Biology subjects

Das, H.

Publications and source records attributed to Das, H..

4 recordsLinked to original sources

bioRxiv2021

A bispecific monomeric nanobody induces SARS-COV-2 spike trimer dimers

Antibodies binding to the severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) spike have therapeutic promise, but emerging variants show the potential for virus escape. This emphasizes the need for therapeutic molecules with distinct and novel neutralization mechanisms. Here we isolated a nanobody that interacts simultaneously with two RBDs from different spike trimers of SARS-CoV-2, rapidly inducing the formation of spike trimer-dimers leading to the loss of their ability to attach to the host cell receptor, ACE2. We show that this nanobody potently neutralizes SARS-CoV-2, including the B.1.351 variant, and cross-neutralizes SARS-CoV. Furthermore, we demonstrate the therapeutic potential of the nanobody against SARS-CoV-2 and the B.1.351 variant in a human ACE2 transgenic mouse model. This naturally elicited bispecific monomeric nanobody establishes a novel strategy for potent inactivation of viral antigens and represents a promising antiviral against emerging SARS-CoV-2 variants.

immunology↗

bioRxiv2020

Modified split application of nitrogen with biochar improved grain yield and nitrogen use efficiency in rainfed maize grown in Vertisols of India

Conventionally, non-judicious and blanket fertilizer nitrogen (N) used in rainfed maize lead to higher N losses, low N use efficiency (NUEs) and poor yields due to substandard agronomic management practices. To avoid such N losses, fertilizer additions are synchronized with plant uptake requirements. In this context, agronomic based management focused on optimizing N rates and biochar application is essential for improved NUEs and crop productivity. Keeping this in view, a field experiment was conducted during 2014, 2015 and 2016 in rainfed maize (Zea mays L.) grown in Vertisols of India. In this study, twelve treatments that comprised of N omission plot (N0), skipping of basal rate, multi-split topdressing at varying time as broadcast and band placement, soil test crop response (STCR) based NPK with target yield 6.0 t ha-1 in maize and biochar application (10 t ha-1) were investigated. The experiment was conducted following a Randomized Complete Block Design (RCBD) set up with three replications. Pooled analysis of three years data revealed that the application of N rates (120 kg Nha-1) in 2 equal splits (60 kg Nha-1) at knee high (V8) and tasseling (VT) stages with skipped basal N rate, achieved higher maize grain yield (5.29 t ha-1) ascribed to the greater growth parameters, yield components and N uptake compared to the recommended practices. Biochar application (10 t ha-1) as soil amendments along with multi top dressed N (120 kg N ha-1) into 3 splits also increased the grain yield. Delayed N application at V8 and VT growth stages, resulted in higher N uptake, agronomy efficiency (AE), partial factor productivity (PFP), physiology efficiency (PE) and recovery efficiency (RE). Biochar along with N fertilizer also improved the soil organic carbon (5.47g kg-1), ammonium-N (2.40 mg kg-1) and nitrate-N (0.52 mg kg-1) concentration in soil (P<0.05) as compared to non-biochar treatments. Application of biochar along with chemical fertilizer (120 kg Nha-1) significantly increased the concentration of ammonium (2.40 mg kg-1) and nitrate (0.52 mg kg-1) in soil (P<0.05) as compared to non-biochar treatments. The perfect positive linear relationship illustrated that the grain yield of rainfed maize was highly dependent (R2=0.99 at p<0.0001) on N availability, as indicated by the fitted regression line of maize grain yield on N uptake. On the other hand, factor analysis revealed, the one to one positive function relationship of biomass with N uptake at V8 and VT growth stages. Principal Component Regression (PCR) analysis showed that PC1 acted as a major predictor variable for total dry matter yield (TDMY) and dominated by LAI and N uptake. Consequently, these results expressed that the agronomic management based multi-top dressed N application and biochar application to achieve higher yield and greater NUEs in rainfed maize is strongly linked with N application into splits.

plant biology↗

bioRxiv2020

Selection, biophysical and structural analysis of synthetic nanobodies that effectively neutralize SARS-CoV-2

The coronavirus SARS-CoV-2 is the cause of the ongoing COVID-19 pandemic. Therapeutic neutralizing antibodies constitute a key short-to-medium term approach to tackle COVID-19. However, traditional antibody production is hampered by long development times and costly production. Here, we report the rapid isolation and characterization of nanobodies from a synthetic library, known as sybodies (Sb), that target the receptor-binding domain (RBD) of the SARS-CoV-2 spike protein. Several binders with low nanomolar affinities and efficient neutralization activity were identified of which Sb23 displayed high affinity and neutralized pseudovirus with an IC50 of 0.6 {micro}g/ml. A cryo-EM structure of the spike bound to Sb23 showed that Sb23 binds competitively in the ACE2 binding site. Furthermore, the cryo-EM reconstruction revealed a novel conformation of the spike where two RBDs are in the up ACE2-binding conformation. The combined approach represents an alternative, fast workflow to select binders with neutralizing activity against newly emerging viruses.

biophysics↗

bioRxiv2020

An alpaca nanobody neutralizes SARS-CoV-2 by blocking receptor interaction

SARS-CoV-2 is the etiologic agent of COVID-19, currently causing a devastating pandemic for which pharmacological interventions are urgently needed. The virus enters host cells through an interaction between the spike glycoprotein and the angiotensin converting enzyme 2 (ACE2) receptor. Directly preventing this interaction presents an attractive possibility for suppressing SARS-CoV-2 replication. Here we report the isolation and characterization of an alpaca-derived single domain antibody fragment, Ty1, that specifically targets the receptor binding domain (RBD) of the SARS-CoV-2 spike, directly preventing ACE2 engagement. The nanobody binds with high affinity in the low nM range to the RBD, occluding ACE2. A cryo-electron microscopy structure of the bound complex at 2.9 Å resolution reveals that Ty1 binds to an epitope on the RBD accessible in both the ‘up’ and ‘down’ conformations and that Ty1 sterically hinders RBD-ACE2 binding. This 12.8 kDa nanobody does not need an Fc domain to neutralize SARS-CoV-2, and can be expressed in high quantities in bacteria, presenting opportunities for manufacturing at scale. Ty1 is therefore an excellent candidate as an intervention against COVID-19.Competing Interest StatementThe authors have declared no competing interest.View Full Text

microbiology↗