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The article discusses details of several medical cases of patients with Autosomal recessive epidermolysis bullosa simplex (AR-EBS) from India. Topics of the article include the family details of the patients, the genetic characterization of the family, along with the use of genomic DNA probing for the exome sequencing.

The demonstrated variable efficacy of the only licensed TB vaccine Mycobacterium bovis bacillus Calmette-Guérin (M. bovis BCG) encourages the need for new vaccine candidates against TB. Antigen specific cellular immune response is often considered imperative during Mycobacterium tuberculosis (M. tuberculosis) infection and antigens that are strongly associated with the latent phase of infection are drawing increasing attention for anti-TB vaccine development. Here, we investigated the phenotypic and functional profiles of two novel mycobacterial antigens Rv2251 and Rv2721c during T cell recall response via multi-color flow cytometry. Healthy household contacts of TB (latent/HHC) and active pulmonary TB (PTB) patients were recruited to investigate the difference in antigen specific T cell recall response. These two antigens induced expansion of CD45RA- CCR7+ central memory subtypes and CD45RA- CCR7- effector memory cells in latent population which suggests their possible association with HHC. Rv2251 and Rv2721c antigen specific IFN-γ, TNF-α and IL-2 response was also significantly high in HHC when compared to the PTB (p < 0.005, p < 0.05 and p < 0.05 respectively). The frequency of multifunctional T cells also was high in HHC compared to the PTB with statistical significance only for the antigen Rv2251. Often, the dominant Th1 immune response in HHC is correlated with the protection against the active TB disease. Collectively, we report the first insights into Rv2251 and Rv2721c antigen specific immune response in human donors of TB and provide the immunologic rationale for selecting them for vaccine development against TB. [ABSTRACT FROM AUTHOR]

Background: Control of the global burden of tuberculosis is obstructed due to lack of simple, rapid and cost effective diagnostic techniques that can be used in resource poor-settings. To facilitate the early diagnosis of TB directly from clinical specimens, we have standardized and validated the use of nested multiplex PCR, targeting gene fragments IS6110, MTP40 and 32kD α-antigen encoding genes specific for Mycobacterium tuberculosis complex and non-tubercular mycobacteria (NTM), in comparison to smear microscopy, solid culture and single step multiplex PCR. The results were evaluated in comparison to a composite reference standard (CRS) comprising of microbiological results (smear and culture), clinical, radiological and cytopathological findings, clinical treatment and response to anti-tubercular therapy.Methods: The nested multiplex PCR (nMPCR) assay was evaluated to test its utility in 600 (535 pulmonary and 65 extra-pulmonary specimens) clinically suspected TB cases. All specimens were processed for smear, culture, single step multiplex PCR and nested multiplex PCR testing.Results: Out of 535 screened pulmonary and 65 extra-pulmonary specimens, 329 (61.5%) and 19 (29.2%) cases were culture positive for M. tuberculosis. Based on CRS, 450 patients had "clinical TB" (definitive-TB, probable-TB and possible-TB). Remaining 150 were confirmed "non-TB" cases. For culture, the sensitivity was low, 79.3% for pulmonary and 54.3% for extra-pulmonary cases. The sensitivity and specificity results for nMPCR test were evaluated taken composite reference standard as a gold standard. The sensitivity of the nMPCR assay was 97.1% for pulmonary and 91.4% for extra-pulmonary TB cases with specificity of 100% and 93.3% respectively.Conclusion: Nested multiplex PCR using three gene primers is a rapid, reliable and highly sensitive and specific diagnostic technique for the detection and differentiation of M. tuberculosis complex from NTM genome and will be useful in diagnosing paucibacillary samples. Nested multiplex PCR assay was found to be better than single step multiplex PCR for assessing the diagnosis of TB. [ABSTRACT FROM AUTHOR]

Summary: Background: Not all patients infected with NDM-1-positive bacteria have a history of hospital admission in India, and extended-spectrum β-lactamases are known to be circulating in the Indian community. We therefore measured the prevalence of the NDM-1 gene in drinking water and seepage samples in New Delhi. Methods: Swabs absorbing about 100 μL of seepage water (ie, water pools in streets or rivulets) and 15 mL samples of public tap water were collected from sites within a 12 km radius of central New Delhi, with each site photographed and documented. Samples were transported to the UK and tested for the presence of the NDM-1 gene, bla NDM-1, by PCR and DNA probing. As a control group, 100 μL sewage effluent samples were taken from the Cardiff Wastewater Treatment Works, Tremorfa, Wales. Bacteria from all samples were recovered and examined for bla NDM-1 by PCR and sequencing. We identified NDM-1-positive isolates, undertook susceptibility testing, and, where appropriate, typed the isolates. We undertook Inc typing on bla NDM-1-positive plasmids. Transconjugants were created to assess plasmid transfer frequency and its relation to temperature. Findings: From Sept 26 to Oct 10, 2010, 171 seepage samples and 50 tap water samples from New Delhi and 70 sewage effluent samples from Cardiff Wastewater Treatment Works were collected. We detected bla NDM-1 in two of 50 drinking-water samples and 51 of 171 seepage samples from New Delhi; the gene was not found in any sample from Cardiff. Bacteria with bla NDM-1 were grown from 12 of 171 seepage samples and two of 50 water samples, and included 11 species in which NDM-1 has not previously been reported, including Shigella boydii and Vibrio cholerae. Carriage by enterobacteria, aeromonads, and V cholera was stable, generally transmissible, and associated with resistance patterns typical for NDM-1; carriage by non-fermenters was unstable in many cases and not associated with typical resistance. 20 strains of bacteria were found in the samples, 12 of which carried bla NDM-1 on plasmids, which ranged in size from 140 to 400 kb. Isolates of Aeromonas caviae and V cholerae carried bla NDM-1 on chromosomes. Conjugative transfer was more common at 30°C than at 25°C or 37°C. Interpretation: The presence of NDM-1 β-lactamase-producing bacteria in environmental samples in New Delhi has important implications for people living in the city who are reliant on public water and sanitation facilities. International surveillance of resistance, incorporating environmental sampling as well as examination of clinical isolates, needs to be established as a priority. Funding: European Union. [Copyright &y& Elsevier]

Abstract: Objective: To compare the utility of cytology and HPV testing in women from Mumbai, India, suspected of having cervical intraepithelial neoplasia (CIN) on visual inspection with acetic acid (VIA), Lugol''s iodine (VILI), or both. Method: The sensitivity, specificity, and predictive values of these tests for the detection of CIN 2 and/or 3 were evaluated in this cross-sectional study with 756 women suspected of having CIN on visual inspection. Results: There were 25 women with CIN 2, 20 with CIN 3, and 21 with invasive cancer. The sensitivity to detect CIN 3 lesions was 85.0% (95% CI, 62.1–96.8) and 70.0% (95% CI, 45.7–88.1) for cytology testing at the ASCUS and LSIL thresholds, respectively, and it was 89.5% (95% CI, 66.9–98.7) for HPV testing. The specificity to detect CIN 3 lesions was 94.5% (95% CI, 92.5–96.1) and 96.1% (95% CI, 94.4–97.5) for cytology testing at the ASCUS and LSIL thresholds, and it was 91.1% (95% CI, 88.5–93.2) for HPV testing. Conclusion: Cytology and HPV testing were both found to be accurate triaging methods for women suspected of having CIN on visual inspection, especially for those with CIN 3 lesions. [Copyright &y& Elsevier]

Isothermal techniques with lateral flow detection have emerged as a point of care (POC) technique for malaria, a major parasitic disease in tropical countries such as India. Plasmodium falciparum and Plasmodium vivax are the two most prevalent malaria species found in the country. An advanced multiplex loop-mediated isothermal amplification (mLAMP) combined with a lateral flow dipstick (LFD) technique was developed for the swift and accurate detection of P. falciparum and P. vivax, overcoming the challenges of the existing RDTs (rapid diagnostic tests). A single set of LAMP primers with a biotinylated backward inner primer (BIP primer) was used for DNA amplification of both malaria species in a single tube. The amplified DNA was hybridized with fluorescein isothiocyanate (FITC) and digoxigenin-labelled DNA probes, having a complemented sequence for the P. falciparum and P. vivax genomes, respectively. A colour band appeared on two separate LFDs for P. falciparum and P. vivax upon running the hybridized solution over them. In total, 39 clinical samples were collected from ICMR-NIMR, New Delhi. Melting curve analysis, with cross primers for both species, was used to ascertain specificity, and the sensitivity was equated with a polymerase chain reaction (PCR). The results were visualized on the LFD for both species within 60 min. We found 100% sensitivity and specificity, when compared with a traditional PCR. Melting curve analysis of mLAMP revealed the lowest detection limit of 0.15 pg/μL from sample genomic DNA. The mLAMP-LFD assays could be a potential point of care (POC) tool for early diagnosis in non-laboratory conditions, with the convenience of a reduced assay time and the simple interpretation of results. [ABSTRACT FROM AUTHOR]

Occurrence of yellow vein mosaic disease of mesta ( Hibiscus cannabinus L. and H. sabdariffa L.) was found to be endemic in parts of India. For rapid and sensitive diagnosis of the Begomovirus associated with this disease, a radiolabelled diagnostic method has been developed. Southern hybridization and nucleic acid spot hybridization using radiolabelled probes to the coat protein (CP) gene of DNA A and DNA β of the virus were able to detect the virus both in plants and in viruliferous whiteflies. These probes detected the presence of the same virus in experimentally infected Vigna plants showing only leaf crumpling symptoms. These probes were also able to detect infection in other crops, ornamentals and weed plants showing characteristic symptoms of whitefly-transmitted geminiviruses. Polymerase chain reaction amplification through primers specific to the CP gene, full-length DNA A and full-length DNA β molecules using DNA isolated from all infected plants and viruliferous whiteflies detected presence of same virus in them. [ABSTRACT FROM AUTHOR]

This article cites a study determining the association of polymorphisms in pulmonary surfactant protein (SP) A1 and A2 genes with high-altitude pulmonary edema (HAPE). The study population consisted of 46 age-matched male volunteers. All of the subjects were unrelated natives of India. The blood samples were drawn from the HAPE patients within 2 to 3 days of occurrence of the symptoms. At the time of collection of the samples, the HAPE patients were still ill and under treatment in the hospital. Genomic DNA was extracted from peripheral blood mononuclear cells following a previously described protocol. Purified genomic DNA samples were used as templates in the polymerase chain reaction amplification of various regions of SP-A1 and SP-A2. Based on the findings of the study, it was concluded that the polymorphisms in SP-A1 and SP-A2 might be one of the genetic factors contributing to susceptibility to HAPE.

We have previously reported an interaction between -514C>T polymorphism at the hepatic lipase (HL) gene and dietary fat on high-density lipoprotein-cholesterol (HDL-C) metabolism in a representative sample of white subjects participating in the Framingham Heart Study. Replication of these findings in other populations will provide proof for the relevance and consistency of this marker as a tool for risk assessment and more personalized cardiovascular disease prevention. Therefore, we examined this gene-nutrient interaction in a representative sample of Singaporeans (1324 Chinese, 471 Malays and 375 Asian Indians) whose dietary fat intake was recorded by a validated questionnaire. When no stratification by fat intake was considered, the T allele was associated with higher plasma HDL-C concentrations (P = 0.001), higher triglyceride (TG) concentrations (P = 0.001) and higher HDL-C/TG ratios (P = 0.041). We found a highly significant interaction (P = 0.001) between polymorphism and fat intake in determining TG concentration and the HDL-C/TG ratio (P = 0.001) in the overall sample even after adjustment for potential confounders. Thus, TT subjects showed higher TG concentrations only when fat intake supplied >30% of total energy. This interaction was also found when fat intake was considered as continuous (P = 0.035). Moreover, in the upper tertile of fat intake, TT subjects had 45% more TG than CC individuals (P < 0.01). For HDL-C concentration, the gene-diet interaction was significant (P = 0.015) only in subjects of Indian origin. In conclusion, our results indicate that there are differences in the association of -514C>T polymorphism with plasma lipids according to dietary intake and ethnic background. Specifically, the TT genotype is associated with a more atherogenic lipid profile when subjects consume diets with a fat content > 30%. [ABSTRACT FROM AUTHOR]

Introduction: Human papilloma virus (HPV) has been associated with oral squamous cell carcinoma (OSCC) as a potential carcinogen. There are several types of HPV, of which type 16 has been strongly implicated in carcinogenesis. HPV16 in saliva can potentially facilitate early detection of subclinical cases that may warrant further diagnosis, monitoring and intervention., Aim: The aim of this study was to evaluate the presence of HPV 16 in saliva and lesional tissue of OSCC and to determine the use of saliva as an alternative non invasive diagnostic tool in HPV16 identification., Materials and Methods: 30 cases of Histopathologically confirmed OSCC with HPV positive on ELISA were taken up for the study. The tumour tissue and saliva sample of each patient were obtained to detect the presence of specific HPV16 genotype by polymerase chain reaction (PCR). The data was subjected to statistical analysis using Student t-test., Results: In our study we found 28/30, 26/30 positive for HPV 16 in tissue and saliva samples respectively on PCR analysis. The P value was statistically significant (0.00)., Conclusion: The study revealed significant prevalence of HPV 16 among both tissue and salivary specimens of OSCC patients in south Indian population. Though, the yielded content was relatively less in saliva, it can be concluded that, saliva being a non invasive tool proved to be as useful as tissue specimen and can be used as an alternative indicator of HPV16 positivity in OSCC., Competing Interests: None

Develops DNA probes to differentiate groups of Giardia lamblia strains present in symptomatic and asymptomatic persons in India. Clinical symptoms; Laboratory findings; Efficacy of the probe.

Setting: Department of Microbiology., Objective: To determine the common mutations responsible for rifampicin resistance in TB cases detected by Xpert MTB/RIF assay., Design: Results of Xpert MTB/RIF assay performed from 2013 to 2017 were analysed for missing probes in different types of specimens containing rifampicin resistant MTB., Results: Successful results were obtained in14872 of the total 15129 specimens processed by Xpert MTB/RIF assay, of which 9458 (63.6%) were sputum and 5414 (36.4%) were extrapulmonary specimens. MTB was detected in 1624 (17.17%) sputum and 1121 (20.70%) extrapulmonary specimens of which 409 (25.18%) and 277 (24.71%) were rifampicin resistant respectively. Probe E (83.82%) was the commonest probe responsible for rifampicin resistance followed by D (3.93%) and B (3.79%). Mutation in probe C (0.29%) was very rare. Combination of missing probes like AB (0.73%), DE (1.16%) and ADE (0.14%) was observed. 22 (3.2%) specimens showed presence of all five probes., Conclusion: Xpert MTB/RIF assay uses various combinations of probe to detect MTB along with rifampicin resistance and is a valuable diagnostic tool. It can become a useful epidemiological tool to identify dynamics of transmission of TB by addition of few more probes to identify mutations at specific codons., (Copyright © 2018 Tuberculosis Association of India. Published by Elsevier B.V. All rights reserved.)

Anthrax is a zoonotic disease caused by Bacillus anthracis, and well recognized as a potential agent for bioterrorism. B. anthracis can be identified by detecting the virulence factors genes located on two plasmids, pXO1 and pXO2. The aim of the present study was to determine the presence of virulence genes in 27 isolates of B. anthracis isolated from clinical and environmental samples. For this purpose, multiplex PCR and DNA probes were designed to detect protective antigen ( pag), edema factor (cya), lethal factor (lef ), and capsule (cap) genes. Our results indicated that all the isolates contained all the above virulence genes, suggesting that the isolates were virulent. To the best our knowledge, this is the first study about the determination of virulence marker genes in clinical and environmental isolates of B. anthracis using multiplex PCR and DNA probes in India. We suggest that the above methods can be useful in specific identification of virulent B. anthracis in clinical and environmental samples.

Background: Most of the quantitation assays for HIV-1 RNA used currently are designed and optimized for HIV-1 subtype B viruses and hence may not be suitable for India, where the predominant subtype is HIV-1 subtype C., Objectives: Development and standardization of HIV-1 TaqMan real time PCR assay suitable for measuring plasma and CSF viral RNA levels in HIV subtype C infected individuals., Study Design: A TaqMan real time PCR was developed using primers and probes selected in the gag region for detection of Indian HIV-1 subtype C strain. Plasma (n=120) and CSF samples (n=46) obtained from HIV infected subjects were used to evaluate the sensitivity and specificity of the assay. A comparative evaluation was carried out with a commercially available quantitative HIV viral load assay (Roche Amplicor Version 1.5)., Results: The TaqMan assay was able to amplify all HIV-1 group M subtypes except subtype E. Viral loads could be estimated in all the plasma (n=120) and 40/46 CSF samples obtained from HIV positive subjects. Sensitivity of this assay was found to be 180 copies/ml. Correlation with the commercially available viral load assay was very good (r=0.885)., Conclusions: A TaqMan real time PCR was standardized for HIV-1 subtype C and it was more sensitive (180 copies/ml) than standard Amplicor monitor assay, Version 1.5 (400 copies/ml).

Southern hybridization with the complex probe Ca3 is a well established tool for molecular subtyping of Candida albicans. Multilocus sequence typing (MLST) is a DNA sequence-based subtyping method recently applied to C. albicans and shown to have a high degree of intraspecies discriminatory power. However, its utility for studying the molecular epidemiology of sequential isolates from recurrent disease has not been established. We compared Ca3 Southern hybridization and MLST using seven housekeeping genes (CaAAT1a, CaACC1, CaADP1, CaPMI, CaSYA1, CaVPS13, CaZWF1b) for their ability to discriminate among 37 C. albicans isolates from recurrent cases of oropharyngeal candidiasis (OPC) in ten HIV-positive patients from India and the US. Among the 37 isolates, MLST identified 23 distinct genotypes (index of diversity = 97%); Ca3 Southern hybridization identified 21 distinct genotypes (index of diversity = 95%). Both methods clustered isolates into seven genetically-related groups and, with one exception, isolates that were indistinguishable by MLST were indistinguishable or highly related by Ca3 Southern hybridization. These results demonstrate that MLST performs equally well or better compared to Ca3 Southern hybridization for defining genetic-relatedness of sequential C. albicans isolates from recurrent cases of OPC in HIV-positive patients.

Lebanon is located at a continental crossroad between Europe, Africa, and Asia. This region has been the center of wide-scale movements of populations as well as the theater of genetic and cultural trade off among neighboring populations. In this study, HLA-C alleles were characterized by a PCR-SSOP (sequence-specific oligonucleotide probes) hybridization protocol in a sample of 97 Lebanese. A total of 23 alleles were identified with four predominant, Cw*0401, Cw*0602, Cw*0701/06, and Cw*1203, accounting for almost 60% of HLA-C allele frequencies. We included the Lebanese data into a broad analysis of the HLA-C genetic structure of a large set of populations located in Europe, the Middle East, and the Indian subcontinent. Our results indicate that Lebanese exhibit an intermediate genetic profile among the populations from the Middle East, which constitute a rather homogeneous genetic group. In Europe, a high correlation coefficient is found between genetic and geographic distances. In this continent, we also identified a significant genetic frontier following a north-east to south-west axis. This frontier cuts through the Alps and the Pyrenees, thus separating the north-western European populations from those located in the eastern and Mediterranean areas. Finally, the populations from India - Pakistan are very heterogeneous, particularly the Dravidians. Their differentiation has probably been caused by rapid genetic drift under complex influences of cultural, linguistic, and/or religious barriers. Overall, the results show that the HLA-C genetic patterns of these three geographic regions, i.e., the Middle East, Europe, and India-Pakistan, have been shaped by very different genetic histories.

The prevalence of hepatopancreatic parvovirus (HPV) in wild penaeid shrimp samples from India was studied by nested polymerase chain reaction (PCR) using primers designed in our laboratory. The virus could be detected in 9 out of 119 samples by non-nested PCR. However, by nested PCR 69 out of 119 samples were positive. The PCR results were confirmed by hybridization with digoxigenin-labelled DNA probe. Shrimp species positive by non-nested PCR included Penaeus monodon, Penaeus indicus and Penaeus semisulcatus and by nested PCR Parapenaeopsis stylifera, Penaeus japonicus, Metapenaeus monoceros, M. affinis, M. elegans, M. dobsoni, M. ensis and Solenocera choprai. This is the first report on the prevalence of HPV in captured wild shrimp from India.

Neptunia natans is a unique aquatic legume indigenous to tropical and sub-tropical regions and is nodulated symbiotically by rhizobia using an unusual infection process unlike any previously described. Previously, isolates of neptunia-nodulating rhizobia from Senegal were characterized as Allorhizobium undicola. Here we report on a different group of neptunia-nodulating rhizobia isolated from India. Sequencing of the 16S rDNA gene from two of these Indian isolates (strains J1T and J2) show that they belong in the genus Devosia rather than Allorhizobium. Currently, the only described Devosia species is D. riboflavina (family Hyphomicrobiaceae, order Rhizobiales). The complete 16S rDNA sequences of strains J1T and J2 are 95.9% homologous to the type strain, D. riboflavina LMG 2277T, suggesting that these neptunia-nodulating strains from India belong to a new Devosia species. This hypothesis was confirmed by further studies of polyphasic taxonomy (DNA-DNA hybridisation, TP-RAPD patterns, SDS-PAGE of cellular proteins, 16S rDNA RFLP patterns, carbon source utilisation, cellular fatty acid analysis and other phenotypic characterisations), all of which support the proposal that these neptunia-nodulating strains constitute a new Devosia species, which we name Devosia neptuniae sp. nov. These gram negative, strictly aerobic short rods are motile by a subpolar flagellum, positive for catalase, oxidase, urease and beta-galactosidase, can utilise several carbohydrates (but not organic acids) as carbon sources and contain C18:0 3-OH, cis-7 C18:1 11-methyl and cis-7 C18:1 as their major cellular fatty acids. Unlike D. riboflavina, the longer-chain C24:1 3-OH and C26:1 3-OH hydroxy fatty acids are not detected. The type strain of D. neptuniae is LMG 21357T (CECT 5650T). Assignment of this new taxon represents the fourth example in the literature of a non-rhizobial genus of bacteria capable of forming a bonafide dinitrogen-fixing root-nodule symbiosis with legume plants.

Molecular mechanisms of multidrug resistance in Vibrio cholerae belonging to non-O1, non-O139 serogroups isolated during 1997 to 1998 in Calcutta, India, were investigated. Out of the 94 strains examined, 22 strains were found to have class I integrons. The gene cassettes identified were dfrA1, dfrA15, dfrA5, and dfrA12 for trimethoprim; aac(6')-Ib for amikacin and tobramycin; aadA1 and aadA2 for streptomycin and spectinomycin; and ereA2 for erythromycin resistance. To our knowledge, this is the first report of the presence of dfrA5, dfrA12, aac(6')-Ib, and ereA2 cassettes in class I integrons of V. cholerae. Forty-three of 94 strains also had plasmids, and out of these, 14 contained both class I integrons and plasmids. Pulsed-field gel electrophoresis followed by Southern hybridization revealed that in the 14 plasmid-bearing strains, class I integrons resided either on chromosomes, on plasmids, or on both. Our results indicated that besides class I integrons and plasmids, a conjugative transposon element, SXT, possibly contributed to the multiple antibiotic resistance.

Biotechnology (BT) has implications in the diagnosis, treatment/cure and prevention of diseases. Based on BT, a wide range of advanced drugs, diagnostics and vaccines have become available and are integral part of the health care system. Many new imaging and surgical intervention techniques also have great positive impact. However, given the limited resources available, especially in developing countries, the new techniques must be prioritized for correct policy decisions. This paper presents an exercise in prioritizing diagnostics and vaccines and comparing them with other high-tech medical care, which often receive the attention and favor of decision-makers and health care providers. This involves assessing the technologies for their beneficence index. This index is derived by accumulating the ratings for seven different factors e.g., need, efficacy, additional QALY, ease of integration. The outcome of the exercise shows diagnostics and vaccines to be more beneficial than surgical procedures and imaging technologies in the Indian context. Such an exercise could form a basis for resource allocation and can be favored by incentive structures for better social benefits.

Ag-NOR staining and fluorescence in situ hybridization with rDNA probes showed an unusually high number of NORs in the Indian pygmy field mice, Mus booduga and the M. terricolor complex. The chromosomal location of the NORs was also altered in terricolor, they were shifted from the proximal regions of the long arms to the tips of the perceptible heterochromatic short arms of the acrocentric autosomes. The results suggested dispersion of the NORs in the booduga-terricolor lineage probably by transposition, and relocalization of the NORs in the terricolor complex by centric reorganization during the process of replacement of the Mus musculus-related AT-rich heterochromatin with the terricolor-specific heterochromatin., (Copyright 2001 S. Karger AG, Basel)

Various tests have been described to differentiate the pathogenic and non-pathogenic types of E. histolytica. Recently DNA hybridization has been described to differentiate between the two subtypes. Using common HMC probe the presence of E. histolytica in stool was confirmed. Then on the basis of hybridization with DNA probe P 145 (pathogenic) and B 133 (non-pathogenic) E. histolytica was characterized as being pathogenic and non pathogenic respectively. Out of 137 patients studied 88 were symptomatic and 49 asymtomatic. 65 patients harboured E. histolytica as proved by microscopic examination of stool. Sixty-eight stool samples tested positive for DNA hybridization with common HMC probe, this included 65 microscopy positive samples and 3 microscopy negative samples. This gives a sensitivity of 100% and 96% specificity. All the 68 samples were then subjected to hybridization with P 145 and B 133 DNA probes. Out of 88 symptomatic patients stool samples of 57 patients were microscopy positive, however 58 were positive by common HMC probe and all of these were P 145 (pathogenic) positive and B 133 (non-pathogenic) negative. Of the 49 asymptomatic cases 8 were E. histolytica positive on microscopy and 10 positive on hybridization with common HMC probe and all 10 were P 145 negative and B 133 positive. It can be thus concluded that DNA hybridization is a reliable way to differentiate between pathogenic and nonpathogenic E. histolytica.

We examined 103 oral squamous cell carcinomas (OSCC), 100 oral lesions consisting primarily of leukoplakia (82 cases), and 76 clinically normal mucosa specimens from the contralateral site in the oral cavity of individuals with oral lesions, for the presence of Epstein-Barr virus (EBV). Polymerase chain reaction (PCR) was used to amplify a 239 bp fragment of the BamHIL region of the EBV genome, followed by Southern blot hybridization with EBV oligonucleotide probe to increase further the specificity and sensitivity of the assay system. Since EBV seropositivity is frequent in populations, we also examined the peripheral blood cells (PBC) from 141 patients (50 oral cancer patients, 91 patients with oral lesions) for the presence of EBV. We detected EBV in 25 of 103 (25%) OSCC, 13 of 100 (13%) oral lesions, 3 of 76 (4%) clinically normal mucosa samples and 10 of 141 (7%) PBC. Our results indicate that EBV may contribute as one of the multiple factors in oral cancers, in a certain proportion of Indian patients.

Previous reports have suggested that Asiatic lions and tigers are highly inbred and exhibit very low levels of genetic variation. Our analyses on these species have shown much higher degrees of polymorphism than reported. Randomly amplified polymorphic DNA (RAPD) analysis of 38 Asiatic lions, which exist as a single population in the Gir Forest Sanctuary in India, shows an average heterozygosity of 25.82% with four primers. Sperm motility studies by our colleagues corroborate this data. In Indian tigers, microsatellite analysis of five CA repeat loci and multilocus fingerprinting using Bkm 2(8) probe on a population of 22 individuals revealed a heterozygosity of 22.65%. Microsatellite analysis of loci Fca 77 and Fca 126 revealed polymorphism amongst the Asiatic x African lion hybrids, which has enabled us to use these as markers to discriminate the pure Asiatic lions from the hybrids. A similar analysis was used to identify hybrids of Indian and Siberian tigers through polymerase chain reaction (PCR) amplification of hair samples. To ascertain the variation which existed before the population bottleneck at the turn of the present century, microsatellite analysis was performed on 50- to 125-year-old skin samples from museum specimens. Our results show similar levels of genetic variability as in the present population (21.01%). This suggests that low genetic variability may be the characteristic feature of these species and not the result of intensive inbreeding. DNA fingerprinting studies of Asiatic lions and tigers have helped in identifying individuals with high genetic variability which can be used for conservation breeding programs.

Sixty-one clinical strains of Vibrio cholerae O1 El Tor isolated in Calcutta before, during, and after the V. cholerae O139 Bengal outbreak were examined to see if the O1 strains of the post-O139 period were different from those in existence before. Comparison of the restriction fragment length polymorphism of the rRNA genes (ribotyping) and the CTX genetic element revealed that all "before" strains except 1 belonged to a single known ribotype, whereas all "after" strains except 2 belonged to a hitherto undescribed ribotype. Also, 23 of 25 "before" strains harbored two or more copies of CTX in tandem and also a "free" RS1 element away from CTX, whereas 19 of 21 "after" strains had a single copy of CTX and no free RS1 element. CTX occupied different chromosomal locations in "before" and "after" strains. These studies clearly showed that El Tor O1 strains, which displaced V. cholerae O139 in Calcutta, belonged to a new clone and suggested that there is a continuous genetic reassortment among El Tor strains of V. cholerae O1.

We have isolated based on reverse genome hybridization, and sequenced a DNA clone, pNZE25, from a partial genomic library of the Asian rice gall midge Orseolia oryzae (Wood-Mason) (O.o.). Clone pNZE25 is highly A+T rich (67%), lacks any open reading frame and does not display homology to sequences in GenBank. Clone pNZE25 detects a 120-bp repeat in the O.o. genome, as seen from the generation of a 120-bp ladder after Southern analysis of HinfI-digested genomic DNA. When used to probe O.o. genomic DNA digested with DraI, HaeIII or AluI, pNZE25 generates individual specific DNA fingerprints on target DNA isolated from gall midge biotypes collected from different parts of India.

The type strains of Vi-phage types E1, M1 and A of Salmonella typhi, together with drug-resistant and drug-sensitive strains of phage types E1 and M1 isolated in 1992 from patients associated with India or Pakistan, and a drug-resistant strain of phage type A isolated in South Africa in 1991, were characterised with respect to the presence of plasmids conferring resistance to antimicrobial drugs and their chromosomal insertion sequence IS200 profiles. The three type strains, the drug-sensitive strains of Vi-phage types E1 and M1, and a strain of phage type M1 resistant to ampicillin and trimethoprim but not to chloramphenicol, did not contain plasmids. In contrast, for strains of phage types E1 and M1 resistant to chloramphenicol, ampicillin and trimethoprim, and for the drug-resistant strain of phage type A, the complete spectrum of resistance was encoded by high molecular mass plasmids belonging to the H1 incompatibility group. Characterisation of IS200 profiles demonstrated that at least 13 IS200 copies were distributed on the chromosome of all strains tested. Although the IS200 profiles of the type strains of Vi-phage types A, E1 and M1 were identical, it was possible to distinguish between drug-sensitive and drug-resistant strains of Vi-phage types E1 and M1 isolated from patients infected in India and Pakistan by this method. It was concluded that although IS200 typing is not as discriminatory as phage typing for the primary subdivision of S. typhi, it may be useful for certain epidemiological investigations and, in particular, for investigating the origins of strains with multiple drug resistance.

Four DNA probes (L754, p99-6, pERT87-1 and pERT87-15) from the short arm of the human X chromosome were studied in two European (English and Spanish) and two Asiatic Indian (Maratha and Parsi) populations. All four RFLPs showed conclusive heterogeneity among the four populations. Nei's genetic distance (d) matrix shows an affinity between the Parsis and the population from southern Europe. There is an interesting suggestion of a west to east clinic for allele *2 detected by probe L754. Genetic heterogeneity found for the X-linked RFLPs prove that these markers are a useful tool for population genetics studies.

A study for screening of beta-thalassaemia mutations by the Amplification Refractory Mutation System (ARMS) and haplotyping by Polymerase Chain Reaction (PCR) was undertaken because there was a paucity of data in Tamil Nadu in Southern India and to initiate a comprehensive prenatal diagnosis programme. A total of 294 alleles were analysed to study the nature of the mutations, of which 146 were beta-thalassaemia alleles. Only four types of beta-thalassaemia mutations were recorded. Of these, 128 alleles were of the variant IVS-1 nt 5 (G-->C). Thirteen had the mutation codon 41/42 (del TCTT), four had the mutation codon 8/9 (insert G) and one had the 619 bp deletion at the 3' end of the gene. The most common mutation, IVS-1 nt 5 (G-->C), was strongly associated with a single haplotype although the association was not absolute. The population of Tamil Nadu in Southern India seems to be ideal for initiating a prenatal diagnosis programme based on direct detection of mutation by ARMS coupled with RFLP linkage analysis.

A collection of 521 environmental isolates of Vibrio cholerae which were previously examined by the suckling mouse assay and found to be negative for the heat-stable enterotoxin NAG-ST were reassessed by a recently developed DNA probe for NAG-ST. A total of 12 (2.3%) of the isolates hybridized with the NAG-ST probe. By using a cholera toxin (CT) DNA probe, the CT gene was detected in six of the strains in the collection, although none of the isolates of V. cholerae non-O1 hybridized with both of the toxin probes. All of the NAG-ST and CT probe-positive strains were hemolysin positive. Thirty-fold-concentrated supernatants of the three representative NAG-ST DNA probe-positive V. cholerae non-O1 strains gave positive fluid accumulation ratios in the suckling mouse assay even after heating (100 degrees C for 5 min) and also inhibited the binding of a NAG-ST monoclonal antibody to the bound NAG-ST in a competitive enzyme-linked immunosorbent assay (ELISA). Likewise, all six CT probe-positive V. cholerae non-O1 strains produced in vitro CT when examined by the CT bead ELISA. HindIII digest patterns of chromosomal DNA from the representative NAG-ST gene-positive strains were visually indistinguishable. Between the groups of NAG-ST probe-positive strains examined, there was a variation in the hybridizable fragments, with one group of strains exhibiting a hybridizable fragment similar to that of the NRT 36 reference strain; a smaller HindIII fragment hybridized with the NAG-ST probe in the other group of strains.(ABSTRACT TRUNCATED AT 250 WORDS)

Five DNA probes (RC8, 754, XJ 1-1, pert 87.8, and L1.28) from the short arm of the human X chromosome were investigated in samples from five populations (English, Nigerian, Chinese, Muslim, and Hindu from India). The variation in the allele frequencies of several probes between different groups was significant. The average heterozygosity in females of the five populations ranged from 32% to 51%. The genetic distance between the five groups was compatible with that using traditional polymorphic systems. There is an interesting suggestion of longitudinal cline for allele *2 (9 kb) detected with probe L1.28. The X-linked RFLPs are useful genetic markers for anthropological studies.

Eight members of a 3-generation kindred of Indian descent with congenital contractural arachnodactyly (Beals syndrome) have been appraised. Considerable variation was noted in the clinical features of affected persons, and the previously unreported associated finding of clubbing of the fingers and toes was evident in two individuals. The family was investigated using conventional serum and protein markers, and RFLP probes for type I and II collagen. No linkage in affected members could be demonstrated with type I collagen probes.

The TaqI/p49 Y-specific RFLPs were studied in 98 Indians coming from 3 locations in the country. A new allele (G0) and five new haplotypes (XX-XXIV) were found, not present in Caucasians and in Africans. In the genealogy of haplotypes, the new Indian haplotypes appear grouped together, and all Indian haplotypes occupy an intermediate position between Caucasian and African haplotypes.

Restriction fragment length polymorphisms were investigated in five racial groups using the X chromosome probes DXS9 and DXS7. The allele frequencies of these polymorphisms showed significant differences and both DNA fragments were found to be highly polymorphic in the populations of south and southeast Asia. In the Marathi population of India, a rare allele B*3 (3 kilobases; kb) and an altered 7-kb fragment instead of the 6.6-kb constant band were found with DXS9. This is the first time that the rare B*3 allele is found in a non-European population.