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.

Is the amelogenin gene reliable for gender identification in forensic casework and prenatal diagnosis?

In humans, the amelogenin gene is present on both the X and the Y chromosomes. However, there are size differences in this gene between these chromosomes, which have been utilised for sexing in forensic casework and prenatal diagnosis. Our study using the AmpFl STR Profiler Plus kit, showed a deletion of Y chromosome-specific amelogenin in five Indian males (1.85%). We propose to call them "deleted-amelogenin males" (DAMs), who but for the detection of the presence of other Y-specific markers (e.g. SRY, STR and 50f2) would have been identified as females. Considering the consequences of the result obtained only using the amelogenin marker, we suggest the use of additional Y chromosome markers for unambiguous gender identification.

Isolation and characterization of Clostridium botulinum type E from soil of Gwalior, India

A strain of Clostridium botulinum type E has been isolated from soil samples of Gwalior, India. The isolated strain shows curved vegetative cells with oval, bulging, and terminal spores. The production of toxin was detected by immunodiffusion test, symptomatic death of mice and mouse protection assay with trivalent antitoxin (A+B+E). The culture supernatant gave 10(3) MLD (minimum lethal dose) per ml without any protease treatment. Group specific and serotype specific primers amplified the DNA fragments of 260 bp and 445 bp, respectively, indicating Clostridium botulinum type 'E.'

Distribution of HIV-1 resistance-conferring polymorphic alleles SDF-1-3'A, CCR2-64I and CCR5-Delta32 in diverse populations of Andhra Pradesh, South India

Polymorphic allelic variants of chemokine receptors CCR2 and CCR5, as well as of stromal-derived factor-1 SDF-1, the ligand for the chemokine receptor CXCR4, are known to have protective effects against HIV-1 infection and to be involved with delay in disease progression. We have studied the DNA polymorphisms at the loci that encode these proteins in 525 healthy individuals without any history of HIV-1 infection from 11 diverse populations of Andhra Pradesh, South India. The two protective alleles SDF-1-3'A and CCR2-64I at the SDF-1 and CCR2 loci, respectively, are present in all populations studied, although their frequencies differ considerably across populations (from 17% to 35% for the SDF-1-3'A allele, and from 3% to 17% for CCR2-64I). In contrast the CCR5-Delta32 allele is observed only in three populations (Yamani, Pathan and Kamma), all in low frequencies (i.e. 1% to 3%). The mean number of mutant alleles (for the three loci together) carried by each individual varies from 0.475 (in Vizag Brahmins) to 0.959 (in Bohra Muslims). The estimated relative hazard values for the populations, computed from the three-locus genotype data, are comparable to those from Africa and Southeast Asia, where AIDS is known to be widespread.

Dorsal free graft urethroplasty for urethral stricture by ventral sagittal urethrotomy approach

OBJECTIVES

To explore the feasibility of applying a dorsal free graft to treat urethral stricture by the ventral sagittal urethrotomy approach without mobilizing the urethra.

METHODS

Twelve patients with long or multiple strictures of the anterior urethra were treated by a dorsal free full-thickness preputial or buccal mucosa graft. The urethra was not separated from the corporal bodies and was opened in the midline over the stricture. The floor of the urethra was incised, and an elliptical raw area was created over the tunica on which a free full-thickness graft of preputial or buccal mucosa was secured. The urethra was retubularized in one stage.

RESULTS

After a follow-up of 8 to 40 months, one recurrence developed and required dilation.

CONCLUSIONS

The ventral sagittal urethrotomy approach for dorsal free graft urethroplasty is not only feasible and successful, but is easy to perform.

Effect of gabapentin-like compounds on development and maintenance of morphine-induced conditioned place preference

RATIONALE

Psychological dependence to the opioid analgesic morphine is attributable to the rewarding properties of the drug, and its evolution can be divided into two distinct phases: development and maintenance. Both phases can be studied using conditioned place preference (CPP).

OBJECTIVES

To determine whether the two phases can be influenced by pre-treatment with gabapentin-like compounds.

METHODS

CPP to morphine was used to demonstrate the rewarding properties of morphine in the presence or absence of gabapentin-like compounds. In-vivo microdialysis in the nucleus accumbens was used to determine the effects of gabapentin or pregabalin on morphine-induced dopamine release.

RESULTS

Pretreatment with either gabapentin (10-100 mg/kg p.o.) or pregabalin (3-30 mg/kg p.o.) attenuated CPP induced by a submaximal dose of morphine (0.75 mg/kg). Neither gabapentin nor pregabalin had any effect alone in the CPP test. Both gabapentin-like compounds blocked the effect of morphine (0.75 mg/kg s.c.) to increase the release of dopamine in the nucleus accumbens. Studies of the maintenance of CPP to morphine showed CPP was maintained for at least 4 days after the initial test. In a second experiment, it was found that pregabalin (injected once, 24 h after CPP had been demonstrated) was able to reverse morphine-induced CPP.

CONCLUSIONS

Neither gabapentin nor pregabalin induced CPP, but both compounds blocked the development of CPP to morphine and also blocked morphine's effects on dopamine release. Furthermore, pregabalin blocked the maintenance of morphine-induced CPP. It is concluded that gabapentin-like compounds, which have no intrinsic rewarding properties, may have some therapeutic use in the treatment of opioid dependence.

Y-chromosome SNP haplotypes suggest evidence of gene flow among caste, tribe, and the migrant Siddi populations of Andhra Pradesh, South India

From observations of lack of haplotype sharing based on Y-chromosome specific short tandem repeat (STR) loci, previous reports suggested negligible gene flow among different geographic populations of India. Using Single Nucleotide Polymorphism (SNP) sites in combination with STRs, we observed evidence of haplotype sharing across caste-tribe boundaries in South India. We examined 27 SNPs in the non-recombining region of the Y chromosome to investigate gene flow in 204 individuals belonging to three caste groups (Vizag Brahmins, Peruru Brahmins, Kammas), three tribes (Bagata, Poroja, Valmiki) and an additional group (the Siddis) of African ancestry. Principal component and AMOVA analyses show that the between group component of variation is non-significant (P>0.05), while that among populations within the caste and tribal groups is significant (P<0.001). In particular, the Valmikis and Siddis are close to the caste groups. Of a total of 11 distinct SNP-haplotypes observed, the two tribal groups (Bagata and Poroja) lack the haplotypes H4, H4A, H5A and H16, which are seen in the caste groups. In contrast, all three tribal groups exhibit the Southeast Asian haplotype H11 that is absent in the caste populations. The presence of haplotypes H4, H5, H14, and H16 in the Siddis indicate that they have assimilated considerable non-African admixture. The evidence of haplotype sharing between castes and tribes is also found when the H14 lineage was further subdivided by five STR loci. We conclude that even though these SNP-based Y-haplotypes are able to distinguish the populations, gene flow in these South Indian populations is not as negligible as that inferred from other studies based on Y-specific short tandem repeat markers.

Utilization of an intramolecular hydrogen bond to increase the CNS penetration of an NK(1) receptor antagonist

This paper describes the synthesis and physical and biological effects of introducing different substituents at the alpha-position of the tryptophan containing neurokinin-1 receptor antagonist [(R)-2-(1H-indol-3-yl)-1-methyl-1-((S)-1-phenyl-ethylcarbamoyl)-ethyl]-carbamic acid benzofuran-2-ylmethyl ester (CI 1021). The described compounds all exhibit less than 5 nM binding affinities for the human neurokinin-1 receptor and selectivity over the tachykinin NK(2) and NK(3) receptor subtypes. Application of variable temperature nuclear magnetic resonance spectroscopy studies of the amide and urethane protons was utilized to determine the existence of an intramolecular hydrogen bond. This intramolecular hydrogen bond increases the apparent lipophilicity to allow increased central nervous system penetration and pharmacological activity (gerbil foot tap test) in the case of the highest affinity compound [(S)-1-dimethylaminomethyl-2-(1H-indol-3-yl)-1-((S)-1-phenyl-ethylcarbamoyl)-ethyl]-carbamic acid benzofuran-2-ylmethyl ester (PD 174424) over those analogues that could not form an intramolecular hydrogen bond.