Genetic variation in South Indian castes: evidence from Y-chromosome, mitochondrial, and autosomal polymorphisms

Background

Major population movements, social structure, and caste endogamy have influenced the genetic structure of Indian populations. An understanding of these influences is increasingly important as gene mapping and case-control studies are initiated in South Indian populations.

Results

We report new data on 155 individuals from four Tamil caste populations of South India and perform comparative analyses with caste populations from the neighboring state of Andhra Pradesh. Genetic differentiation among Tamil castes is low (R_ST = 0.96% for 45 autosomal short tandem repeat (STR) markers), reflecting a largely common origin. Nonetheless, caste- and continent-specific patterns are evident. For 32 lineage-defining Y-chromosome SNPs, Tamil castes show higher affinity to Europeans than to eastern Asians, and genetic distance estimates to the Europeans are ordered by caste rank. For 32 lineage-defining mitochondrial SNPs and hypervariable sequence (HVS) 1, Tamil castes have higher affinity to eastern Asians than to Europeans. For 45 autosomal STRs, upper and middle rank castes show higher affinity to Europeans than do lower rank castes from either Tamil Nadu or Andhra Pradesh. Local between-caste variation (Tamil Nadu R_ST = 0.96%, Andhra Pradesh R_ST = 0.77%) exceeds the estimate of variation between these geographically separated groups (R_ST = 0.12%). Low, but statistically significant, correlations between caste rank distance and genetic distance are demonstrated for Tamil castes using Y-chromosome, mtDNA, and autosomal data.

Conclusion

Genetic data from Y-chromosome, mtDNA, and autosomal STRs are in accord with historical accounts of northwest to southeast population movements in India. The influence of ancient and historical population movements and caste social structure can be detected and replicated in South Indian caste populations from two different geographic regions.     

The rarity concept and the commonness of rarity in freshwater zooplankton

1. Regional distribution, frequency of occurrence and relative abundance were scored in 2467 Norwegian lakes for all the recorded 130 species of crustacean zooplankton. The majority of species were rare in the sense that 65% of species were recorded in fewer than 10% of localities. Only six species were recorded in more than 50% of localities, and the median number of species in a given locality was 14 (i.e. 10% of the total species pool). 2. Abundances of all species were scored according to the fraction of lakes in which they were recorded, their geographical range of distribution, and their numerical abundance. Typically the most rare species were rare by all three criteria, and vice versa for the common species, pointing to rarity as an inherent property of some species. For some species this rarity reflects being on the edge of their distributional range, while for others rarity seems to be a consequence of their life cycle strategies. 3. Some of the truly rare species have high dispersal rates and high colonization abilities, but are rapidly replaced by other species. Others are confined to specific habitats, often highly eutrophic, pointing to highly specialized niche adaptations. 4. A major cause for the few truly common species seems to be the limited number of species that are able to coexist within a given locality, reflecting ‘the ghost of competition past’ and predation pressure. 5. While species composition and species richness may reflect colonization abilities and stochastic events, the presence or absence of species is not only a random lottery but also a consequence of species‐specific attributes.     

Inhibitors of advanced glycation end product-associated protein cross-linking

The reaction of lens proteins with sugars over time results in the formation of protein-bound advanced glycation end products (AGEs). The most damaging element of AGE formation may be the synthesis of protein-protein cross-links in long-lived proteins, such as collagen or lens crystallins. A quantitative cross-linking assay, involving the sugar-dependent incorporation of [U-(14)C]lysine into protein, was employed to determine the efficacy of a variety of potential cross-linking inhibitors. Reaction mixtures contained 5.0 mM L-threose, 2.5 microCi [(14)C]lysine (1.0 mCi/mmole), 5.0 mg/ml bovine lens proteins, 0-10 mM inhibitor and 1.0 mM DTPA in 100 mM phosphate buffer, pH 7.0. Of 17 potential inhibitors tested, 11 showed 50% inhibition or less at 10 mM. The dicarbonyl-reactive compounds 2-aminoguanidine, semicarbazide and o-phenylenediamine inhibited 50% at 2.0 mM, whereas 10 mM dimethylguanidine had no effect. Several amino acids failed to compete effectively with [(14)C]lysine in the cross-linking assay; however, cysteine inhibited 50% at 1.0 mM. This was likely due to the sulfhydryl group of cysteine, because 3-mercaptopropionic acid and reduced glutathione exhibited similar activity. Sodium metabisulfite had the highest activity, inhibiting 50% at only 0.1-0.2 mM. Protein dimer formation, as determined by SDS-PAGE, was inhibited in a quantitatively similar manner. The dicarbonyl-reactive inhibitors and the sulfur-containing compounds produced similar inhibition curves for [(14)C]lysine incorporation over a 3 week assay with 250 mM glucose. A much lesser effect was observed on either the incorporation of [(14)C]glucose, or on fluorophore formation (360/420 nm), suggesting that non-cross-link fluorophores were also formed. The inhibitor data were consistent with cross-linking by a dicarbonyl intermediate. This was supported by the fact that the inhibitors were uniformly less effective when the 5.0 mM threose was replaced by either 3.0 mM 3-deoxythreosone or 3.0 mM threosone.     

2-ammonio-6-(3-oxidopyridinium-1-yl)hexanoate (OP-lysine) is a newly identified advanced glycation end product in cataractous and aged human lenses

Post-translational modifications of proteins take place during the aging of human lens. The present study describes a newly isolated glycation product of lysine, which was found in the human lens. Cataractous and aged human lenses were hydrolyzed and fractionated using reverse-phase and ion-exchange high performance liquid chromatography (HPLC). One of the nonproteinogenic amino acid components of the hydrolysates was identified as a 3-hydroxypyridinium derivative of lysine, 2-ammonio-6-(3-oxidopyridinium-1-yl)hexanoate (OP-lysine). The compound was synthesized independently from 3-hydroxypyridine and methyl 2-[(tert-butoxycarbonyl)amino]-6-iodohexanoate. The spectral and chromatographic properties of the synthetic OP-lysine and the substance isolated from hydrolyzed lenses were identical. HPLC analysis showed that the amounts of OP-lysine were higher in water-insoluble compared with water-soluble proteins and was higher in a pool of cataractous lenses compared with normal aged lenses, reaching 500 pmol/mg protein. The model incubations showed that an anaerobic reaction mixture of Nalpha-tert-butoxycarbonyllysine, glycolaldehyde, and glyceraldehyde could produce the Nalpha-t-butoxycarbonyl derivative of OP-lysine. The irradiation of OP-lysine with UVA under anaerobic conditions in the presence of ascorbate led to a photochemical bleaching of this compound. Our results argue that OP-lysine is a newly identified glycation product of lysine in the lens. It is a marker of aging and pathology of the lens, and its formation could be considered as a potential cataract risk-factor based on its concentration and its photochemical properties.     

Bill morphology reflects adaptation to a fibrous diet in the kākāpō (Strigops: Psittaciformes)

We describe the upper portion of the bill sheath (rhinotheca) of the kākāpō (Strigops habroptilus) from three adult female specimens. The external buccal surface of the rhinotheca is deeply concave with a prominent palatal stop and hardened chevrons creating a ‘milling apparatus’ that the kākāpō uses to grind food. The palatal stop presents a working face of 40–50?mm². The internal surface of the rhinotheca mirrors the overlying premaxilla and provides a distinct thickened abutment consistent with resistance against the increased workload of the mandibles (gnathotheca) due to the kākāpō’s fibrous diet and chewing style. Along the midline, the rhinotheca at the abutment is up to 5.6?mm thick, compared with as thin as 2.1?mm elsewhere on the midline. The closely related Nestor parrots have less developed palatal stops, chevrons and abutments on their rhinothecas consistent with their lower preference for fibrous plant material. The form of the rhinotheca agrees with the kākāpō’s feeding ecology as a generalist herbivore that grinds locally available fibrous material to assist digestion.     

Molecular evolution modeled as a fractal Poisson process in agreement with mammalian sequence comparisons

The fractal doubly stochastic Poisson process (FDSPP) model of molecular evolution, like other doubly stochastic Poisson models, agrees with the high estimates for the index of dispersion found from sequence comparisons. Unlike certain previous models, the FDSPP also predicts a positive geometric correlation between the index of dispersion and the mean number of substitutions. Such a relationship is statistically proven herein using comparisons between 49 mammalian genes. There is no characteristic rate associated with molecular evolution according to this model, but there is a scaling relationship in rates according to a fractal dimension of evolution. The FDSPP is a suitable replacement for the homogeneous Poisson process in tests of the lineage dependence of rates and in estimating confidence intervals for divergence times. As opposed to other fractal models, this model can be interpreted in terms of Darwinian selection and drift.      

Transfer RNA(4lys) and cell cycle progression: characterization of ts-694 cells

Lysine tRNA modification has been studied in mammalian ts-694 cells with respect to cell cycle progression in temperature downshift and upshift experiments. The modification of tRNA(lys) measured in temperature downshift experiments showed that tRNA(4lys) levels start to increase 6 h following the temperature shift, approximately 10-12 h prior to the cells entry into S phase. Ts-694 cells showed a gradual decrease in the level of tRNA(4lys) and the rates of DNA synthesis following a temperature upshift. The cells became growth arrested following incubation for 36-45 h at the rt. Cell cycle mapping of the temperature restriction point suggests a G1 block prior to the serum deprivation restriction point. Depletion of cellular tRNA(4lys) by serum deprivation followed by simultaneously shifting cells to the rt and feeding medium containing 10% serum showed that cells with low tRNA(4lys) levels and no mechanism for the synthesis of tRNA(4lys) could not enter S phase and synthesize DNA. Blocking of ts-694 at the G1/S boundary with aphidicolin indicates that cells that have passed through G1 are capable of entering S phase and synthesizing DNA independent of the incubation temperature. These results indicate that tRNA(4lys) is not needed during S phase for DNA replication but suggests that tRNA(4lys) is required for cells to progress through G1.     

Glycation of MP26 and MP22 in bovine lens membranes.

Alkali treated membranes were isolated from mature bovine lenses and incubated with different sugars for 3 weeks to study the effect of glycation on the lens intrinsic membrane proteins, MP26 and MP22. The obtained results show that a) [1-14C] ascorbic acid (ASA) was able to glycate the intrinsic membrane proteins as rapidly as soluble lens proteins; b) on 15% acrylamide gels in SDS, glucose, fructose, galactose and ribose exhibited low activity for crosslinking membrane proteins; whereas ASA, dehydroascorbate (DHA), diketogulonate (DKG), xylosone and threose, all showed not only the formation of protein multimers, but also highly crosslinked products, which did not enter the spacer gel; c) except glycated MP22, all of the crosslinks of MP26 or MP22, and also the glycated MP26, showed cross reactivity with polyclonal MP26 antibody; d) the extent of crosslinking correlated with an equal loss of lysine and arginine contents by amino acid analysis.     

Glycation of lens proteins by the oxidation products of ascorbic acid

Bovine lens water-soluble proteins were incubated with [I-14C]ascorbic acid (ASA) for 6 days, and the incorporation into protein was measured at daily intervals. Aliquots were also withdrawn to determine the distribution of label among the various ASA oxidation products. A linear incorporation into protein was observed in the presence of NaCNBH3, however, little or no incorporation was seen in its absence. TLC analysis showed a complete loss of ASA by day 3, whereas both dehydroascorbate (DHA) and diketogulonic acid (DKG) remained constant for 6 days, consistent with the linear incorporation into protein. The amino acid composition of the proteins glycated in the presence of NaCNBH3 was identical to controls except for a 70% reduction in lysine residues and a corresponding increase in an unknown product which eluted slightly earlier than methionine. In the absence of NaCNBH3 lysine decreased linearly to 20% with an additional decrease in arginine and histidine at later times concurrent with protein crosslinking. DHA and DKG were prepared and incubated directly with lens proteins for an 8 day period. Both compounds glycated lens protein as evidenced by an increased binding to a boronate affinity column. SDS-PAGE showed that both compounds were also capable of causing protein crosslinking. DHA is apparently capable of reacting directly with protein since glycation was observed with the ASA analog, reductic acid, which can be oxidized to dehydroreductic acid, but which cannot be hydrolyzed to an open chain structure. DHA also produced a lysine adduct which was not obtained with DKG, supporting the idea that both species have glycating ability.