The charms of sex chromosomes in snakes

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L859F mutation in androgen receptor gene results in complete loss of androgen binding to the receptor

Androgens drive male secondary sexual differentiation and maturation. Mutations in the androgen receptor (AR) gene cause an array of abnormal sex differentiation phenotypes in humans, ranging from mild through partial to complete androgen insensitivity. Earlier, we reported a C3693T missense mutation in the AR gene in a familial case of complete androgen insensitivity syndrome (CAIS), resulting in the replacement of a highly conserved leucine residue with phenylalanine (L859F) in ligand-binding domain (LBD) of the receptor. In silico analysis and the information from the crystal structure of AR-LBD indicated that the residue L859, located in helix 10 of AR protein, plays a significant role in overall architecture of the ligand-binding pocket. From this information we anticipated that the mutation might have resulted in the loss of the ligand binding to the receptor. In the present study, we have conducted the in vitro functional assays for this mutation. The mutation resulted in highly significant loss of the ligand binding to the receptor. The loss of ligand binding and subsequent AR function was confirmed by the transactivation assay, in which we observed very little activation of the reporter gene expressed under the control of the ligand-AR complex

Complex genetic origin of Indian populations and its implications

Indian populations are classified into various caste, tribe and religious groups, which altogether makes them very unique compared to rest of the world. The long-term firm socio-religious boundaries and the strict endogamy practices along with the evolutionary forces have further supplemented the existing high-level diversity. As a result, drawing definite conclusions on its overall origin, affinity, health and disease conditions become even more sophisticated than was thought earlier. In spite of these challenges, researchers have undertaken tireless and extensive investigations using various genetic markers to estimate genetic variation and its implication in health and diseases. We have demonstrated that the Indian populations are the descendents of the very first modern humans, who ventured the journey of out-of-Africa about 65,000 years ago. The recent gene flow from east and west Eurasia is also evident. Thus, this review attempts to summarize the unique genetic variation among Indian populations as evident from our extensive study among approximately 20,000 samples across India

Association of CYO1A1 gene polymorphism with recurrent pregnancy loss in the South Indian population

Background: We investigated the relationship between idiopathic recurrent pregnancy loss (RPL) and genetic polymorphisms in phase I and phase II detoxification genes which include CYP1A1, CYP2D6, GSTM1, GSTP1 and GSTT1. Method: A case-control study comprised 160 females with RPL and 63 healthy controls with a successful reproductive history. Results: The CYP1A1 variant allele was present at frequencies of 0.61 and 0.44 in cases and controls, respectively (odds ratio=1.93; P=0.023, 95% confidence interval 1.10-3.38). The CYP2D6 variant allele was present at a frequency of 0.17 in females with RPL, while in the control population the frequency was 0.16. The GSTM1 and GSTT1 null genotypes were present at frequencies of 0.39 and 0.26 in RPL cases, whereas in controls the frequencies were 0.37 and 0.17, respectively. The mutant GSTP1 frequencies in case and control women were 0.38 and 0.40, respectively. We report a significant association of the CYP1A1∗2A allele with RPL which is confirmed by logistic regression analysis. No association was observed for the other polymorphisms or in their combinations studied. Conclusions: The present study suggests the occurrence of the CYP1A1∗2A allele as a probable risk factor in idiopathic recurrent miscarriages

The use of Y-chromosome-specific repeated DNA sequences in the analysis of testis development in an XX/XY mouse

A study, by means of Y-chromosome-specific repeated DNA probes, of mouse (ST) with small testes is reviewed. Mouse ST was shown to be a somatic mosaic of 10 % XY and 90 % XX cells. The cellular composition of the azoospermic testis reflected the overall proportions of XX and XY cells but it was found that XY cells predominated in the Sertoli cells of the testis tubules. These findings have been interpreted to indicate a fundamental role for the Sertoli cell in inducing testis organization in the indifferent gonadal rudiment, involving the expression of the Y chromosome

Genome-wide analysis of microsatellite repeats in humans: their abundance and density in specific genomic regions

BACKGROUND: Simple sequence repeats (SSRs) are found in most organisms, and occupy about 3% of the human genome. Although it is becoming clear that such repeats are important in genomic organization and function and may be associated with disease conditions, their systematic analysis has not been reported. This is the first report examining the distribution and density of simple sequence repeats (1-6 base-pairs (bp)) in the entire human genome. RESULTS: The densities of SSRs across the human chromosomes were found to be relatively uniform. However, the overall density of SSR was found to be high in chromosome 19. Triplets and hexamers were more predominant in exonic regions compared to intronic and intergenic regions, except for chromosome Y. Comparison of densities of various SSRs revealed that whereas trimers and pentamers showed a similar pattern (500-1,000 bp/Mb) across the chromosomes, di- tetra- and hexa-nucleotide repeats showed patterns of higher (2,000-3,000 bp/Mb) density. Repeats of the same nucleotide were found to be higher than other repeat types. Repeats of A, AT, AC, AAT, AAC, AAG, AGC, AAAC, AAAT, AAAG, AAGG, AGAT predominate, whereas repeats of C, CG, ACT, ACG, AACC, AACG, AACT, AAGC, AAGT, ACCC, ACCG, ACCT, CCCG and CCGG are rare. CONCLUSIONS: The overall SSR density was comparable in all chromosomes. The density of different repeats, however, showed significant variation. Tri- and hexa-nucleotide repeats are more abundant in exons, whereas other repeats are more abundant in non-coding regions

Genome-wide analysis of Bkm sequences (GATA repeats): predominant association with sex chromosomes and potential role in higher order chromatin organization and function

Motivation: Bkm (Banded krait minor) satellite DNA sequences (GATA repeats) have been shown to be associated with the sex determining chromosomes of various eukaryotes and have been implicated in the evolution and differentiation of sex chromosomes in snakes. The objective of the study is to analyze the GATA repeats of human genome specifically, the Y-chromosome, and other model organisms to understand the possible function and potential role in higher order chromatin organization. Results: Our extensive analysis of GATA repeats in the prokaryotic and eukaryotic genomes, which have been completely sequenced so far, has revealed that GATA repeats are absent in prokaryotes and have been gradually accumulated in higher organisms during the course of evolution. In human, the Y-chromosome has the highest GATA repeat density, which predominantly exists in the Yq centromeric region. Generally, occurrence of repeats in the genomes decreases steadily as the length of the repeat increases. In contrast, we report, that the occurrence of GATA repeats increases as the length of the repeat increases from six tandem repeats onwards and peaks at (GATA)10-12. This has not been observed with any other simple repeat. Distribution of (GATA)10-12 along the chromosome and their close proximity to Matrix Associated Regions (GATA-MAR) suggests that it may be demarking chromatin domains for a coordinated expression of genes residing in these domains

Tree species diversity, distribution and population structure in a tropical dry deciduous forests of Chhatisgarh, India

Tree species diversity, distribution and population structure of tropical forests of Bharnawapara wildlife sanctuary was investigated. The study analyzed the structure of a tropical dry deciduous forest in Chhatisgarh at different sites i.e. closed natural forest, open natural forest and plantation forests of teak. The study was conducted by laying 30 quadrats, each 10 m × 10 m in size at different sites. In total, 246 trees belonging to 28 species of 17 families were recorded from 0.3 ha sampling area. Density ranged between 520 to 990 trees ha-1 subsequently, basal area ranged between 21.50 to 47.30 m2 ha-1. The dominant tree species was Cleistanthus collinus with an importance value index (IVI) of 57.70. Other important species were Terminalia tometosa (IVI 47.10), Lagerstroemia parviflora (36.92), Diospyros melanoxylon (28.42) and Madhuca indica(26.03). The Shannon-Wiener index (H?) ranged between 0.19 to 3.35 and Simpson’s index (C) between 0.12 to 0.95 indicating high tree species diversity of tropical dry deciduous forests. It is evident from the study that natural forest has an edge over plantation forest in terms of species diversity, dominance and richness. Tree species diversity, distribution and population structure provide baseline information for conservation and management of tropical dry deciduous forests in India. Efforts are needed to conserve the natural forest for their diversity and existence. They can also be supplemented with plantation forests to lower the biotic pressure

Mitochondrial DNA sequence divergence among big cats and their hybrids

Mitochondrial DNA sequence variation was used to distinguish between various big catspecies and their hybrids. Mitochondrial D loop sequencing revealed the presence of only one haplotype among the Asiatic lions while the hybrids (Asiatic×African) exhibited a number of haplotypes, which showed homology with the African lion sequence. this strongly indicates the population. the sequence divergence reveals the two subspecies must have split about 80,000 to 100,000 years ago. Similar analysis also helped in distinguishing between Indian and Siberian tigers. Microsatellite studies had earlier shown the presence of siberian tiger alleles in the Dhudhwa tiger reserve population. Mitochondrial cytochrome b gene sequence analysis of the hair samples from suspected Indian and Siberian tigerhybrids of the Dhudhwa tiger reserve revealed the presence of Indian tiger mitochondrial DNA haplotype