Biology subjects

DAS, S.

Publications and source records attributed to DAS, S..

8 recordsLinked to original sources

bioRxiv2026

Experimental and In Silico Analysis of the Structural Dynamics of Dengue NS2B-NS3 Protease

The Dengue virus (DENV), a major global health concern, causes dengue fever, predominantly affecting tropical and subtropical regions. The NS2B-NS3 protease complex of DENV is critical for viral replication, making it a promising target for antiviral drug development. This study investigates the structural dynamics of the NS2B-NS3 protease under varying pH conditions, integrating experimental and computational approaches. The recombinant NS2B-NS3 protease was expressed in E. coli, purified using affinity chromatography, and analysed for purity via SDS-PAGE. Circular dichroism (CD) spectroscopy revealed pH-dependent secondary structural changes, indicating stability at neutral to slightly basic pH and destabilization under acidic and highly basic conditions. Dynamic light scattering (DLS) analysis demonstrated protein aggregation and structural heterogeneity under extreme pH levels. Complementary in silico techniques, including homology modelling and molecular dynamics (MD) simulations, provided detailed insights into the conformational changes of the protease. The modelled structure, validated and refined through computational tools, revealed structural stability at physiological pH, with notable disruptions at pH extremes. DSSP (Dictionary of Secondary Structure of Proteins) and principal component analyses highlighted significant secondary structural transitions, especially at acidic pH where -helices and {beta}-sheets transformed into random coils Docking and MD simulation was carried out with the small molecule for therapeutic analysis between Dengue NS2bNS3 and small molecule. This study emphasizes the pH-dependent conformational plasticity of the NS2B-NS3 protease, contributing to the understanding of its functional mechanisms and providing a foundation for the rational design of pH-specific inhibitors. These findings underscore the importance of structural biology in advancing therapeutic strategies against dengue fever.

bioinformatics↗

bioRxiv2026

Ancient IL-6-STAT5 signaling orchestrates inflammation in jawless vertebrates

Interleukin-6 (IL-6) is a central regulator of vertebrate immunity, yet its existence in jawless vertebrates has remained obscure because of extreme sequence divergence. The extant jawless vertebrates (lampreys and hagfish), which deploy variable lymphocyte receptors (VLRs) instead of immunoglobulins and T cell receptors, provide a unique window into the earliest interface between cytokines and adaptive immunity. Here, we identify IL-6-like genes in jawless vertebrates by combining computational structural comparisons, phylogenetic reconstruction, and conserved local and long-range synteny analyses. The encoded proteins adopt the canonical four-helix bundle characteristic of immune-related IL-6 family cytokines and align topologically with mammalian IL-6. In sea lamprey, three IL-6 paralogs show distinct leukocyte and tissue expression patterns and are differentially induced by pathogen-associated molecular patterns and skin injury, indicating early functional diversification of IL-6-mediated inflammatory responses. Stimulation of myeloid peritoneal leukocytes with recombinant lamprey IL-6 induces STAT5 phosphorylation and rapid upregulation of SOCS1/3 genes, consistent with an IL-6/STAT5/SOCS regulatory axis. These findings extend the repertoire of immune-related four-helix bundle cytokines to jawless vertebrates and indicate that IL-6-dependent inflammatory programs were already in place before the divergence of VLR-based and Ig/TCR-based adaptive immune systems in vertebrates.

immunology↗

bioRxiv2023

Emerging Antifungal Resistance in Falco Species: A Novel Model for Human Medicine

Antifungal resistance is a growing concern in the medical community, as fungal infections are becoming increasingly difficult to treat. In this study, Falco species were used as novel models for studying antifungal resistance since Aspergillosis, a fungal disease is common in falcons. The most isolated fungi in this study were A. fumigatus, A. flavus, A. niger, and A. terreus, all of which can cause aspergillosis in falcons. Isavuconazole, posaconazole, and voriconazole had the lowest MICs among the drugs tested, suggesting that they may be effective treatment options. However, this study showed that 34% of the isolates were resistant to itraconazole, which is an increase from 21% in 2006. There is no resistance to voriconazole found in 2006 and 2011, but a 9% resistance rate was noted in 2022. Similarly, there is no resistance to posaconazole and isavuconazole was noticed in 2011, but resistance of 4.7% and 5.8%, respectively was noticed in 2022. Amphotericin B, which showed a 51% resistance rate in 2006, became even more resistant with an 80% rate in 2011, leading to its discontinuation from the treatment of falcons against aspergillosis. This study highlights a significant rise in antifungal resistance, which is a challenging problem in both falcon and human medicine.

microbiology↗

bioRxiv2022

A mechanistic insight into Nigella sativa mediated anticancer effect on breast cancer through regulation of various miRNAs: An in vitro & in vivo study

BackgroundCancer continues to threat the mortal alongside scientific community with its burgeoning grasp. Although efforts have been directed to tame cancer by radiotherapy, photodynamic therapy, chemotherapy it came at a cost of fatal side effects. PurposePlant derived bioactive compounds carries an inevitable advantage of being safer, bioavailable & less toxic compared to contemporary chemotherapeutics. This study analyzed anti-cancerous potential of volatile oil, extracted from Nigella sativa, in-vitro against MDA-MB-231, MCF-7 & in-vivo on tumor growth in mice after successful oral administration. Study DesignOur strategic approach employed solvent extraction of black seed oil (BSO) to highlight orchestrated use of its potent integrants - TQ, Carvacrol & TA which in modest amounts show anti-cancerous properties compared to their individual treatment. We attempted to show this cost effective, safe & bioavailable form of dealing with the atrocities of breast cancer by means of MTT, Apoptotic, Western Blot Assays besides Transwell & Wound healing Assay. Reduction in the solid tumour in-vivo & near normalcy restoration of tissue section architecture from the BSO treated tumour sets are indicative of the better anti-tumorigenic potential of BSO. MethodsBSOs Solvent extraction was performed followed by its characterization. MTT aided cytotoxicity study of BSO alongside major components in PBMC & cancer cells while its efficacy was presented by flow cytometric ROS analysis, cell cycle arrest & apoptosis assessment. Anti-migratory potential evaluated by Wound Healing, Transwell Migration & Western Blot while the expression study of a wide range of proteins, miRNAs & the in-vivo studies undertaken climaxed the confirmation of the anti-cancerous potential of BSO. ResultsComparatively reduced concentrations of TQ, TA & Carvacrol in BSO played a synergistic role to enhance apoptotic potential via Caspase 7 & 9, through enhanced ROS & expression of apoptotic family of proteins, miRNAs besides uplifting the anti-migratory perspective by effectively enhancing E-cad & downregulating lamellipodia, filopodia assembly & MMPs in MCF-7 & MDA-MB-231. Similar observations in-vivo outlined the therapeutic potential of BSO. ConclusionThis study culminates isolation & processing of BSO in a simplified procedure, thereby aiming at a more lucrative paradigm to be accepted in contemporary phytomedicine research.

cancer biology↗

bioRxiv2020

Analyses of spike protein from first deposited sequences of SARS-CoV2 from West Bengal, India

India has recently started sequencing SARS-CoV2 genome from clinical isolates. Currently only few sequences are available from three states in India. Kerala was the first state to deposit complete sequence from two isolates followed by one from Gujarat. On April 27, 2020, the first five sequences from the state of West Bengal (Eastern India) were deposited on a global initiative on sharing avian flu data (GISAID) platform. In this paper we have analysed the spike protein sequences from all these five isolates and also compared for their similarities or differences with other sequences reported in India and with isolates of Wuhan origin. We report one unique mutation at position 723 and the other at 1124 in the S2 domain of spike protein of the isolates from West Bengal only and one mutation downstream of the receptor binding domain at position 614 in S1 domain which was common with the sequence from Gujarat (a state of western part of India). Mutation in the S2 domain showed changes in the secondary structure of the spike protein at region of mutation. We also studied molecular dynamics using normal mode analyses and found that this mutation decreases the flexibility of S2 domain. Since both S1 and S2 are important in receptor binding followed by entry in the host cells, such mutations may define the affinity or avidity of receptor binding.

molecular biology↗

bioRxiv2020

Specific mutations in SARS-CoV2 RNA dependent RNA polymerase and helicase alter protein structure, dynamics and thus function: Effect on viral RNA replication

1.The open reading frame (ORF) 1ab of SARS-CoV2 encodes non-structural proteins involved in viral RNA functions like translation and replication including nsp1-4; 3C like proteinase; nsp6-10; RNA dependent RNA polymerase (RdRp); helicase and 3-5 exonuclease. Sequence analyses of ORF1ab unravelled emergence of mutations especially in the viral RdRp and helicase at specific positions, both of which are important in mediating viral RNA replication. Since proteins are dynamic in nature and their functions are governed by the molecular motions, we performed normal mode analyses of the SARS-CoV2 wild type and mutant RdRp and helicases to understand the effect of mutations on their structure, conformation, dynamics and thus function. Structural analyses revealed that mutation of RdRp (at position 4715 in the context of the polyprotein/ at position 323 of RdRp) leads to rigidification of structure and that mutation in the helicase (at position 5828 of polyprotein/ position 504) leads to destabilization increasing the flexibility of the protein structure. Such structural modifications and protein dynamics alterations might alter unwinding of complex RNA stem loop structures, the affinity/ avidity of polymerase RNA interactions and in turn the viral RNA replication. The mutation analyses of proteins of the SARS-CoV2 RNA replication complex would help targeting RdRp better for therapeutic intervention.

molecular biology↗

bioRxiv2019

Prevalence, risk factors and health seeking behaviour of pulmonary tuberculosis in four tribal dominated districts of Odisha

AimTo determine the prevalence of pulmonary tuberculosis, socio-cultural practices and health seeking behaviour of tribal people in four districts of Odisha. MethodologyThis was an action research study with qualitative and quantitative design following a sequential approach implemented in a 4-phased manner. It was carried out in the 6 selected villages from July,2015 to June,2017. The screening for active TB among chest symptomatics is followed as per the guidelines of the (RNTCP) Revised National Tuberculosis Control Program in India. ResultsIn all, 1455 households were surveyed in the 6 tribal dominated villages of 4 districts, namely Balangir, Dhenkanal, Kandhmal and Mayurbhanj. Total population of the villages was 6681. Based on the eligibility, 5144 (97.7%) individuals were screened. About 139 (2.3%) could not be screened due to non-availability in their households during day time. Out of these, 126 chest symptomatic individuals were identified. Sputum samples were collected from these and sent to the National Reference Laboratory, RMRC, Bhubaneswar using public transport and maintaining cold chain. 35 patients were found to be having active TB disease. 18 were culture positive. The prevalence of pulmonary TB is 0.68%. The risk factors seemed to be ignorance about TB symptoms, addiction to alcoholic drinks, difficulty reaching the health facilities owing to the long distances, lack of communication and transport. In addition, other morbidities like Malaria, diabetes, hypertension, malnutrition, etc. were observed in the tribes of the study sites. ConclusionObserved prevalence suggests further strengthening of TB control program. This study is the first of its kind in this State.

microbiology↗

bioRxiv2019

Pre-Innervated Tissue Engineered Muscle Promotes a Pro-Regenerative Microenvironment Following Volumetric Muscle Loss

Volumetric Muscle Loss (VML) is defined as traumatic or surgical loss of skeletal muscle tissue beyond the inherent regenerative capacity of the body, generally leading to a severe functional deficit. Autologous muscle grafts remain the prevalent method of treatment whereas recent muscle repair techniques using biomaterials and tissue engineering are still at a nascent stage and have multiple challenges to address to ensure functional recovery of the injured muscle. Indeed, appropriate somato-motor innervations remain one of the biggest challenges for both autologous muscle grafts as well as tissue engineered muscle constructs. We aim to address this challenge by developing Pre-Innervated Tissue Engineered Muscle comprised of long aligned networks of spinal motor neurons and skeletal myocytes. Here, we developed methodology to biofabricate long fibrils of pre-innervated tissue engineered muscle using a co-culture of myocytes and motor neurons on aligned nanofibrous scaffolds. Motor neurons lead to enhanced differentiation and maturation of skeletal myocytes in vitro. These pre-innervated tissue engineered muscle constructs when implanted in vivo in a rat VML model significantly increase satellite cell migration, micro-vessel formation, and neuromuscular junction density in the host muscle near the injury area at an acute time point as compared to non-pre-innervated myocyte constructs and nanofiber scaffolds alone. These pro-regenerative effects can potentially lead to enhanced functional neuromuscular regeneration following VML, thereby improving the levels of functional recovery following these devastating injuries.

bioengineering↗