Legacies of domestication, Neolithic diffusion and trade between Indian subcontinent and Island Southeast Asia shape maternal genetic diversity of Andaman cattle.

Andaman cattle is a precious indigenous livestock species endemic to Andaman and Nicobar Islands, India. Till date, origin and genetic makeup of the breed which is warranted for breed conservation is not known. Moreover, the spread of zebu cattle from Indus valley to different parts of Island Southeast Asia (ISEA) is not properly understood. Here, we report the genetic diversity, population structure of Andaman cattle and their evolution in the context of epicentre of zebu domestication and ISEA. High genetic diversity in complete mitochondrial D-loop sequences indicated the ability of the breed to withstand impending climate change. Total 81 haplotypes were detected and all of them except three belonged to Bos indicus. The presence of taurine haplotypes in Andaman cattle indicate introgression by European-derived cattle. A poor phylogenetic signal of Andaman cattle with genetic affinities with cattle of Indian subcontinent and ISEA was observed. The poor phylogenetic structure may be due to multidirectional gene flow from Indian subcontinent and ISEA, with which Andaman shares a close cultural and trade relationship from Neolithic age. We hypothesize that Andaman cattle is the outcome of Neolithic diffusion from centre of zebu domestication along with multidirectional commercial exchange between Indian subcontinent and ISEA.

Molecular characterization of Rhipicephalus microplus in Andaman and Nicobar Islands, India: an insight into genetic assemblages.

The tick, Rhipicephalus microplus is considered as the most notorious ectoparasite of veterinary importance in tropical and sub-tropical regions of the world. The present study deals with the molecular characterization of R. microplus in different regions of Andaman and Nicobar Islands using sequence information of mitochondrial cytochrome C oxidase subunit I (COX1) and their phylogenetic relationship with other Indian R. microplus genotypes. DNA polymorphism study identified a total of eight haplotypes with haplotype diversity of 0.909 ± 0.065 and nucleotide diversity of 0.01911 ± 0.00493. Currently, R. microplus complex consists of five taxa; R. microplus clade A sensu Burger et al. (2014), R. microplus clade B sensu Burger et al. (2014), R. microplus clade C sensu Low et al. (2015), R. australis and R. annulatus. Phylogenetic analysis revealed the presence of two clades (clade A and clade C) of R. microplus in Andaman and Nicobar isolates; Nicobar isolates belonged to clade A whereas Andaman isolates belonged to clade C of R. microplus complex. All the other Indian sequences retrieved from GenBank belonged to clade C of R. microplus complex. Andaman isolates under clade C of R. microplus were phylogenetically distinct from Indian isolates, which indicates independent speciation under isolated island milieu. In Indian isolates, no host-specific or geographical location-specific sub-clustering was observed which indicates the species jumping potential of the R. microplus tick. Therefore, this study indicated the presence of two different genetic makeup of R. microplus complex in two areas of the Andaman and Nicobar archipelago separated by a natural geographical barrier. This indicates presence of two different founding populations of ticks, one in the south and north-middle Andaman and the other in Nicobar Island.

Exploring broilers and native fowls of Andaman and Nicobar Islands as a source of ß-lactamase-producing Enterobacteriaceae even with limited anthropogenic activities and docking-based identification of catalytic domains in novel ß-lactamase variants.

Objectives: The present study was conducted to detect the occurrence of ß-lactamase and biofilm-producing Escherichia coli, Salmonella, and Klebsiella in broilers and native fowl reared in the Andaman and Nicobar Islands, India. The study also included molecular docking experiments to confirm the nature of the catalytic domains found in the ß-lactamase variants obtained and to reveal the clonal relationship of the isolates with human clinical strains from the database. Materials and methods: A total of 199 cloacal swabs were collected from five poultry breeds/varieties (broiler, Vanraja, Desi, Nicobari, and layer) in three districts of the Andaman and Nicobar Islands. E. coli, Salmonella enterica, and Klebsiella pneumoniae were isolated by standard techniques and confirmed by PCR. Phenotypical ß-lactamase producers were identified by a double-disc test. The genes (bla CTX, bla SHV, bla TEM , and bla AmpC) were screened, and selected sequences of ß-lactamase variants were submitted to DDBJ. Homology modeling, model validation, and active site identification of different ß-lactamase variants were done by the SWISS-MODEL. Molecular docking was performed to identify the catalytic domains of the ß-lactamase variants. The selected ß-lactamase sequences were compared with the Indian ESBL sequences from human clinical strains in NCBI-GenBank. Results: In total, 425 Enterobacteriaceae strains were isolated from the collected samples. Klebsiella pneumoniae (42.58%) was found to be the most prevalent, followed by Salmonella enterica (30.82%) and E. coli (26.58%). The phenotypical antibiogram of all 425 isolates showed the highest resistance against oxytetracycline (61-76%) and the lowest against gentamicin (15-20%). Phenotypical production of ß-lactamase enzymes was observed in 141 (33.38%) isolates. The isolation rate of ß-lactamase producing E. coli, Salmonella enterica, and Klebsiella pneumoniae was significantly higher (p < 0.05) in the birds reared in the South Andaman district (25.6, 17.5, and 18.7%, respectively) than in Nicobar (11.5, 7.6, 7.1%, respectively). Genotyping of the ß-lactamase-producing isolates revealed the maximum possession of bla TEM, followed by bla SHV and bla CTX - M. The nucleotide sequences were found to be similar with bla CTX - M-15, bla SHV - 11, bla SHV - 27, bla SHV - 228, bla TEM - 1, and bla AmpC in BLAST search. Distribution of studied biofilm-associated genes in Enterobacteriaceae strains from different varieties of the birds revealed that the layer birds had the maximum possession, followed by Vanraja, Desi, broilers, and Nicobari fowls. The phylogenetic analysis of selected sequences revealed a partial clonal relationship with human clinical strains of the Indian subcontinent. Molecular docking depicted the Gibbs free energy release for 10 different macromolecules (proteins) and ligand (antibiotic) complexes, ranging from -8.1 (SHV-27 + cefotaxime) to -7 (TEM-1 + cefotaxime) kcal/mol. Conclusion and relevance: The study revealed ß-lactamase variants circulating in the fowl population of the Andaman and Nicobar Islands (India), even in remote places with low anthropogenic activity. Most of the strains possessed bla TEM - 1, followed by bla CTX - M-15. Possession of bla SHV - 11, bla SHV - 27, and bla SHV - 228 in poultry Enterobacteriaceae strains was not reported earlier from any part of the world. The phylogenetic analysis revealed a partial clonal relationship of ß-lactamase sequences with the human clinical strains isolated from the Indian subcontinent.

Origin, genetic diversity and evolution of Andaman local duck, a native duck germplasm of an insular region of India.

Domestic ducks are of paramount importance as a cheap source of protein in rural India. Andaman local duck (ALD) is an indigenous avian genetic resource of Andaman and Nicobar islands (ANI) and is mainly distributed in Middle and Northern parts of these islands. Negligence has brought this breed on the edge of extinction necessitating immediate conservation efforts. Here, we report the genetic diversity, population structure and matrilineal genetic root of ALD. Partial mtDNA D-loop sequences were analyzed in 71 ALD samples and analysis revealed 19 polymorphic sites and 13 haplotypes. Estimated haplotype (Hd ± SD) and nucleotide diversity (π ± SD) were 0.881 ± 0.017 and 0.00897 ± 0.00078 respectively. The high genetic diversity of ALD indicates introgression of genetic material from other local duck breeds. In addition, it can be postulated that ALD bearing high genetic diversity has strong ability to adapt to environmental changes and can withstand impending climate change. Phylogenetic and network analysis indicate that ALD falls under Eurasian clade of mallard and ALD forms three clusters; one cluster is phylogenetically close to Southeast Asian countries, one close to Southern part of mainland India and the third one forms an independent cluster. Therefore, ALD might have migrated either from Southeast Asian countries which enjoy a close cultural bondage with ANI from time immemorial or from Southern part of India. The independent cluster may have evolved locally in these islands and natural selection pressure imposed by environmental conditions might be the driving force for evaluation of these duck haplotypes; which mimics Darwin's theory of natural selection. The results of the study will be beneficial for formulating future breeding programme and conservation strategy towards sustainable development of the duck breed.

Tracing the genetic root of Trinket cattle: an endangered cattle population of a small isolated island of Nicobar group of islands.

Trinket cattle are the inhabitant of a small island called Trinket, which is one of the picturesque islands of Andaman. This herd is thought to be of Danish leftover during their dynasty in Nicobar archipelago. When the island was abandoned by foreign invaders, indigenes utilized the animals for the purpose of meat. As a result, the cattle became semi-feral in nature. After the Great Sumatra earthquake and tsunami of Indian Ocean in 2004, Trinket island was left abandoned by indigenes and the cattle became totally feral in nature. To trace the genetic root of the cattle, this study has been undertaken based on the sequence information of the mitochondrial D-loop and cytochrome b gene. The genomic DNA was extracted from the blood samples of the Trinket cattle and was used for amplification of mitochondrial markers, and the sequence information was generated by Sanger sequencing. The analysis of sequence information revealed that the Trinket cattle belongs to Bos indicus (I) haplotype, sub-haplotype I2. The presence of I2 sub-haplotype in Trinket cattle may be due to the expansion of this I2 haplotype towards Southeast Asian countries. This is a novel input for the formulation of breeding strategy towards conservation of eco-friendly sustainable livestock in the isolated island ecosystem.

Assessment of Protein Profiles of RNAlater Stored and Fresh PBMC Cells Using Different Protein Extraction Buffers.

For proteome analyses, the tissue samples are mostly preserved either snap frozen or formalin-fixed, paraffin-embedded form. Use of RNAlater-a non-toxic solution primarily used to stabilize the RNA content of samples-in tissue preservation for proteome analysis recently described equally reliable with snap-frozen preservation in human tissues. Even though RNALater storage has great potential in the preservation of Peripheral Blood Mononuclear Cells (PBMC), its impact on the results of proteome analysis is poorly described at qualitative and quantitative measures. The present study investigated protein profiles of RNAlater preserved and fresh PBMCs using three extraction buffers viz. Triton X-100, RIPA and SDS. Proteins are separated in SDS-PAGE and quantified using densitometry. On an average 19.3 bands from fresh and 15.6 bands from RNAlater storage cells were obtained with a molecular weight ranging from 25 to > 250 kDa. RNAlater storage generated a fewer number and lesser quantity of low molecular weight proteins while yielded a similar or high quantity of high molecular weight protein fractions. The principal component analysis showed that Triton X-100 is inferior as compared to SDS and RIPA with respect to their protein bands and quantity yielded. While RNAlater is effective in preserving PBMC for proteome analysis, our findings warrant caution in its use in proteomics experiments especially if the target is low molecular weight proteins.

Effect of designer diets on egg yolk composition of 'White Leghorn' hens.

A study was made on 96 'White Leghorn' hens on the influence of designer diets enriched with omega-3 fatty acids and antioxidants from natural sources on egg yolk composition. The birds were divided into four equal groups viz. Control (without enrichment); FSE - (150 g flaxseeds + 200 mg vitamin E + 3 g spirulina/kg diet); FOSe (20 g fish oil + 0.2 mg organic Se (Sel-Plex) + 3 g spirulina/kg diet) and FSE + FOSe (75 g flaxseed + 10 g fish oil + 100 mg vitamin E + 0.1 mg organic Se + 3 g spirulina/kg diet). All three designer diets increased (p < 0.01) the yolk carotenoid pigments and omega-3 fatty acid levels with proportionate reduction in saturated fatty acid levels and no significant change in the oleic acid levels in the yolk lipids. The three diets also reduced (p < 0.01) the yolk cholesterol levels. Boiled eggs from all four groups had comparable sensory acceptability. Dietary Se and vitamin E supplementation acted synergistically in increasing omega-3 fatty acid levels in the egg.

T-DNA tagging and characterization of a cryptic root-specific promoter in Arabidopsis.

From a T-DNA tagged Arabidopsis population, a line, M-57 showing GUS (beta-glucuronidase) expression in the vascular regions of young roots was identified. Southern analysis revealed presence of a single T-DNA insert. Using inverse PCR, the plant sequence flanking the T-DNA insertion was cloned. The insertion was identified to be in the intergenic area between loci At4G13940 and At4G13930, coding for SAHH (S-Adenosyl-l-Homocysteine Hydrolase) and SHMT (Serine Hydroxy Methyl Transferase) genes, respectively. A 452-bp fragment immediately upstream of the T-DNA insertion when cloned and mobilized as a GUS fusion was capable of driving a similar root-specific expression of reporter gene in transgenic Arabidopsis plants and their progenies. This cryptic promoter element does not show the presence of any known root-specific promoter element.

Energy expenditure on household, childcare and occupational activities of women from urban poor households.

This present study attempts to measure the energy cost of activities of women from the poor socio-economic group in India. Women in the age group of 18-40 years (n 98) either working for incomes or classified as homemakers were randomly selected. Time disposition studies were conducted by a 24 h observation of their activities on a typical day. Predominant activities were identified from the activity profiles and standardized for posture and duration. The BMR (Douglas bag method) and energy cost of the activities (Kofranyi-Michaelis meter) were measured by indirect calorimetry. The energy consumption during these activities ranged from 2.94-12.51 kJ/min. The tasks were divided into standard, household, childcare, occupational and other activities. Using the World Health Organization/Food and Agriculture Organization/United Nations University (1985) criteria, attempts were made to categorize the activities into light, moderate and heavy. It was significant that except for walking, the standard activities and occupational work could be classified into the light category (< 2.2 BMR). Most of the household and childcare activities except cooking were classified into the moderate to heavy (2.2-> 2.8 BMR). The energy expenditure of activities did not differ significantly between women with different occupations. This present study provides an important database on energy costs of activities for computing energy requirements of women involved in similar activity patterns.

Spindle damaging effect of salbutamol sulphate on bone marrow cells of mice.

In vivo assessment and identification of aneuploidy are important phases of genotoxicity evaluation. Considerable effort has been devoted to assess the utility of the existing bioassays and to develop simpler techniques for identifying environmental aneugens. Salbutamol sulphate--an antiasthmatic drug was tested for its spindle damaging effects in bone marrow cells of mice using an in vivo technique, for the evaluation of mitotic index, C-mitotic effects, anaphase reduction and hyperdiploidy. Doses of 0.12, 0.24, 1.2, 2.4, mg/kg body weight were dissolved in bidistilled water and administered intraperitoneally to the mice. Colchicine was taken as positive control for its known aneuploidy-inducing effects. The drug showed positive C-mitotic effects accompanied with increases of mitotic index and decreased frequencies of anaphase in higher doses. Significant levels of hypodiploidy also noted at higher doses. The preliminary results indicated that Salbutamol is capable of inducing C-mitotic effects in mouse bone marrow cells, which is suggestive of possible induction of aneuploidy.

C-mitotic effects of trichloroethylene (TCE) on bone marrow cells of mice.

The possible aneuploidy inducing activity of Trichloroethylene (TCE, CAS No. 79-01-6) an industrial chemical was investigated by employing three cytogenetic end points i.e., C-mitotic effects, Micronuclei (MN) and parallel chromosome structural aberration (CA) analysis in vivo. The experiments were conducted in mouse bone marrow cells. The animals were treated with TCE in the dose of 500, 1000, 2000 and 4000 mg/kg for 6, 12, 24, 48 hr. Colchicine (COL) was taken as positive control for its known aneuploidy-inducing effects and Cyclophosphamide as a model mutagen. TCE showed positive CM effects accompanied with increases of Mitotic Index and decreased frequencies of anaphases in higher doses. The chemical showed a positive MN response in bone marrow polychromatic erythrocytes but was negative in CA analysis. The preliminary results indicated that TCE is capable of inducing C-mitotic effects in mouse bone marrow cells which is suggestive of its possible aneuploidy induction potential.

Interaction between vitamin A and iron: effects of supplements in pregnancy.

Very few reports are available on the vitamin A status of Indian pregnant women in the rural population. The present study was carried out to assess the vitamin A status and the effect of vitamin A and iron supplementation in pregnancy on serum vitamin A levels in the rural women. It was observed that serum vitamin A levels showed a marginal decrease with advancing gestation. Though satisfactory as per WHO guidelines, supplementation with 60 mg of iron prevented this decrease. A higher dose of iron (120 mg) actually resulted in a similar vitamin A status as seen in vitamin A supplemented women. If this preliminary study can be confirmed it would appear that interactions between vitamin A and iron in pregnancy have a positive effect on the vitamin A nutriture.

In-vivo genotoxicity of the alkaloid drug pilocarpine nitrate in bone marrow cells and male germ cells of mice.

Pilocarpine nitrate, an alkaloid drug of plant origin induces spindle disfunction in bone marrow cells of mice. Further studies were carried out to investigate its mutagenic effects in somatic and germ cells of mice by assessing chromosome aberrations at mitotic metaphase and as micronuclei in bone marrow cells and sperm-shape abnormality in cauda epididymides. The dose and time yield effects of the drug were investigated. The statistically significant results that were obtained for both chromosomal aberrations and micronucleus test but not for the sperm-shape abnormality test, indicated the genotoxicity of this compound in somatic cells but not in germ cells.

Iron nutritional status of adolescent girls from rural area and urban slum.

Iron nutritional status of adolescent girls belonging to an urban slum and rural areas was assessed by measuring serum ferritin levels. Overall anemia was observed in 25% of the girls irrespective of their urban rural residence. A higher percentage of rural girls (37.5%) especially below the age of 12 years showed evidence of anemia. Thereafter, the prevalence was similar in both urban and rural girls who had not attained menarche. With increasing age, urban girls who had attained menarche showed an increase in the prevalence of anemia. The prevalence of iron deficiency (serum ferritin < 12 micrograms/dl) showed a progressive increase from 60% at < 12 to 28% at > 14 yrs especially in the girls not attained menarche in the girls not attained menarche in the rural area. Overall iron deficiency was of much higher order in the rural girls irrespective of the menarcheal status. Distribution of iron/folate tablets to cover girl population may go a long way to correct the anemia and iron deficiency in the vulnerable groups.