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North Eastern states of India are blessed with extensive ecoclimatic conditions and much of India’s endemic flora and fauna. This region is rich in fish diversity with plenty of species of ornamental importance, including model species zebrafish. Among the potential ornamental fishes, Ctenops nobilis is designated as Near Threatened and Danio dangila is included in the Least Concern list by IUCN. Cytogenetic profiling was undertaken here to provide complementary data for precise species identification and to study genetic inheritance, genome organization and evolution of the species. The cytogenetic analyses revealed diploid chromosome numbers 44 and 50 with karyotype formula 8m+20sm+10st+6t (FN=72) and 20m+24sm+6st (FN=94), respectively, in C. nobilis and D. dangila. The staining of nucleolar organizer regions revealed the presence of Ag-NORs, CMA3 sites and 18S rDNA probe signals on one pair sub-telocentric chromosome and one pair sub-metacentric chromosome in C. nobilis and D. dangila, respectively. These biomarkers are an important resource for molecular taxonomy, evolutionary/phylogenetic studies and conservation genetics of C. nobilis and D. dangila.

The wild stock of Indian major carps is declining in major rivers of India due to pollution, overexploitation, and inbreeding depression. In the present study, the comparative population structure, genetic diversity, and historical demographics of IMCs, Labeo rohita, Labeo catla, and Cirrhinus mrigala were characterized by analyzing partial 307bp sequences of Cytochrome b gene of 357 individuals collected from seven geographically isolated sites from Indian river basins and two culture zones. The DNA sequences alignment among three species revealed comparative divergence and evolution in these heterogeneous species in terms of over transition to transversion ratio of 6.25. The study implicated the occurrence of 35 haplotypes with haplotype diversity of 0.7333 in L. rohita at Brahmaputra basin showing allelic richness, while no nucleotide diversity (π) 0.000 was observed in L. catla of two geographically isolated locations of Rivers Ganga and Narmada. The analysis of molecular variance (AMOVA) revealed the genetic diversity of IMCs is to be very low (9.40%) within the species, as compared to among the three species (80.76%). The Fst scores ranged between 0.000 and 0.996, indicating low to high genetic structure of IMCs. The Haplotype-1, Haplotype-13, and Haplotype-19 in L. rohita, L. catla, and C. mrigala were considered as ancestral haplotypes, respectively. The expansion factor was found to be 0.45000 and 0.90000 for L. rohita stocks at Farakka-Ganga and Allahabad-Ganga, respectively. The present study provides the first report on genealogical biogeography, evolutionary divergence, and expansion of three IMCs, which could help to formulate the strategies for conservation of fisheries biodiversity in the Indian riverine ecosystems.

Snakehead fishes are important food fishes from freshwater ecosystems with their significant contribution in capture fisheries. They also have high potential for aquaculture. Cytogenetic variability between the Channa punctata and C. striata was assessed in the present investigation. The study revealed diploid chromosome number, karyotype configuration and fundamental arm numbers as 32, 18m + 10sm + 4st and 64, respectively, in C. punctata and 40, 6m + 2sm + 10st + 22t and 68 in C. striata without any heteromorphic pair(s) in both the species. Rhodamine-labeled 18S rDNA probe was constructed and hybridized on the metaphase chromosome spreads of both the species. The signals of the hybridized probe were observed on two sub-metacentric and two sub-telocentric chromosome pairs in C. punctata and C. striata, respectively. The study revealed that 18S ribosomal genes are present on morphologically different chromosome pairs which have evolved by means of chromosome fragmentation and their rearrangements during the evolution of the species. The information is useful for 18S gene-bearing chromosomes identification, in cytotaxonomy and documentation of the hybrids of the two species.

BAC library has always been an important genomic source for preserving the genetic material of an organism for sequencing, developing physical map as well as addressing the novel evolutionary biology questions. Here, the end sequences of BAC clones were generated using a set of primers and mapped on the genome scaffolds of C. magur using bioinformatics tool. Numbers of genes present on the clones were identified using scaffolds’ annotation information. Further, the clone insert DNA was labeled through nick translation using tetra methyl rhodamine-5-dUTP (Pool A contained 6 clones possessing 36 genes mapped on scaffold A) and fluorescein 12-dUTP (Pool B contained 4 clones possessing 15 genes mapped on scaffold B) fluorophores for probe construction and was subsequently hybridized on metaphase chromosomes using FISH. The BAC-FISH revealed the mapping of red color probe on 19th sub-telocentric chromosome and green color on 14th sub-metacentric chromosome. These findings will be useful in understanding the chromosomes organization and evolution of genomic structure as well as function of the species in comparison to its closely related and well studies species, such as channel catfish and zebrafish.

Fluctuation in water temperature can create thermal stress, which may impact many aspects of fish life, such as survival, growth, reproduction, disease occurrence etc. The endangered catfish, Clarias magur, has been reported to survive at higher thermal stress, even though the exact mechanism is unknown. The genes coding for Nuclear protein 1 (Nupr1) and Parkin E3 ubiquitin protein ligase (Park2) have been reported to protect cells from stress-induced damage and death. In this study, we characterized both the genes and assessed their quantitative expression in C. magur. Structural features of both the genes were found similar to a related catfish, Ictalurus punctatus, and model fish zebrafish. The genes were fairly conserved in fishes as observed through phylogenetic analysis. The real time expression of the two stress-associated genes were also assessed in brain, kidney, liver and muscle tissues of C. magur exposed to warm (34 °C) and cold (15 °C) water. RT-PCR analysis revealed up-regulation in the relative expression levels of Nupr1 and Park2 genes at both temperatures with maximum positive fold change during stress to cold water, even though the posteriori Dunnett's test after ANOVA revealed that there were significant differences between the control and challenged groups. The study indicated that Nupr1 gene plays role in muscle tissue at both high and low thermal stress, but at high thermal stress in liver, while Park2 plays role in muscle, brain and kidney at low temperature and in liver at high temperature stress in C. magur. The study has generated first-hand information under warm- and cold water, which pave the way to understand the expression response of these genes to thermal vacillations and to establish evolutionary significance in catfishes and other species.

The Glossogobius giuris (Gobiidae), tank goby—a species of goby fish, is native mainly to freshwater and estuaries and has importance in the aquarium trade. It is classified as least concern under IUCN Red List. Live individuals of this species were collected from Loktak Lake in Manipur for cytogenetic investigation to reveal the nucleolar organizer region (NOR) through silver nitrate (AgNO3) and chromomycin A3 (CMA3) staining as well as DAPI staining and single-color fluorescence in situ hybridization (FISH) using 18S rDNA sequence as probe. Analysis of more than 50 metaphase chromosome complement (obtained from colchicine–potassium chloride–Carnoy’s fixation–Giemsa staining procedures) showed the presence of 46 diploid chromosome numbers with all telocentric having fundamental arm number as 46 without any heteromorphic pair. One pairs of silver-stained NORs, situated terminally on the telocentric chromosome, were observed. Similarly, one pair of CMA3-positive sites were observed on the chromosome that suggested abundance of GC-rich repetitive DNAs in this region. One pair of 18S rDNA positive sites was observed on the telocentric chromosomes using FISH. These karyological features can be useful markers in cytotaxonomy and conservation of this species.

Striped snakehead (Channa striata) is a freshwater species of early Miocene period belonging to family Channidae. The genetic variability of the snakehead populations in India was not well known. Present study was undertaken using 149 sequences of control region of mitochondrial DNA from seven geographically distinct populations of Indian water, which resulted in 46 haplotypes with 137 variable nucleotide sites (60 singletons and 77 parsimony informative) and the nucleotide frequencies was: A = 33.0, T = 28.1, G = 15.4, and C = 23.5%. The presence of low-frequency of younger haplotypes with a large number of singletons indicates the absence of dominant haplotype. Hierarchical AMOVA showed highly significant genetic differentiation (F

The freshwater snakehead fishes are members of the family Channidae and order Perciform, which are native to parts of Africa and Asia with widespread distributions. The present study was aimed to assess the genetic variability and molecular phylogeny among 22 species of genus Channa, viz. C. argus, C. asiatica, C. aurantimaculata, C. bankanensis, C. barca, C. bleheri, C. burmanica, C. diplogramma, C. gachua, C. lucius, C. maculata, C. marulius, C. melasoma, C. micropeltis, C. orientalis, C. ornatipinnis, C. panaw, C. pleurophthlama, C. pulchra, C. punctata, C. stewartii and C. striata, using partial 513 bp long consensus sequence of cytochrome-c oxidase subunit I mitochondrial DNA retrieved from NCBI (March, 2018). The study showed 281 haplotypes with 267 variable sites (i.e., 33 singletons and 234 parsimoniously informative) in nucleotide positions. Most of the sequences were A + T rich, except in C. argus which is G + C rich (50.25%). The NJ and MP trees showed similar topology with discrete branches, each as a distinct species of the Channa with slight differences in bootstrap values. Maximum K2P distance was found between the C. ornatipinnis and the C. melasoma. The maximum numbers of polymorphic loci were present in C. gachua.

The complete mitogenome of Heteropneustes fossilis is described using Ion Torrent (PGM sequencer), which showed it was 16,489 bp in size comprising 13 mRNAs, 22 tRNAs, 2 rRNA genes, and 858 bp as D-Loop control region, along with gene order and organization, being similar to most of the other related Siluriformes fish mitogenome of NCBI databases. The 20 RNAs were packed into a typical cloverleaf structure. The mitogenome in the present study has 99% similarity to the complete mitogenome sequence of H. fossilis mitogenome reported earlier and also would be helpful in understanding the population genetics, phylogenetics, and evolution of catfishes.

The complete mitogenome of Osteobrama belangeri is described using Ion Torrent (PGM sequencer), which was 16,609 bp in size comprising 13 mRNAs, teo rRNA genes, 22 tRNAs, and 926 bp as D-Loop control region, in addition to gene order and organization, being similar to most of the other related Cypriniformes fish mitogenome of NCBI databases. The all 22 tRNAs were packed into a typical clover-leaf structure. In the present study, the mitogenome has 99% similarity to the complete mitogenome sequence of O. belangeri mitogenome details previously and also would be helpful in understanding the phylogenetics, population genetics, and evolution of family Cyprinidae fishes.

A wide range of diploid number of chromosomes and the body size of

A wide range of diploid number of chromosomes and the body size of Channa congeners are useful combination of characters for studying the factors controlling the body size. In this study, the karyological information was superimposed on the evolutionary tree generated by 16S rRNA mitochondrial gene sequences. Here, the metaphase chromosome complements stained with Giemsa, AgNO3 and CMA3 were prepared from six snakehead murrel fish species collected from northeast India. The diploid chromosome numbers and the fundamental arms of C. aurantimaculata (2n = 52, NF = 98), C. gachua (2n = 56, NF = 84), C. marulius (2n = 44, NF = 58), C. orientalis (2n = 52, NF = 74), C. punctata (2n = 32, NF = 60) and C. striata (2n = 40, NF = 48) were calculated by the analysis of metaphase chromosome complements. Both methods of nucleolar organizer region (NOR) localization, silver nitrate and chromomycin A3, revealed NOR pairs of 1, 2, 3, 1, 4 and 3 in C. aurantimaculata, C. gachua, C. marulius, C. orientalis, C. punctata and C. striata, respectively. The subject species showed primitive type of asymmetrical chromosomes, except the C. punctata. The variation in 2n for C. orientalis (2n = 52, 78) and C. gachua (2n = 52, 78, 104) of a complete haploid set indicates the possibility of either ploidy change in C. orientalis and C. gachua, if we consider 2n = 52 or the Robertsonian rearrangements in different populations of these two species. The chromosome evolution tree was constructed on 16S rRNA ML-phylogenetic tree using ChromEvol 1.3. The analysis of chromosome evolution explained the loss or gain of chromosome, duplications or semiduplications mechanism. For time scaling the chromosomeevolution, the node age of available 16S rRNA gene of Channa species were estimated, which was also used for estimating the time when chromosomal changes occurred in context of geological time-scale.

The snakehead murrel Channa striata, with extensive distribution in Asia, is important in both culture and capture fisheries. Wild sub-populations of C. striata from Indian waters were analyzed in the present study using mitochondrial cytochrome b gene and nuclear microsatellite loci for genetic diversity assessment and sub-population structuring with the expectations that this fish have resulted in isolated sub-populations. A total of 191 specimens were collected for the study from eight distinctly located rivers from India. The cyt b analyses showed moderate to high, while microsatellites indicated low to moderate levels of inter-sub-populations' diversity. Tapti sub-population showed high level of genetic variation in cyt b analyses but low in SSRs, with a recent bottleneck. Betwa sub-population showed minimum haplotype variation, while Brahmaputra exhibited minimum expected heterozygosity at all the loci. Cyt b gene revealed 45 polymorphic sites with overall nucleotide diversity 0.00924 and haplotype diversity 0.9301. In phylogenetic analysis and haplotypes network, Chaliyar population appeared in different lineage. Chaliyar sub-population revealed maximum mean private alleles for microsatellite loci, while Tapti showed one private allele and Brahmaputra without private allele. The results indicate a gradual loss in number of private alleles within the species, which might be a concern for its conservation in the future.

In eukaryotes, the serine/threonine kinases (STKs) belonging to cyclin-dependent protein kinases (CDKs) play significant role in control of cell division and curb transcription in response to several extra and intra-cellular signals indispensable for enzymatic activity. The zebrafish cyclin-dependent protein kinase-like 1 protein (zCDKL1) shares a high degree of sequence and structural similarity with mammalian orthologs and express in brain, ovary, testis, and low levels in other tissues. Regardless of its importance in the developmental process, the structure, function and mode of ATP recognition have not been investigated yet due to lack of experimental data. Henceforth, to gain atomistic insights in to the structural dynamics and mode of ATP binding, a series of computational techniques involving theoretical modeling, docking, molecular dynamics (MD) simulations and MM/PBSA binding free energies were employed. The modeled bi-lobed zCDKL1 shares a high degree of secondary structure topology with human orthologs where ATP prefers to lie in the central cavity of the bi-lobed catalytic domain enclosed by strong hydrogen bonding, electrostatic and hydrophobic contacts. Long range MD simulation portrayed that catalytic domain of zCDKL1 to be highly rigid in nature as compared to the complex (zCDKL1-ATP) form. Comparative analysis with its orthologs revealed that conserved amino acids i.e., Ile10, Gly11, Glu12, Val18, Arg31, Phe80, Glu 130, Cys143 and Asp144 were crucial for ATP binding mechanism, which needs further investigation for legitimacy. MM/PBSA method revealed that van der Waals, electrostatic and polar solvation energy mostly contributes towards negative free energy. The implications of ATP binding mechanism inferred through these structural bioinformatics approaches will help in understanding the catalytic mechanisms of important STKs in eukaryotic system.

The freshwater snakehead murrel fish, Channa striata, is a commercially important and potential candidate species for aquaculture. Sequences of 655 bp long cytochrome oxidase I fragments from 115 individuals, belonging to nine geographically isolated from riverine ecosystems of India, was used for genetic diversity studies. The result indicated 33 polymorphic sites with 31 parsimonious-info and 8 singletons, which revealed the presence of 16 haplotypes with haplotype diversity (H) range from 0.4190 to 0.7424. H2 was found as ancestral haplotype with frequency of 18 individuals. C. striata populations in river Chaliyar showed distinct mitochondrial lineage with maximum 23 points mutations between mv1 to H12 and H3 to H13. The Analysis of Molecular Variance and Fst scores represented the genetic dispersal of C. striata in Indian water. Generally, moderate to high Fst scores were observed in geographically isolated C. striata populations. The finding of analysis suggests a single panmictic population of C. striata across the nine rivers of India.

The present study explains the population structure and genetic diversity of medium carp Labeo gonius by analyzing partial sequence of mitochondrial DNA cytochrome b gene. Labeo gonius is a lower risk Near Threatened species, distributed throughout the North Indian major rivers, reservoirs and lakes. This species has a larger scope as an alternative candidate species in carp aquaculture system. In the present investigation, 223 individuals of Labeo gonius were collected from five locations of phylo-geographically isolated riverine ecosystems of India resulted in 12 haplotypes. These haplotypes showed 14 variables, out of which 9 were singletons and 5 were parsimony informative sites of nucleotide positions. The haplotypes H1 was considered as ancestral haplotype. All the haplotypes were connected to each other by 1-4 nucleotide mutations. The Narmada haplotypes (H10; H11 and H12) were isolated from H1 by four nucleotide mutations. The analyses resulted maximum expansion events (τ = 4.13672) in Narmada, with Fst scores more than other population pairs. The analysis of molecular variance (AMOVA) showed significant genetic differentiation among populations (ØST = 0.69470, p .000). The genetic differentiation patterns were significantly consistence with geographical distributions. This study rejected the null hypothesis of single panmictic population of medium carp, Labeo gonius in Indian water.

Catla (Catla catla) is a one of the most harvested Indian major carps and is widely cultured fish species in Indian subcontinent. In the present study, genetic variability between hatchery and wild stocks of Catla was surveyed using sequence data of mitochondrial DNA of partial 307 bp of cytochrome b region. A total of 174 Catla individuals were examined from three different river basins and hatcheries. Significant genetic heterogeneity was observed for the sequence data (F

The cytogenetic investigations of Cyprinus carpio, collected from river Gomti, Lucknow, India, was undertaken in the present study using giemsa/silver nitrate/chromomycin A3 staining and 18S rDNA probe hybridization on the chromosomes. The metaphase chromosome compliment analyses revealed the presence of diploid chromosome number 100. The karyotype consisted of 24m+26sm+18st+32t chromosomes. The silver nitrate stained nucleolar organizer regions were found at terminal position on the short arms of two sub-metacentric homologous chromosomes, and the chromomycin A3 positive sites suggested abundance of GC-rich repetitive DNAs in this region. The fluorescence in situ hybridization confirmed the location of 18S rDNA probe on one pair of metaphase chromosomes. Negative-DAPI staining of NORs indicated lack of AT-rich sequence in this region. The cytogenetic evidence of polyploidization reported previously in C. carpio has been proved using molecular cytogenetic approach in this study leaving behind little or no contradiction. The FISH technique with 18S rDNA probe, performed first time in this species, showed the importance of biomarkers in using phylogenetic and evolutionary studies useful in taxonomy and conservation of C. carpio.

Bacterial artificial chromosome (BAC) library is an important genomic resource useful in targeted marker development, positional cloning, physical mapping and a substrate for genome sequencing for better understanding the genome organization of a species. The present manuscript elucidates the improvement in protocols for economical and efficient BAC insert DNA isolation, BAC end sequencing and FISH for physical localization on the metaphase chromosome complements. BAC clones of Clarias magur, maintained in 384-well plate format in our laboratory, were used in this study. The protocols gave consistent and efficient results. We use routinely these protocols for BAC insert DNA extraction, generating end sequence data of the clone and constructing DNA probes to hybridize on the metaphase spreads of C. magur using FISH for physical their localization.

The world has shown growing interest in generating the energy using renewable sources of energy. Due to many advantages like reduced cost higher system efficiency, controllability, DFIG has become a popular concept and has become an interesting research topic. This paper deals with comparison of three different models of MATLAB using Sim Power Systems of Simulink. Firstly Phasor, Average & Detailed models has been presented which uses a (DFIG) having a capacity of 12 MW that is supplied to the distribution system. Different models are studied, reviewed, simulated & compared properly.

Documentation of genetic differentiation among the populations of a species can provide useful information that has roles in conservation, breeding, and management plans. In the present study, we examined the genetic structure and phylogenetic relationships among the 149 individuals of Ompok bimaculatus belonging to 24 populations, collected from Indian waters, using cytochrome b gene. The combined analyses of data suggested that the Indian O. bimaculatus consist of three distinct mtDNA lineages with star-like haplotypes network, which exhibited high genetic variation and haplotypic diversity. Analysis of molecular variance indicated that most of the observed genetic variation was found among the populations suggesting restricted gene flow. Long-term interruption of gene flow was also evidenced by high overall Fst values (0.82367) that could be favored by the discontinuous distributions of the lineages.

The HMOX1 gene plays role in several biological processes and is also responsive to hypoxia stress. Freshwater carp fish, Labeo rohita, is reported as hypoxia sensitive, but the information of annotated hypoxia genes in public domain is very scanty for this species. Here, an attempt was made to isolate and characterize HMOX1 gene in L. rohita using information from zebrafish. HMOX1 gene was obtained by mapping HMOX1 protein of zebrafish over assembled genome of L. rohita. Aligned region was used for designing primers for HMOX1 amplification. Eight overlapping sets of primers were designed for amplifying ~540 bp long successive overlapping fragments. Splicing of overlapping amplicons generated 3715 bp fragment that was confirmed as HMOX1 gene having full coding region with 6 exons between 184 and 2156 bp positions. HMOX1 characterization is an initiative for L. rohita genes annotation to support the characterization of new genes in the important species.

The connective tissue growth factor gene plays important role in several biological processes and also responsive to hypoxia stress in fishes. The freshwater fish, Labeo rohita, highly cultured in Indian subcontinent for food, is reported as hypoxia sensitive but annotation and sequences of nuclear genes were not available for this species so far in the public domain, except some transcripts. In this study, an attempt was made for isolation and annotation of the CTGF gene in L. rohita using information of zebrafish from the same family. The CTGF gene sequence was obtained by aligning assembled genome of L. rohita, (NCBI BioProject ID: PRJNA437789), with the CTGF protein of zebrafish. Eight overlapping sets of forward and reverse primers from aligned region were designed for amplification of around 600 bp long successive overlapping fragments of CTGF gene in L. rohita. Assembly and annotation of overlapping fragments confirmed a complete 2421 bp long CTGF gene sequence with a full coding region that comprised of five exons between 308 and 1921 positions. This annotated CTGF gene sequence was submitted to GenBank (Acc. No. KY940466). Characterization of CTGF will be an initiative in identification of hypoxia response genes in L. rohita which may further help in understanding the mechanism of hypoxia tolerability in this species.

In this paper, we consider a wireless sensor network (WSN) that consists of sensor nodes (SN), cluster head (CH), forward node (FN) and a base station (BS). The information acquired by the sensor node is sent to the CH, all the CH’s send the information to a FN which forwards it to the BS. Fast detection of malicious nodes is imperative to the performance of a WSN and therefore we study the weighted trust method for malicious node detection. We have considered two scenarios one with single cluster head without grid and other with multiple cluster head with non-overlapping grid. The results indicates that the scenario with multiple cluster heads with non-overlapping grid requires less time for malicious node detection with better accuracy as compared to the scenario with single cluster head without grid.