Journal of Biosciences最新文献

{"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":"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}

{"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":"Mungbean in Central Asia: It went there from East Asia, not South Asia.","authors":"Geeta R, E Roshini Nayar","doi":"","DOIUrl":"","url":null,"abstract":"<p><p>The migration and dispersal of organisms is fascinating from many perspectives and, in the case of crop plants, intersects with the movement of human beings. As they explore new areas, agricultural peoples carry seeds of crops, which move and may establish ('diffuse') where they go. In order to understand the movement of the crop across regions, we need to understand the pattern and rate of diffusion of the crop, as well as that of the people involved, both those who carried it and those who adopted it. What determines whether a particular crop will establish in a new region with a different climate and other environmental factors (e.g., precipitation), likely necessitating genetic change through natural or artificial selection (e.g., Rendo´n-Anaya et al. 2017)? The extent to which the rate of diffusion is determined by evolutionary and environmental processes, on the one hand, and human migratory processes, on the other, is a complex question that has not been resolved even for as intensively studied a crop as maize (Stoneking et al. 2023).</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":"139575444","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":"Screening of quinoa (<i>Chenopodium quinoa</i> Willd.) germplasms under high-SAR saline water on the basis of growth, yield, and multivariate analysis.","authors":"Kailash Prajapat, Satish Kumar Sanwal, Parbodh Chander Sharma","doi":"","DOIUrl":"","url":null,"abstract":"<p><p>Increasing soil and underground water salinization with decreasing availability of fresh water has become a potential threat to sustainable crop production in arid and semi-arid areas globally. Introduction and evaluation of salt-tolerant halophytic crops is one of the sustainable ways to preserve productivity in saline ecosystems. This study was aimed to screen quinoa germplasms under high-sodium adsorption ratio (SAR) saline stress. Thirteen quinoa germplasms were evaluated under four levels [best available water (BAW), 8, 16, and 24 dSm^-1] of high-SAR saline water irrigation. The evaluation was carried out based on growth, yield, and ionic content parameters along with statistical tools such as multivariate analysis, salt tolerance indices, and correlation. The results showed that the salinity levels of 16 and 24 dSm^-1 resulted in increase of chlorophyll content relative to BAWand 8 dSm^-1. The germplasm CSQ2 recorded the highest proline content (163.7 mg g^-1 FW) at 24 dSm^-1. Increasing levels of salinity reduced relative water content in plant leaves, and the germplasm CSQ2 showed minimal reduction of 4% at 24 dSm^-1. Na⁺ and K⁺ contents in the plants increased with increasing salinity levels, while the K⁺/Na⁺ ratio decreased. The grain yield of quinoa germplasms ranged between 3.5 and 14.1 g plant^-1. The germplasm EC507740 recorded the highest grain yield (7.0 g plant^-1) followed by CSQ1 and CSQ2 at a maximum stress of 24 dSm^-1. Principal component analysis (PCA) and correlation elucidated that Na⁺ content in plants was negatively correlated with all the studied traits except SPAD, proline content, and K⁺ content. The different salt tolerance indices indicated that the germplasms EC507740, CSQ1, CSQ2, EC507738, and IC411825 were more stable at high-SAR salinity, while PCA showed the germplasms EC507740 and CSQ2 as the most salt-tolerant germplasms.</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":"139575446","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":"Mitochondrial alternative oxidase pathway helps in nitrooxidative stress tolerance in germinating chickpea.","authors":"Josepheena Joseph, Sanjib Bal Samant, Kapuganti Jagadis Gupta","doi":"","DOIUrl":"","url":null,"abstract":"<p><p>Mitochondrial alternative oxidase (AOX) is an important protein that can help in regulating reactive oxygen species and nitric oxide in plants. The role of AOX in regulation of nitro-oxidative stress in chickpea is not known. Using germinating chickpea as a model system, we investigated the role of AOX in nitro-oxidative stress tolerance. NaCl treatment was used as an inducer of nitro-oxidative stress. Treatment of germinating seeds with 150 mM NaCl led to reduced germination and radicle growth. The AOX inhibitor SHAM caused further inhibition of germination, and the AOX inducer pyruvate improved growth of the radicle under NaCl stress. Isolated mitochondria from germinated seeds under salt stress not only increased AOX capacity but also enhanced AOX protein expression. Measurement of superoxide levels revealed that AOX inhibition by SHAM can enhance superoxide levels, whereas the AOX inducer pyruvate reduced superoxide levels. Measurement of NO by gas phase chemiluminescence revealed enhanced NO generation in response to NaCl treatment. Upon NaCl treatment there was enhanced tyrosine nitration, which is an indicator of nitrosative stress response. Taken together, our results revealed that AOX induced under salinity stress in germinating chickpea can help in mitigating nitro-oxidative stress, thereby improving germination.</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":"140898409","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":"Predicting and reducing potential parasite infection between migratory livestock and resident Asiatic ibex of Pin valley, India.","authors":"Munib Khanyari, Rodrigo Oyanedel, Abhirup Khara, Manvi Sharma, E J Milner-Gulland, Kulbhushansingh R Suryawanshi, Hannah Rose Vineer, Eric R Morgan","doi":"","DOIUrl":"","url":null,"abstract":"<p><p>Disease cross-transmission between wild and domestic ungulates can negatively impact livelihoods and wildlife conservation. In Pin valley, migratory sheep and goats share pastures seasonally with the resident Asiatic ibex (<i>Capra sibirica</i>), leading to potential disease cross-transmission. Focussing on gastro-intestinal nematodes (GINs) as determinants of health in ungulates, we hypothesized that infection on pastures would increase over summer from contamination by migrating livestock. Consequently, interventions in livestock that are well-timed should reduce infection pressure for ibex. Using a parasite life-cycle model, that predicts infective larval availability, we investigated GIN transmission dynamics and evaluated potential interventions. Migratory livestock were predicted to contribute most infective larvae onto shared pastures due to higher density and parasite levels, driving infections in both livestock and ibex. The model predicted a <i>c.</i>30-day antiparasitic intervention towards the end of the livestock's time in Pin would be most effective at reducing GINs in both hosts. Albeit with the caveats of not being able to provide evidence of interspecific parasite transmission due to the inability to identify parasite species, this case demonstrates the usefulness of our predictive model for investigating parasite transmission in landscapes where domestic and wild ungulates share pastures. Additionally, it suggests management options for further investigation.</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":"140898417","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":"Clinical trial registries: The good, and the not so good.","authors":"Gayatri Saberwal","doi":"","DOIUrl":"","url":null,"abstract":"<p><p>Clinical trial registries are a vital part of the infrastructure of a robust clinical research ecosystem, itself essential for biomedical translational research. We describe what clinical trial registries are, provide a brief history of the major registries, list the major registries today, mention some of the flaws in these registries, comment on the economics of trial registries, give details of the Indian registry, Clinical Trials Registry - India, and catalogue three examples of research done with data in the Indian registry.</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":"142466263","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}