Autosomal STR data on the enigmatic Andaman Islanders

We have analyzed nine autosomal STR loci (D3S1358, vWA, FGA, D8S1179, D21S11, D18S51, D5S818, D13S317, and D7S820) in 97 samples of enigmatic Andaman islanders including: 15 Great Andamanese, 46 Onge and 36 Nicobarese. Data was compared with the available data on Indian and South East Asian populations. Heterozygosity (H), power of discrimination (PD), probability exclusion (PE), typical paternity index (TPI), polymorphism information content (PIC), AMOVA and Arlequin analysis were carried out. Average heterozygosity observed was high and almost equal in all the populations. Similarly, PD, PE, TPI and PIC have been almost equal in all the populations.

Mutational analysis of the betaglycan gene-coding region in susceptibility for ovarian failure

BACKGROUND

Elevation of FSH is frequently a consequence of impaired ovarian follicle growth. Down-regulation of the FSH levels by inhibins is mediated through its receptor betaglycan in the gonadotrophs. Understanding of germline status of the betaglycan gene (TGFBR3) is essential for ovarian failure pathophysiology.

METHODS

Sequence analysis was performed for the coding region of TGFBR3 gene in a cohort of 196 ovarian failure cases that include 133 premature ovarian failure (POF) cases, 63 primary amenorrhoea (PA) cases compared with 200 controls.

RESULTS

Forty-six variants including six novel exonic variants and 16 novel intronic variants were revealed. Two variants were missense: (i) p.Iso184Val in a control and (ii) p.Pro775Ser in a POF case. Genotypic distribution of three variants (c.382-81C>T, c.382-77T>C and c.1200G>A) was significantly different in the patients as compared with the controls. Five variants c.382-81C>T, c.382-77T>C, c.566-216G>A, c.1200G>A and c.2022T>C were chosen for haplotyping. The CCAAT haplotype was significantly higher in the patient population as compared with the controls (P = 0.00007).

CONCLUSION

This study establishes the first mutational report of the TGFBR3 gene in correlation with ovarian failure. Significant diversity of genotype distribution and haplotype analysis suggested susceptibility of the TGFBR3 gene for ovarian failure aetiology.

Direct immunofluorescence assay for rapid environmental detection of Vibrio cholerae O1

An immunofluorescence assay for direct detection of V. cholerae O1 was developed using polyclonal antibodies raised against outer membrane proteins (OMPs) of V. cholerae O1. Production of OMPs varied with growth media used; maximum production was found in tryptic soy broth. The detection system was specific because no cross-reactivity was observed with other bacteria including V. cholerae O139, E. coli, S. dysenteriae and Salmonella enterica subsp. enterica serovar Typhi. The technique was able to detect 240 CFU/mL of V. cholerae O1 suspended in phosphate-buffered saline. The assay coupled with bacterial enrichment in APW for 6 h detected as few as 5 CFU of V. cholerae in spiked samples. Moreover, a 2-h incubation of enriched bacterial cells in 0.1% yeast extract with 10 ppm nalidixic acid enhanced the bacterial size and helped in morphological identification of V. cholerae. Among 32 potable water samples from afflicted hand pumps and wells collected from a cholera-plagued area 12 were found to be contaminated with V. cholerae by immunofluorescence assay as well as by conventional culture methods. The proposed method could thus be employed in environmental surveillance of V. cholerae O1.

Asian and non-Asian origins of Mon-Khmer- and Mundari-speaking Austro-Asiatic populations of India

In the present study, we analyzed 1,686 samples from 31 tribal populations of India for the mitochondrial DNA 9-base-pair deletion/insertion polymorphism, and characterized them based on the relevant mitochondrial DNA coding-region single nucleotide polymorphisms and hypervariable region I motifs, to test the genetic origins of the ethnically and linguistically heterogeneous Austro-Asiatic tribes of India. A comparative analysis of our results with the existing data suggests multiple origins of Austro-Asiatic tribes in India, and particularly the Asian and non-Asian origins of the Mon-Khmer and the Mundari populations. We also identified a novel subclade of haplogroup B in the Mon-Khmer Khasi tribes that distinguishes them from the Nicobarese, indicating two different waves of migration of the Mon-Khmer tribes in India.

Major histocompatibility complex class I polymorphism in Asiatic lions

Asiatic lions (Panthera leo persica), whose only natural habitat in the world is the Gir forest sanctuary of Gujarat State in India, are highly endangered and are considered to be highly inbred with narrow genetic diversity. An objective assessment of genetic diversity in their immune loci will help in assessing their survivability and may provide vital clues in designing strategies for their scientific management and conservation. We analyzed the comparative sequence polymorphism at exon 2 and exon 3 of major histocompatibility complex (MHC) class I in three groups of lions, i.e. wild Asiatic (from Gir forest), captive-bred Asiatic (from zoological parks in India), and Afro-Asiatic hybrid groups (from zoological parks in India) through polymorphism chain reaction-assisted sequence-based typing. The two exons were amplified, cloned, sequenced, and analyzed for polymorphism at nucleotide and putative translated product level. The analysis revealed extensive sequence polymorphism not only between clones derived from different lions but also the clones derived from a single lion. Furthermore, the wild Asiatic lions of Gir forest exhibited abundant sequence polymorphism at MHC class I comparable with that of Afro-Asiatic hybrid lions and significantly higher than that of captive-bred Asiatic lions. We hypothesize that Asiatic lions of Gir forest are not highly inbred as thought earlier and they possess abundant sequence polymorphism at MHC class I loci. During this study, 52 new sequences of the multigene MHC class I family were also identified among Asiatic lions.

STR data for the Amp FlSTR Profiler Plus loci among 27 populations of different social hierarchy from southern part of Andhra Pradesh, India

Allele frequency for the 9 STR loci (D3S1358, vWA, FGA, D8S1179, D21S11, D18S51, D5S818, D13S317, D7S820) were estimated from a total of 1096 individuals belonging to 27 endogamous populations from the state of Andhra Pradesh, India, covering the entire gamut of socio-economic variation of the linguistic region. These loci are found to be highly polymorphic within the populations with high levels of average heterozygosity (>0.80). However, the allele frequency distributions are fairly uniform across the populations in case of these loci suggesting relatively greater homogeneity among the populations. Regrouping populations into five broad socio-economic categories further reiterated the homogenous pattern of genetic diversity.

Structure-based design in drug discovery - the application of a peptoid drug design strategy for the development of non-peptide neuropeptide receptor ligands

Over the last decade the increasing availability of metabolically- stable non-peptide antagonists targeted at neuropeptide receptors has led directly to a more thorough understanding of the role of neuropeptides in mammalian physiology. By far the majority of these non-peptide neuropeptide receptor antagonists thus far disclosed have been developed from leads identified from broad screening of company compound files or natural product collections, and may thus bear little obvious structural resemblance to the endogenous peptide ligand. This review will focus on an alternative structure-based approach to non-peptide neuropeptide receptor ligand design, referred to as the 'peptoid' drug design strategy, in which an appreciation of the structure of the neuropeptide is the key to the success of this approach. The development and current clinical progress of peptoid cholecystokinin and tachykinin receptor ligands that have thus far resulted from this process will be highlighted and used to exemplify the importance of this novel approach.

Phylogeography of olive ridley turtles (Lepidochelys olivacea) on the east coast of India: implications for conservation theory

Orissa, on the east coast of India, is one of the three mass nesting sites in the world for olive ridley turtles (Lepidochelys olivacea). This population is currently under threat as a result of fishery-related mortality; more than 100 000 olive ridleys have been counted dead in the last 10 years in Orissa. In general, the globally distributed olive ridley turtle has received significantly less conservation attention than its congener, the Kemp's ridley turtle (L. kempi), because the latter is recognized as a distinct species consisting of a single endangered population. Our study of mitochondrial DNA haplotypes suggests that the ridley population on the east coast of India is panmictic, but distinct from all other populations including Sri Lanka. About 96% of the Indian population consisted of a distinct 'K' clade with haplotypes not found in any other population. Nested clade analysis and conventional analysis both supported range expansions and/or long-distance colonization from the Indian Ocean clades to other oceanic basins, which suggested that these are the ancestral source for contemporary global populations of olive ridley turtles. These data support the distinctiveness of the Indian Ocean ridleys, suggesting that conservation prioritization should be based on appropriate data and not solely on species designations.

Occurrence of Cucumber mosaic virus in Gerbera jamesonii in India

Gerbera jamesonii (family Asteraceae) is a popular perennial ornamental cut flower and potted plant with considerable economic importance. In a survey of gerbera grown in floriculture fields at the Institute of Himalayan Bioresource Technology (IHBT), Palampur and nearby nurseries, color break symptoms on the petals, asymmetrical ray florets, and deformed flowers were observed during 2003-2004. The virus evoked chlorotic local lesions on Chenopodium album, C. amaranticolor, and C. quinoa, while systemic mosaic was observed on Cucumis sativus, Nicotiana benthamiana, N. clevelandii, N. glutinosa, and N. tabacum cv. Samsun. The virus was transmitted nonpersistently by Myzus persicae and Aphis gossypii and was identified as Cucumber mosaic virus (CMV) using enzyme-linked immunosorbent assay (ELISA) with CMV-specific antibodies (Agdia, Elkhart, IN). Polyhedral particles approximately 29 nm were observed with electron microscopy of leaf dips from symptomatic gerbera leaves. Total RNA was isolated from the infected gerbera plants and N. glutinosa by using RNAqueous (Ambion, Austin, TX). CMV-specific primers (1) were used to detect the virus with reverse transcription-polymerase chain reaction that produced an amplicon predicted size of approximately 540 bp, but the virus was not detected in healthy controls. Sequence alignment of the amplicons (533 bp) utilizing BLAST resulted in 91 to 99% homology with the partial intercistronic region and partial coat protein gene (1042-1574 bp) (gene sequence submitted to EMBL database with Accession no. AJ634532) of CMV RNA3 in subgroup I. To our knowledge, this is the first report of CMV on gerbera in India. Reference: (1) C. De Blas et al. J. Phytopathol. 141:323, 1994.

Mutational analysis of the mature peptide region of inhibin genes in Indian women with ovarian failure

BACKGROUND

Clinically, premature ovarian failure (POF) is defined as unexplained amenorrhoea (> 6 months) with a high FSH level (> 40 IU) before the age of 40 years. POF is a heterogeneous genetic disease with unknown aetiology. Inhibin and activin regulate the FSH level by their opposing actions and thus have been considered as strong candidate genes in the aetiology of POF.

METHODS

We have screened inhibin genes in patients with POF (n = 80), primary amenorrhoea (n = 33) and secondary amenorrhoea (n = 4).

RESULTS

INHbetaB and INHbetaA genes do not show any association with ovarian failure. We found the Ala257Thr missense mutation in INHalpha gene with high statistical significance in POF (nine out of 80, 11.2%) (Fisher's exact test, P = 0.0005), primary amenorrhoea (three out of 33, 9.1%) (Fisher's exact test, P = 0.014) and secondary amenorrhoea (two out of four, 50%) (Fisher's exact test, P = 0.001) with complete absence of this mutation in controls (none out of 100).

CONCLUSION

The INHalpha gene is a strong candidate gene for ovarian failure. Mutations in INHbetaB and INHbetaA genes are not associated with ovarian failure.

Absence of PRSS1 mutations and association of SPINK1 trypsin inhibitor mutations in hereditary and non-hereditary chronic pancreatitis

BACKGROUND AND AIMS

Mutations in the cationic trypsinogen (protease, serine, 1 (trypsin 1); PRSS1) gene are causally associated with recurrent acute and chronic pancreatitis. We investigated whether mutations in the PRSS1 gene are associated with hereditary and non-hereditary pancreatitis. As a modifier role has been proposed for trypsin inhibitor (serine protease inhibitor, Kazal type I; SPINK1) mutations, the role of SPINK1 mutations in these patients was also analysed.

SUBJECTS AND METHODS

The coding regions of PRSS1 and SPINK1 genes were sequenced in 290 controls and 198 patients, of whom 120 were diagnosed as idiopathic (ICP), 41 as alcoholic (ACP), and 37 as hereditary pancreatitis (HP). Twenty four unaffected relatives of HP probands were also analysed and genotype-phenotype correlations and statistical analyses were performed.

RESULTS

No mutations in the PRSS1 gene were detected in any of the patients, including HP patients, while the N34S mutation was observed in the SPINK1 gene in the majority of HP patients (73%). Similarly, 26.8% of ACP (11 of 41) and 32.5% (39 of 120) of ICP patients also had SPINK1 mutations. The N34S mutation was observed in both homozygous and heterozygous conditions. In comparison, only 2.76% of the control population had the N34S allele (p<0.001). The P55S mutation was observed in one ICP and one ACP patient, and in three normal individuals. Genotype-phenotype correlations did not suggest any significant difference in the age of onset, severity of disease, or pancreatic endocrine insufficiency in patients with or without mutated SPINK1 and irrespective of the allelic status of N34S SPINK1.

CONCLUSIONS

Irrespective of the aetiology, mutations in the PRSS1 gene are not associated with chronic pancreatitis, including HP. In contrast, the N34S mutation in the SPINK1 gene shows a significant correlation in these patients. A comparable phenotype in terms of age of onset, diabetes mellitus, and other phenotypic features in patients with or without SPINK1 mutations and N34S homozygotes and heterozygotes suggests that there may still be involvement of other genetic or environmental factors.

A GATA-binding protein expressed predominantly in the pupal ovary of the silkworm, Bombyx mori

Preferential localization of Bkm (Banded krait minor-satellite) DNA sequences on Y/W chromosomes of higher eukaryotes, which remain highly condensed in somatic cells but undergo extensive decondensation in the germ cells during early stages of development, led to the postulation for the existence of a sex- and tissue-specific Bkm-binding protein (BBP). Accordingly, we purified and characterized a BmBBP expressed predominantly in pupal ovary of the silkworm (Bombyx mori). 2D-PAGE revealed BmBBP as moderately basic (pI 7.8-8, in the range expected for DNA-binding proteins) and Matrix Assisted Laser Desorption/Ionization Time of Flight exhibited a value of 37.5-kDa. BmBBP neither contains nor requires divalent metal ions for its DNA-binding activity, suggesting that it does not belong to the well-studied GATA-family of transcription factors. BmBBP is unusually strong in its DNA-binding characteristics to Bkm (GATA-repeats), which suggests its probable role in bringing about coordinated chromatin conformational changes to activate genes present in associated chromosomal domains. Fluorescence immuno-localization studies employing specific anti-BmBBP antibodies revealed its presence in the follicle cells and in the ooplasm, as well as the nucleus of different developmental stages of oocytes.

Molecular characterization of some Indian Basmati and other elite rice genotypes using fluorescent-AFLP

Cultivated rice is a high-volume, low-value cereal crop providing staple food to more than 50% of the world populace. A small group of rice cultivars, traditionally produced on the Indo-Gangetic plains and popularly known as Basmati, have exquisite quality grain characteristics and are a prized commercial commodity. Efforts to improve the yield potential of Basmati have led to the development of several crossbred Basmati-like cultivars. In this study we have analysed the genetic diversity and interrelationships among 33 rice genotypes consisting of the traditional Basmati, improved Basmati-like genotypes developed in India and elsewhere, American long-grain rice and a few non-aromatic rice using a DNA marker-based approach - fluorescent-amplified fragment length polymorphism (f-AFLP). Using a set of nine primer-pairs we scored a total of 10,672 data points over all of the genotypes in the size range of 75-500 bp. The scored data points corresponded to a total of 501 AFLP markers (putative loci/genome landmarks) of which 327 markers (65%) were polymorphic. The f-AFLP marker data, which were analysed using different clustering algorithms and principal component analysis, indicate that: (1) considerable genetic variability exists in the analysed genotypes; (2) traditional Basmati cultivars could be distinctly separated from the crossbred Basmati-like genotypes as well as from the non-aromatic rice; (3) the crossbred Basmati-like cultivars from the subcontinent and elsewhere are genetically very distinct; (4) f-AFLP-based clustering, in general, conforms to the putative pedigree of the improved genotypes. Moreover, analysis to ascertain the scope of AFLP as a technique suggests that the polymorphism revealed by three selective primer-pair combinations is sufficient to obtain reliable estimates of genetic diversity for the type of material used in this study. However, its utility to identify group-specific DNA markers was discounted due to a low frequency of observed group-specific discrete markers.

Apolipoprotein E and presenilin-1 allelic variation and Alzheimer's disease in India

As part of a larger epidemiological survey to study the prevalence of dementia in a suburb of Mumbai, Western India, we identified 78 cases with a Clinical Dementia Rating (CDR) > or = 1.0. Of these, 49 Alzheimer's disease (AD) cases were analyzed for risk association with APOE E*4 allele at apolipoprotein E gene (APOE) and presenilin-1 (PS-1) intron-8 polymorphism and were compared with 100 age- and sex-matched nondemented controls. Genotype analysis confirmed the association of APOE E*4 allele with AD as has been reported by various studies. We report a low frequency of APOE E*4 allele, consistent with a low prevalence of AD in this study. Comparisons with other similar studies on APOE from India suggest common risk factors for AD in the Indian population, which is diverse in its ethnic and racial characteristics. The frequency for allele 1 at PS-1 intron-8 polymorphism is the highest among all studies reported. This first report of PS-1 intron-8 polymorphism and AD from India demonstrates no significant association.

Infants' Listening Preferences: Baby Talk or Happy Talk?

The most robust finding on infants' listening preferences has been widely characterized as a preference for baby talk (BT) over adult-directed speech (ADS). Although prosodic modifications characteristic of BT also convey positive affect, differences in affect across BT and ADS speech registers have not been controlled in previous studies. This set of experiments sought to elucidate the basis for 6-month-olds' listening preference by independently manipulating affect and speech register. When affect was held constant, no preference for any speech register was observed. Moreover, when ADS stimuli presented more positive affect than BT stimuli, infants' preferences followed the positive affect. Higher and more variable pitch was neither necessary nor sufficient for determining infants' preferences, although pitch characteristics may modulate affect-based preferences. The BT preference is thus attributable to a more general preference for speech that imparts relatively positive affect, a preference perhaps ascribable to a preexisting general-purpose mechanism opportunistically exploited by language.