SummaryWe have examined the patterns of DNA sequence variation in and around the genes coding for ICAM1 and TNF, which play functional and correlated roles in inflammatory processes and immune cell responses, in 12 diverse ethnic groups of India. We aimed to (a) quantify the nature and extent of the variation, and (b) analyse the observed patterns of variation in relation to population history and ethnic background. At the ICAM1 and TNF loci, respectively, the total numbers of SNPs that were detected were 28 and 12. Many of these SNPs are not shared across ethnic groups and are unreported in the dbSNP or TSC databases, including two fairly common non-synonymous SNPs at positions 13487 and 13542 in the ICAM1 gene. Conversely, the TNF-376A SNP that is reported to be associated with susceptibility to malaria was not found in our study populations, even though some of the populations inhabit malaria endemic areas. Wide between-population variation in the frequencies of shared SNPs and coefficients of linkage disequilibrium have been observed. These findings have profound implications in case-control association studies.
We have studied DNA sequence variation in and around the genes ICAM1 and TNF, which play functional and correlated roles in inflammatory processes and immune cell responses, in 12 diverse ethnic groups of India, with a view to investigating the relative roles of demographic history and natural selection in shaping the observed patterns of variation. The total numbers of single nucleotide polymorphisms (SNPs) detected at the ICAM1 and TNF loci were 29 and 12, respectively. Haplotype and allele frequencies differed significantly across populations. The site frequency spectra at these loci were significantly different from those expected under neutrality, and showed an excess of intermediate-frequency variants consistent with balancing selection. However, as expected under balancing selection, there was no significant reduction of F S T values compared to neutral autosomal loci. Mismatch distributions were consistent with population expansion for both loci. On the other hand, the phylogenetic network among haplotypes for the TNF locus was similar to expectations under population expansion, while that for the ICAM1 was as expected under balancing selection. Nucleotide diversity at the ICAM1 locus was an order of magnitude lower in the promoter region, compared to the introns or exons, but no such difference was noted for the TNF gene. Thus, we conclude that the pattern of nucleotide variation in these genes has been modulated by both demographic history and selection. This is not surprising in view of the known allelic associations of several polymorphisms in these genes with various diseases, both infectious and noninfectious.[Sengupta S., Farheen S., Mukherjee N. and Majumder P. P. 2007 Patterns of nucleotide sequence variation in ICAM1 and TNF genes in twelve ethnic groups of India: roles of demographic history and natural selection. J. Genet. 86,[225][226][227][228][229][230][231][232][233][234][235][236][237][238][239]
The influence of the Sn(II) ion on the formation and morphology of an arachidic acid (AA) monolayer was investigated using Langmuir film formation technology, pressure−area (Π−A) isotherm measurements, and Brewster angle microscopy (BAM). Our findings indicate that AA Langmuir monolayers exhibit organization that depends on subphase pH and Sn 2+ concentration. There are multiple equilibria that are relevant to the complexation of AA monolayers, and the balance of Sn(OH) n equilibria and Sn(AA) n equilibria gives rise to unusual monolayer structural effects. With Sn 2+ in the subphase, the AA monolayer exhibits an isotherm characterized by the absence of a collapse point and with a pH-dependent change in isotherm shape not consistent with the formation of an ordered solid phase. The amphiphile headgroup equilibrium mediates the absence of collapse seen experimentally and the ability of the monolayer to retain organization at a surface pressure of ca. 70 mN/m. BAM images show that the morphology of the monolayer depends on the Sn 2+ concentration, consistent with several species of Sn(AA) n , where n = 1, 2, or 3, contributing to the overall monolayer order.
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