Biology subjects

Yadav, P.

Publications and source records attributed to Yadav, P..

At least 73 records · Page 4Linked to original sources

bioRxiv2021

ZRC3308 monoclonal antibody cocktail shows protective efficacy in Syrian hamsters against SARS-CoV-2 infection

We have developed a monoclonal antibody (mAb) cocktail (ZRC-3308) comprising of ZRC3308-A7 and ZRC3308-B10 in the ratio 1:1 for COVID-19 treatment. The mAbs were designed to have reduced immune effector functions and increased circulation half-life. mAbs showed good binding affinities to non-competing epitopes on RBD of SARS-CoV-2 spike protein and were found neutralizing SARS-CoV-2 variants B.1, B.1.1.7, B.1.351, B.1.617.2 and B.1.617.2 AY.1 in vitro. The mAb cocktail demonstrated effective prophylactic and therapeutic activity against SARS-CoV-2 infection in Syrian hamsters. The antibody cocktail appears to be a promising candidate for the prophylactic use and for therapy in early COVID-19 cases which have not progressed to severe disease.

microbiology↗

bioRxiv2021

Human - murine concordance of molecular signatures in nerve-sparing murine partial bladder outlet obstruction (NeMO)

Recently we demonstrated the utility of a nerve-sparing mid-urethra model of partial outlet obstruction (NeMO) that has high consistency and minimal mortalities, unlike the traditional model proximal to the bladder neck. Our goal was to uncover potential therapeutic targets by investigating the genome wide transcriptional changes and pathways altered in NeMO to compare with published human bladder obstruction data. We performed RNAseq and analysed the differentially upregulated and downregulated genes for associated pathways, transcription factor binding site analysis (TFBS), upstream regulators and Gene Set Enrichment Analysis (GSEA). NeMO increased bladder mass, relative bladder mass and hyperactivity, and decreased voiding efficiency. In NeMO vs. sham, 831 genes were differentially expressed (adjusted p<0.05) and correlated significantly with at least one physiologic parameter. Gene ontology revealed an enrichment for matrix pathways in the upregulated genes, and for cardiac contraction, oxidative phosphorylation and pyruvate metabolism in downregulated genes. TFBS analysis revealed a differential regulation of up vs downregulated genes, with KLF4 strongly associated with the downregulated genes. Downregulated genes of Human bladder obstruction were also associated with the TFBS of KLF4. GSEA of the NeMO gene set confirmed the DAVID results, but also showed a cluster of cytokine activation genes. In human bladder underactive obstruction, cytokines were also highly upregulated. The common cytokine pathway upregulation provided an example of the use of RNAseq for uncovering potential new therapeutic targets. As TNF and the innate immune pathways were strongly implicated in both human and mouse, and TNF is produced by macrophages, we depletion macrophages with clodronate (CL) during NeMO. Although CL did not block hypertrophy, it significantly decreased NeMO-induced hyperactive voiding (p<0.01) and increased voiding efficiency (p<0.05). The expression of several cytokines/chemokines correlated significantly with bladder functional parameters such as residual volumes, and hyperactivity. Conclusions: Gene expression signatures of NeMO were consistent with human bladder obstruction, supporting the use of the nerve-sparing mouse obstruction model for therapeutic exploration.

molecular biology↗

bioRxiv2021

Isolation of SARS-CoV-2 B.1.1.28.2 P2 variant and pathogenicity comparison with D614G variant in hamster model

BackgroundConsidering the potential threat from emerging SARS-CoV-2 variants and the rising COVID-19 cases, SARS-CoV-2 genomic surveillance is ongoing in India. We report herewith the isolation of the P.2 variant (B.1.1.28.2) from international travelers and further its pathogenicity evaluation and comparison with D614G variant (B.1) in hamster model. MethodsVirus isolation was performed in Vero CCL81 cells and genomic characterization by next generation sequencing. The pathogenicity of the isolate was assessed in Syrian hamster model and compared with B.1 variant. ResultsB.1.1.28.2 variant was isolated from nasal/throat swabs of international travelers returned to India from United Kingdom and Brazil. The B.1.1.28.2 variant induced body weight loss, viral replication in the respiratory tract, lung lesions and caused severe lung pathology in infected Syrian hamster model in comparison, with B.1 variant infected hamsters. The sera from B.1.1.28.2 infected hamsters efficiently neutralized the D614G variant virus whereas 6-fold reduction in the neutralization was seen in case of D614G variant infected hamsters sera with the B.1.1.28.2 variant. ConclusionsB.1.1.28.2 lineage variant could be successfully isolated and characterization could be performed. Pathogenicity of the isolate was demonstrated in Syrian hamster model and in comparison, with B.1 variant was found more pathogenic. The findings of increased disease severity and neutralization reduction is of great concern and point towards the need for screening the vaccines for efficacy.

microbiology↗

bioRxiv2021

Isolation and characterization of SARS-CoV-2 VOC, 20H/501Y.V2, from UAE travelers

Multiple SARS-CoV-2 variants have been emerged and created serious public health in the affected countries. The variant of Concern associated with high transmissibility, disease severity and escape mutations is threat to vaccination program across the globe. Travel has been important factor in spread of SARS-CoV-2 variants worldwide. India has also witnessed the dreadful effect of these SARS-CoV-2 variants. Here, we report the Isolation and characterization of SARS-CoV-2 VOC, 20H/501Y.V2 (B.1.351), from UAE travelers to India. The virus isolate would be useful to determine the efficacy of the currently available vaccines in India.

microbiology↗

bioRxiv2021

Neutralization potential of Covishield vaccinated individuals against B.1.617.1

Covishield comprises the larger proportion in the vaccination program in India. Hence, it is of utmost importance to understand neutralizing capability of vaccine against the B.1.617.1 variant which is considered to responsible for surge of the cases in India. The neutralizing-antibody (NAb) titer against B.1.167.1 and prototype B.1 variant (D614G) was determined of the vaccine sera (4 weeks after second dose) of COVID-19 naive subjects (n=43) and COVID-19 recovered subjects (n=18). The results demonstrated that sera of COVID-19 recovered subjects (n=18) who received two doses of Covishield have higher NAb response compared to the COVID-19 naive with a significant difference (p<0.0001) in NAb titer against B.1 and B.1.617.1 In-spite of reduction in the neutralizing titer against B.1.617.1 variant; Covishield vaccine-induced antibodies are likely to be protective to limit the severity and mortality of the disease in the vaccinated individuals.

immunology↗

bioRxiv2021

Neutralization of B.1.1.28 P2 variant with sera of natural SARS-CoV-2 infection and recipients of BBV152 vaccine

The emergence of new SARS-CoV-2 variants has been a serious threat to the public health system and vaccination program. The variant of concerns have been the under investigation for their neutralizing potential against the currently available COVID-19 vaccines. Here, we have determined the neutralization efficacy of B.1.1.28.2 variant with the convalescent sera of individuals with natural infection and BBV152 vaccination. The two-dose vaccine regimen significantly boosted the IgG titer and neutralizing efficacy against both B.1.1.28.2 and D614G variants compared to that seen with natural infection. The study demonstrated 1.92 and 1.09 fold reductions in the neutralizing titer against B.1.1.28.2 variant in comparison with prototype D614G variant with sera of vaccine recipients and natural infection respectively.

microbiology↗

bioRxiv2021

Convergent evolution of SARS-CoV-2 spike mutations, L452R, E484Q and P681R, in the second wave of COVID-19 in Maharashtra, India

As the global severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) pandemic expands, genomic epidemiology and whole genome sequencing are being constantly used to investigate its transmissions and evolution. In the backdrop of the global emergence of "variants of concern" (VOCs) during December 2020 and an upsurge in a state in the western part of India since January 2021, whole genome sequencing and analysis of spike protein mutations using sequence and structural approaches was undertaken to identify possible new variants and gauge the fitness of current circulating strains. Phylogenetic analysis revealed that the predominant clade in circulation was a distinct newly identified lineage B.1.617 possessing common signature mutations D111D, G142D, L452R, E484Q, D614G and P681R, in the spike protein including within the receptor binding domain (RBD). Of these, the mutations at residue positions 452, 484 and 681 have been reported in other globally circulating lineages. The structural analysis of RBD mutations L452R and E484Q along with P681R in the furin cleavage site, revealed that these may possibly result in increased ACE2 binding and rate of S1-S2 cleavage resulting in better transmissibility. The same two RBD mutations indicated decreased binding to select monoclonal antibodies (mAbs) and may affect their neutralization potential. Experimental validation against a wider panel of mAbs, sera from vaccinees and those that recovered from natural infection needs to be studied. The emergence of such local variants through the accumulation of convergent mutations during the COVID-19 second wave needs to be further investigated for their public health impact in the rest of the country and its possibility of becoming a VOC.

molecular biology↗

bioRxiv2021

Neutralization of variant under investigation B.1.617 with sera of BBV152 vaccinees

The drastic rise in the number of cases in Maharashtra, India has created a matter of concern for public health experts. Twelve isolates of VUI lineage B.1.617 were propagated in VeroCCL81 cells and characterized. Convalescent sera of the COVID-19 cases and recipients of BBV152 (Covaxin) were able to neutralize VUI B.1.617.

immunology↗

bioRxiv2021

Ozone Stress Responsive Gene Database (OSRGD ver. 1.1): a literature curated database for crop improvement

Ozone (O3) is a major abiotic stress which severely affects the growth and development of plants. In order to cope up with ozone stress, plants exhibit a plethora of morphological, physiological and molecular changes. Various molecular studies have been performed and a variety of genes exhibiting expression in response to ozone stress have been identified. However, no existing database has been designed yet to present information on ozone stress responsive genes differentially expressed across different plant species. The lack of a curated database limits the research potential in the area and therefore a cohesive database should be designed as a data repository of the ozone responsive genes. OSRGD ver. 1.1 is a user friendly web interface to explore ozone stress specific transcriptome dataset of different plant species. It allows users to retrieve the ozone stress responsive gene data by keyword based search. Each entry upon keyword query contains detailed information about the specific species, its foliar injury symptoms, pattern of gene expression, and platform used for gene expression analysis with reference literature. This comprehensive biocuration will offer researchers a better biological insight into plants response to ozone stress which will focus on development of climate smart crops through crop breeding.

plant biology↗

bioRxiv2021

Comparison of SARS-CoV-2 VOC 202012/01 (UK variant) and D614G variant transmission by different routes in Syrian hamsters

Many SARS-CoV-2 variants of concern has been reported recently which were linked to increased transmission. In our earlier study on virus shedding using VOC 202012/01(UK variant) and D614G variant in hamster model, we observed significantly higher viral RNA shedding through nasal wash in case of UK variant. Hence, we compared the transmission of both the UK and D614G variant by various routes in Syrian hamsters to understand whether the high viral RNA shedding could enhance the transmission efficiency of the variant. The current study demonstrated comparable transmission efficiency of both UK and D614G variants of SARS-CoV-2 in Syrian hamsters.

microbiology↗

bioRxiv2021

Assessment of immunogenicity and protective efficacy of ZyCoV-D DNA vaccine candidates in Rhesus macaques against SARS-CoV-2 infection

Vaccines remain the key protective measure to achieve herd immunity to control the disease burden and stop COVID-19 pandemic. We have developed and assessed the immunogenicity and protective efficacy of two formulations (1mg and 2mg) of ZyCoV-D (a plasmid DNA based vaccine candidates) administered through Needle Free Injection System (NFIS) and syringe-needle (intradermal) in rhesus macaques with three dose vaccine regimens. The vaccine candidate 2mg dose administered using Needle Free Injection System (NFIS) elicited a significant immune response with development of SARS-CoV-2 S1 spike region specific IgG and neutralizing antibody (NAb) titers during the immunization phase and significant enhancement in the levels after the virus challenge. In 2 mg NFIS group the IgG and NAb titers were maintained and showed gradual rise during the immunization period (15 weeks) and till 2 weeks after the virus challenge. It also conferred better protection to macaques evident by the viral clearance from nasal swab, throat swab and bronchoalveolar lavage fluid specimens in comparison with macaques from other immunized groups. In contrast, the animals from placebo group developed high levels of viremia and lung disease following the virus challenge. Besides this, the vaccine candidate also induced increase lymphocyte proliferation and cytokines response (IL-6, IL-5).The administration of the vaccine candidate with NFIS generated a better immunogenicity response in comparison to syringe-needle (intradermal route). The study demonstrated immunogenicity and protective efficacy of the vaccine candidate, ZyCoV-D in rhesus macaques.

microbiology↗

bioRxiv2021

Neutralization of UK-variant VUI-202012/01 with COVAXIN vaccinated human serum

We performed the plaque reduction neutralization test (PRNT50) using sera collected from the 26 recipients of BBV152/COVAXIN against hCoV-19/India/20203522 (UK-variant) and hCoV27 19/India/2020Q111 (heterologous strain). A comparable neutralization activity of the vaccinated individuals sera showed against UK-variant and the heterologous strain with similar efficiency, dispel the uncertainty of possible neutralization escape.

molecular biology↗

bioRxiv2020

Molecular evidence indicates the existence of multiple lineages of Sperata species in Indian Rivers

Sperata seenghala (Giant river-catfish) and Sperata aor (Long-whiskered catfish) are commercially important freshwater catfishes of India, belongs to family Bagridae. Due to high nutritional significance and the low number of intramuscular bones, both fishes have considerable demand in South Asian countries. Both of the Sperata species are morphologically close and well adapted to the same habitat. In this study, we have assessed the level of genetic diversity and differentiation of S. seenghala and S. aor in the Ganga River based on the mitochondrial DNA (mtDNA) control region and compared with the other major Indian rivers. We found high haplotypes diversity for both the species in the Ganga. However, it was comparatively low for S. seenghala in Mahanadi and Brahmaputra populations. The phylogenetic and median-joining network strongly indicated the presence of two distinct maternal lineages of S. seenghala from the Ganga river. Interestingly, the genetic differentiation between S. seenghala of Ganga-Brahmaputra was much higher (~25.3%) than the S. seenghala and S. aor (~17%), whereas it was comparatively low between Ganges-Mahanadi (~8.0%). Our finding provided evidence that all the three rivers: Ganga, Mahanadi, and the Brahmaputra sustain a highly diverse and genetically distinct stock of giant river catfish; therefore, all populations should be considered as a different management unit for the protection of stocks. Our findings indicated that Brahmaputra lineages qualify the species level variations. This study can be further used as a reference database for proper lineage identification of S. seenghala and S. aor that could formulate the appropriate conservation and management plans.

genetics↗

bioRxiv2020

Evaluation of Safety and Immunogenicity of an Adjuvanted, TH-1 Skewed, Whole Virion Inactivated SARS-CoV-2 Vaccine - BBV152

We report the development and evaluation of safety and immunogenicity of a whole virion inactivated SARS-COV-2 vaccine (BBV152), adjuvanted with aluminium hydroxide gel (Algel), or a novel TLR7/8 agonist adsorbed Algel. We used a well-characterized SARS-CoV-2 strain and an established vero cell platform to produce large-scale GMP grade highly purified inactivated antigen, BBV152. Product development and manufacturing were carried out in a BSL-3 facility. Immunogenicity was determined at two antigen concentrations (3g and 6g), with two different adjuvants, in mice, rats, and rabbits. Our results show that BBV152 vaccine formulations generated significantly high antigen-binding and neutralizing antibody titers, at both concentrations, in all three species with excellent safety profiles. The inactivated vaccine formulation containing TLR7/8 agonist adjuvant-induced Th1 biased antibody responses with elevated IgG2a/IgG1 ratio and increased levels of SARS-CoV-2 specific IFN-{gamma}+ CD4 T lymphocyte response. Our results support further development for Phase I/II clinical trials in humans.

immunology↗

bioRxiv2020

Bio-informed Protein Sequence Generation for Multi-class Virus Mutation Prediction

Viral pandemics are emerging as a serious global threat to public health, like the recent outbreak of COVID-19. Viruses, especially those belonging to a large family of +ssRNA viruses, have a high possibility of mutating by inserting, deleting, or substituting one or multiple genome segments. It is of great importance for human health worldwide to predict the possible virus mutations, which can effectively avoid the potential second outbreak. In this work, we develop a GAN-based multi-class protein sequence generative model, named ProteinSeqGAN. Given the viral species, the generator is modeled on RNNs to predict the corresponding antigen epitope sequences synthesized by viral genomes. Additionally, a Graphical Protein Autoencoder (GProAE) built upon VAE is proposed to featurize proteins bioinformatically. GProAE, as a multi-class discriminator, also learns to evaluate the goodness of protein sequences and predict the corresponding viral species. Further experiments show that our ProteinSeqGAN model can generate valid antigen protein sequences from both bioinformatics and statistics perspectives, which can be promising predictions of virus mutations.

bioinformatics↗

bioRxiv2020

Bioengineered ciprofloxacin loaded chitosan nanoparticles for the treatment of Bovine Mastitis

Mastitis is the most devastating economic disease of dairy cattle. Mastitis in dairy cattle frequently occurs during the dry period or in early lactation. E. coli. and S. aureus is the main causative agent of mastitis. S. aureus has an ability to form encapsulated focuses in the udder and develop subclinical form of mastitis. This property of bacteria hinders the effective cure during lactation period. Antibiotics used for treatments have a short half-life span at the site of action because of frequent milking, therefore unable to maintain desired drug concentration for effective clearance of bacteria. We demonstrated the potential of ciprofloxacin encapsulated nanocarriers which can improve availability of drugs and could provide effective means of the treatment of mastitis. These drug loaded nanoparticles show low toxicity & slow clearance from the site of action. Antimicrobial studied against clinical strain of E.coli. and Staphylococcus aureus zone of inhibition depend on dose 0.5 mg to 2 mg/ml nanoparticles solution from 11.6 to 14.5 mm and 15 to 18mm. These nanoparticles show good antimicrobial activity in broth culture as well against bacteria.

pharmacology and toxicology↗

bioRxiv2020

Protein stability and functional activity during nebulization: A comparative study of three nebulizer!

Delivery of therapeutics protein to the lung offers effective treatments of lungs disease. Efficacy of delivered therapeutics molecules depends on integrity and stability of protein during nebulization. In this study, we compared three nebulizers: compressed air nebulizer (CAN), ultrasonic nebulizer (USN) and mesh nebulizer (MAN) to deliver aerosol dose, stability and functional activity of a model protein lysozyme. Lysozyme/BSA delivered dose assessed by indirect and direct method. It was shown CAN deliver 0.142{+/-}0.027 to 0.632{+/-} 0.09 ml of protein, USN deliver 0.511{+/-}0.119 to 1.688{+/-}0.173 ml and MAN deliver 0.238{+/-}0.006 to 0.731{+/-}0.013 ml of protein in the same time. Integrity of nebulized proteins were assessed by gel electrophoresis and circular diochorism. It was found integrity of lysozyme compromised in all three nebulizer maximum in CAN and minimum with MAN. The functional activity of protein was assessed after nebulization by turbidometry assay. The functional activity was compromised by all three nebulizer upto some extent. In conclusion, nebulization compromise protein stability: this impact depend on nebulization techniques as well as nature of protein. The CAN deliver protein more precisely in small amount in comparison to the other nebulizer. O_FIG O_LINKSMALLFIG WIDTH=200 HEIGHT=122 SRC="FIGDIR/small/085720v1_ufig1.gif" ALT="Figure 1"> View larger version (30K): org.highwire.dtl.DTLVardef@5b230forg.highwire.dtl.DTLVardef@15ac79corg.highwire.dtl.DTLVardef@e7130forg.highwire.dtl.DTLVardef@94684e_HPS_FORMAT_FIGEXP M_FIG Graphical Abstract C_FIG

bioengineering↗

bioRxiv2020

Potential Neutralizing Antibodies Discovered for Novel Corona Virus Using Machine Learning

The fast and untraceable virus mutations take lives of thousands of people before the immune system can produce the inhibitory antibody. Recent outbreak of novel coronavirus infected and killed thousands of people in the world. Rapid methods in finding peptides or antibody sequences that can inhibit the viral epitopes of COVID-19 will save the life of thousands. In this paper, we devised a machine learning (ML) model to predict the possible inhibitory synthetic antibodies for Corona virus. We collected 1933 virus-antibody sequences and their clinical patient neutralization response and trained an ML model to predict the antibody response. Using graph featurization with variety of ML methods, we screened thousands of hypothetical antibody sequences and found 8 stable antibodies that potentially inhibit COVID-19. We combined bioinformatics, structural biology, and Molecular Dynamics (MD) simulations to verify the stability of the candidate antibodies that can inhibit the Corona virus.

immunology↗