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The emergence of the Severe Acute Respiratory Syndrome Coronavirus 2 (SARS-CoV-2) as a serious pandemic has altered the global socioeconomic dynamics. The wide prevalence, high death counts, and rapid emergence of new variants urge for the establishment of research infrastructure to facilitate the rapid development of efficient therapeutic modalities and preventive measures. In agreement with this, SARS-CoV-2 strains were isolated from patient swab samples collected during the first COVID-19 wave in Odisha, India. The viral isolates were adapted to in vitro cultures and further characterized to identify strain-specific variations in viral growth characteristics. The neutralization susceptibility of viral isolates to vaccine-induced antibodies was determined using sera from individuals vaccinated in the Government-run vaccine drive in India. The major goal was to isolate and adapt SARS-CoV-2 viruses in cell culture with minimum modifications to facilitate research activities involved in the understanding of the molecular virology, host–virus interactions, drug discovery, and animal challenge models that eventually contribute toward the development of reliable therapeutics.

Coronavirus disease 2019 (COVID-19), caused by the severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) virus, has emerged as a global pandemic worldwide. In this study, we used ARTIC primers–based amplicon sequencing to profile 225 SARS-CoV-2 genomes from India. Phylogenetic analysis of 202 high-quality assemblies identified the presence of all the five reported clades 19A, 19B, 20A, 20B, and 20C in the population. The analyses revealed Europe and Southeast Asia as two major routes for introduction of the disease in India followed by local transmission. Interestingly, the19B clade was found to be more prevalent in our sequenced genomes (17%) compared to other genomes reported so far from India. Haplotype network analysis showed evolution of 19A and 19B clades in parallel from predominantly Gujarat state in India, suggesting it to be one of the major routes of disease transmission in India during the months of March and April, whereas 20B and 20C appeared to evolve from 20A. At the same time, 20A and 20B clades depicted prevalence of four common mutations 241 C > T in 5′ UTR, P4715L, F942F along with D614G in the Spike protein. D614G mutation has been reported to increase virus shedding and infectivity. Our molecular modeling and docking analysis identified that D614G mutation resulted in enhanced affinity of Spike S1–S2 hinge region with TMPRSS2 protease, possibly the reason for increased shedding of S1 domain in G614 as compared to D614. Moreover, we also observed an increased concordance of G614 mutation with the viral load, as evident from decreased Ct value of Spike and the ORF1ab gene.

Abstract Aberrant immune responses characterize autoimmune disorders like Rheumatoid Arthritis (RA) wherein lymphocytes are recognized as key players. Role of CD8+ T cells in RA has been less defined however we found that these cells are activated in RA patients with increased expression of cytolytic granules and inflammatory mediators thereby modulating immune responses contributing to disease severity. Though unconventional expression of different Toll Like Receptors (TLRs) on CD8+ T cells has been proposed but their expression and role in T cell activation and differentiation in RA still remains obscure. Herein we report, for the first time, an increased expression of TLR4 on peripheral CD8+ T cells of RA patients and its role in skewing CD8+ T cells towards activated and inflammatory phenotype thereby playing a significant role in pathogenesis and progression of RA. We found that the surface expression of TLR4 on CD8+ T cells directly correlates with disease severity. Moreover, these CD8+ T cells respond to the TLR4 ligand LPS and express robust amounts of cytotolytic and inflammatory molecules including TNFα and IFNγ. Our study hence identifies an important role for CD8+ T cells in orchestrating RA through TLR4 mediated activation and differentiation.

Many organisms exhibit temporal rhythms in gene expression that propel diurnal cycles in physiology. In the liver of mammals, these rhythms are controlled by transcription-translation feedback loops of the core circadian clock and by feeding-fasting cycles. To better understand the regulatory interplay between the circadian clock and feeding rhythms, we mapped DNase I hypersensitive sites (DHSs) in the mouse liver during a diurnal cycle. The intensity of DNase I cleavages cycled at a substantial fraction of all DHSs, suggesting that DHSs harbor regulatory elements that control rhythmic transcription. Using chromatin immunoprecipitation followed by DNA sequencing (ChIP-seq), we found that hypersensitivity cycled in phase with RNA polymerase II (Pol II) loading and H3K27ac histone marks. We then combined the DHSs with temporal Pol II profiles in wild-type (WT) and Bmal1-/- livers to computationally identify transcription factors through which the core clock and feeding-fasting cycles control diurnal rhythms in transcription. While a similar number of mRNAs accumulated rhythmically in Bmal1-/- compared to WT livers, the amplitudes in Bmal1-/- were generally lower. The residual rhythms in Bmal1-/- reflected transcriptional regulators mediating feeding-fasting responses as well as responses to rhythmic systemic signals. Finally, the analysis of DNase I cuts at nucleotide resolution showed dynamically changing footprints consistent with dynamic binding of CLOCK:BMAL1 complexes. Structural modeling suggested that these footprints are driven by a transient heterotetramer binding configuration at peak activity. Together, our temporal DNase I mappings allowed us to decipher the global regulation of diurnal transcription rhythms in the mouse liver.

Background: Rheumatoid arthritis (RA) is an autoimmune disease characterized by abnormal immune responses to self-antigens. Though the pathogenesis of RA is not yet fully elucidated, it is known to be induced by environmental factors on a genetically susceptible background. Toll-like Receptors (TLRs) have been established to recognize specific patterns of microbial components and lead to systemic immune responses in Rheumatoid arthritis (RA). TLRs are expressed by cells in inflamed joints of RA patients and variety of endogenous TLR ligands is present within those joints. This study suggests that the over expression of TLR4 in CD8+T cells from RA patients may contribute to the abnormal immune activation of pro inflammatory cytokines and enhance the acute inflammation. Methods: Eighty seven RA patients and 70 healthy donors participated in this study. Clinical variations like disease duration, number of actively inflamed joints, number, and type of bones deformities, CRP, RF, Anti-CCP, ESR (Erythrocyte Sedimentation Rate), and therapeutic interventions were recorded for each patient and DAS 28 scores were calculated with the help of the clinician. We analyzed the expression of TLR4 in transcript level by real-time PCR and protein level by flow cytometry in CD8+T cells of RA patients. Different cytokines level was checked after stimulation of CD8+T cells in TLR4 agonist. We have checked the MAP Kinase – ERK signal transduction in CD8+Tcells. Results: A significant increase of TLR4 in both transcript level and protein level in patients with RA compared to healthy donors. We got a strong positive correlation between TLR4 expression and DAS 28 score. The ROC curve analysis confirmed the significance of TLR4 expression in RA patients. We found that TLR4 ligand responsiveness significantly increased the expression of different inflammatory mediators in purified CD8+T cells of RA patients compared with healthy individuals after in vitro stimulation. Our result showed TLR4 stimulation induces ERK phosphorylation in CD8+T cells. Conclusion: In summary, our data suggest an increased expression of TLR4 in CD8+T cells play a major role in inflammation of RA patients.

In the current scenario, a decline in the natural deposits of copper and its alloys has called for the efficient usage of bronze in mechanical components. The development of additive manufacturing processes such as Directed Energy Deposition (DED) provides an opportunity to address this issue by replacing complete bronze components such as worm wheels with parts made of less critical raw materials and provided with bronze coatings on the wear-active interfaces. Therefore, this current work focuses on evaluating the deposition of CuSn10 on a steel substrate using DED. Four types of specimens are manufactured, three having deposition of CuSn10 on the steel substrate and one specimen having an initial deposition of CuSn10 + 316L mixture followed by CuSn10. The laser power for the deposition process was varied through the thickness of the deposition with values varying between a minimum of 600 W to a maximum of 1100 W. The specimens were subjected to wear testing under dry conditions to evaluate their friction behavior and to check for debonding between the substrate and deposition. The effect of different laser power on porosity, microstructure, and microhardness was evaluated. The results, when compared with wrought CuSn10, indicated that the DED CuSn10 can be a probable replacement for wrought CuSn10 in worm wheels.

The present work investigates cellular materials that can be potentially used as a replacement of solid implants owing to their mechanical properties and biocompatibility. More specifically, titanium alloy (Ti6Al4V) cellular materials of three different topologies were considered to study the effect of the degree of irregularity. Cubic regular, cubic irregular and trabecular structures were manufactured using Laser based powder bed fusion (LB-PBF) process. The LB-PBF process had an impact on the strut thickness of the samples. Samples were subjected to micro computed tomography to understand the geometrical deviations and to use the actual geometry for finite element analysis. Mechanical properties such as Young's modulus and strength were derived from compression and tensile testing. The results indicate that the Young's modulus was between 6 and 17 GPa, which were closer to the values of human cortical bone. The finite element analysis results showed a good correlation with the tensile test results as well. Furthermore, Gibson–Ashby model is used to study the effect of cell topology on the structural behavior. The model indicated that the misalignment of nodes of cubic regular structures to form irregular structure, transformed the stretching dominated behavior of cubic structures to bending dominated behavior like trabecular structures. Finally, the regular structures appeared to be much more prone to catastrophic failure than irregular and trabecular structures. Both visual observation of experimental testing and FE analysis explained this difference as result of different modes and zones of failures.