Biology subjects

Pawar, P.

Publications and source records attributed to Pawar, P..

8 recordsLinked to original sources

bioRxiv2026

A novel vaccine and drug targets for global eradication of bovine tuberculosis: Holistic frameworks for construction of a potent vaccine and identification of drug targets

Bovine tuberculosis (TB), caused by Mycobacterium bovis, has become a global concern over the last two decades. Bovine TB primarily affects cattle, but other domestic livestock are also affected and it is more common in less developed and developing countries. The significant loss of livestock leads to trade restrictions and economic crises. Zoonotic potential of bovine TB raises health concerns for the public. Currently, no effective treatment is available and animal slaughtering is usually undertaken to reduce the burden of it in the environment. Antibiotic therapy can be used on animals living in captivity, but it is not reliable for herd or free-grazing animals. The BCG vaccine is another option available for treating the disease, but it shows limited efficacy in cattle. The prevention of bovine TB is a long-term goal that can only be accomplished by developing a more effective vaccine than BCG and designing new drugs. In this research, we propose therapeutic drug targets and vaccine for treating bovine TB. The conceptual framework for vaccine developed in this study uses a number of bioinformatics approaches to identify potential vaccine candidates and construct an in-silico epitope-based vaccine. Our holistic framework identified potential therapeutic candidates by directly analysing the proteome of TB bacterial strains. Specifically, we performed a comparative proteomic analysis of 11 Mycobacterium bovis strains to cover the diversity and identify conserved proteins among those strains for developing the bovine TB vaccine. An extensive reverse vaccinology and immunoinformatics analysis provided 26 highly immunogenic, non-toxic and non-allergenic epitopes (CTL epitopes-8, HTL epitopes-2 and B-cell epitopes-16) for Mycobacterium bovis required for three-dimensional structure construction of TB vaccine. The constructed epitope-based vaccine showed a potent interaction inside the host, thus generating efficient cell-mediated and humoral immune responses. Next, a framework based on a novel subtractive proteomic approach was developed for identifying bovine TB drug targets. We performed this approach on the 11 Mycobacterium bovis strains and identified nine drug targets that are conserved, essential, antigenic and have unique metabolic pathways in Mycobacterium bovis. These drug targets could further help investigate therapeutic drugs for the treatment of bovine TB. Several bioinformatics prediction tools were used together to ensure checks and balances, aiming to reduce the chance of errors and provide accurate results. The vaccine and drug targets developed in this study can be tested experimentally with confidence for further validation as therapeutics with the potential to eradicate bovine TB globally. The strategies implemented in the study are generic and can be used for other zoonotic infectious diseases. This study would be a game changer in the field of bovine tuberculosis treatment.

bioinformatics↗

bioRxiv2026

A vaccine for global eradication of TB - A novel conceptual framework and design of a potent peptide-based vaccine with universal coverage through advanced computational vaccinology

Tuberculosis (TB) remains a formidable global health challenge, exacerbated by the emergence of drug-resistant Mycobacterium tuberculosis strains that threaten to render existing drug therapies and vaccine ineffective. Despite the availability of the Bacillus Calmette-Guerin (BCG) vaccine, its limited efficacy--primarily in infants and young children--falls short of reducing TB prevalence or offering adequate protection to adults. Therefore, developing a new TB vaccine with enhanced efficacy and the capability to generate a robust reservoir of memory cells is essential. Addressing the challenge of drug-resistant tuberculosis requires a deep understanding of bacterial evolution and developing robust countermeasures. This study aims to design a next-generation TB vaccine that provides broad-spectrum protection against various Mycobacterium tuberculosis strains, including drug-resistant ones. By conducting an in-depth investigation into pathogen-human interactions, the research proposes a holistic framework that leverages computational vaccinology to tackle challenges posed by pathogen polymorphism and overcome the limitations of conventional vaccines. By targeting conserved proteins across diverse TB strains and enhancing both humoral and cell-mediated immunity, this study proposes a new strategy for an epitope-based vaccine that provides long-lasting, universal coverage. An extensive proteomic, reverse vaccinology and immunoinformatics analysis of 159 TB strains yielded 27 highly conserved, immunogenic, non-toxic, and non-allergenic epitopes. These epitopes, consisting of 14-cytotoxic T-lymphocytes (CTL), 5-helper T-lymphocytes (HTL), and 8-B-cell epitopes, were used to construct a three-dimensional, multi-epitope TB vaccine designed based on a new concept introduced in this research for maximising vaccine efficacy. Molecular docking and immune simulation studies demonstrated a significant affinity between the vaccine constructs and toll-like receptors, indicating a strong potential for effective immune system engagement. The crucial features of the epitope-based TB vaccine constructed in this research include sequence conservancy, robust antigenicity, exclusion of self-peptides and potential for diverse allelic interactions. The proposed epitope-based vaccine is poised to be highly effective, safe, and capable of providing universal coverage, potentially paving the way for global TB eradication. Validation in laboratory and clinical settings will be essential to confirm its efficacy and real-world applicability.

bioinformatics↗

bioRxiv2026

Confronting global eradication of TB head on: Uncovering the root of drug resistance and bacterial survival strategies through a comprehensive computational study of first-line TB drug resistant mutations

Tuberculosis (TB) is fast becoming incurable affecting millions globally. Mycobacterium tuberculosis (Mtb), causative agent of TB, has evolved elusive survival strategies through point mutations in the drug targets leading to a daunting scenario of resistance towards first-line TB drugs, exacerbated by global differences in mutation patterns. Drug resistance studies have focussed only on few mutations; however, hundreds of mutations have been reported in the last three decades. WHOs goal of global eradication of TB therefore now requires a deep understanding of mechanisms of drug resistance, involving many mutations, addressed in a global context. This study addresses bacterial survival strategies by following bacteria-drug interaction to probe into how bacteria evolve drug resistance mechanisms through mutations. We hypothesise that bacteria favour mutations that protect them from a drug while making the drug ineffective. To test the hypothesis, we quantify the impact of mutations on both bacterial function and drug binding affinity to get to the root of drug resistance revealing how bacteria may evolve an arsenal of mutations towards an optimal survival strategy. This first comprehensive and systematic in-depth study global patterns of mutation and drug resistance mechanisms from mutation data for Mtb reported over the last 30 years. These were collected for 31,073 drug-resistant Mtb isolates from 149 published studies for the four first line drugs isoniazid (INH), pyrazinamide (PZA), rifampicin (RIF), and ethambutol (EMB). We found 821 single frequency non-synonymous mutations for INH (n= 202), RIF (n=120), EMB (n=226) and PZA (n=273). We then investigated the prevalence and diversity of these mutations in the drug targets across the globe. We found S315T in the target katG (60%) to be the most prevalent mutation in INH resistance followed by S450L in rpoB (56%) and M306V in embB (29%) associated with RIF and EMB resistance, respectively; these were also the highly occurring mutations across the six WHO regions, except for the most common mutation Q10P in pncA (1.4%) (PZA resistance; with shorter exposure to drug) showing a variable pattern of occurrence globally. We found the highest mutational burden in the Western Pacific and South-East Asia regions for INH and RIF resistance. Frequent mutations had also undergone frequent amino acid substitutions. Accordingly, we developed a comprehensive atlas of mutation spread across the globe and their evolution over the last 30 years. We then probed into the impact of mutations on TB bacteria and drug binding with a comprehensive bioinformatics analysis for understanding crucial changes caused by mutation at the molecular level affecting function and structural stability of bacteria and the drug binding affinity. We found that the most prevalent mutations occur in non-conserved areas in the drug binding region indicating a choice of a less dramatic level of change in target protein function and stability. All mutations reduced drug binding affnity. For characterising drug resistance mechanisms, we introduced a new concept of ranking drug-resistant TB mutations into lethal, moderate, mild and neutral considering the combined effect on Mtb viability and drug binding. We identified 340 mutations as lethal, 284 as moderate, 185 as mild and 12 as neutral. We observed that frequently occurring mutations occur in non-conserved regions causing a mild effect on target proteins (such as S315T of katG, S450L of rpoB and M306V in embB), while reducing drug binding affinity. With these we uncovered a universal strategy of drug resistance and bacterial survival: Mtb favours less harmful mutations in the drug binding region without compromising conservancy while destabilising the drugs, thus striking a balance between fitness and drug resistance. This ingenuous strategy seems successful and reasonable persisting globally over three decades and provides a holistic understanding of drug resistance and a strong foundation for designing efficacious drugs and therapies towards global eradication of TB.

bioinformatics↗

bioRxiv2025

Understudied and underprotected: biodiversity and conservation challenges in the Konkan region of Maharashtra

In biodiversity hotspots, such as the Western Ghats, periodic synthesis of existing ecological research can help identify knowledge gaps and address critical threats to biodiversity. The Maharashtra part of the Konkan region, situated between the Sahyadri foothills and the west coast, with diverse tropical vegetation, harbours unique open ecosystems, such as lateritic plateaus, and supports a multitude of threatened species, including hornbills and tigers. However, the region remains relatively understudied and has not received adequate protection through state or national conservation policies and laws. The area is undergoing rapid human-driven land-use change. These activities can impact the regions biodiversity, necessitating an effort to identify knowledge gaps and critical threats. Through a combination of a literature review and focus group discussions with 44 participants from various institutions and non-governmental organisations, we synthesised existing published information on the Konkan region of Maharashtra and identified key research gaps and conservation challenges. Our review of 138 studies found that while agroforestry and human-wildlife interactions have received some research attention, the effects of climate change on the regions biodiversity remain poorly understood. Focus group discussions highlighted major threats, including land-use changes due to expanding monoculture plantations, clear-felling of forests, forest fires, environmental pollution, and rapid infrastructure development, which are leading to habitat loss and fragmentation. Some of these concerns were validated by publicly available regional data, which revealed a 30% increase in roads, a 14% expansion of cashew plantations, and associated forest loss. This synthesis offers valuable insights for government and non-governmental organisations to inform future research and conservation efforts in the region.

ecology↗

bioRxiv2025

The role of MYB46 in modulating polysaccharide acetylation by mediating the transcriptional regulation of cell wall-related genes in Arabidopsis

Understanding the mechanism behind the transcriptional regulation of polysaccharide O-acetylation remains a key challenge that might be regulated through transcription factors. Our earlier work revealed the upregulation of AtGELP7 in MYB46 overexpression lines, prompting us to investigate how MYB46 transcriptionally controls AtGELP7 including other cell wall acetylation pathway genes in Arabidopsis. In MYB46 overexpression lines, we observed alteration in acetylation levels on xylan, xyloglucan and pectin in different tissue types, which suggests complex and tight regulation of acetylation homeostasis in the cell wall. Further, our transcriptomic data revealed the simultaneous upregulation of both AtGELP7 (acetyl xylan esterase) and xylan-specific TBLs (xylan O-acetyltransferases) indicating sophisticated regulation of cell wall acetylation homeostasis. Using transactivation studies in Nicotiana and pAtGELP7::GUS stable lines, we found that MYB46 enhances AtGELP7 expression probably through downstream regulators which could be either MYB103 or other MYBs. In addition, extensive cell wall analysis of MYB46 overexpression lines showed differential sugar distribution, preferably to major cell wall components such as cellulose, xyloglucan, and xylan across different tissue types of different developmental stages. Moreover, the integration of RNA-sequencing and ChIP-sequencing data uncovered previously unknown, novel probable direct gene targets of MYB46 that may be involved in polysaccharide acetylation and cell wall remodeling.

plant biology↗

bioRxiv2020

Analysis of Genetically Determined Gene Expression Suggests Role of Inflammatory Processes in Exfoliation Syndrome

Exfoliation syndrome (XFS) is an age-related systemic disorder characterized by excessive production and progressive accumulation of abnormal extracellular material, with pathognomonic ocular manifestations. It is the most common cause of secondary glaucoma, resulting in widespread global blindness. We performed Transcriptomic Wide Association Studies (TWAS) using PrediXcan models trained in 48 GTEx tissues to identify genetically- determined gene expression changes associated with XFS risk, leveraging on results from a global GWAS that included 123,457 individuals from 24 countries. We observed twenty-eight genes in a three-Megabase chr15q22-25 region that showed statistically significant associations, which were further whittled down to ten genes after additional statistical validations. In experimental analysist of these ten genes, mRNA transcript levels for ARID3B, CD276, LOXL1, NEO1, SCAMP2, and UBL7 were significantly decreased in iris tissues from XFS patients compared to control samples. Genes with genetically determined expression changes in XFS were significantly enriched for genes associated with inflammatory conditions. We further explored the health consequences of high susceptibility to XFS using a large electronic health record and observed a higher incidence of XFS comorbidity with inflammatory and connective tissue diseases. Our results implicate a role for connective tissues and inflammation in the etiology of XFS. Targeting the inflammatory pathway may be a potential therapeutic option to reduce progression in XFS.

genetics↗

bioRxiv2019

A RETINOBLASTOMA-RELATED transcription factor network governs egg cell differentiation and stress response in Arabidopsis

The multicellular embryo, and ultimately the entire organism, is a derivative of the fertilized egg cell. Unlike in animals, transcription factor networks orchestrating faithful egg development are still largely unknown in plants. We have identified that egg cell differentiation in Arabidopsis require interplay between evolutionarily conserved onco-protein homologs RETINOBLASTOMA-RELATED (RBR) and redundant MYB proteins MYB64/MYB119. RBR physically interacts with the MYBs; and with plant-specific transcription factors belonging to the RWP-RK-domain (RKD) family and LEAFY COTYLEDON1 (LEC1), which participate in development of egg cells and inherent stress response. RBR binds to most of these egg cell-expressed loci at the DNA level, partially overlapping with sites of histone methylation H3K27me3. Since deregulation of RKDs phenocopies mutants of RBR and the MYBs in terms of cell proliferation in the egg cell spatial domain, all the corresponding proteins are likely required to restrict parthenogenetic cell divisions of the egg cells. Cross-talk among these transcription factors, and direct regulation by RBR, govern egg cell development and expression of egg-to-zygotic polarity factors of the WUSCHEL RELATED HOMEOBOX family. Together, a network of RBR-centric transcription factors underlies egg cell development and stress response, possibly, in combination with several other predicted nodes.\n\nAuthor summaryThe RETINOBLASTOMA protein is one of the core components of the Eukaryotic cell cycle, and corresponding evolutionary homologs have been implicated not only to repress cell division but also to control differentiation and development. How RETINOBLASTOMA RELATED (RBR) associate with other higher order regulators to control faithful egg cell development in sexual plants is pivotal for manipulation of successful reproduction in general, and engineering of parthenogenesis when asexual or apomictic seed progeny are desirable over sexual plants. Using a suite of molecular methods, we show that a RBR-associated transcription factor network operates to specify egg cells in Arabidopsis. Complex cross-regulation within these transcription factors seems to be necessary for successful maternal egg cell to zygotic transition and reproductive stress response. Detailed genetic analysis implicate that RBR and its interactive partners belonging to MYB and RWP-RK transcription factor families are possibly required to prevent parthenogenesis of the sexual egg cells. Novel RBR networks and stress nodes explained in this study might help to improve our understanding of sexual and asexual reproduction.

genetics↗

bioRxiv2019

A deconvolution algorithm for multiecho functional MRI: Multiecho Sparse Paradigm Free Mapping

This work introduces a novel algorithm for deconvolution of the BOLD signal in multiecho fMRI data: Multiecho Sparse Paradigm Free Mapping (ME-SPFM). Assuming a linear dependence of the BOLD percent signal change on the echo time (TE) and using sparsity-promoting regularized least squares estimation, ME-SPFM yields voxelwise time-varying estimates of the changes in the transverse relaxation [Formula] without prior knowledge of the timings of individual BOLD events. Our results in multi-echo fMRI data collected during a multi-task event-related paradigm at 3 Tesla demonstrate that the maps of [Formula] changes obtained with ME-SPFM at the times of the stimulus trials show high spatial and temporal concordance with the activation maps and BOLD signals obtained with standard model-based analysis. This method yields estimates of [Formula] having physiologically plausible values. Owing to its ability to blindly detect events, ME-SPFM also enables us to map [Formula] associated with spontaneous, transient BOLD responses occurring between trials. This framework is a step towards deciphering the dynamic nature of brain activity in naturalistic paradigms, resting-state or experimental paradigms with unknown timing of the BOLD events.

neuroscience↗