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Lalji Singh

Publications and source records attributed to Lalji Singh.

At least 55 records · Page 3Linked to original sources
PubMed2004

Phylogenetic position of Platanista gangetica: insights from the mitochondrial cytochrome b and nuclear interphotoreceptor retinoid-binding protein gene sequences.

The evolutionary relationship of peculiar and poorly known Ganges River dolphin with extinct and extant cetaceans has been in the state of confusion for more than a century. The close resemblance of platanistidae with some of the extinct taxon viz., Dalpiaziniidae and Waipatiidae and their sister group relationship with many of the extant lineages of cetaceans has been reported but none of the alternative hypotheses provide an unambiguous placement for this species. The present study provides insights into the molecular relationships of Platanista with other cetaceans based on comprehensive analyses of the mitochondrial cytochrome b and nuclear interphotoreceptor retinoid-binding protein gene sequences, obtained from 15 specimens of Ganges dolphin from India and Bangladesh. The mean substitution distance analysis of phylogenetically informative characters in the cytochrome b sequences suggested that Platanista gangetica is significantly closer (P<0.001) to Mysticeti than to any other group of toothed whales. However, the conventional methods of phylogenetic reconstruction supported this finding with low to moderate (41-69%) bootstrap values.

Animals↗
PubMed2004

CYP1A1, GSTM1 and GSTT1 genetic polymorphism is associated with susceptibility to polycystic ovaries in South Indian women.

Polymorphic variants in the phase I enzyme, cytochrome P450 gene, may lead to increased toxification, whereas polymorphisms in the phase II enzyme, glutathione S-transferase genes, may result in impaired detoxification. Alterations in the activities of phase I drug metabolizing enzymes and phase II detoxification enzymes may cause abnormal functioning and formation of follicular cysts in the ovaries and thus causing an imbalance in the hormone profiles. This study aimed to investigate the relationship between genetic polymorphisms of CYP1A1 (T6235C), GSTM1 and GSTT1 in South Indian women with polycystic ovaries (PCO) using polymerase chain reaction-restriction fragment length polymorphism. The frequencies of variants of these genes were studied in 180 women with confirmed PCO and in 72 healthy fertile women with successful pregnancy record. No significant difference was found between the frequencies of GSTM1 and GSTT1 null genotypes in PCO cases and healthy controls. However, CYP1A1 Msp I homozygous mutants were strongly associated (P = 0.0139) with increased susceptibility to PCO. Three genotype combinations, CYP1A1 (mt/mt) with GSTM1 [-] and GSTT1 [-], CYP1A1 (wt/mt) with GSTM1 [-] and GSTT1 [-] and CYP1A1 (mt/mt) with GSTM1 [-], GSTT1 [+], were also observed in women with PCO. In conclusion, the presence of hyperinducible CYP1A1 (T6235C) mutant genotype and its mutants in combination with GSTM1 and GSTT1 null genotypes might cause an imbalance between phase I and phase II enzymes, and therefore may represent a risk factor for PCO.

Adolescent↗
PubMed2004

Genetic diversity and relationships among the tribes of Meghalaya compared to other Indian and Continental populations.

The autosomal AmpFLSTR markers validated and widely used for forensic applications are used in this study to examine the extent of diversity and genetic relationships among nine Meghalaya populations. Altogether, 932 chromosomes from 9 populations were analyzed using 9 tetrameric AmpFLSTR loci. The included populations were all seven subtribes of the Austro-Asiatic Mon-Khmer-speaking Khasi and the neighboring Tibeto-Burman Garo. The Lyngngam, which are linguistically closer to the Khasi but are culturally intermediate between the Khasi and the Garo, are also included in the study. Although most of the microsatellite loci are highly polymorphic in each of these populations, the allele distributions are fairly uniform across the Meghalaya populations, suggesting relative homogeneity among them. Concurrent with this, the coefficient of gene differentiation (G(ST)) is observed to be low (0.026+/-0.002). This is naturally reflected in the lack of clear differentiation and clustering pattern of the Meghalaya tribes based on either geographic proximity or the historical or current affiliations of these tribes. Analysis of molecular variance (AMOVA) suggests no significant population structure. The structure analysis further suggests that, barring War-Khasi and Pnar, no other population shows any semblance of genetic identity. Even the position of the linguistically distinct Garo is not portrayed as separate from the Khasi. However, when comparable data from other Indian, Southeast Asian, and other continental populations were analyzed, the Meghalaya populations formed a compact cluster clearly separated from other populations, suggesting genetic identity of the Meghalaya populations as a whole. These results are concurrent with the hypothesis of a common and recent origin of these Meghalaya populations, whose genetic differentiation is overwhelmed by the homogenizing effect of continuous gene flow.

Alleles↗
PubMed2004

Mutation in the STR locus D21S1 1 of father causing allele mismatch in the child.

We analyzed a case of paternity dispute with 15 autosomal STR loci and found a mismatch in one of the alleles of the locus D21S11 in the child. The composition of the alleles of this locus in the mother, suspicious father, and child were 29/32, 29/29, and 29/30, respectively. The combined paternity index (2.4 x 10(10)) and paternity probability (0.9999) suggest that the suspicious father is the biological father of the child. Further analysis of 6 Y chromosome STR loci revealed matching of all the Y chromosomal alleles of the child with that of the suspicious father. Since there was a perfect match of all the paternal alleles inherited (15 autosomal and 6 Y chromosomal) in the child with that of the suspicious father except the allele D21S11, it is suggested that this might be a case of mutation. Cloning and sequencing of all the alleles of the locus D21S11 of the suspicious father, mother, and the child helped in determining that the suspicious father contributed the mutated allele.

Alleles↗
PubMed2003

Phylogeography and origin of Indian domestic goats.

The Indian subcontinent contains 20 well-characterized goat breeds, which vary in their genetic potential for the production of milk, meat, and fibre; disease resistance; heat tolerance; and fecundity. Indian goats make up 20% of the world's goat population, but there has been no extensive study of these economically important animals. Therefore, we have undertaken the present investigation of 363 goats belonging to 10 different breeds from different geographic regions of India using mtDNA sequence data from the HVRI region. We find evidence for population structure and novel lineages in Indian goats and cannot reconcile the genetic diversity found within the major lineage with domestication starting 10,000 years ago from a single mtDNA ancestor. Thus, we propose a more complex origin for domestic goats.

Analysis of Variance↗
PubMed2003

Was elusive carnivore a panther? DNA typing of faeces reveals the mystery.

In this study, we report the findings of a recent case in which the officials of an Indian zoo claimed that an animal, possibly a carnivore, is periodically visiting the zoo from a nearby vast forest area and causing panic in zoo and nearby villages. They collected some elusive faecal material from the vicinity of an herbivore enclosure. Looking to the pugmarks found in that area and faecal matter ceased, the officials could not decide whether it was a lioness, a tiger or a panther. We resolved this mystery by DNA-based analysis of the faecal material, using our recently developed novel universal primers to amplify and sequence a specific fragment of mitochondrial cytochrome b gene. The findings of the DNA-based analyses were confirmed after few days when the zoo officials trapped the animal of same species as suggested in our report. The potential of our procedure to investigate the cases related to wildlife offence is discussed.

Animals↗
PubMed2003

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.

Animals↗
PubMed2003

Triplet repeats in human genome: distribution and their association with genes and other genomic regions.

MOTIVATION: Simple sequence repeats (SSRs) or microsatellite repeats are found abundantly in many prokaryotic and eukaryotic genomes. Among SSRs, triplet repeats are of special significance because some of them have been linked to various genetic disorders. The objective of the study is to analyze the triplet repeats of complete human genome and to identify the genes that contain the triplet repeats in their coding region. The analysis will help us to identify the candidate genes that have potential for repeat expansion. RESULTS: We have analyzed triplet repeats in the complete human genome from the publicly available sequences. Our analysis revealed that AGC and CCG repeat were predominantly present in the coding regions of the genome while UTRs and the upstream sequences contained CCG repeats in relative abundance. Analysis of density of triplet repeats (bp/Mb) revealed that AAT and AAC were the abundant repeats whereas ACT and ACG were the rare repeats found in human genome. We could identify about 2135 known or predicted genes that were associated with at least one of the triplet repeat types. A large proportion of putative transcripts that were identified by gene finding programs were found to be associated with triplet repeats. These transcripts will be the candidate genes for analysis of triplet repeat expansion and a possible association with disease phenotypes. Identification of 171 genes which contain a minimum of ten repeat units will be of particular interest in future in correlating their association with any disease phenotype due to the expansion potential of repeats present in them. The list of genes and other details of analysis are given in the online supplementary data (http://www.ingenovis.com/tripletrepeats).

Databases, Nucleic Acid↗
PubMed2003

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.

Dinucleotide Repeats↗
PubMed2003

Genetic affinities of the Andaman Islanders, a vanishing human population.

BACKGROUND: The Andaman Islands in the Bay of Bengal are inhabited by hunter-gatherers of unknown origin, now on the verge of extinction. The Andamanese and other Asian small-statured peoples, traditionally known as "Negritos," resemble African pygmies. However, it is generally believed that they descend from the early Australo-Melanesian settlers of Southeast Asia and that their resemblance to some Africans is due to adaptation to a similar environment, rather than shared origins. RESULTS: We analyzed mitochondrial DNA (mtDNA) sequences and RFLP polymorphisms, and Y chromosome biallelic markers and microsatellites, in present-day Andamanese of the Onge, Jarawa, and Great Andamanese tribes, and of inhabitants of the neighboring Nicobar Islands. We also analyzed mtDNA sequences from Andamanese hair samples collected by an ethnographer during 1906-1908. Living Andamanese exhibit low genetic variability that is consistent with their small population size and reproductive isolation. CONCLUSIONS: Our data indicate that the Andamanese have closer affinities to Asian than to African populations and suggest that they are the descendants of the early Palaeolithic colonizers of Southeast Asia. In contrast, the Nicobarese have genetic affinities to groups widely distributed throughout Asia today, presumably descended from Neolithic agriculturalists.

Alleles↗
PubMed2003

A highly conserved human gene encoding a novel member of WD-repeat family of proteins (WDR13).

We have identified and characterized a novel member of the WD-repeat motif gene family, WDR13, which contains 9 exons and 8 introns. The gene has been mapped to the genomic locus Xp11.23 by fluorescent in situ hybridization and in silico mapping. Sequence analysis has revealed a continuous open reading frame (ORF) encoding for 485 amino acids with six WD motifs. The expression of this gene has been detected in all the tissues analyzed with significantly varied expression levels among the tissues studied. Analysis of EST clones from various tissues, showing significant homology to WDR13, has identified two spliced variants. The transcription start point has been mapped. Promoter analysis has identified high activity in the 5' UTR, which interestingly showed a testis-specific activity in the transgenic animals studied. The subcellular localization of the WDR13 protein in the nucleus suggests that it may also have a regulatory role in nuclear function along with protein-protein interaction like other members of the WD family of proteins.

5' Untranslated Regions↗
PubMed2003

Phylogeography and conservation genetics of Eld's deer (Cervus eldi).

Eld's deer (Cervus eldi) is a highly endangered cervid, distributed historically throughout much of South Asia and Indochina. We analysed variation in the mitochondrial DNA (mtDNA) control region for representatives of all three Eld's deer subspecies to gain a better understanding of the genetic population structure and evolutionary history of this species. A phylogeny of mtDNA haplotypes indicates that the critically endangered and ecologically divergent C. eldi eldi is related more closely to C. e. thamin than to C. e. siamensis, a result that is consistent with biogeographic considerations. The results also suggest a strong degree of phylogeographic structure both between subspecies and among populations within subspecies, suggesting that dispersal of individuals between populations has been very limited historically. Haplotype diversity was relatively high for two of the three subspecies (thamin and siamensis), indicating that recent population declines have not yet substantially eroded genetic diversity. In contrast, we found no haplotype variation within C. eldi eldi or the Hainan Island population of C. eldi siamensis, two populations which are known to have suffered severe population bottlenecks. We also compared levels of haplotype and nucleotide diversity in an unmanaged captive population, a managed captive population and a relatively healthy wild population. Diversity indices were higher in the latter two, suggesting the efficacy of well-designed breeding programmes for maintaining genetic diversity in captivity. Based on significant genetic differentiation among Eld's deer subspecies, we recommend the continued management of this species in three distinct evolutionarily significant units (ESUs). Where possible, it may be advisable to translocate individuals between isolated populations within a subspecies to maintain levels of genetic variation in remaining Eld's deer populations.

Animal Population Groups↗
PubMed2003

Conservation of wild animals by assisted reproduction and molecular marker technology.

Wild animals are an integral component of the ecosystem. Their decimation due to abrupt natural calamities or due to gradual human intervention would be disastrous to the ecosystem and would alter the balance in nature between various biotic components. Such an imbalance could have an adverse effect on the ecosystem. Therefore, there is an urgent need to put an end to the ever increasing list of endangered species by undertaking both in situ and ex situ conservation using tools of modern biology, to ascertain the degree of genetic variation and reproductive competence in these animals. This review highlights the development and use of molecular markers such as microsatellites, minisatellites, mitochondrial control region, cytochrome b and MHC loci to assess the genetic variation in various Indian wild animals such as the lion, tiger, leopard and deer. The review also presents data on the semen profile of the big cats of India. Reproductive technologies such as cryopreservation of semen and artificial insemination in big cats are also highlighted.

Animals↗
PubMed2002

MRD: a microsatellite repeats database for prokaryotic and eukaryotic genomes.

MRD is a database system to access the microsatellite repeats information of genomes such as archea, eubacteria, and other eukaryotic genomes whose sequence information is available in public domains. MRD stores information about simple tandemly repeated k-mer sequences where k= 1 to 6, i.e. monomer to hexamer. The web interface allows the users to search for the repeat of their interest and to know about the association of the repeat with genes and genomic regions in the specific organism. The data contains the abundance and distribution of microsatellites in the coding and non-coding regions of the genome. The exact location of repeats with respect to genomic regions of interest (such as UTR, exon, intron or intergenic regions) whichever is applicable to organism is highlighted. MRD is available on the World Wide Web at http://www.ccmb.res.in/mrd and/or http://www.ingenovis.com/mrd. The database is designed as an open-ended system to accommodate the microsatellite repeats information of other genomes whose complete sequences will be available in future through public domain.

Animals↗
PubMed2002

The mutational spectrum of brachydactyly type C.

Growth/differentiation factor-5 (GDF5), also known as cartilage-derived morphogenetic protein-1 (CDMP-1), is a secreted signaling molecule that participates in skeletal morphogenesis. Heterozygous mutations in GDF5, which maps to human chromosome 20, occur in individuals with autosomal dominant brachydactyly type C (BDC). Here we show that BDC is locus homogeneous by reporting a GDF5 frameshift mutation segregating with the phenotype in a family whose trait was initially thought to map to human chromosome 12. We also describe heterozygous mutations in nine additional probands/families with BDC and show nonpenetrance in a mutation carrier. Finally, we show that mutant GDF5 polypeptides containing missense mutations in their active domains do not efficiently form disulfide-linked dimers when expressed in vitro. These data support the hypothesis that BDC results from functional haploinsufficiency for GDF5.

Animals↗
PubMedDate not supplied

Sperm mitochondrial mutations as a cause of low sperm motility.

We report the unique case of a 28-year-old man who, in spite of having a varicocele and a sperm concentration of 5 million/mL, of which 10% were motile and 20% had normal forms (oligoasthenoteratozoospermia [OAT]), was fertile. This was confirmed by paternity testing using 16 autosomal and 6 Y-chromosomal short tandem repeat (STR) loci. An analysis of mitochondrial genes that included cytochrome oxidase I (COI), cytochrome oxidase II (COII), adenosine triphosphate synthase6 (ATPase6), ATPase8, transfer ribonucleic acid (tRNA) serine I, tRNA lysine, and NADH dehydrogenase3 (ND3) revealed, for the first time, 9 missense and 27 silent mutations in the sperm's mitochondrial DNA (mtDNA) but not in the DNA from the blood cells. There was a 2-nucleotide deletion in the mitochondrial COII genes, introducing a stop codon, which might be responsible for low sperm motility.

Adult↗
PubMedDate not supplied

Y chromosome deletions in azoospermic men in India.

Genetic factors cause about 10% of male infertility. Azoospermia factors (AZFa, AZFb, AZFc) are considered to be the most important for spermatogenesis. We therefore made an attempt to evaluate the genetic cause of azoospermia, Y chromosome deletion in particular, in Indian men. We have analyzed a total of 570 men, including 340 azoospermic men and 230 normal control subjects. DNA samples were initially screened with 30 sequence-tagged site (STS) markers representing AZF regions (AZFa, AZFb, AZFc). Samples, with deletion in the above regions were mapped by STS walking. Further, the deletions were confirmed by Southern hybridization using the probes from both euchromatic and heterochromatic regions. Of the total 340 azoospermic men analyzed, 29 individuals (8.5%) showed Y chromosome deletion, of which deletion in AZFc region was the most common (82.8%) followed by AZFb (55.2%) and AZFa (24.1%). Microdeletions were observed in AZFa, whereas macrodeletions were observed in AZFb and AZFc regions. Deletion of heterochromatic and azoospermic regions was detected in 20.7% of the azoospermic men. In 7 azoospermic men, deletion was found in more than 8.0 Mb spanning AZFb and AZFc regions. Sequence analysis at the break points on the Y chromosome revealed the presence of L1, ERV, and other retroviral repeat elements. We also identified a approximately 240-kb region consisting of 125 bp tandem repeats predominantly comprised of ERV elements in the AZFb region. Histological study of the testicular tissue of the azoospermic men, who showed Y chromosome deletion, revealed complete absence of germ cells and presence of only Sertoli cells.

Adult↗