FBIS: A regional DNA barcode archival & analysis system for Indian fishes

DNA barcode is a new tool for taxon recognition and classification of biological organisms based on sequence of a fragment of mitochondrial gene, cytochrome c oxidase I (COI). In view of the growing importance of the fish DNA barcoding for species identification, molecular taxonomy and fish diversity conservation, we developed a Fish Barcode Information System (FBIS) for Indian fishes, which will serve as a regional DNA barcode archival and analysis system. The database presently contains 2334 sequence records of COI gene for 472 aquatic species belonging to 39 orders and 136 families, collected from available published data sources. Additionally, it contains information on phenotype, distribution and IUCN Red List status of fishes. The web version of FBIS was designed using MySQL, Perl and PHP under Linux operating platform to (a) store and manage the acquisition (b) analyze and explore DNA barcode records (c) identify species and estimate genetic divergence. FBIS has also been integrated with appropriate tools for retrieving and viewing information about the database statistics and taxonomy. It is expected that FBIS would be useful as a potent information system in fish molecular taxonomy, phylogeny and genomics

Fish Karyome: A karyological information network database of Indian Fishes

‘Fish Karyome’, a database on karyological information of Indian fishes have been developed that serves as central source for karyotype data about Indian fishes compiled from the published literature. Fish Karyome has been intended to serve as a liaison tool for the researchers and contains karyological information about 171 out of 2438 finfish species reported in India and is publically available via World Wide Web. The database provides information on chromosome number, morphology, sex chromosomes, karyotype formula and cytogenetic markers etc. Additionally, it also provides the phenotypic information that includes species name, its classification, and locality of sample collection, common name, local name, sex, geographical distribution, and IUCN Red list status. Besides, fish and karyotype images, references for 171 finfish species have been included in the database. Fish Karyome has been developed using SQL Server 2008, a relational database management system, Microsoft's ASP.NET-2008 and Macromedia's FLASH Technology under Windows 7 operating environment. The system also enables users to input new information and images into the database, search and view the information and images of interest using various search options. Fish Karyome has wide range of applications in species characterization and identification, sex determination, chromosomal mapping, karyo-evolution and systematics of fishes

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Not AvailableBackground. The Ganga River (Ganges) is known of its rich fish diversity which is adversely affected by degrading environmental and ecological conditions. There are more than 300 exotic fish species in India. Many of them (particularly Cyprinus carpio) escaped from confinement and are now present in the Ganga River, challenging its ecological equilibrium. The aim of this project was to study the population characteristics of Cyprinus carpio (i.e., the abundance, size range, food and feeding, gonado-somatic index (GSI), gonad maturity stage, maturity and breeding) and the altered fishery dynamics. Materials and Methods. The commercially caught fishes, including the exotic ones, were identified, examined and measured. Important indices such as: the abundance index of exotic fishes, the gonado-somatic index (IG), as well as the gonad maturity stage of the escapee C. carpio were determined. The gut content was also analyzed to identify food items and there after the food richness, diet breadth, and gut repletion index (GRI%) were calculated using the Simpson's diversity index. Results. C. carpio introduced about sixty years ago for aquaculture has now been found to invade into the Ganga, the largest river of the country contributing significantly to the fishery. The abundance index of C. carpio ranged from 12.2% to 45.5% in 250 km long river stretch of the Ganga River flowing along Kanpur to Varanasi in the state of Uttar Pradesh. The gut content analysis revealed the presence of Eichhornia (9.8%), Pistia (11.6%), Nymphaea (8.5%), annelids worms (7.8%), algae (20.2%), mud and detritus (14.8%). The calculated diet breadth ranged from 0.82% to 0.91%; food richness ranged from 12 to 16, and the gut repletion index (GRI%) was 100% at different sampling sites. Mature females represented all the six reproductive stages with varying gonado-somatic index (IG) (0.5 to 30) in different catches. Presence of spent, ripe, and mature females was recorded. Conclusion. Abundance of exotic fish primarily C. carpio and Oreochromisniloticus in the fishery of the Ganga River was observed. The gonado-somatic index (IG) and the presence of all the six gonadal stages confirmed that C. carpio established its breeding population. The dominant catch of exotic fishes negatively impacted on the important indigenous fishes particularly Indian major carps (Catla catla, Labeo rohita, and Cirrhinus mrigala). The change in dynamics of the fishery due to the presence of common carp attracted attention to conserve rich indigenous germplasm facing threats of shifting from their natural habitats .Not Availabl

Secondary metabolites interference on potential of Solanum lycopersicum grown under UV-B stress and its impact on developmental attributes of Capsicum annuum

Ultraviolet-B (UV–B) radiation contributes only a minor fraction of the solar radiation that shows functional duality. It can induce negative effects directly by degrading DNA and protein or can strengthen UV-light mediated stress acclimation responses through activation of series of secondary metabolic pathways. In this experiment, we examined the secondary metabolites profile of Solanum lycopersicum (tomato) grown in doses of 15 min, 30 min, 45 min and 60 min of UV-B and the effects of its extracts on growth and metabolism of Capsicum annuum (chilli). The chief secondary metabolites of the tomato plants were determined by using gas-chromatography mass spectroscopy. Several biophysical, biochemical and histochemical analyses were performed to evaluate the effects of UV-B on secondary metabolism of the tomato and impact of its extract on chilli plants. The results indicated that the chilli plant showed negative growth responses against the aqueous extracts of tomato. These decrease in growth parameters are related to enhanced effects of secondary metabolites found in extracts which induce oxidative stress in the chilli plants. Moreover, histochemical imaging of chilli leaves and roots also showed the increased generation of reactive oxygen species and lignin accumulation. In conclusion our results highlight the presence of miscellaneous secondary metabolites which increased under UV-B stress and improved its herbicidal potency against chilli plants

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Not AvailableWorldwide, global databases on fishes lack fish diversity information at regional scale of a country, which hasfascinated many fishery workers to know the regional scale fish diversity. Databases are essential part of thebiodiversity science and have been used widely in the biological research. The present study discusses development,services and utility of the database application (UPFBase) providing information on the freshwater fish biodiversityof Uttar Pradesh. To develop UPFBase, data on the fish biodiversity of this region was compiled from differentsources that include primary data generated from different projects and secondary data from published literatures.The collected data were screened and then digitized. Microsoft ACCESS relational database and Visual Basiclanguage technologies were used for designing and implementing the standalone database application with the datamanagement capability. Presently, UPFBase provides taxonomy, synonyms, local name, common name, morphology,biology, distribution, habitat, economic importance, conservation status and other fishery information on 129 fishesbelonging to 11 orders and 27 families. UPFBase is user friendly and provides ease in working through search,query and action command button tools. It can easily be deployed on the mobile storages devices like CD-ROM,Pen drive, PCMCIA etc and can be installed on any Windows based Intel x86 machines. This version of UPFBasewas built for countries, where computational hardware and software resources are in scare and it is expected that itmight play imperious role in knowing and managing the indigenous fish diversity for decision making and posterity.Not Availabl

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Not AvailableThe 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.CABin Scheme of ICAR and CABin Division of ICAR-IASRI, New Delhi

Green synthesis of zinc oxide nanoparticles using Vernonia cinerea leaf extract and evaluation as nano-nutrient on the growth and development of tomato seedling

abstract: In the present study, the leaves of Vernonia cinerea were utilized as an efficacious bio-reductant, stabilizing, and capping agent for biological/green synthesis of zinc oxide nanoparticles (ZnO NPs). The nanoparticle (NPs) characteristics show that phytocapped ZnO NPs are in the nano-size range (1–100 nm). Fourier transforms infrared studies reveal the outline of the synthesis mechanism for ZnO NPs whereas X-ray diffraction analysis approved the crystalline structure of ZnO-NPs. Energy-dispersive X-ray analysis defined the pureness and chemical constituent of ZnO-NPs. The microscopic analysis of ZnO NPs confirmed the spherical and non-agglomeration attributes of nano-particles. The commenced study reveals the outcome of phytocapped ZnO NPs on the growth of tomato seedlings. Results showed ZnO-NPs boost the morphological as well as physiological characteristics as compared to the bulk Zn. At lower doses, ZnO NPs give better results as compared to higher doses. The higher doses showed obstruction in the growth and development thereby recommending the 50 mg/L−1of ZnO NPs exposed to tomato seedlings is beneficial

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Not AvailableThe 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.CABin Scheme of ICAR and CABin Division of ICAR-IASRI, New Delhi