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Biology subjects

Santra, D.

Publications and source records attributed to Santra, D..

4 recordsLinked to original sources

A breeder in the sky: scoring flowering with fewer flights

Flowering time is a trait of broad interest and importance to both plant breeders and plant biologists. Unlike many other traits, flowering time cannot be scored accurately from a single observation; its measurement requires repeated observations of the same experiments over time. Both classification- and object-detection-based approaches have demonstrated the potential to estimate flowering time from Unmanned aerial vehicle (UAV) imagery rather than by manual observation, but they still require data collection at many time points. Here, we train and deploy a regression-based framework for scoring flowering time. Using a dataset of more than 200,000 UAV images and associated flowering-time records collected across 27 environments, we demonstrate that this approach enables the prediction of flowering time from as few as one observation per field experiment and successfully generalizes to field experiments in environments not represented in the training dataset. These results indicate that regression-based approaches for predicting flowering time from sparse UAV observations have the potential to substantially reduce the data-collection burden in field experiments

plant biology↗

Proliferative and Motile Cell Interplay in Glioma Invasion: Go-or-Grow Switching Caps the Invasion Speed

On the cellular level, glioma cells seem to be either in a "go" state or in a "grow" state. It is observed that the outer edge of the tumor grows over time. A general rule c [≤] 1/2c_F was proven by Thiessen, Conte, Stepien, and Hillen via a substitution argument; however, they weren't able to derive the exact formula for the tumor's speed or determine exactly what conditions would cause a tumor to reach its maximum speed. In this article, it is assumed that the cells switch back and forth between moving and growing very fast, and the exact equation for the speed of the tumor expansion is c* = 2{surd}{phi}i_m {phi}_p rD. It is found that the same rate of maximum possible growth occurs when cells move for 50\% of the time and grow for 50% of the time. If the cells spend more of their time doing one than the other, it grows even more slowly. Moreover, a dimensionless parameter is introduced: {chi} = c/2{surd}rD, to determine the exact hidden phenotype balance through plugin the speed at which one individual cell moves (D), the cell division rate (r), and the tumor expansion rate (c). The outcome will be near 1 if the old standard tumor model is correct. If it is 0.5 or below, our model is correct; it is either a "go" or "grow" state. In addition, the exact number indicates the percentage of tumour cells that are moving. In the human brain, tumors do not spread evenly in a circle; they spread much faster along with the white-matter tracts apparent through diffusion tensor imaging (DTI). It is shown that our 50% speed limit remains valid along these "brain highways" a result that has not been previously shown in a mathematical study. Lastly, we address a theoretical question that was left unanswered by past studies using computer simulations and discuss the implications for clinical interpretation of MRI growth rates from real patients using our results.

biophysics↗

Conserved in 186 countries the RBD fraction of SARS CoV-2 S-protein with in-silicoT500S mutation strongly blocks ACE2 rejecting the viral spike; A Molecular-docking analysis.

SARS-CoV-2 developed global-pandemic with millions of infections/deaths. Blocker/inhibitor of ACE2 and viral-spikes Receptor-Binding-Domain RBD-blockers are helpful. Here, conserved RBD (CUTs) from 186-countries were compared with WUHAN-Hu-1 wild-type by CLUSTAL-X2 and Structural-alignment using Pymol. The RBD of ACE2-bound nCOV2 crystal-structure (2.68[A]) 6VW1 was analyzed by Haddock-PatchDock. Extensive structural study/trial to introduce point/double/triple mutations in the following locations (Y489S/Y453S/T500S/T500Y)/(Y489S,Y453S/Y489S,T500S/Y489S,T500Y/Y453S,T500S/Y453S, T500Y)/ (Y489S,Y453S,T500S/Y489S,Y453S,T500Y) of CUT4 (most-effective) were tested with Swiss-Model-Expacy. Blind-docking of mutated-CUTs to ACE2 (6VW1) by Haddock-Hawkdock was performed and optimally complete-rejection of nCOV2 to ACE2 was noticed. Further, competitive-docking/binding-analyses were done by PRODIGY. Present results suggest that compared to the wild-spike, CUT4 showed extra LYS31-PHE490/GLN42-GLN498 bonding and lack of TYR41-THR500 interaction (in wild H-bond:2.639[A]) with ACE2 RBD. Mutated-CUT4 strongly binds with the ACE2-RBD, promoting TYR41-T500S (H-bond: 2.0[A] and 1.8[A])/T500Y (H-bond:2.6[A]) interaction and complete inhibition of ACE2 RBD-nCOV2. Mutant combinations T500S,Y489S,T500S and Y489S,Y453S,T500Y mostly blocked ACE2. Conclusively, CUT4-mutant rejects whole glycosylated-nCoV2 pre-dock/post-dock/competitive-docking conditions.

bioinformatics↗

Energetics based epitope screening in SARS CoV-2 (COVID 19) spike glycoprotein by Immuno-informatic analysis aiming to a suitable vaccine development.

The recent outbreak by SARS-CoV-2 has generated a chaos in global health and economy and claimed/infected a large number of lives. Closely resembling with SARS CoV, the present strain has manifested exceptionally higher degree of spreadability, virulence and stability possibly due to some unidentified mutations. The viral spike glycoprotein is very likely to interact with host Angiotensin-Converting Enzyme 2 (ACE2) and transmits its genetic materials and hijacks host machinery with extreme fidelity for self propagation. Few attempts have been made to develop a suitable vaccine or ACE2 blocker or virus-receptor inhibitor within this short period of time. Here, attempt was taken to develop some therapeutic and vaccination strategies with a comparison of spike glycoproteins among SARS-CoV, MERS-CoV and the SARS-CoV-2. We verified their structure quality (SWISS-MODEL, Phyre2, Pymol) topology (ProFunc), motifs (MEME Suite, GLAM2Scan), gene ontology based conserved domain (InterPro database) and screened several epitopes (SVMTrip) of SARS CoV-2 based on their energetics, IC50 and antigenicity with regard to their possible glycosylation and MHC/paratopic binding (Vaxigen v2.0, HawkDock, ZDOCK Server) effects. We screened here few pairs of spike protein epitopic regions and selected their energetic, IC50, MHC II reactivity and found some of those to be very good target for vaccination. A possible role of glycosylation on epitopic region showed profound effects on epitopic recognition. The present work might be helpful for the urgent development of a suitable vaccination regimen against SARS CoV-2.

immunology↗