Genome-wide identification and characterization of tissue specific long non-coding RNAs and circular RNAs in common carp (Cyprinus carpio L.)

Cyprinus carpio is regarded as a substitute vertebrate fish model for zebrafish. A varied category of non-coding RNAs is comprised of long non-coding RNAs (lncRNAs) and circular RNAs (circRNAs). These ncRNAs were once considered non-functional “junk DNA” but research now shows they play important roles in gene expression regulation, chromatin modification, and epigenetic regulation. The systemic tissue-specific research of the lncRNAs and circRNAs of C. carpio is yet unexplored. A total of 468 raw RNA-Seq dataset across 28 distinct tissues from different varieties of common carp retrieved from public domain were pre-processing, mapped and assembled for lncRNA identification/ classification using various bioinformatics tools. A total of 33,990 lncRNAs were identified along with revelation of 9 miRNAs having 19 unique lncRNAs acting as their precursors. Additionally, 2,837 miRNAs were found to target 4,782 distinct lncRNAs in the lncRNA-miRNA-mRNA interaction network analysis, which resulted in the involvement of 3,718 mRNAs in common carp. A total of 22,854 circRNAs were identified tissue-wise across all the 28 tissues. Moreover, the examination of the circRNA-miRNA-mRNA interaction network revealed that 15,731 circRNAs were targeted by 5,906 distinct miRNAs, which in turn targeted 4,524 mRNAs in common carp. Significant signaling pathways like necroptosis, NOD-like receptor signaling pathway, hypertrophic cardiomyopathy, small cell lung cancer, MAPK signaling pathway, etc. were identified using Gene Ontology and Kyoto Encyclopedia of Genes and Genomes. The web resource of common carp ncRNAs, named CCncRNAdb and available at http://backlin.cabgrid.res.in/ccncrnadb/ gives a comprehensive information about common carp lncRNAs, circRNAs, and ceRNAs interactions, which can aid in investigating their functional roles for its management

Synthesis and study of Structural, Microstructural and Dielectric Properties of Ce3+ doped Co-Ni Ferrites for automotive applications

Nano crystalline spinel ferrites of Co0.5Ni0.5CexFe2−xO4 (x=0.01, 0.015, 0.02, 0.025 and 0.03) was prepared by modified solution combustion method using a mixture of fuels for the first time. The influence of rare earth Ce3+ substitution at the Fe3+ site on the structural, microstructural and dielectric properties of Co0.5Ni0.5CexFe2-xO4 was investigated. The X-ray diffraction (XRD) studies confirmed the formation of monophasic nano crystalline samples without any secondary phases. The crystallite size decreases and density increases with the increases of Ce3+ contents. Surface morphology was studied through Scanning Electron Microscopy (SEM). Dielectric properties of these ferrites have been studied at room temperature using impedance analyzer in the frequency range up to 20 MHz. The effect of frequency and composition on dielectric constant (ε’), dielectric loss (tanδ) and ac conductivity (σac) have been discussed in terms of hopping of charge carriers (Fe2+↔Fe3+). The decrease in dielectric loss with frequency follows Debye's relaxation phenomena. Both the variation in tan loss and dielectric loss with frequency shows a similar. AC conductivity increases with the increases of frequency which directly proportional to concentration of Ce3+ ions follows Jonscher law. These Cerium doped Cobalt-nickel ferrites are very helpful for automotive applications

Double-digest restriction-associated DNA sequencing-based genotyping and its applications in sesame germplasm management

Sesame (Sesamum indicum L.) is an ancient oilseed crop belonging to the family Pedaliaceae and a globally cultivated crop for its use as oil and food. In this study, 2496 sesame accessions, being conserved at the National Genebank of ICAR-National Bureau of Plant Genetic Resources (NBPGR), were genotyped using genomics-assisted double-digest restriction-associated DNA sequencing (ddRAD-seq) approach. A total of 64,910 filtered single-nucleotide polymorphisms (SNPs) were utilized to assess the genome-scale diversity. Applications of this genome-scale information (reduced representation using restriction enzymes) are demonstrated through the development of a molecular core collection (CC) representing maximal SNP diversity. This information is also applied in developing a mid-density panel (MDP) comprising 2515 hyper-variable SNPs, representing almost equally the genic and non-genic regions. The sesame CC comprising 384 accessions, a representative set of accessions with maximal diversity, was identified using multiple criteria such as k-mer (subsequence of length “k” in a sequence read) diversity, observed heterozygosity, CoreHunter3, GenoCore, and genetic differentiation. The coreset constituted around 15% of the total accessions studied, and this small subset had captured >60% SNP diversity of the entire population. In the coreset, the admixture analysis shows reduced genetic complexity, increased nucleotide diversity (π), and is geographically distributed without any repetitiveness in the CC germplasm. Within the CC, India-originated accessions exhibit higher diversity (as expected based on the center of diversity concept), than those accessions that were procured from various other countries. The identified CC set and the MDP will be a valuable resource for genomics-assisted accelerated sesame improvement program

Nitrogen Use in Durum and Selected Brassicaceae Oilseeds in Two-Year Rotations

Brassicaceae oilseeds can serve as potential feedstocks for renewable biofuels to offset demand for petroleum-based alternatives. However, little is known about oilseed crop yield potential and N use in semiarid, wheat (Triticum spp.)-based cropping systems that dominate the northern Great Plains (NGP). A 5-yr study was conducted in northeast Montana to investigate the yield potential of a direct seeded system of durum (T. durumDesf.) in rotation with either chemical fallow or three Brassicaceae oilseeds: camelina [Camelina sativa (L.) Crantz], crambe (Crambe abyssinica Hochst. ex R.E. Fries), and canola-quality Brassica juncea L. Overall, results from the study indicated that seed yield in the three Brassicaceae oilseeds tested in rotation with durum was related (P \u3c 0.001; r2 = 0.68) to a nitrogen recovery index (NRI), indicating the importance of nitrogen use (NU) efficiency in dryland oilseed production, and that B. juncea generally used N more efficiently than crambe and camelina. Similarly, NRI was related (P \u3c 0.001; r2 = 0.72) to grain yield in durum following oilseeds. Grain yield of durum following B. juncea was similar to durum following fallow and greater than durum following camelina or crambe. Durum following crambe tended to use N more inefficiently than durum following camelina, B. juncea, or fallow. Differences in yield and N use of durum and oilseeds varied among years, which underscores the need to further develop management tools to optimize durum-oilseed cropping systems in highly variable rainfall environments typical of the NGP

Uncovering Genomic Regions Associated With 36 Agro-Morphological Traits in Indian Spring Wheat Using GWAS

Wheat genetic improvement by integration of advanced genomic technologies is one way of improving productivity. To facilitate the breeding of economically important traits in wheat, SNP loci and underlying candidate genes associated with the 36 agro-morphological traits were studied in a diverse panel of 404 genotypes. By using Breeders’ 35K Axiom array in a comprehensive genome-wide association study covering 4364.79 cM of the wheat genome and applying a compressed mixed linear model, a total of 146 SNPs (-log10P ≥ 4) were found associated with 23 traits out of 36 traits studied explaining 3.7–47.0% of phenotypic variance. To reveal this a subset of 260 genotypes was characterized phenotypically for six quantitative traits [days to heading (DTH), days to maturity (DTM), plant height (PH), spike length (SL), awn length (Awn_L), and leaf length (Leaf_L)] under five environments. Gene annotations mined ∼38 putative candidate genes which were confirmed using tissue and stage specific gene expression data from RNA Seq. We observed strong co-localized loci for four traits (glume pubescence, SL, PH, and awn color) on chromosome 1B (24.64 cM) annotated five putative candidate genes. This study led to the discovery of hitherto unreported loci for some less explored traits (such as leaf sheath wax, awn attitude, and glume pubescence) besides the refined chromosomal regions of known loci associated with the traits. This study provides valuable information of the genetic loci and their potential genes underlying the traits such as awn characters which are being considered as important contributors toward yield enhancement

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Not AvailableThe livestock production system has a multi-faceted role in promoting livelihoods, alleviating poverty, building nutritional security & health and improving crop husbandry. The demand for animal-based food and animal products is rapidly growing more notably in developing countries due to rising incomes and urbanization. However, meeting such an upward demand, there is need of socially, economically and technically feasible system for sustainable and environment friendly smart livestock production system. Smart livestock farming envisages the harnessing of Information and Communication Technologies (ICT) as a decision support tool for more efficient, productive and profitable.Not Availabl

Development of a Tool for Comparison of Protein 3D Structure using graph theoretic approach

Project reportWe have illustrated in detail about two novel methods for comparison of 3D structure using (1) graph partition and (2) graph properties. The both proposed methods have been implemented in MATLAB by writing codes for various functions. The performance of the developed methodologies are tested with two existing best methods such as CE and jFATCAT on 100 proteins benchmark dataset with SCOP (Structural Classification Of Proteins) database. First method “graph partitioning” method is comprises conversion of 3D graph into 2D graph, partitioning of 2D graph into sub-graphs and then aligning sub-graphs. Finally structure similarity has been calculated by identify local structural similarities between sub-graphs to global similarity of the whole graph. The proposed method has shown significant improvement over jFATCAT and accuracy has increased up to 12-15%. Prime notion of the method is the decomposition of structure to clusters than single residues and SSE, this could be basic interaction of non-bonded residues in the arrangement of structure elements within a structure. These interaction leads protein fold space and arrangement of SSE elements in 3D space. Then, aligned the structures based on atoms positions and association with other atoms within clusters and between clusters to identify similar geometry and similarity of the two structures. The proposed method performed better in terms of classification accuracy due to the inclusion of all atoms but CE and jFATCAT uses only backbone C-α atoms and non-bonded atoms in a cluster may plays important role to inclusion of folding information of protein while comparing the 3D structures. In second method, is based on concepts of construction of graph from real world problems, database for graph and graph mining, pattern recognition are rich fields of computational techniques to study structures, topologies and properties of graphs. In this method, we have demonstrated that converting protein 3Dstructures into graphs and into properties such as total degree, maximum degree, no of adjacencies, average number of degree, cluster coefficient, graph energy, spectrum and number of components etc. Exploitation of the graph properties and data mining technique to perform complex studies on protein 3D structure. The proposed method is fast in terms of computation time complexity. Regarding accuracy is little improved over jFATCAT method. In future, this work can be extended for including more number of graph properties and more research can be done to find out the best structural identity or similarity among protein structures.Not Availabl

Delineation of molecular interactions of plant growth promoting bacteria induced β-1,3-glucanases and guanosine triphosphate ligand for antifungal response in rice: a molecular dynamics approach

Financiado para publicación en acceso aberto: Universidade de Vigo/CISUGAbstract Background The plant growth is influenced by multiple interactions with biotic (microbial) and abiotic components in their surroundings. These microbial interactions have both positive and negative effects on plant. Plant growth promoting bacterial (PGPR) interaction could result in positive growth under normal as well as in stress conditions. Methods Here, we have screened two PGPR’s and determined their potential in induction of specific gene in host plant to overcome the adverse effect of biotic stress caused by Magnaporthe grisea , a fungal pathogen that cause blast in rice. We demonstrated the glucanase protein mode of action by performing comparative modeling and molecular docking of guanosine triphosphate (GTP) ligand with the protein. Besides, molecular dynamic simulations have been performed to understand the behavior of the glucanase-GTP complex. Results The results clearly showed that selected PGPR was better able to induce modification in host plant at morphological, biochemical, physiological and molecular level by activating the expression of β-1,3-glucanases gene in infected host plant. The docking results indicated that Tyr75, Arg256, Gly258, and Ser223 of glucanase formed four crucial hydrogen bonds with the GTP, while, only Val220 found to form hydrophobic contact with ligand. Conclusions The PGPR able to induce β-1,3-glucanases gene in host plant upon pathogenic interaction and β-1,3-glucanases form complex with GTP by hydrophilic interaction for induction of defense cascade for acquiring resistance against Magnaporthe grisea. Graphical abstractMinistry of Agriculture and Farmers’ Welfare, India | Ref. 4-1/2013-A&PUniversidade de Vigo | Ref. 50110000676