Conservation categories of siluroid fishes in North-East Sundarbans,India

In stock fishery of North-East Sundarbans, siluroid fishes hold a remarkable position owing to the culture potentiality of many of them. Scales in fishes play significant role in protection and resistance against environmental stresses and the lack of scalation in case of siluroid fishes is supposed to be one of the reasons for their decline in eco-degraded aquatic habitats. 11 species of fishes belonging to 9 genera, 8 families under the order Siluriformes have been recorded from different water bodies of North-East Sundarbans, India. Fish Magnitude Value (FMV) of those catfishes were recorded especially by information harvested from local fishermen community and stakeholders as well as from market survey on fish landing. The extensive damage to the population of catfishes in the area has placed the fishes under threat categories. Following the IUCN guidelines and also through Participatory Rural Appraisal (PRA) methods, an attempt has been made to assess the status of such fishes. Trend analysis, Fish Magnitude Value (FMV) and Rank Based Quotient (RBQ) revealed 1 catfish as Endangered, 5 as Vulnerable and 5 as Near Threatened species. The situation warrants immediate attention of ecologists, administrators, managers and entrepreneurs to propose remedial measures for revival of the fishes. The study also delineates distribution, present status and conservation measures for revival of the fishes in North-East Sundarbans wet-land environment of West Bengal, India.     

Comparison of the rapidly evolving KIR locus in Parsis and natives of India

The extreme variability at the Killer cell Immunoglobulin-like Receptor (KIR) locus along with that of the genes encoding their ligands, HLA class I, appears to modulate risk for viral, autoimmune, and malignant diseases, and reproductive failure. Differences in KIR gene and haplotype frequencies across world populations may reflect some combination of ancestral genotypes, locale-specific selection pressures, and genetic drift. We genotyped unrelated healthy Parsis and Maharashtrian Hindus, neighboring peoples from Western India. These two populations showed remarkable similarity in KIR gene frequencies despite their distinct ethnic background and the fairly recent migration of Parsis to Western India from Persia around 900 A.D. One clear exception is KIR3DS1, which is found at a significantly higher frequency in the Parsis than in the Maharashtrians, previously characterized North Indians, and most other world populations. The high KIR3DS1 frequency of Parsis corresponds with a low frequency of its putative HLA-B ligand group, an inverse correlation that has been observed previously across other world populations. Thus, KIR3DS1 frequency in Parsis may be a remnant of their distinct ancestral Persian origin. KIR gene frequencies and profiles of the Parsis and Maharashtrians were more similar to one another than they were to North Indians, suggesting a potential effect of local environmental factors on KIR evolution and/or some degree of admixture between Parsis and populations from Western India. Overall, these data support other studies indicating the rapid evolution of the KIR locus and the apparent dependency of this evolution on the loci encoding HLA class I ligands.     

In vitro testing of anthelmintic efficacy of Flemingia vestita (Fabaceae) on carbohydrate metabolism in Rallietina echinobothrida

The root tuber peel of Flemingia vestita has been in use in local traditional medicine against intestinal worm infections in Meghalaya (North-East India). In order to evaluate and authenticate the anthelminitc efficacy of the isoflavones of F. vestita, the root peel extract of this putative plant was tested against several helminth parasites, extensively on Rallietina echinobothrida, with respect to different parameters of these parasites. In this paper, we describe various methods to evaluate the anthelmintic efficacy of this medicinal plant with respect to carbohydrate metabolism in R. echinobothrida at paralytic time caused by the isoflavones of F. vestita. To meet the high energy demand by the parasite due to the anthelmintic stress, glucose breakdown follows the PEPCK-malate pathway in the parasite.     

New record of nucleopolyhedroviruses in tea looper caterpillars in India

Tea production in North-East India hit a record loss due to the widespread severe outbreak of a mixed brood of three species of looper caterpillar pests of geometrid moths (Lepidoptera) in 2008-2010. In addition to Buzura suppressaria, two newly recorded geometrids, viz., Hyposidra infixaria and Hyposidra talaca have caused widespread severe damage in recent years. In the present study we report the nucleopolyhedroviruses (NPV) isolated from the tea looper caterpillar from North-East India. We identified and characterized the NPV by cloning and sequencing a partial segment of polyhedrin gene of virus infected larvae of B. suppressaria, H. talaca and H. infixaria. A comparison of deduced amino acids of polyhedrin gene among H. talaca, H. infixaria and B. suppressaria showed that same strain was found to infect all the three loopers in India, which show high sequence identity with B. suppressaria Chinese isolates. Based on the polyhedrin sequence homology, it is predicted that a variant of B. suppressaria Chinese isolate of NPV found to infect H. talaca, H. infixaria and B. suppressaria in India.     

Study of unscheduled DNA synthesis following exposure of human cells to arecoline and extracts of betel nut in vitro.

Aqueous, acetic acid, hydrochloric acid and ethanol extracts of betel nut (Areca catechu L.) have been found to induce unscheduled DNA synthesis in Hep 2 cells obtained from human larynx carcinoma, in vitro. Different concentrations of extracts of betel nut induced dose-dependent unscheduled DNA synthesis in Hep 2 cells. Together with the viability of the Hep 2 cells, our results indicate that the aqueous and acetic acid extracts of betel nut induce relatively more unscheduled DNA synthesis than the hydrochloric acid and ethanol extracts and arecoline. The carcinogenic potency of raw and unprocessed betel nut of North-East India used in this study is discussed.     

A Rare HBV Subgenotype D4 with Unique Genomic Signatures Identified in North-Eastern India –An Emerging Clinical Challenge?

Background/Aims

HBV has been classified into ten genotypes (A–J) and multiple subgenotypes, some of which strongly influence disease outcome and their distribution also correlate with human migration. HBV infection is highly prevalent in India and its diverse population provides an excellent opportunity to study the distinctiveness of HBV, its evolution and disease biology in variegated ethnic groups. The North-East India, having international frontiers on three sides, is one of the most ethnically and linguistically diverse region of the country. Given the paucity of information on molecular epidemiology of HBV in this region, the study aimed to carry out an in-depth genetic characterization of HBV prevailing in North-East state of Tripura.

Methods

From sera of chronically HBV infected patients biochemical/serological tests, HBV DNA quantification, PCR-amplification, sequencing of PreS/S or full-length HBV genomes were done. HBV genotype/subgenotype determination and sequence variability were assessed by MEGA5-software. The evolutionary divergence times of different HBV subgenotypes were estimated by DNAMLK/PHYLIP program while jpHMM method was used to detect any recombination event in HBV genomes.

Results

HBV genotypes D (89.5%), C (6.6%) and A (3.9%) were detected among chronic carriers. While all HBV/A and HBV/C isolates belonged to subgenotype-A1 and C1 respectively, five subgenotypes of HBV/D (D1–D5) were identified including the first detection of rare D4. These non-recombinant Indian D4 (IndD4) formed a distinct phylogenetic clade, had 2.7% nucleotide divergence and recent evolutionary radiation than other global D4. Ten unique amino acids and 9 novel nucleotide substitutions were identified as IndD4 signatures. All IndD4 carried T¹²⁰ and R¹²⁹ in ORF-S that may cause immune/vaccine/diagnostic escape and N¹²⁸ in ORF-P, implicated as compensatory Lamivudine resistance mutation.

Conclusions

IndD4 has potential to undermine vaccination programs or anti-viral therapy and its introduction to North-East India is believed to be linked with the settlement of ancient Tibeto-Burman migrants from East-Asia.     

Fast recovery of transgenic submergence tolerant rice cultivars of North-East India by early co-cultivation of <Emphasis Type="Italic">Agrobacterium</Emphasis> with pre-cultured callus

Agro-climatic conditions of North-East India are very complex and rice cultivars present in the region have been adapted to grow under harsh environmental conditions. Germplasm present in the region is considered to possess several important and unique traits that are of importance in rice improvement programs. Genetic engineering is a powerful tool to introduce new traits into crop plants. However, not much information is available on the methods to introduce foreign genes into North-East rice cultivars. Therefore, the main objective of this study is to develop transformation procedures for fast recovery of transgenic plants from North-East rice cultivars. To achieve this objective, a systematic study was carried out to identify media components and culture conditions for efficient embryogenic callus induction from the mature seeds and differentiation of callus into plantlets from two North-East deep water rice cultivars, Taothabi and Khongan. Also, role of preculture of callus on Agrobacterium-mediated transformation was studied. Co-cultivation of Agrobacterium with 1–5 days precultured callus was found to result in high frequency of transformation. Detailed characterization of transgenic lines confirmed stable integration of transgenes and expression of reporter gfp gene. The whole process starting from callus induction to regenerating of transgenic rice plants that can be established in the soil was achieved in about 35–45 days. The procedures developed were found to be applicable to a popular variety IR 64. Therefore, methods developed in this study should be useful not only to introduce new traits quickly but also to validate the function(s) of several candidate gene(s) identified under the functional genomics of rice.     

Sometimes Similar,Sometimes Dangerously Different: Exploring Resonance,Laminations and Subject-Formation in South India

This paper explores the ways in which particular individuals or groups are cast as problematically other at certain times by exploring the relationship between empathy and antipathy – identified as products of ‘resonance’, or a certain kind of responsiveness to embodied encounters with others and also to concerns, ideas and discourses that originate locally or from elsewhere. Consequent effects on subject-formation and affordances of social possibilities are explored through an intensive focus on one Muslim man. The notion of a ‘laminated subjectivity’ is presented and elucidated. The paper draws on ethnography conducted in a Tamil town and is set against the backdrop of Hindu–Muslim relations in India.     

In vitro testing of anthelmintic efficacy of Flemingia vestita (Fabaceae) on carbohydrate metabolism in Rallietina echinobothrida

The root tuber peel of Flemingia vestita has been in use in local traditional medicine against intestinal worm infections in Meghalaya (North-East India). In order to evaluate and authenticate the anthelminitc efficacy of the isoflavones of F. vestita, the root peel extract of this putative plant was tested against several helminth parasites, extensively on Rallietina echinobothrida, with respect to different parameters of these parasites. In this paper, we describe various methods to evaluate the anthelmintic efficacy of this medicinal plant with respect to carbohydrate metabolism in R. echinobothrida at paralytic time caused by the isoflavones of F. vestita. To meet the high energy demand by the parasite due to the anthelmintic stress, glucose breakdown follows the PEPCK-malate pathway in the parasite.     

Modeling potential invasion range of alien invasive species,Hyptis suaveolens (L.) Poit. in India: Comparison of MaxEnt and GARP

Bushmint (Hyptis suaveolens (L.) Poit.) is one among the world's most noxious weeds. Bushmint is rapidly invading tropical ecosystems across the world, including India, and is major threat to native biodiversity, ecosystems and livelihoods. Knowledge about the likely areas under bushmint invasion has immense importance for taking rapid response and mitigation measures. In the present study, we model the potential invasion range of bushmint in India and investigate prediction capabilities of two popular species distribution models (SDM) viz., MaxEnt (Maximum Entropy) and GARP (Genetic Algorithm for Rule-Set Production). We compiled spatial layers on 22 climatic and non-climatic (soil type and land use land cover) environmental variables at India level and selected least correlated 14 predictor variables. 530 locations of bushmint along with 14 predictor variables were used to predict bushmint distribution using MaxEnt and GARP. We demonstrate the relative contribution of predictor variables and species-environmental linkages in modeling bushmint distribution. A receiver operating characteristic (ROC) curve was used to assess each model's performance and robustness. GARP had a relatively lower area under curve (AUC) score (AUC: 0.75), suggesting its lower ability in discriminating the suitable/unsuitable sites. Relative to GARP, MaxEnt performed better with an AUC value of 0.86. Overall the outputs of MaxEnt and GARP matched in terms of geographic regions predicted as suitable/unsuitable for bushmint in India, however, predictions were closer in the spatial extent in Central India and Western Himalayan foothills compared to North-East India, Chottanagpur and Vidhayans and Deccan Plateau in India.     

Some studies on three known and a new species of the genus Binema Travassos, 1925 (Travassosinematidae: Thelastomatoidea) from Manipur, North-East India

During the investigation of insect nematodes of North-East India, a new species of Binema (Travassosinematidae: Thelastomatoidea) was recovered from the intestine of Gryllotalpa africana Beauv. It is described and illustrated as Binema anulinervus n.sp. Three known species namely B. ornata Travassos, 1925, B. mirzaia (Basir, 1942) Basir, 1956 and B. korsakowi (Sergiev, 1923) Basir, 1956 have also been collected, redescribed and illustrated in the present study. The new species differs from all known species and only comes close to B. pseudornatum Leibersperger, 1960 for having caudal flagellate appendage. Key to species of the genus and a comparative measurement chart are given in Table 1.     

Potential toxicity of heavy metals in beach and intertidal sediments: A comparative study

The spatial distributions of heavy metals, magnetic susceptibility and granulometric contents have been assessed for beach and intertidal sectors of North-East coast of Tamilnadu, India. Metal concentrations and magnetic susceptibility are high, moderate and low in WER, MER and LER respectively. The measured concentrations are compared with background and toxicological reference values, results insist that in both sectors adverse biological effect is possible in some sites due to the excess Ni and Pb. Calculated three different indexes (PLI, PER and mERM-Q) indicate that in beach and intertidal samples shows moderate and low degree of potential ecological risk respectively. The studied metals might have 21% probability of being toxic in both sectors. Studied metal concentrations, calculated indexes, magnetic susceptibility and clay content are low in intertidal sector. Dominant factors for calculated indexes have been assessed in both sectors. In both cases, all the calculated indexes are positively (low) correlated with magnetic susceptibility and clay.     

Diversity of Streptomyces spp. in Eastern Himalayan region - computational RNomics approach to phylogeny

Isolation and characterization of actinomycetes from soil samples from altitudinal gradient of North-East India were investigated for computational RNomics based phylogeny. A total of 52 diverse isolates of Streptomyces from the soil samples were isolated on four different media and from these 6 isolates were selected on the basis of cultural characteristics, microscopic and biochemical studies. Sequencing of 16S rDNA of the selected isolates identified them to belong to six different species of Streptomyces. The molecular morphometric and physico-kinetic analysis of 16S rRNA sequences were performed to predict the diversity of the genus. The computational RNomics study revealed the significance of the structural RNA based phylogenetic analysis in a relatively diverse group of Streptomyces.     

Alcohol and Tobacco Increases Risk of High Risk HPV Infection in Head and Neck Cancer Patients: Study from North-East Region of India

Background

Human papilloma virus (HPV) associated Head and Neck Cancers (HNCs) have generated significant amount of research interest in recent times. Due to high incidence of HNCs and lack of sufficient data on high-risk HPV (hr-HPV) infection from North -East region of India, this study was conceived to investigate hr-HPV infection, its types and its association with life style habits such as tobacco, alcohol consumption etc.

Methods

A total of one hundred and six primary HNC tumor biopsy specimens were collected. These samples were analyzed for hr-HPV DNA (13 HPV types) using hybrid capture 2 (HC2) assay and genotyping was done by E6 nested multiplex PCR (NMPCR).

Results

The presence of hr-HPV was confirmed in 31.13% (n = 33) and 24.52% (n = 26) of the HNC patients by nested multiplex PCR (NMPCR) and HC2 assay respectively. Among hr-HPV positive cases, out of thirteen hr- HPV types analyzed, only two prevalent genotypes, HPV-16 (81.81%) followed by HPV-18 (18.18%) were found. Significant association was observed between hr-HPV infection with alcohol consumption (p <0.001) and tobacco chewing (p = 0.02) in HNC cases. Compared to HPV-18 infection the HPV-16 was found to be significantly associated with tobacco chewing (p = 0.02) habit.

Conclusions

Our study demonstrated that tobacco chewing and alcohol consumption may act as risk factors for hr-HPV infection in HNCs from the North-East region of India. This was the first study from North-East India which also assessed the clinical applicability of HC2 assay in HNC patient specimens. We suggest that alcohol, tobacco and hr- HPV infection act synergistically or complement each other in the process of HNC development and progression in the present study population.     

Effect of maternal Tp53 gene G412C polymorphism on neural tube defects: A study from North India

CONTEXT:

Tumor protein 53 (tp53) is one of the candidate gene proposed for neural tube defects, which affects central nervous system during early embryonic development, on the basis of mouse models.

AIMS:

The present study is an attempt to unfold the possible role of tp53 G412C polymorphism in the incidence of neural tube defect (NTDs) in humans.

SETTINGS AND DESIGN:

Case-control study was carried out in government hospitals of Delhi, India.

MATERIALS AND METHODS:

Subjects comprised of 100 mothers of NTD children and 100 matched control mothers. Information on some environmental exposures was collected along with blood samples. After DNA extraction, the genotyping of tp53 G412C polymorphism was carried out by PCR-RFLP method.

Statistical Analysys:

Fisher Exact or Chi square test, binary logistic model, and odds ratio (95% confidence interval) calculations were used to evaluate effect of risk factors on NTDs using SPSS v17.0.

RESULTS:

The ‘CC’ genotype of tp53 G412C showed protective effect towards the development of anencephaly and/or encephalocele (OR: 0.44; 95% CI: 0.19-1.00); however, no significant difference among overall NTD cases and controls was observed (P>0.05). Further segregation of all subjects based on 2 different communities, Hindus and Muslims, the association of ‘CC’ genotype of the polymorphism with reduced NTD risk was observed among Hindu community (OR: 0.33; 95% CI: 0.13-0.79).

CONCLUSION:

The study highlights the selective advantage provided by maternal ‘CC’ genotype, thereby reducing risk of cephalic NTDs, probably due to the lower apoptotic activity of the protein, however, more specifically in the presence of community-specific microenvironment.     

Genetic heterogeneity among the Hindus and their relationships with the other “Caucasoid” populations: New data on Punjab-Haryana and Rajasthan Indian States

The genetic structure of Rajasthan Hindus and Punjab-Haryana Hindus and Sikhs has been studied for ABO, RH, APOC2, C6, C7, F13A, F13B, HP, ORM1, ACP1, ADA, AK1, ESD, GLO1, PGD, PGM1 subtyping, and PGP. This is the first genetic survey on Hindus of Rajasthan. Furthermore, many of these markers have never been studied on Hindus before (APOC2, C6, 07, F13A, F13B, ORMl, PGP). These data, together with those previously available for Hindus, have been utilized to analyze the within-Hindus genetic heterogeneity by R_ST statistic and correspondence analysis. The genetic relationships of Hindus to other Causcasoid populations were also investigated. In the first analysis, two eastern states (Orissa and Andhra Pradesh) were found to be quite separate from each other and clearly distinct from the northwestern and western states. Out of the markers which could not be utilized in this analysis, PGM1 subtyping turned out to discriminate between the Dravidian—speaking and the Indo-Aryan-speaking Hindus. The second analysis shows a clear-cut separation of Hindus from Europeans, with Near Eastern and Middle Eastern populations genetically in an intermediate position. © 1995 Wiley-Liss, Inc.     

NeMedPlant: a database of therapeutic applications and chemical constituents of medicinal plants from north-east region of India

The North-East region of India is one of the twelve mega biodiversity region, containing many rare and endangered species. A curated database of medicinal and aromatic plants from the regions called NeMedPlant is developed. The database contains traditional, scientific and medicinal information about plants and their active constituents, obtained from scholarly literature and local sources. The database is cross-linked with major biochemical databases and analytical tools. The integrated database provides resource for investigations into hitherto unexplored medicinal plants and serves to speed up the discovery of natural productsbased drugs. AVAILABILITY: The database is available for free at http://bif.uohyd.ac.in/nemedplant/orhttp://202.41.85.11/nemedplant/     

A Study on the nature of genetic divergence in rice from assam and North East Himalayas

Summary A representative group of 190 rice types collected from North-East India along with four standard varieties, three of which were indicas and one japonica, was studied to understand the nature of genetic divergence. Preliminary grouping was done by canonical analysis and the resultant 42 groups were further classified using the D² statistic.The final grouping resulted in nine divergent clusters. The three indica standards were found in three different clusters indicating the wide available variability among them. The japonica standard formed a separate group by itself. A majority of the North-East Indian types formed clusters with indicas, whereas some were intermediate and still others were closer to japonica or indica, thus indicating a series of intergrades bridging indica and japonica.Height followed by leaf area was found to be important for primary and 100-grain weight, followed by amylose content for secondary differentiation. It appears that natural selection as well as human selection might have operated for characters differentiating rice types in Assam and North Eastern Himalayas. Geographical distance was not found to be related to genetic divergence. The study suggests that O. sativa contains innumerable but divergent forms, and its classification into definite varietal groups on an arbitrary basis such as isolation barrier, sexual affinity or geographic distribution would be far from reality.     

Phylogenetic relationships among Neoechinorhynchus species (Acanthocephala: Neoechinorhynchidae) from North-East Asia based on molecular data

Phylogenetic and statistical analyses of DNA sequences of two genes, cytochrome oxidase subunit 1 (cox 1) of the mitochondrial DNA and 18S subunit of the nuclear ribosomal RNA (18S rRNA), was used to characterize Neoechinorhynchus species from fishes collected in different localities of North-East Asia. It has been found that four species can be clearly recognized using molecular markers—Neoechinorhynchus tumidus, Neoechinorhynchus beringianus, Neoechinorhynchus simansularis and Neoechinorhynchus salmonis. 18S sequences ascribed to Neoechinorhynchus crassus specimens from North-East Asia were identical to those of N. tumidus, but differed substantially from North American N. crassus. We renamed North-East Asian N. crassus specimens to N. sp., although the possibility that they represent a subspecies of N. tumidus cannot be excluded, taking into account a relatively small distance between cox 1 sequences of North-East Asian specimens of N. crassus and N. tumidus. Maximum likelihood, maximum parsimony and Bayesian inference analyses were performed for phylogeny reconstruction. All the phylogenetic trees showed that North-East Asian species of Neoechinorhynchus analyzed in this study represent independent clades, with the only exception of N. tumidus and N. sp. for 18S data. Phylogenetic analysis has shown that the majority of species sampled (N. tumidus + N. sp., N. simansularis and N. beringianus) are probably very closely related, while N. salmonis occupies separate position in the trees, possibly indicating a North American origin of this species.