Journal of Biosciences最新文献

{"title":"NMR-based comparative metabolomics of quiescent muscle cells.","authors":"Gunjan Purohit, Akila Ramesh, Anant B Patel, Jyotsna Dhawan","doi":"","DOIUrl":"","url":null,"abstract":"<p><p>Adult muscle tissue largely comprised of differentiated myofibers also harbors quiescent muscle-resident stem cells (MuSCs) that are responsible for its maintenance, repair and regeneration. Emerging evidence suggests that quiescent MuSCs exhibit a specific metabolic state, which is regulated during physiological and pathological alterations. However, a detailed understanding of the metabolic state of quiescent MuSCs and its alteration during activation and repair is lacking. Direct profiling of MuSCs <i>in vivo</i> is challenging because the cells are rare and dispersed, while isolation and enrichment leads to their activation and loss of quiescence. In this study, we employed 1H-nuclear magnetic resonance (NMR) spectroscopy to profile metabolites in an established culture model of quiescent MuSC-derived myoblasts and compared with activated, proliferative and differentiated muscle cells to determine the state-specific metabolome. We report that the proliferating and differentiated cells are highly enriched in metabolites involved in energy generation, the quiescent state is enriched in metabolites related to phospholipid catabolism (glycerophosphocholine and choline) and depleted for phosphocholine which is enriched in proliferating cells. We propose that the ratio of these metabolites may be useful as a biomarker of MuSC quiescence.</p>","PeriodicalId":15171,"journal":{"name":"Journal of Biosciences","volume":"49 ","pages":""},"PeriodicalIF":2.9,"publicationDate":"2024-01-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"141179771","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Collaborative action between noradrenergic and serotoninergic systems in peripheral antinociception in mice.","authors":"Danielle Diniz Aguiar, Cristina DA Costa Oliveira, Julia Alvarenga Petrocchi, Marina Gomes Miranda E Castor, Andrea Castro Perez, Igor Dimitri Gama Duarte, Thiago Roberto Lima Romero","doi":"","DOIUrl":"","url":null,"abstract":"<p><p>Noradrenaline (NA) and serotonin (5-HT) induce nociception and antinociception. This antagonistic effect can be explained by the dose and type of activated receptors. We investigated the existence of synergism between the noradrenergic and serotonergic systems during peripheral antinociception. The paw pressure test was performed in mice that had increased sensitivity by intraplantar injection of prostaglandin E₂ (PGE₂). Noradrenaline (80 ng) administered intraplantarly induced an antinociceptive effect, that was reversed by the administration of selective antagonists of serotoninergic receptors 5-HT_1B isamoltan, 5-HT_1D BRL15572, 5-HT_2A ketanserin, 5-HT₃ ondansetron, but not by selective receptor antagonist 5-HT₇ SB-269970. The administration of escitalopram, a serotonin reuptake inhibitor, potentiated the antinociceptive effect at a submaximal dose of NA. These results, indicate the existence of synergism between the noradrenergic and serotonergic systems in peripheral antinociception in mice.</p>","PeriodicalId":15171,"journal":{"name":"Journal of Biosciences","volume":"49 ","pages":""},"PeriodicalIF":2.1,"publicationDate":"2024-01-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"141450586","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Cell membrane proteome analysis in HEK293T cells challenged with α-synuclein amyloids.","authors":"Harshit Vaish, Shemin Mansuri, Aanchal Jain, Swasti Raychaudhuri","doi":"","DOIUrl":"","url":null,"abstract":"<p><p>Amyloids interact with plasma membranes. Extracellular amyloids cross the plasma membrane barrier. Internalized extracellular amyloids are reported to trigger amyloidogenesis of endogenous proteins in recipient cells. To what extent these extracellular and intracellular amyloids perturb the plasma membrane proteome is not investigated. Using α-synuclein as a model amyloid protein, we performed membrane shaving followed by mass spectrometry experiments to identify the conformational changes in cell surface proteins after extracellular amyloid challenge. We also performed membrane proteomics after the biogenesis of intracellular α-synuclein amyloids. Our results suggest that promiscuous interactions with extracellular amyloids stochastically alter the conformation of plasma membrane proteins. This affects the biological processes through the plasma membrane and results in loss of cell viability. Cells that survive the extracellular amyloid shock can grow normally and gradually develop intracellular amyloids which do not directly impact the plasma membrane proteome and associated biological processes. Thus, our results suggest that α-synuclein amyloids can damage the plasma membrane and related processes during cell-to-cell transfer and not during their intracellular biogenesis.</p>","PeriodicalId":15171,"journal":{"name":"Journal of Biosciences","volume":"49 ","pages":""},"PeriodicalIF":2.1,"publicationDate":"2024-01-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"141554883","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Lafora progressive myoclonus epilepsy: Disease mechanism and therapeutic attempts.","authors":"Rashmi Parihar, Subramaniam Ganesh","doi":"","DOIUrl":"","url":null,"abstract":"<p><p>Lafora disease (LD) is a life-threatening autosomal recessive and progressive neurodegenerative disorder that primarily affects adolescents, resulting in mortality within a decade of onset. The symptoms of LD include epileptic seizures, ataxia, dementia, and psychosis. The underlying pathology involves the presence of abnormal glycogen inclusions in neurons and other tissues, which may contribute to neurodegeneration. LD is caused by loss-of-function mutations in either the <i>EPM2A</i> gene or the <i>NHLRC1</i> gene. These two genes, respectively, code for laforin phosphatase and malin ubiquitin ligase, and are thought to function, as a functional complex, in diverse cellular pathways. One of the major pathways affected in LD is glycogen metabolism; defects here lead to abnormally higher levels of glycogen and its hyperphosphorylation and aggregation, resulting in the formation of Lafora inclusion bodies. Currently, there is no effective therapy for LD. Studies, particularly from animal models, provide distinct insights into the fundamental mechanisms of diseases and potential avenues for therapeutic interventions. The purpose of this review is to present a comprehensive overview of our current knowledge regarding the disease, its genetics, the animal models that have been developed, and the therapeutic strategies that are being developed based on an understanding of the disease mechanism.</p>","PeriodicalId":15171,"journal":{"name":"Journal of Biosciences","volume":"49 ","pages":""},"PeriodicalIF":2.9,"publicationDate":"2024-01-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"139575354","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Rare genetic diseases in India: Steps toward a nationwide mission program.","authors":"Anjana Kar, Sundaravadivel P, Ashwin Dalal","doi":"","DOIUrl":"","url":null,"abstract":"<p><p>Rare genetic diseases are rare by themselves with prevalence of 1 in 25,000, but collectively they are a significant cause of morbidity and mortality. Till date, collectively there are more than 9,000 rare diseases documented, which impose a devastating impact on patients, their families, and the healthcare system, including enormous societal burden. Obtaining a conclusive diagnosis for a patient with a rare genetic disease can be long and gruelling. For some patients it takes months or years to receive a definite diagnosis, and around 50% of the patients remain undiagnosed even with expert clinical and advanced high-end laboratory investigations. Owing to the large population and practice of consanguinity the Indian population is a pool of indigenous variants and unreported phenotypes or diseases. A mission program on pediatric rare diseases is an unparalleled initiative to study unique clinical conditions via the use of latest state-of-art technologies and with the combination of a mulit-omics approach. Our initiative will not only provide diagnosis to patients with rare disease but also build a platform for translational research for rare disease screening, management, and treatment.</p>","PeriodicalId":15171,"journal":{"name":"Journal of Biosciences","volume":"49 ","pages":""},"PeriodicalIF":2.9,"publicationDate":"2024-01-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"139931312","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"<i>IRF9</i> and <i>STAT1</i> as biomarkers involved in T-cell immunity in atherosclerosis.","authors":"Wei Xie, Xiang Gao, Liang Zhao, Shifei Song, N A Li, Junming Liu","doi":"","DOIUrl":"","url":null,"abstract":"<p><p>Atherosclerosis is a common cardiovascular disease in which the arteries are thickened due to buildup of plaque. This study aims to identify programmed cell death (PCD)-related biomarkers and explore the crucial regulatory mechanisms of atherosclerosis. Gene expression profiles of atherosclerosis and control groups from GSE20129 and GSE23746 were obtained. Necroptosis was elevated in atherosclerosis. Weighted gene coexpression network analysis (WGCNA) was conducted in GSE23746 and GSE56045 to identify PCD-related modules and to perform enrichment analysis. Two necroptosis-related genes (<i>IRF9</i> and <i>STAT1</i>) were identified and considered as biomarkers. Enrichment analysis showed that these gene modules were mainly related to immune response regulation. In addition, single-cell RNA sequencing data from GSE159677 were obtained and the characteristic cell types of atherosclerosis were identified. A total of 11 immune cell types were identified through UMAP dimension reduction. Most immune cells were mainly enriched in plaque samples, and <i>STAT1</i> and <i>IRF9</i> were primarily expressed in T-cells and macrophages. Moreover, the roles of <i>IRF9</i> and <i>STAT1</i> were assessed and found to be significantly upregulated in atherosclerosis, which was associated with increased risk of atherosclerosis. This study provides a molecular feature of atherosclerosis, offering an important basis for further research on its pathological mechanisms and the search for new therapeutic targets.</p>","PeriodicalId":15171,"journal":{"name":"Journal of Biosciences","volume":"49 ","pages":""},"PeriodicalIF":2.1,"publicationDate":"2024-01-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142132783","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"CDCA: Community detection in RNA-seq data using centrality-based approach.","authors":"Tonmoya Sarmah, Dhruba K Bhattacharyya","doi":"","DOIUrl":"","url":null,"abstract":"<p><p>One of the integral part of the network analysis is finding groups of nodes that exhibit similar properties. Community detection techniques are a popular choice to find such groups or communities within a network and it relies on graph-based methods to achieve this goal. Finding communities in biological networks such as gene co-expression networks are particularly important to find groups of genes where we can focus on further downstream analysis and find valuable insights regarding concerned diseases. Here, we present an effective community detection method called community detection using centrality-based approach (CDCA), designed using the graph centrality approach. The method has been tested using four benchmark bulk RNA-seq datasets for schizophrenia and bipolar disorder, and the performance has been proved superior in comparison to several other counterparts. The quality of communities are determined using intrinsic graph properties such as modularity and homogeneity. The biological significance of resultant communities is decided using the pathway enrichment analysis.</p>","PeriodicalId":15171,"journal":{"name":"Journal of Biosciences","volume":"49 ","pages":""},"PeriodicalIF":2.1,"publicationDate":"2024-01-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142080403","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Seasonal variation in expression patterns of anti-microbial peptides and activity of anti-oxidant defence enzymes in muga silkworm larvae, <i>Antheraea assamensis</i> Helfer.","authors":"Deepshikha Keot, Aashis Dutta, Manas DAS","doi":"","DOIUrl":"","url":null,"abstract":"<p><p>Muga is a semi-domesticated multi-voltine silkworm cultivated in different seasons of the year. Crops are reared in specific months and are traditionally named Jarua (spring), Chotua, Bohogua, Jethua, Aherua, Saonia, Bhodia, Ahinia, Katia (autumn) and Aghonia. Seasonal variation forces silkworm larvae to face harsh environmental conditions manifested by generation of oxidative stress and occurrence of microbial diseases. Anti-oxidant enzymes like superoxide dismutase (SOD), catalase (CAT), and glutathione-S-transferase (GST) along with anti-microbial peptides like cecropin, gloverin, and defensin in lepidopterans play a significant role in fighting against free radicals as well as disease-causing microbes, and hence this study has focussed on the expression of anti-oxidant enzyme activity and different anti-microbial peptides in three distinct crops, namely, Jarua and Aherua (seed crops) and Katia (commercial crop) collected from the same site, Khanapara (26°09'34.62″N; 91°41'27.23″E) in Assam, India. The results of biochemical enzyme assays revealed the Jarua crop to possess the highest enzyme activity with respect to SOD and GST in particular, followed by the Katia and Aherua crops. Malondialdehyde lipid peroxidase and reduced glutathione were also expressed notably in the Jarua crop. The quantitative polymerase chain reaction (qPCR) study involving analysis of anti-microbial peptide (AMP) expression revealed the Jarua crop to possess the highest expression of three AMPs, viz., gloverin, moricin 1 and gallerimycin pro, followed by Katia with the highest expression of attacin and defensin. Total haemocyte count revealed Jarua to induce the least haemocyte count, Katia to induce moderate, and Aherua to induce the highest count. Thus, our findings indicate that although the Jarua crop is considered a seed crop, it can be reconsidered as a commercial crop due to its high concentration of anti-oxidant enzymes and higher expression of AMPs. This study was carried out to focus on the immunological response of the muga silkworm with varying seasons. Their innate immunity helps them fight against diseases that emerge under different environmental conditions in which anti-microbial peptides play a crucial role. Muga larvae are reared for silk and are used commercially to produce various commodities for which the best silk thread should always be identified to obtain a higher market value.</p>","PeriodicalId":15171,"journal":{"name":"Journal of Biosciences","volume":"49 ","pages":""},"PeriodicalIF":2.1,"publicationDate":"2024-01-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142466267","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Abundance and age structure of critically endangered long-billed (<i>Gyps indicus</i>) and white-rumped (<i>G. bengalensis</i>) vultures at the breeding colonies of Kaghaznagar Forest Division and its adjoining areas in the Deccan Plateau, India.","authors":"Manchiryala Ravikanth, Nagarajan Baskaran","doi":"","DOIUrl":"","url":null,"abstract":"<p><p>Kaghaznagar and Sironcha Forest Divisions in the Deccan Plateau of India support large breeding colonies of critically endangered species of long-billed <i>Gyps indicus</i> (LBV) and white-rumped <i>G. bengalensis</i> (WRV) vultures. To assess their abundance and age-structure, that are important population parameters, they were surveyed every month at their breeding colonies; LBV at Palarapu cliff during 2010-2021 and Lakkameda cliff during 2015-2021, and WRV at Dechilpeta during 2014-2021. Breeding colonies of LBV supported a mean of 32 ± 1.3 individuals during 2015-2021. Although its number increased from 34 individuals in 2015 to 42 in 2017, it declined significantly to 10 in 2021. In contrast, WRV with a mean of 49 ± 3.35 individuals between 2014 and 2021 increased from 22 to 66. Data on the population structure show that adults constitute bulk of the population in both LBV (78 ± 1.2%) and WRV (80 ± 2.1%) with a low proportion of young age-classes of sub-adults, juveniles and chicks. With a declining trend and low proportion of young-age classes, the LBV breeding colonies are likely to decrease over time. Although WRV showed an increasing trend during the study period, the high adult proportion (80%) cannot guarantee its sustained growth.</p>","PeriodicalId":15171,"journal":{"name":"Journal of Biosciences","volume":"49 ","pages":""},"PeriodicalIF":2.9,"publicationDate":"2024-01-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"141087662","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Harnessing the innate immune system by revolutionizing macrophage-mediated cancer immunotherapy.","authors":"Gayatri Reghu, Praveen Kumar Vemula, Sarita Ganapathy Bhat, Sreeja Narayanan","doi":"","DOIUrl":"","url":null,"abstract":"<p><p>Immunotherapy is a promising and safer alternative to conventional cancer therapies. It involves adaptive T-cell therapy, cancer vaccines, monoclonal antibodies, immune checkpoint blockade (ICB), and chimeric antigen receptor (CAR) based therapies. However, most of these modalities encounter restrictions in solid tumours owing to a dense, highly hypoxic and immune-suppressive microenvironment as well as the heterogeneity of tumour antigens. The elevated intra-tumoural pressure and mutational rates within fastgrowing solid tumours present challenges in efficient drug targeting and delivery. The tumour microenvironment is a dynamic niche infiltrated by a variety of immune cells, most of which are macrophages. Since they form a part of the innate immune system, targeting macrophages has become a plausible immunotherapeutic approach. In this review, we discuss several versatile approaches (both at pre-clinical and clinical stages) such as the direct killing of tumour-associated macrophages, reprogramming pro-tumour macrophages to anti-tumour phenotypes, inhibition of macrophage recruitment into the tumour microenvironment, novel CAR macrophages, and genetically engineered macrophages that have been devised thus far. These strategies comprise a strong and adaptable macrophage-toolkit in the ongoing fight against cancer and by understanding their significance, we may unlock the full potential of these immune cells in cancer therapy.</p>","PeriodicalId":15171,"journal":{"name":"Journal of Biosciences","volume":"49 ","pages":""},"PeriodicalIF":2.1,"publicationDate":"2024-01-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC10961329/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"141305971","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}