FMiR: A Curated Resource of Mitochondrial DNA Information for Fish

Mitochondrial genome sequences have been widely used for evolutionary and phylogenetic studies. Among vertebrates, fish are an important, diverse group, and their mitogenome sequences are growing rapidly in public repositories. To facilitate mitochondrial genome analysis and to explore the valuable genetic information, we developed the Fish Mitogenome Resource (FMiR) database to provide a workbench for mitogenome annotation, species identification and microsatellite marker mining. The microsatellites are also known as simple sequence repeats (SSRs) and used as molecular markers in studies on population genetics, gene duplication and marker assisted selection. Here, easy-to-use tools have been implemented for mining SSRs and for designing primers to identify species/habitat specific markers. In addition, FMiR can analyze complete or partial mitochondrial genome sequence to identify species and to deduce relational distances among sequences across species. The database presently contains curated mitochondrial genomes from 1302 fish species belonging to 297 families and 47 orders reported from saltwater and freshwater ecosystems. In addition, the database covers information on fish species such as conservation status, ecosystem, family, distribution and occurrence downloaded from the FishBase and IUCN Red List databases. Those fish information have been used to browse mitogenome information for the species belonging to a particular category. The database is scalable in terms of content and inclusion of other analytical modules. The FMiR is running under Linux operating platform on high performance server accessible at URL http://mail.nbfgr.res.in/fmir.     

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. AVAILABILITY: The database is available for free at http://mail.nbfgr.res.in/fbis/     

Salinity-Induced Attenuation in Secondary Metabolites Profile and Herbicidal Potential of Brassica nigra L. on Anagallis arvensis L.

Studies on plant defense mechanisms in stressful conditions predict that plant cope up with increasing stress for survival. Under environmental stress plants interact with problems like competition and survival under resource constraints or utilization of these resources in production of secondary compounds. In this experiment, we examined the costs of defense by evaluating variation in production of secondary compounds of Brassica nigra grown in the saline (B1?=?100 mM NaCl and B2?=?150 mM NaCl) and control (C?=?0 mM) soils and impact of its extracts on weed Anagallis arvensis L. The main allelopathic compounds in Brassica were determined using gas chromatography–mass spectroscopy (GC–MS). The results indicated that A. arvensis was adversely affected by the aqueous extracts of B. nigra. These observations might be related to extracts induced oxidative stress indicated by superoxide (O₂^?) production through nitroblue tetrazolium, cell integrity by Evans blue staining, malondialdehyde estimation by Schiff reagent, lipid peroxidation, lignin deposition, and antioxidant enzyme activities assay. We observed that soil salinity reduced the phytotoxicity of aqueous extract and decreased its potential. The presence of different bioactive compounds improved the natural herbicidal properties of B. nigra and it can be used in various medicinal and agricultural practices.

     

Green synthesis of nanoparticles and its potential application

Nanotechnology is a new and emerging technology with wealth of applications. It involves the synthesis and application of materials having one of the dimensions in the range of 1–100 nm. A wide variety of physico–chemical approaches are being used these days for the synthesis of nanoparticles (NPs). However, biogenic reduction of metal precursors to produce corresponding NPs is eco-friendly, less expensive, free of chemical contaminants for medical and biological applications where purity of NPs is of major concern. Biogenic reduction is a “Bottom Up” approach similar to chemical reduction where a reducing agent is replaced by extract of a natural products with inherent stabilizing, growth terminating and capping properties. Furthermore, the nature of biological entities in different concentrations in combination with reducing organic agents influence the size and shape of NPs. Present review focuses on microbes or plants based green synthesis of Ag, Au, Cu, Fe, Pd, Ru, PbS, CdS, CuO, CeO₂, Fe₃O₄, TiO₂, and ZnO NPs and their potential applications.     

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.     

Mitigating Strategies of Gibberellins in Various Environmental Cues and Their Crosstalk with Other Hormonal Pathways in Plants: a Review

Plant Molecular Biology Reporter - Phytohormones are chemical substances that in minute concentration instruct a plethora of developmental and physiological responses in plants. These signal...     

Interaction between shrimp and white spot syndrome virus through PmRab7-VP28 complex: an insight using simulation and docking studies

White spot disease is a devastating disease of shrimp Penaeus monodon in which the shrimp receptor protein PmRab7 interacts with viral envelop protein VP28 to form PmRab7–VP28 complex, which causes initiation of the disease. The molecular mechanism implicated in the disease, the dynamic behavior of proteins as well as interaction between both the biological counterparts that crafts a micro-environment feasible for entry of virus into the shrimp is still unknown. In the present study, we applied molecular modeling (MM), molecular dynamics (MD) and docking to compute surface mapping of infective amino acid residues between interacting proteins. Our result showed that α-helix of PmRab7 (encompassing Ser74, Ile143, Thr184, Arg53, Asn144, Thr184, Arg53, Arg79) interacts with β-sheets of VP28 (containing Ser74, Ile143, Thr184, Arg53, Asn144, Thr184, Arg53, Arg79) and Arg69-Ser74, Val75-Ile143, Leu73-Ile143, Arg79-Asn144, Ala198-Ala182 bonds contributed in the formation of PmRab7–VP28 complex. Further studies on the amino acid residues and bonds may open new possibilities for preventing PmRab7–VP28 complex formation, thus reducing chances of WSD. The quantitative predictions provide a scope for experimental testing in future as well as endow with a straightforward evidence to comprehend cellular mechanisms underlying the disease.