Biology subjects

Kalita, P.

Publications and source records attributed to Kalita, P..

6 recordsLinked to original sources

bioRxiv2023

Evaluation of morpho-physiological and yield-associated traits of rice (Oryza sativa L.) landraces combined with marker-assisted selection under high temperature stress and elevated atmospheric CO2 levels

Rice (Oryza sativa L.) has a tremendous domestication history and is presently used as a major cereal all over the world. In Asia, India is considered as one of the centers of origin of indica rice and has several native landraces, especially in North-Eastern India (NEI), which have the potential to cope with the negative impact of present-day climate change. The current investigation aimed to evaluate the NEI rice landraces potential under high temperatures and elevated CO2 levels in comparison with a check variety for phenological, morphological, physiological and yield-associated parameters and molecularly validated with marker-assisted genotyping. The initial experiment was carried out with 75 rice landraces to evaluate their high heat tolerance ability. Seven better-performing landraces along with the check variety (N22) were further evaluated for aforesaid traits across two years (2019 and 2020) under control (or T1) and two stress treatments - (i) mild stress or T2 [CO2 550 ppm + 4{degrees} C more than ambient temperature] and (ii) severe stress or T3 [CO2 750 ppm + 6{degrees} C more than ambient temperature] using bioreactors. In the molecular analysis, the eight selected genotypes were evaluated through 25 Start Codon Targeted (SCoT) markers. The results revealed that the mild stress (T2) had a positive impact on various morpho-physiological parameters like plant height, number of leaves, leaf area and yield parameters like spikelets panicle-1 (S/P), thousand-grain weight (TGW) and grain yield (GY). This effect could be attributed to the genotypes ability to maintain a higher photosynthetic rate and possess better tolerance ability to moderately high temperatures. However, under high-temperature conditions in T3, all genotypes exhibited a significant decrease in the studied parameters including GY. It was found that pollen traits were significantly and positively correlated to spikelet fertility% at maturity, which was further significantly associated with GY under applied stress conditions. The physiological traits including shoot biomass were evident to have a significant positive effect on yield-associated parameters like S/P, harvest index (HI), TGW and GY. Overall, two landraces Kohima special and Lisem were found to be better responsive compared to other landraces as well as the check variety N22 under stress conditions. SCoT genotyping amplified a total of 77 alleles out of which 55 were polymorphic with the PIC value ranging from 0.22 to 0.67. The investigation suggests the presence of genetic variation among the tested rice lines and further supports evidence of the closely relatedness of Kohima special and Lisem. These two are two better-performing rice landraces from North-East India based on their improving morpho-physiological parameters and yield attributes in mild and severe high temperature and elevated CO2 stress environments. The shortlisted two rice landraces can be used as valuable pre-breeding materials for future rice breeding programs to improve the stress tolerance properties, particularly to high temperatures and elevated CO2 levels under ongoing changing climatic scenarios.

plant biology↗

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

A highly thermotolerant, trimeric SARS-CoV-2 receptor binding domain derivative elicits high titers of neutralizing antibodies

The Receptor Binding Domain (RBD) of SARS-CoV-2 is the primary target of neutralizing antibodies. We designed a trimeric, highly thermotolerant glycan engineered RBD by fusion to a heterologous, poorly immunogenic disulfide linked trimerization domain derived from cartilage matrix protein. The protein expressed at a yield of [~]80-100 mg/liter in transiently transfected Expi293 cells, as well as CHO and HEK293 stable cell lines and formed homogeneous disulfide-linked trimers. When lyophilized, these possessed remarkable functional stability to transient thermal stress of upto 100 {degrees}C and were stable to long term storage of over 4 weeks at 37 {degrees}C unlike an alternative RBD-trimer with a different trimerization domain. Two intramuscular immunizations with a human-compatible SWE adjuvanted formulation, elicited antibodies with pseudoviral neutralizing titers in guinea pigs and mice that were 25-250 fold higher than corresponding values in human convalescent sera. Against the beta (B.1.351) variant of concern (VOC), pseudoviral neutralization titers for RBD trimer were [~] three-fold lower than against wildtype B.1 virus. RBD was also displayed on a designed ferritin-like Msdps2 nanoparticle. This showed decreased yield and immunogenicity relative to trimeric RBD. Replicative virus neutralization assays using mouse sera demonstrated that antibodies induced by the trimers neutralized all four VOC to date, namely B.1.1.7, B.1.351, P.1 and B.1.617.2 without significant differences. Trimeric RBD immunized hamsters were protected from viral challenge. The excellent immunogenicity, thermotolerance, and high yield of these immunogens suggest that they are a promising modality to combat COVID-19, including all SARS-CoV-2 VOC to date.

microbiology↗

bioRxiv2020

Design of a highly thermotolerant, immunogenic SARS-CoV-2 spike fragment

Virtually all SARS-CoV-2 vaccines currently in clinical testing are stored in a refrigerated or frozen state prior to use. This is a major impediment to deployment in resource-poor settings. Several use viral vectors or mRNA. In contrast to protein subunit vaccines, there is limited manufacturing expertise for these novel, nucleic acid based modalities, especially in the developing world. Neutralizing antibodies, the clearest known correlate of protection against SARS-CoV-2, are primarily directed against the Receptor Binding Domain (RBD) of the viral spike protein. We describe a monomeric, glycan engineered RBD protein fragment that is expressed at a purified yield of 214mg/L in unoptimized, mammalian cell culture and in contrast to a stabilized spike ectodomain, is tolerant of exposure to temperatures as high as 100{degrees}C when lyophilized, upto 70{degrees}C in solution and stable for over four weeks at 37{degrees}C. In prime:boost guinea pig immunizations, when formulated with the MF59 like adjuvant AddaVax, the RBD derivative elicited neutralizing antibodies with an endpoint geometric mean titer of ~415 against replicative virus, comparing favourably with several vaccine formulations currently in the clinic. These features of high yield, extreme thermotolerance and satisfactory immunogenicity suggest that such RBD subunit vaccine formulations hold great promise to combat COVID-19.

biophysics↗

bioRxiv2020

High Throughput Designing and Mutational Mapping of RBD-ACE2 Interface Guide Non-Conventional Therapeutic Strategies for COVID-19

Considering the current status of the SARS-CoV-2 pandemic, sequence variations and possibly structural changes in the rapidly evolving SARS-CoV-2 is highly expected in the coming months. The SARS-CoV-2 spike (S) protein is responsible for mediating viral attachment and fusion with cell membranes. Mutations in the receptor-binding domain (RBD) of the S-protein occur at the most variable part of the SARS-CoV-2 genome, and specific sites of S-protein have undergone positive selection impacting the viral pathogenicity. In the present work, we used high-throughput computation to design 100,000 mutants in RBD interfacial residues and identify novel affinity-enhancing and affinity-weakening mutations. Our data suggest that SARS-CoV-2 can establish a higher rate of infectivity and pathogenesis when it acquires combinatorial mutations at the interfacial residues in RBD. Mapping of the mutational landscape of the interaction site suggests that a few of these residues are the hot-spot residues with a very high tendency to undergo positive selection. Knowledge of the affinity-enhancing mutations may guide the identification of potential cold-spots for this mutation as targets for developing a possible therapeutic strategy instead of hot-spots, and vice versa. Understanding of the molecular interactions between the virus and host protein presents a detailed systems view of viral infection mechanisms. The applications of the present research can be explored in multiple antiviral strategies, including monoclonal antibody therapy, vaccine design, and importantly in understanding the clinical pathogenesis of the virus itself. Our work presents research directions for the exploitation of non-conventional solutions for COVID-19.

biophysics↗

bioRxiv2018

Draft genome of the liver fluke Fasciola gigantica

Fascioliasis is a neglected food-borne disease caused by liver flukes (genus Fasciola) and affects more than 200 million people worldwide. Despite technological advances, little is known about the molecular biology and biochemistry of the fluke. We present the draft genome of Fasciola gigantica for the first time. The assembled draft genome has a size of ~1.04 Gb with an N50 of 129 kb. A total of 20,858 genes were predicted. The de novo repeats identified in the draft genome were 46.85%. In pathway analysis, all the genes of glycolysis, Krebs cycle and fatty acid metabolism were found to be present, but the key genes for fatty acid production in fatty acid biosynthesis were missing. This indicates that the fatty acid required for the survival of the fluke may be acquired from the host bile. The genomic information will provide a comprehensive resource to facilitate the development of novel interventions for fascioliasis control.

bioinformatics↗