Molecular characterization of lymphocystis disease virus in Indian glass fish: first report from the Andaman Islands.

Here, we report the first detection of lymphocystis disease virus (LCDV) in Indian glass fish in the Andaman Islands, India. Microscopic examination revealed the presence of whitish clusters of nodules on the fish's skin, fins, and eyes. The histopathology of the nodules revealed typical hypertrophied fibroblasts. Molecular characterization of the major capsid protein (MCP) gene of the virus showed a significant resemblance to known LCDV sequences from Korea and Iran, with 98.92% and 97.85% sequence identity, respectively. Phylogenetic analysis confirmed that the MCP gene sequence of the virus belonged to genotype V. This study represents the first documented case of LCDV in finfish from the Andaman Islands, emphasizing the necessity for continued monitoring and research on the health of aquatic species in this fragile ecosystem.

Progress and future perspectives of livestock genomics in India: a mini review.

The field of genetics has evolved a lot after the emergence of molecular and advanced genomic technologies. The advent of Next Generation Sequencing, SNP genotyping platforms and simultaneous reduction in the cost of sequencing had opened the door to genomic research in farm animals. There are various applications of genomics in livestock, such as the use of genomic data: (i) to investigate genetic diversity and breed composition/population structure (ii) to identify genetic variants and QTLs related to economically important and ecological traits, genome-wide association studies (GWAS) and genomic signatures of selection; (iii) to enhance breeding programs by genomic selection. Compared to traditional methods, genomic selection is expected to improve selection response by increasing selection accuracy and reducing the generation interval due to early selection. Genomic selection (GS) in developed countries has led to rapid genetic gains, especially in dairy cattle, due to a well-established genetic evaluation system. Indian livestock system is still lagging behind developed nations in adopting these technologies. This review discusses the current status, challenges, and future perspectives of livestock genomics in India.

Genome-wide detection of copy number variations in Tharparkar cattle.

Copy number variations (CNVs) are major forms of genetic variation with an increasing importance in animal genomics. This study used the Illumina BovineSNP 50 K BeadChip to detect the genome-wide CNVs in the Tharparkar cattle. With the aid of PennCNV software, we noticed a total of 447 copy number variation regions (CNVRs) across the autosomal genome, occupying nearly 2.17% of the bovine genome. The average size of detected CNVRs was found to be 122.2 kb, the smallest CNVR being 50.02 kb in size, to the largest being 1,232.87 Kb. Enrichment analyses of the genes in these CNVRs gave significant associations with molecular adaptation-related Gene Ontology (GO) terms. Most CNVR genes were significantly enriched for specific biological functions; signaling pathways, sensory responses to stimuli, and various cellular processes. In addition, QTL analysis of CNVRs described them to be linked with economically essential traits in cattle. The findings here provide crucial information for constructing a more comprehensive CNVR map for the indigenous cattle genome.

Biological methylation: redefining the link between genotype and phenotype.

The central dogma of molecular biology is responsible for the crucial flow of genetic information from DNA to protein through the transcription and translation process. Although the sequence of DNA is constant in all organs, the difference in protein and variation in the phenotype is mainly due to the quality and quantity of tissue-specific gene expression and methylation pattern. The term methylation has been defined and redefined by various scientists in the last fifty years. There is always huge excitement around this field because the inheritance of something is beyond its DNA sequence. Advanced gene methylation studies have redefined molecular genetics and these tools are considered de novo in alleviating challenges of animal disease and production. Recent emerging evidence has shown that the impact of DNA, RNA, and protein methylation is crucial for embryonic development, cell proliferation, cell differentiation, and phenotype production. Currently, many researchers are focusing their work on methylation to understand its significant role in expression, disease-resistant traits, productivity, and longevity. The main aim of the present review is to provide an overview of DNA, RNA, and protein methylation, current research output from different sources, methodologies, factors responsible for methylation of genes, and future prospects in animal genetics.

Hydrogeochemical characteristics and risk evaluation of potential toxic elements in groundwater from Shanmughanadhi, Tamilnadu, India.

Hydrogeochemical and Health Risk Assessments of trace elements are integral to groundwater resource assessment, utilization, and human health. Investigation of groundwater chemistry and trace elemental impact on local inhabitants were attempted in Shanmuganadhi basin, Tamilnadu, India. About 60 groundwater samples were collected during the pre-monsoon period and analyzed for hydrochemical composition, including major and trace elements (Fe, Cr, Ni, Cu Pb, Mn, and As) to isolate chemical characteristics and human health risk assessment. Groundwater geochemistry is prejudiced by geochemical reactions uniting cation exchange, dissolution and precipitation, adsorption, and anthropogenic contributions. About thirty-two percent of groundwater samples recorded higher F-(>1.5 mg/L) than the prescribed limit suggests sources from rock weathering and silicate dissolution. Nitrates (>45.0 mg/L) suggest sources from agricultural influences. Water types indicate alkalis (Na+ + K+) dominating alkali earth (Ca2+ - Mg2+) and strong acids (Cl- and SO42-) looming weak acid (CO32- and HCO3-) irrespective of water samples. The geochemical stability diagram suggests precipitation of silica, carbonate, and magnesium and dissolution of sulphate minerals along the groundwater flow path. Significant correlation between major ions and trace elements (Pb, Mn, Ni, and Cu) suggests origin from rock weathering, human impacts, and cultivation practices. Non-carcinogenic human risk for trace elements was higher in children compared with adults via ingestion and dermal exposure. The carcinogenic result suggests that Cr in CHK (7.1 × 10-2) and HBG (4.3 × 10-2) have the most excellent chance of cancer risk. The environmental risk category attempted using Comprehensive risk factor (CRI) suggests Pb (3.2-CHK, 2.6-HBG) with potential cancer risk. The comprehensive evaluation index recommends environmental damage between mild to moderate, indicating continuous exposure of traceable elements might result in cancer cause to the inhabitants. The study suggests water quality seems to be prejudiced by various geological and anthropogenic causes and endorses counteractive measures and proper execution of existing laws to protect groundwater resources in the study area.

Signatures of selection in riverine buffalo populations revealed by genome-wide SNP data.

The detection of selection signatures assists in understanding domestication, evolution, and the identification of genomic regions related to adaptation and production traits in buffaloes. The emergence of high-throughput technologies like Next Generation Sequencing and SNP genotyping had expanded our ability to detect these signatures of selection. In this study, we sought to identify signatures of selection in five buffalo populations (Brazilian Murrah, Bulgarian Murrah, Indian Murrah, Nili-Ravi, and Kundi) using Axiom Buffalo 90 K Genotyping Array data. Using seven different methodologies (Tajima's D, CLR, ROH, iHS, FST, FLK and hapFLK), we identified selection signatures in 374 genomic regions, spanning a total of 381 genes and 350 quantitative trait loci (QTLs). Among these, several candidate genes were associated with QTLs for milk production, reproduction, growth and carcass traits. The genes and QTLs reported in this study provide insight into selection signals shaping the genome of buffalo breeds. Our findings can aid in further genomic association studies, genomic prediction, and the implementation of breeding programmes in Indian buffaloes.

Genome-wide assessment of genetic diversity, linkage disequilibrium and haplotype block structure in Tharparkar cattle breed of India.

Knowledge about genetic diversity is very essential for the management and sustainable utilization of livestock genetic resources. In this study, we presented a comprehensive genome-wide analysis of genetic diversity, ROH, inbreeding, linkage disequilibrium, effective population size and haplotype block structure in Tharparkar cattle of India. A total of 24 Tharparkar animals used in this study were genotyped with Illumina BovineSNP50 array. After quality control, 22,825 biallelic SNPs were retained, which were in HWE, MAF > 0.05 and genotyping rate >90%. The overall mean observed (HO) and expected heterozygosity (HE) were 0.339 ± 0.156 and 0.325 ± 0.129, respectively. The average minor allele frequency was 0.234 with a standard deviation of ± 0.131. We identified a total of 1832 ROH segments and the highest autosomal coverage of 13.87% was observed on chromosome 23. The genomic inbreeding coefficients estimates by FROH, FHOM, FGRM and FUNI were 0.0589, 0.0215, 0.0532 and 0.0160 respectively. The overall mean linkage disequilibrium (LD) for a total of 133,532 pairwise SNPs measured by D' and r2 was 0.6452 and 0.1339, respectively. In addition, we observed a gradual decline in effective population size over the past generations.

Genomic scans for selection signatures revealed candidate genes for adaptation and production traits in a variety of cattle breeds.

Domestication and selection are the major driving forces responsible for the determinative genetic variability in livestock. These selection patterns create unique genetic signatures within the genome. BovineSNP50 chip data from 236 animals (seven indicine and five taurine cattle breeds) were analyzed in the present study. We implemented three complementary approaches viz. iHS (Integrated haplotype score), ROH (Runs of homozygosity), and FST, to detect selection signatures. A total of 179, 56, and 231 regions revealed 518, 277, and 267 candidate genes identified by iHS, ROH, and FST methods, respectively. We found several candidate genes (e.g., NCR3, ARID5A, HIST1H2BN, DEFB4, DEFB7, HSPA1L, HSPA1B, and DNAJB4) related to production traits and the adaptation of indigenous breeds to local environmental constraints such as heat stress and disease susceptibility. However, further studies are warranted to refine the findings using a larger sample size, whole-genome sequencing, and/or high density genotyping.

Policy framework and development strategy for freshwater aquaculture sector in the light of COVID-19 impact in Andaman and Nicobar archipelago, India.

The present study was aimed at understanding the impact of COVID-19 pandemic related restrictions on the freshwater aquaculture sector of Andaman and Nicobar archipelago (ANI). We interviewed the freshwater fish farmers (N = 211) covering all the three districts (North and Middle, South Andaman, Nicobar district) of the archipelago. The results revealed the critical issues faced by the stakeholders such as fish seed unavailability, limitations in feeding, insufficient logistical support, movement related restrictions, lack of inputs, manpower shortages, etc. as the important constraints during lockdown. Our surveys also revealed that there was a significant reduction in the income of the farmers post COVID-19 outbreak (p < 0.001). Possible reform strategies that could promote the sector development and resilience were outlined to recover from the COVID-19 impacts. The study also highlights the significance of effective networking among the stakeholders and necessary preparedness measures to be undertaken by the fish farmers to deal with the exigencies. The study also recommends a policy framework to strengthen the planning and management of freshwater aquaculture sector towards the path of sustainability.

Outbreak of hirudiniasis in aquarium-reared albino red-bellied pacu Piaractus brachypomus.

We report hirudiniasis caused by the leech Hemiclepsis marginata asiatica Moore, 1924 in albino red-bellied pacu (pirapitinga) Piaractus brachypomus (Cuvier, 1818), constituting the first documentation of a freshwater fish species being affected in India. The outbreak occurred in a tank of an aquarium-fish retailer; infested fish appeared asphyxiated, unable to swim or swimming upside down, with cloudy eyes and body with thick mucus secretion. The prevalence and mortality was 100%, with a mean intensity of 81 leeches per fish. The histopathology of the morbid fish revealed degenerative necrosis, eosinophilic infiltration in the muscle tissue and haemorrhages in the fin membrane. The leech mitochondrial 18S rDNA and 12S rDNA genes were characterised and submitted to GenBank under accession numbers MN380443 (18S) and MK733282 (12S). A maximum likelihood tree was constructed using 12S rDNA gene sequences to demonstrate the phylogenetic position of Hemiclepsis marginata asiatica among its congeners.

Submarine Groundwater Discharge from an Urban Estuary to Southeastern Bay of Bengal, India: Revealed by Trace Element Fluxes.

Submarine groundwater discharge and associated trace element fluxes from the Coleroon River estuary to south bay, India, has been attempted, because increasing trace elements could result in harmful algal blooms and eutrophication. Trace elements (Al, Cr, Mn, Fe, Ni, Cu, Zn, Sr, Mo, Ba, Pb, Th, and U) in surface water, pore, and groundwater samples were monitored for 10 days in three locations (A, B, and C) by considering tidal fluctuations. The trace elements Al, Cr, Fe, Ni, Zn, Sr, Mo, Pb, Th, and U were greater and found to be influenced by processes, such as fresh groundwater discharge and seawater intrusion. Lower Mn, Cu, and Ba signifies impact due to sediment adsorption, mixing, and elemental exchange during fresh groundwater and seawater mixing. Salinity versus trace element plot infers greater trace element mobility with cumulative salinity influenced by the conformist behavior of freshwater, seawater, and mixing. The calculated submarine groundwater discharge supported dissolved trace elements fluxes were 107,047.8 n mol d-1 m-1 for location A, 183,520.2 n mol d-1 m-1 for location B, and 181,474.4 n mol d-1 m-1 for location C, respectively. Variations in dissolved trace elements fluxes are attributed to variations in pH, free redox environment in the aquifer, adsorption or desorption by sediments, and the environmental cycle of marine organisms.

Chemical weathering and atmospheric carbon dioxide (CO2) consumption in Shanmuganadhi, South India: evidences from groundwater geochemistry.

Chemical weathering in a groundwater basin is a key to understanding global climate change for a long-term scale due to its association with carbon sequestration. The present study aims to characterize and to quantify silicate weathering rate (SWR), carbon dioxide consumption rate and carbonate weathering rate (CWR) in hard rock terrain aided by major ion chemistry. The proposed study area Shanmuganadhi is marked with superior rainfall, oscillating temperature and runoff with litho-units encompassing charnockite and hornblende-biotite gneiss. Groundwater samples (n = 60) were collected from diverse locations and analysed for major chemical constituents. Groundwater geochemistry seems to be influenced by geochemical reactions combining dissolution and precipitation of solids, cation exchange and adsorption along with minor contribution from anthropogenic activities. The SWR calculated for charnockite and hornblende-biotite gneiss was 3.07 tons km-2 year-1 and 5.12 tons km-2 year-1, respectively. The calculated CWR of charnockite and hornblende-biotite gneiss was 0.079 tons km-2 year-1 and 0.74 tons km-2 year-1, respectively. The calculated CO2 consumption rates via silicate weathering were 1.4 × 103 mol km-2 year-1 for charnockite and 5.8 × 103 mol km-2 year-1 for hornblende-biotite gneiss. Lithology, climate and relief were the key factors isolated to control weathering and CO2 consumption rates.

Molecular characterization and expression analysis of secretory immunoglobulin M (IgM) heavy chain gene in rohu, Labeo rohita.

Immunoglobulin M (IgM) is the major isotype among teleost immunoglobulins. The present study was aimed to explore IgM heavy chain gene and its expression profile in rohu. Full-length IgM heavy chain cDNA of rohu consisted of 1994 bp encoding a polypeptide of 576 amino acid residues including a leader peptide, variable (VH) and constant (CH1-CH2-CH3-CH4) domains confirming the secretory form of IgM. The sequence carries conserved residues such as cysteine, tryptophan and amino acid motifs like 'YYCAR' and 'FDYWGKGT-VTV-S'. The predicted 3 D model confirmed various domains of rohu IgM heavy chain. Phylogenetic tree analysis revealed that IgM heavy chain gene of rohu shared the same cluster with that of other cyprinid fishes. Tissue distribution analysis showed the predominant level of IgM heavy chain gene expression in kidney, spleen and intestine. IgM heavy chain gene expression in rohu kidney was found to be up-regulated and reached a maximum at 7 days post-challenge with Aeromonas hydrophila. These findings demonstrate the first report of full-length secretory IgM heavy chain gene in rohu. Besides, IgM heavy chain gene was highly expressed in major lymphoid tissues and bacterial challenge influenced its expression which further confirmed its role in the adaptive humoral immune response.

Tunable electronic, electrical and optical properties of graphene oxide sheets by ion irradiation.

The tunable electronic, electrical and optical properties of graphene oxide (GO) sheets were investigated using a controlled reduction by 500 keV Ar+-ion irradiation. The carbon to oxygen ratio of the GO sheets upon the ion beam reduction has been estimated using resonant Rutherford backscattering spectrometry analyses and its effect on the electrical and optical properties of GO sheets has been studied using sheet resistance measurements and photoluminescence (PL) measurements. The restoration of sp 2-hybridized carbon atoms within the sp 3 matrix is found to be increases with increasing the Ar+-ion fluences as evident from Fourier transform infrared, and x-ray absorption near-edge structure measurements. The decrease in the number of disorder-induced local density of states (LDOSs) within the π-π* gap upon the reduction causes the shifting of PL emission from near infra-red to blue region and decreases the sheet resistance. The improved electrical and optical properties of GO sheets were correlated to the decrease in the number of LDOSs within the π-π* gap. Our experimental investigations suggest ion beam irradiation is one of an effective approaches to reduce GO to RGO and to tailor its electronic, electrical and optical properties.

A novel green approach for reduction of free standing graphene oxide: electrical and electronic structural investigations.

Ion beam irradiation technique has been proposed, for efficient, fast and eco-friendly reduction of graphene oxide (GO), as an alternative to the conventional methods. 5 MeV, Au+ ion beam has been used to reduce the free standing GO flake. Both electronic and nuclear energy loss mechanisms of the irradiation process play a major role in removal of oxygen moieties and recovery of graphene network. Atomic resolution scanning tunnelling microscopy analysis of the irradiated GO flake shows the characteristic honeycomb structure of graphene. X-ray absorption near edge structure analysis at C K-edge reveals that the features of the irradiated GO flake resemble the few layer graphene. Resonant Rutherford backscattering spectrometry analysis evidenced an enhanced C/O ratio of ∼23 in the irradiated GO. In situ sheet resistance measurements exhibit a sharp decrease of resistance (few 100 s of Ω) at a fluence of 6.5 × 1014 ions cm-2. Photoluminescence spectroscopic analysis of irradiated GO shows a sharp blue emission, while pristine GO exhibits a broad emission in the visible-near IR region. Region selective reduction, tunable electrical and optical properties by controlling C/O ratio makes ion irradiation as a versatile tool for the green reduction of GO for diverse applications.

Real-time water quality monitoring using Internet of Things in SCADA.

Water pollution is the root cause for many diseases in the world. It is necessary to measure water quality using sensors for prevention of water pollution. However, the related works remain the problems of communication, mobility, scalability, and accuracy. In this paper, we propose a new Supervisory Control and Data Acquisition (SCADA) system that integrates with the Internet of Things (IoT) technology for real-time water quality monitoring. It aims to determine the contamination of water, leakage in pipeline, and also automatic measure of parameters (such as temperature sensor, flow sensor, color sensor) in real time using Arduino Atmega 368 using Global System for Mobile Communication (GSM) module. The system is applied in the Tirunelveli Corporation (Metro city of Tamilnadu state, India) for automatic capturing of sensor data (pressure, pH, level, and energy sensors). SCADA system is fine-tuned with additional sensors and reduced cost. The results show that the proposed system outperforms the existing ones and produces better results. SCADA captures the real-time accurate sensor values of flow, temperature, and color and turbidity through the GSM communication.

Pairwise contact energy statistical potentials can help to find probability of point mutations.

To adopt a particular fold, a protein requires several interactions between its amino acid residues. The energetic contribution of these residue-residue interactions can be approximated by extracting statistical potentials from known high resolution structures. Several methods based on statistical potentials extracted from unrelated proteins are found to make a better prediction of probability of point mutations. We postulate that the statistical potentials extracted from known structures of similar folds with varying sequence identity can be a powerful tool to examine probability of point mutation. By keeping this in mind, we have derived pairwise residue and atomic contact energy potentials for the different functional families that adopt the (α/ß)8 TIM-Barrel fold. We carried out computational point mutations at various conserved residue positions in yeast Triose phosphate isomerase enzyme for which experimental results are already reported. We have also performed molecular dynamics simulations on a subset of point mutants to make a comparative study. The difference in pairwise residue and atomic contact energy of wildtype and various point mutations reveals probability of mutations at a particular position. Interestingly, we found that our computational prediction agrees with the experimental studies of Silverman et al. (Proc Natl Acad Sci 2001;98:3092-3097) and perform better prediction than iMutant and Cologne University Protein Stability Analysis Tool. The present work thus suggests deriving pairwise contact energy potentials and molecular dynamics simulations of functionally important folds could help us to predict probability of point mutations which may ultimately reduce the time and cost of mutation experiments. Proteins 2016; 85:54-64. © 2016 Wiley Periodicals, Inc.

Design, synthesis and biological evaluation of 2-(4-phenylthiazol-2-yl) isoindoline-1,3-dione derivatives as anti-prostate cancer agents.

The structural modification and molecular docking-based screening approaches on thiazole-based isoindolinediones were imposed to find the novel 2-(4-phenylthiazol-2-yl) isoindoline-1,3-dione derivatives. The best fit compounds (6a-n) were synthesized and evaluated their antiproliferative activities on the prostate cancer cell lines (PC-3 & LNCaP). Among them, the compound, 6m exhibited good activity, particularly on LNCaP (IC50=5.96±1.6µM), moderately active against PC-3 cell lines as compared to bicalutamide. The compound, 6m decreased the androgen-mediated transcription of ARE-mRNA in PSA, TMPRSS2, c-myc and cyclin D1 than R-bicalutamide. The compounds, 6e and 6f were reconfirmed through single crystal XRD analysis. The ADME profiling of the test compounds was evaluated to find the drug-likeness and pharmacokinetic parameters. These findings may provide vital information for the development of anti-prostate cancer agents.

High voltage generation from lead-free magnetoelectric coaxial nanotube arrays and their applications in nano energy harvesters.

Harvesting energy from surrounding vibrations and developing self-powered portable devices for wireless and mobile electronics have recently become popular. Here the authors demonstrate the synthesis of piezoelectric energy harvesters based on nanotube arrays by a wet chemical route, which requires no sophisticated instruments. The energy harvester gives an output voltage of 400 mV. Harvesting energy from a sinusoidal magnetic field is another interesting phenomenon for which the authors fabricated a magnetoelectric energy harvester based on piezoelectric-magnetostrictive coaxial nanotube arrays. Piezoelectric K0.5Na0.5NbO3 (KNN) is fabricated as the shell and magnetostrictive CoFe2O4 (CFO) as the core of the composite coaxial nanotubes. The delivered voltages are as high as 300 mV at 500 Hz and at a weak ac magnetic field of 100 Oe. Further tailoring of the thickness of the piezoelectric and magnetic layers can enhance the output voltage by several orders. Easy, single-step wet chemical synthesis enhances the industrial upscaling potential of these nanotubes as energy harvesters. In view of the excellent properties reported here, the lead-free piezoelectric component (KNN) in this nanocomposite should be explored for eco-friendly piezoelectric as well as magnetoelectric power generators in nanoelectromechanical systems (NEMS).