Dinesh Yadav | Deen Dayal Upadhyay Gorakhpur University, Gorakhpur, Uttar Pradesh, INDIA (original) (raw)

Papers by Dinesh Yadav

Genetic Engineering and Biotechnology Journal, 2010

The genetic relatedness of three varieties of finger millet (Eleusine coracana L.) with varying s... more The genetic relatedness of three varieties of finger millet (Eleusine coracana L.) with varying seed coat color namely PRM-1 (Brown), PRM-701 (White) and PRM-801 (Golden) were assessed with 10 RAPD and 10 ISSR markers. Molecular parameters viz., total number of bands, average polymorphic bands, average percent polymorphism, average polymorphic information content (PIC) and average expected gene diversity (Hi) generated from RAPD and ISSR markers has been compared. The RAPD profiling of ...

Yadav SK, Dubey AK, Yadav S, Bisht D, Darmwal NS, Yadav D., Amino acid sequences based phylogenet... more Yadav SK, Dubey AK, Yadav S, Bisht D, Darmwal NS, Yadav D., Amino acid sequences based phylogenetic and motif assessment of lipases from different organisms, Online J Bioinform., 13(3):400-417, 2012. Bacterial, fungal, plant and animal lipases amino acid sequences retrieved from different databases were analyzed for homology search, multiple sequence alignment, phylogenetic and motif assessment using different bioinformatics tools. The multiple sequence alignment revealed different conserved stretches of amino acids exclusively for each groups along with a highly conserved glycine residue for plant and animal lipases. The phylogenetic tree constructed for different groups uniformly showed two major clusters divided into several sub-clusters based on the closeness of the lipases protein sequences irrespective of the source organisms. The 64 bacterial lipases protein sequences were distributed into two main clusters with various sub-clusters revealing the rich diversity of lipases among diverse bacterial strains. The fungal lipase protein sequences based phylogenetic tree revealed two major clusters for representing two important groups namely ascomycota and basidomycota with several sub-clusters. The Aspergillus species were placed closely in the cluster along with Penicillium species. The distributions of three conserved motifs were analyzed among these lipases. Bacterial lipases motifs represented α/β hydrolase fold family while fungal, animal and plant lipases revealed lipase 3 families though all represented the same Clan 0028. The motif sequences of these lipases also showed five conserved amino acids residues GHSAG for bacterial, fungal and plant lipases though it was not observed in the case of animal lipases.

The Dof (DNA binding with one finger) transcription factor family represents a typical example of... more The Dof (DNA binding with one finger) transcription factor family represents a typical example of zinc finger transcription factors associated with diverse functions exclusively in plants. In the present study three dimensional structure of twenty one Dof proteins of sorghum were predicted by I-TASSER server based multiple threading method and the resulting modelled structures were validated by PROCHECK, Ramachandran Plot and QMEAN Z-score. These models were assigned PMDB IDs PM0079009 to PM0079021 and PM0079023 to PM0079030. The secondary structure revealed diversity in terms of sheets, beta-alpha-beta units, beta hairpin, beta bulges, strands, helices, helix-helix interactions, beta turns and gamma turns. The structural motif scan revealed presence of specific amino acid rich profile for each SbDof proteins along with a typical zinc finger Dof type profile. The putative functions were also predicted based on gene ontology (GO) terms in I-TASSER server. In-silico expression profili...

Bacterial, fungal, plant and animal lipases amino acid sequences retrieved from different databas... more Bacterial, fungal, plant and animal lipases amino acid sequences retrieved from different databases were analyzed for homology search, multiple sequence alignment, phylogenetic and motif assessment using different bioinformatics tools. The multiple sequence alignment revealed different conserved stretches of amino acids exclusively for each groups along with a highly conserved glycine residue for plant and animal lipases. The phylogenetic tree constructed for different groups uniformly showed two major clusters divided into several sub-clusters based on the closeness of the lipases protein sequences irrespective of the source organisms. The 64 bacterial lipases protein sequences were distributed into two main clusters with various sub-clusters revealing the rich diversity of lipases among diverse bacterial strains. The fungal lipase protein sequences based phylogenetic tree revealed two major clusters for representing two important groups namely ascomycota and basidomycota with seve...

The genetic diversity analysis of eight populations of Nardostachys jatamansi DC. collected from ... more The genetic diversity analysis of eight populations of Nardostachys jatamansi DC. collected from different altitude of Central Himalaya has been attempted using 24 sets of random amplified polymorphic DNA (RAPD) primers. These sets of RAPD marker generated a total of 346 discernible and reproducible bands across the analysed population with 267 polymorphic and 75 monomorphic bands. The unweighted pair group method with arithmetic average (UPGMA) cluster analysis revealed three distinct clusters: I, II and III. The cluster I was represented by N. jatamansi population collected from Panwali Kantha (3200 m asl) and Kedarnath (3584 m asl), India together with Jumla (2562 m asl) from Nepal. Cluster II included collections from Har Ki Doon (3400 m asl) and Tungnath (3600 m asl) from India while Cluster III was represented by collections from Munsiyari (2380 m asl), Dayara (3500 m asl) and Valley of Flowers (3400 m asl) from India. The clustering of these populations was independent of variations in altitude and geographical locations. The genetic variations observed in different populations of Jatamansi might be due to environmental influences (biotic and abiotic), rather than altitude level differences. The abiotic (geographical or climatic differentiation) and biotic (pollination between population and seed dispersal) factors might be responsible for the genetic variations among these accessions of Jatamansi.

A total of 64 protein sequences of α-L-rhamnosidase representing different source organisms avail... more A total of 64 protein sequences of α-L-rhamnosidase representing different source organisms available in GenBank were downloaded and in silico characterized for homology search, multiple sequence alignment, domain analysis and phylogenetic tree construction to reveal sequence level similarity. Two major clusters representing bacterial and fungal α-L-rhamnosidase were observed. The multiple accessions of different bacterial and fungal sources formed clusters revealing a sequence level similarity. The multiple sequence alignment of α-L-rhamnosidase protein sequences from different source organisms showed conserved regions at different stretches indicating homology at sequence level. A total of seven motifs were observed in MEME which showed similarity with Bacrhamnosid family belonging to clan six hairpin glycosidase hydrolases super family which is conserved in all the fungal and bacterial α-L-rhamnosidase protein sequences. One of the motifs showed similarity with Bac_rhamnoside_N d...

Sugar Tech, 2014

ABSTRACT A total of 25 Dof genes were retrieved from GRASSIUS grass regulatory information server... more ABSTRACT A total of 25 Dof genes were retrieved from GRASSIUS grass regulatory information server. These sequences were in silico characterized for homology search, multiple sequence alignment for conserved Dof DNA binding domains, distribution of conserved motifs and phylogenetic relatedness with sorghum, rice and Arabidopsis. A highly conserved four cysteine residues associated with typical zinc finger of Dof family was observed on multiple sequence alignment of Dof domains. A highly conserved cysteine residue at positions 3 and 6 along with proline and sulfur at positions 4 and 8, respectively were observed. The phylogenetic tree of 119 Dof protein sequences of sugarcane, rice, sorghum and Arabidopsis revealed ten distinct clades with several orthologs and paralogs. The distributions of 25 conserved motifs were analyzed for Dof proteins of sugarcane. Dof proteins with closely related members in the phylogenetic tree shared common motif distribution revealing the possibility of functional similarities within the same subgroup. The motif 1 representing the conserved Dof domain of 50 amino acids was uniformly observed in all the Dof proteins of sugarcane except ScDof8 and ScDof14.

Research Journal of Soil Biology, 2009

Abstract The diversity of Aspergillus from soil of teak dominated kusmi forest an Indian subtropi... more Abstract The diversity of Aspergillus from soil of teak dominated kusmi forest an Indian subtropical teak forest of Gorakhpur, has been studied and compared with earlier reports. The nine species of Aspergillus namely A. aculeatus, A. carbonarius, A. deflectus, A. fischeri, A. niger, A. phoenicis, A. puniceus, A. sparsus and A. wentii were unaffected and uniformly distributed over the time period. There has been substantial loss of 12 species of Aspergillus namely A. carneus, A. deflectus, A. melleus, A. panamensis, A. petrakii, A. puniceus, A. ...

Plant Systematics and Evolution, 2014

ABSTRACT The genetic diversity among cereals and millets were assessed based on PCR amplification... more ABSTRACT The genetic diversity among cereals and millets were assessed based on PCR amplification pattern derived from 4 Dof domain and 20 Dof genes specific primers. Multiple bands showing variability in terms of both number and sizes of bands ranging from 0.1 to 3.0 kbp were observed. Out of a total of 906 bands, 894 polymorphic and 12 monomorphic bands were obtained and the percentage of polymorphism ranged from 69.23 to 100 %. A very high degree of polymorphism was observed with all the primers except Dof-24 primer and the genetic diversity ranged from 0.0601 to 0.2118 among these crops. The Jaccard’s similarity matrices based dendrogram obtained using UPGMA method revealed two major clusters designated as A and B. The major cluster A comprises of rice, sorghum, maize, finger millet, foxtail millet, barnyard millet and proso millet representing Oryzoideae, Panicoideae, Chloridoideae subfamilies while cluster B with wheat, barley, oat, little millet and kodo millet represents predominantly pooideae subfamily. These major clusters were further bifurcated into two sub-clusters each having members representing almost the same subfamilies.

Asian Journal of Biotechnology, 2011

Plant Systematics and Evolution, 2011

... S Afr J Bot 61:58 Asare AT, Gowda BS, Galyuon IKA, Aboagye LL, Takrama JF, Timko MP (2010) A... more ... S Afr J Bot 61:58 Asare AT, Gowda BS, Galyuon IKA, Aboagye LL, Takrama JF, Timko MP (2010) Assessment of the genetic diversity in cowpea (Vigna unguiculata (L.) Walp.) germplasm from Ghana using simple sequence repeat markers. ...