature of mitochondrial DNA (mtDNA) variability in human populations have shown that protein­coding genes are under negative (purifying) selection, since their mutation spectra are characterized by a pro­ nounced predominance of synonymous substitutions over non­synonymous ones (Ka/Ks < 1). Meanwhile, a number of studies have shown that the adaptation of populations to various environmental conditions may be accompanied by a relaxation of negative selection in some mtDNA genes. For example, it was previously found that in Arctic populations, negative selection is relaxed in the mitochondrial ATP6 gene, which encodes one of the subunits of ATP synthase. In this work, we performed a Ka/Ks analysis of mitochondrial genes in large samples of three regional population groups in Eurasia: Siberia (N = 803), Western Asia/Transcaucasia (N = 753), and Eastern Europe (N = 707). The main goal of this work is to search for traces of adaptive evolution in the mtDNA genes of aboriginal peoples of Siberia represented by populations of the north (Koryaks, Evens) and the south of Siberia and the adjacent territory of Northeast China (Bu­ryats, Barghuts, Khamnigans). Using standard Ka/Ks analysis, it was found that all mtDNA genes in all studied regional population groups are subject to negative selection. The highest Ka/Ks values in different regional samples were found in almost the same set of genes encoding subunits of ATP synthase (ATP6, ATP8), NADH dehydrogenase complex (ND1, ND2, ND3), and cytochrome bc1 complex (CYB). The highest Ka/Ks value, indicating a relaxation of negative selection, was found in the ATP6 gene in the Siberian group. The results of the analysis performed using the FUBAR method (HyPhy software package) and aimed at searching for mtDNA codons under the influence of selection also showed the predominance of negative selection over positive selection in all population groups. In Siberian populations, nucleotide sites that are under positive selection and associated with mtDNA haplogroups were registered not in the north (which is expected under the assumption of adaptive evolution of mtDNA), but in the south of Siberia

Polymorphism of the trehalase gene (TREH) in native populations of Siberia

Deficiency of some carbohydrates in the traditional diet of native populations of the Far North contributed to a high population prevalence of inactive variants of genes encoding, for example, amylase (AMY2A gene) and sucrase­isomaltase (SI gene). Trehalose, which is found in algae, higher fungi, lichens and some higher plants, is another of the disaccharides, poorly digested by native people of the Far North. Here, in native populations of Siberia, we studied the polymorphism of the TREH gene, which encodes trehalase, an enzyme that cleaves trehalose. The analysis of exome polymorphism showed the presence of seven haplotypes of the TREH gene in the population. Three of them are determined by the variant rs2276064­A, which is associated with the lowest activity of trehalase. The maximum frequency of this group of haplotypes is observed in the samples of native populations of Northeast Asia (about 60 %), in the remaining samples of the Siberian populations, its frequency is 30–40 %. Thus, the high frequency of variant rs2276064­A, associated with a low­activity trehalase, explains why Northern aboriginal peoples avoid food containing trehalose. It is assumed that the increase in the frequency of this variant in the populations of Northeast Asia can have been facilitated by gene drift acting in populations of a small effective size. However, it is possible that artificially induced trehalose deficiency in the traditional diet of the indigenous peoples of the Far North (due to the tradition of rejecting fungi) could also cause an increase in the frequency of low­activity trehalase, provided that this tradition has been existing among Northern aboriginal peoples for many generations

The Peopling of Europe from the Mitochondrial Haplogroup U5 Perspective

It is generally accepted that the most ancient European mitochondrial haplogroup, U5, has evolved essentially in Europe. To resolve the phylogeny of this haplogroup, we completely sequenced 113 mitochondrial genomes (79 U5a and 34 U5b) of central and eastern Europeans (Czechs, Slovaks, Poles, Russians and Belorussians), and reconstructed a detailed phylogenetic tree, that incorporates previously published data. Molecular dating suggests that the coalescence time estimate for the U5 is ∼25–30 thousand years (ky), and ∼16–20 and ∼20–24 ky for its subhaplogroups U5a and U5b, respectively. Phylogeographic analysis reveals that expansions of U5 subclusters started earlier in central and southern Europe, than in eastern Europe. In addition, during the Last Glacial Maximum central Europe (probably, the Carpathian Basin) apparently represented the area of intermingling between human flows from refugial zones in the Balkans, the Mediterranean coastline and the Pyrenees. Age estimations amounting for many U5 subclusters in eastern Europeans to ∼15 ky ago and less are consistent with the view that during the Ice Age eastern Europe was an inhospitable place for modern humans

Mitogenomic diversity in Tatars from the Volga-Ural region of Russia

To investigate diversity of mitochondrial gene pool of Tatars inhabiting the territory of the middle Volga River basin, 197 individuals from two populations representing Kazan Tatars and Mishars were subjected for analysis of mitochondrial DNA (mtDNA) control region variation. In addition, 73 mitochondrial genomes of individuals from Mishar population were sequenced completely. It was found that mitochondrial gene pool of the Volga Tatars consists of two parts, but western Eurasian component prevails considerably (84% on average) over eastern Asian one (16%). Eastern Asian mtDNAs detected in Tatars belonged to a heterogeneous set of haplogroups (A, C, D, G, M7, M10, N9a, Y, and Z), although only haplogroups A and D were revealed simultaneously in both populations. Complete mtDNA variation study revealed that the age of western Eurasian haplogroups (such as U4, HV0a, and H) is less than 18,000 years, thus suggesting re-expansion of eastern Europeans soon after the Last Glacial Maximum. © 2010 The Author

Origin and Post-Glacial Dispersal of Mitochondrial DNA Haplogroups C and D in Northern Asia

More than a half of the northern Asian pool of human mitochondrial DNA (mtDNA) is fragmented into a number of subclades of haplogroups C and D, two of the most frequent haplogroups throughout northern, eastern, central Asia and America. While there has been considerable recent progress in studying mitochondrial variation in eastern Asia and America at the complete genome resolution, little comparable data is available for regions such as southern Siberia – the area where most of northern Asian haplogroups, including C and D, likely diversified. This gap in our knowledge causes a serious barrier for progress in understanding the demographic pre-history of northern Eurasia in general. Here we describe the phylogeography of haplogroups C and D in the populations of northern and eastern Asia. We have analyzed 770 samples from haplogroups C and D (174 and 596, respectively) at high resolution, including 182 novel complete mtDNA sequences representing haplogroups C and D (83 and 99, respectively). The present-day variation of haplogroups C and D suggests that these mtDNA clades expanded before the Last Glacial Maximum (LGM), with their oldest lineages being present in the eastern Asia. Unlike in eastern Asia, most of the northern Asian variants of haplogroups C and D began the expansion after the LGM, thus pointing to post-glacial re-colonization of northern Asia. Our results show that both haplogroups were involved in migrations, from eastern Asia and southern Siberia to eastern and northeastern Europe, likely during the middle Holocene