Biology subjects

Sharma, D. K.

Publications and source records attributed to Sharma, D. K..

3 recordsLinked to original sources

bioRxiv2020

Foraging analysis of Endangered Greater Adjutant Stork Leptotilus dubios Gemlin in certain habitat of Assam, India.

The endangered Greater Adjutant Stok Leptotilus dubius Gemlin confined only in some pockets in Assam and Bihar in India and in certain areas of Laos and Cambodia has poorly understood in its foraging activities in its natural habitats. Attempt has been made to address the forage pattern in its natural habitat wetlands in the Kamup district and in a city garbage dump in Guwahati in Assam, India. The various forage methods like walking, visual tactile etc and their relation with the body metrices like beak length, tibia tarsus length and its mass were assessed in terms of foraging habits. Forage actvities were evaluated during the breeding (May to September) and non breeding (October to April) time of the study period of 2012-2017 at different water level of the wetland(s). The foraging range of this stork assessed at an confinement of aerial distance of 15 km from the nesting sites appears as resident non migratory birds by habits. Types of diet composition obtained from the regurgitated food at the ground of the nesting sites were mostly the fish group channa and cyprinids. Profitability index was determined at the captive stork showed in favour of these two groups within the size group of 5 to 15 cm. Larger food item showed lesser profitability index. PCA analysis showed negative foraging correlation with the Prey size greater than 8cm and 15 cm, while the captivity study was conducted Thus the present findings on the foraging assessment of Greater Adjutant might be the baseline information for conservation action plan.Competing Interest StatementThe authors have declared no competing interest.View Full Text

zoology↗

bioRxiv2020

In silico Proteome analysis of Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2)

Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) (2019-nCoV), is a positive-sense, single-stranded RNA coronavirus. The virus is the causative agent of coronavirus disease 2019 (COVID-19) and is contagious through human-to-human transmission. The present study reports sequence analysis, complete coordinate tertiary structure prediction and in silico sequence-based and structure-based functional characterization of full SARS-CoV-2 proteome based on the NCBI reference sequence NC_045512 (29903 bp ss-RNA) which is identical to GenBank entry MN908947 and MT415321. The proteome includes 12 major proteins namely orf1ab polyprotein (includes 15 proteins), surface glycoprotein, ORF3a protein, envelope protein, membrane glycoprotein, ORF6 protein, ORF7a protein, orf7b, ORF8, Nucleocapsid phosphoprotein and ORF10 protein. Each protein of orf1ab polyprotein group has been studied separately. A total of 25 polypeptides have been analyzed out of which 15 proteins are not yet having experimental structures and only 10 are having experimental structures with known PDB IDs. Out of 15 newly predicted structures six (6) were predicted using comparative modeling and nine (09) proteins having no significant similarity with so far available PDB structures were modeled using ab-initio modeling. Structure verification using recent tools QMEANDisCo 4.0.0 and ProQ3 for global and local (per-residue) quality estimates indicate that the all-atom model of tertiary structure of high quality and may be useful for structure-based drug designing targets. The study has identified nine major targets (spike protein, envelop protein, membrane protein, nucleocapsid protein, 2-O-ribose methyltransferase, endoRNAse, 3-to-5 exonuclease, RNA-dependent RNA polymerase and helicase) for which drug design targets could be considered. There are other 16 nonstructural proteins (NSPs), which may also be percieved from the drug design angle. The protein structures have been deposited to ModelArchive. Tunnel analysis revealed the presence of large number of tunnels in NSP3, ORF 6 protein and membrane glycoprotein indicating a large number of transport pathways for small ligands influencing their reactivity.

bioinformatics↗

bioRxiv2020

WD 40 domain of RqkA regulates its kinase activity and role in extraordinary radioresistance in Deinococcus radiodurans

RqkA, a DNA damage responsive Serine / Threonine kinase is characterized for its role in DNA repair and cell division in D. radiodurans. It has a unique combination of a kinase domain at N-terminus and a WD40 type domain at C-terminus joined through a linker. WD40 domain is comprised of eight {beta} propeller repeats held together via "tryptophan-docking motifs" and forming a typical velcro closure structure. RqkA mutants lacking the WD40 region (hereafter referred to as WD mutant) could not complement RqkA loss in {gamma} radiation resistance in D. radiodurans and lacked {gamma} radiation mediated activation of kinase activity in vivo. WD mutants failed to phosphorylate its cognate substrate (e.g. DrRecA) in surrogate E. coli cells. Further, unlike wild type enzyme, the kinase activity of its WD40 mutants was not stimulated by Pyrroloquinoline quinine (PQQ) indicating the role of the WD motifs in PQQ interaction and stimulation of its kinase activity. Together, results highlighted the importance of the WD40 domain in the regulation of RqkA kinase signaling functions in vivo and thus the role of WD40 domain in the regulation of any STPK is the first time demonstrated in bacteria. ImportanceThis study highlights the importance of the WD40 domain in activity regulation and signaling activity of bacterial serine/ threonine kinase for the first time in the bacterial response to gamma radiation and DNA damage.

molecular biology↗