Analysis of plastid DNA-like sequences within the nuclear genomes of higher plants

A wide-ranging examination of plastid (pt)DNA sequence homologies within higher plant nuclear genomes (promiscuous DNA) was undertaken. Digestion with methylation-sensitive restriction enzymes and Southern analysis was used to distinguish plastid and nuclear DNA in order to assess the extent of variability of promiscuous sequences within and between plant species. Some species, such as Gossypium hirsutum (cotton), Nicotiana tabacum (tobacco), and Chenopodium quinoa, showed homogenity of these sequences, while intraspecific sequence variation was observed among different cultivars of Pisum sativum (pea), Hordeum vulgare (barley), and Triticum aestivum (wheat). Hypervariability of plastid sequence homologies was identified in the nuclear genomes of Spinacea oleracea (spinach) and Beta vulgaris (beet), in which individual plants were shown to possess a unique spectrum of nuclear sequences with ptDNA homology. This hypervariability apparently extended to somatic variation in B. vulgaris. No sequences with ptDNA homology were identified by this method in the nuclear genome of Arabidopsis thaliana.      

Incidence and levels of fumonisin contamination in Colombian corn and corn products

A survey was conducted to determine the levels of fumonisins B1 and B2 in corn and corn-based products available in Colombia for human and animal consumption. A total of 120 samples were analyzed by acetonitrile-water extraction, cleanup with a strong-anion-exchange column, and liquid chromatography with o-phthaldialdehyde-2-mercaptoethanol derivatization and fluorescence detection. The samples of corn and corn-based products for animal intake were taken at different feed manufacturing plants, whereas the samples used for human foods where purchased from local retail stores. The number of positive samples for fumonisin B1 was 20.0% higher in corn and corn-based products for animal intake (75.0%) than in corn and corn-based products for human consumption (55.0%). The levels of fumonisin B1 were also higher in corn and corn-based products for animal intake (mean = 694 μg/kg; range = 32–2964 μg/kg), than in corn and corn-based products for human intake (mean = 218 μg/kg; range = 24–2170 μg/ kg). The incidence and levels of fumonisin B2 were lower than those for fumonisin B1. Corn and corn-based products for animal consumption had an incidence of fumonisin B2 of 58.3%, with a mean value of 283 μg/kg, and a range of 44–987 μg/kg. The incidence of fumonisin B2 in corn-based products for human intake was 35.0%, with a mean value of 118 μg/kg and a range of 21–833 μg/kg. The highest incidence and levels of fumonisins were found in samples of hominy feed, with concentrations ranging from 86 to 2964 μg/kg fumonisin B1 and 57 to 987 μg/kg fumonisin B2.     

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.     

Genetic relatedness among fish species of Genus Channa using mitochondrial DNA genes

The family Channidae is represented by 26 species, out of which 23 species are found in Asia. However, the taxonomy and phylogeny of the Channid fishes found in India are poorly understood. In the present study, eight species of Channa (Channa striata, Channa punctatus, Channa marulius, Channa gachua, Channa stewartii, Channa aurantimaculata, Channa barca and Channa bleheri) were investigated using partial sequences of 16S rRNA and Cytochrome c Oxidase subunit I (COI) of mitochondrial genes to differentiate among the eight species and study their relationships. The sequence analysis of the genes revealed two distinct groups, which are genetically distant from each other and exhibit identical phylogenetic resolution. The partial sequences of both the genes provided sufficient phylogenetic information to distinguish all the eight species of Channa.     

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/     

Predicting Calendar Aging in Lithium Metal Secondary Batteries: The Impacts of Solid Electrolyte Interphase Composition and Stability

Calendar aging of lithium metal batteries, in which cells' components degrade internally due to chemical reactions while no current is being applied, is a relatively unstudied field. In this work, a model to predict calendar aging of lithium metal cells is developed using two sets of readily obtainable data: solid electrolyte interphase (SEI) layer composition (measured via X‐ray photoelectron spectroscopy) and SEI stability (measured as a degradation rate using a simple constant current–constant voltage charging protocol). Electrolyte properties such as volume and salt concentration are varied in order to determine their effect on SEI stability and composition, with subsequent impacts to calendar aging. Lower salt concentrations produce a solvent‐based, more soluble SEI, while the highest concentration produces a salt‐based, less soluble SEI. Higher electrolyte volumes promote dissolution of the SEI and thus decrease its stability. The model predicts that lithium metal would be the limiting factor in calendar aging, depleting long before the electrolyte does. Additionally, the relative composition of the electrolyte during aging is modeled and found to eventually converge to the same value independent of initial salt concentration.     

Chromosomal localization of 18S and 5S rDNA using FISH in the genus <Emphasis Type="Italic">Tor</Emphasis> (Pisces,Cyprinidae)

Dual color fluorescence in situ hybridization (FISH) was performed to study the simultaneous chromosomal localization of 18S and 5S ribosomal genes in the genus Tor for the first time. The 18S and 5S rDNAs in four Tor species were amplified, sequenced and mapped on the metaphase chromosomes. The number and distribution of 18S and 5S rDNA clusters were examined on metaphase chromosome spreads using FISH. The specimens of T. chelynoides, T. putitora and T. progeneius showed six bright fluorescent signals of 18S rDNA and T. tor exhibited ten such signals. The 5S rDNA signals were present only on one pair of chromosomes in all the four Tor species. Ag-NORs were observed on two pairs of chromosomes in T. chelynoides, T. putitora, T. progeneius and four pairs in T. tor. Comparison of the observed 18S rDNA FISH signals and Ag-NORs strongly suggested a possible inactivation of NORs localized at the telomeres of a subtelocentric and telocentric chromosome pairs in all four species. The 5S rDNA contained an identical 120 bp long coding region and 81 bp long highly divergent non-transcribed spacers in all species examined. 18S and 5S rDNA sequencing and chromosomal localization can be a useful genetic marker in species identification as well as phylogenetic and evolutionary studies.     

Mutagenic,genotoxic and bioaccumulative potentials of tannery effluents in freshwater fishes of River Ganga

The tannery industries are the reason of major environmental concerns as they release toxic heavy metals, like chromium, in rivers posing risks of genotoxicity and mutagenicity in aquatic organism and indirectly in humans through food chain. In the present analysis, the freshwater inhabitant fishes of River Ganges, viz., Labeo calbasu, Puntius sophore, and Mystus vittatus, were examined for assessing the genotoxic, mutagenic, and bioaccumulative potentials of tannery effluents. For genotoxicity assessment, the blood and gill samples of fishes prevailed from polluted sites of River Ganges adjoining Kanpur city were utilized for comet assay and micronucleus test. The present investigation revealed the presence of significantly (p < 0.05) higher micronuclei induction and % tail DNA in erythrocytes and gill cells of the fishes collected from the polluted sites. The bioaccumulation studies revealed chromium concentration in muscle (0.89 µg/g) and gill tissues (0.24 µg/g) of L. calbasu; muscle (0.44 µg/g) and gills (1.23 µg/g) of P. sophore; and muscle (0.9617 µg/g) and gills (0.3628 µg/g) of M. vittatus, quite higher than the permissible limits of the World Health Organization. Consequently, the present study indicates strongly that River Ganges is contaminated with harmful tannery pollutants causing genotoxicity and mutagenicity in freshwater fishes.