Journal of Biosciences最新文献_第6页

Whole exome sequencing reveals novel and rare variants in nonsyndromic hearing loss-related genes: A focus on GPSM2 compound heterozygosity. 全外显子组测序揭示了非综合征性听力损失相关基因的新颖和罕见变异：关注GPSM2复合杂合性。

IF 2.1 4区生物学

Journal of Biosciences Pub Date : 2025-01-01

Sudipta Chakraborty, Sukanya Mitra, Arnab Ghosh, Krishna Kumar, Shamita Sanga, Atanu Kumar Dutta, Suchandra Mukherjee, Nidhan Kumar Biswas, Saikat Chakrabarti, Moulinath Acharya

{"title":"Whole exome sequencing reveals novel and rare variants in nonsyndromic hearing loss-related genes: A focus on GPSM2 compound heterozygosity.","authors":"Sudipta Chakraborty, Sukanya Mitra, Arnab Ghosh, Krishna Kumar, Shamita Sanga, Atanu Kumar Dutta, Suchandra Mukherjee, Nidhan Kumar Biswas, Saikat Chakrabarti, Moulinath Acharya","doi":"","DOIUrl":"","url":null,"abstract":"Non-syndromic hearing loss (NSHL) is a genetically heterogeneous disorder affecting millions worldwide. Recent advances in genetic technologies have expanded our understanding of its molecular basis, but challenges remain in identifying and interpreting causative variants. This study aimed to investigate the genetic etiology of NSHL using comprehensive genetic screening, with a focus on identifying rare and potentially pathogenic variants. We performed genetic analysis on 43 participants diagnosed with NSHL using whole exome sequencing (WES) technology. Variant filtering, in silico prediction tools, and segregation analysis were employed to evaluate the pathogenicity of identified variants. Our analysis revealed 20 rare and deleterious variants (4 novel and 16 previously reported) in 16 NSHL-related genes among 43 participants. These variants included 3 known pathogenic, 4 likely pathogenic, and 13 variants of uncertain significance (VUS). Notably, we identified compound heterozygous variants in the GPSM2 gene (NM_013296:c.185G>A;p.Ser62Asn and NM_013296:c.1264delG;p.Val422Tyrfs*28) in one participant, with segregation analysis confirming their trans configuration. This study expands our understanding of the genetic landscape of NSHL by identifying several rare variants in known NSHL-related genes. Notably, we report the first case of compound heterozygous variants in the GPSM2 gene in the Indian population, a finding not previously documented. This discovery underscores the importance of comprehensive genetic screening in diverse populations and contributes to the growing body of evidence for the role of GPSM2 in NSHL.","PeriodicalId":15171,"journal":{"name":"Journal of Biosciences","volume":"50 ","pages":""},"PeriodicalIF":2.1,"publicationDate":"2025-01-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144275038","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}

引用次数: 0

Thirty years of the Baranyi and Roberts model: Predictions, precautions, risk assessment, and beyond. Baranyi和Roberts模型的三十年：预测、预防、风险评估及其他。

IF 1.9 4区生物学

Journal of Biosciences Pub Date : 2025-01-01

Dhruba Dey, Debapriya Mukherjee, Pallab Ghosh, Dipshikha Chakravortty

{"title":"Thirty years of the Baranyi and Roberts model: Predictions, precautions, risk assessment, and beyond.","authors":"Dhruba Dey, Debapriya Mukherjee, Pallab Ghosh, Dipshikha Chakravortty","doi":"","DOIUrl":"","url":null,"abstract":"In today's world, food safety is of paramount importance. Even a slight lapse can lead to significant economic losses and place a heavy burden on the healthcare system. Over the years, multiple mathematical models have been developed to predict microbial growth in commercial foods. However, each of these models had to give up at least one of the factors, i.e., generality, realism, or precision. The Baranyi and Roberts model was proposed in the 1990s and was an extension of the logistic model. It took 'realism' into account and bridged the gap between the conditions affecting populations in nature and how they are represented on paper. The realistic attributes of the model allowed it to model, for the first time, the lag time. In this review, we have discussed the model in detail, along with its extrapolations that made it flexible. We have further discussed how the Baranyi model is still important in food safety regimes. We have also discussed how one can explain the setting up of the adjustment factor used in this model. Our literature review has revealed how the Baranyi and Roberts model continues to be relevant even after 30 years of its proposition, and further insights on the biochemical aspects of the model's assumptions might help in strengthening its predictions.","PeriodicalId":15171,"journal":{"name":"Journal of Biosciences","volume":"50 ","pages":""},"PeriodicalIF":1.9,"publicationDate":"2025-01-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144821538","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}

引用次数: 0

Bite size of Caenorhabditis elegans regulates feeding, satiety and development on a diet of live yeast. 秀丽隐杆线虫的咬口大小调节着以活酵母为食的摄食、饱腹感和发育。

IF 1.9 4区生物学

Journal of Biosciences Pub Date : 2025-01-01

Atreyee DE, Amit K Sahu, Varsha K Singh

{"title":"Bite size of Caenorhabditis elegans regulates feeding, satiety and development on a diet of live yeast.","authors":"Atreyee DE, Amit K Sahu, Varsha K Singh","doi":"","DOIUrl":"","url":null,"abstract":"In the wild, the nematode Caenorhabditis elegans primarily feeds on microbes, which are abundant in rotting vegetation. Studies show that several gram-positive and gram-negative bacterial populations predominantly constitute the C. elegans gut microbiome, but surprisingly lack any yeast species. To understand the lack of yeast in the intestine of C. elegans, we studied the behaviour of worms on pathogenic and non-pathogenic yeast diets. We show that C. elegans displays low satiety on a yeast diet of Cryptococcus neoformans, Cryptococcus laurentii or Saccharomyces cerevisiae. We find that the average size of cells of budding yeast is much larger than that of Escherichia coli, which constitute the laboratory diet of C. elegans. We have shown that yeast cells cause pharyngeal obstruction, diminished feeding, and lower level of neutral lipids in adult C. elegans. Using scanning electron microscopy, we show that the mouth size of C. elegans larvae is smaller than the average yeast cell. The larvae have no detectable yeast in their alimentary canal, and they undergo delayed development on a yeast diet. We propose that microbial cell size or bite size could be crucial factors in the regulation of feeding in C. elegans, and the composition of the microbiome in its intestine.","PeriodicalId":15171,"journal":{"name":"Journal of Biosciences","volume":"50 ","pages":""},"PeriodicalIF":1.9,"publicationDate":"2025-01-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144955408","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}

引用次数: 0

Modulation of the biphasic pattern of cortical reorganization in spinal cord-transected rats by external magnetic fields. 外磁场对脊髓横断大鼠皮质重组双相模式的调节。

IF 1.9 4区生物学

Journal of Biosciences Pub Date : 2025-01-01

Sajeev Kaur, Suman Jain, Ritika Bhardwaj, Senthil S Kumaran, Kanwal Preet Kochhar

{"title":"Modulation of the biphasic pattern of cortical reorganization in spinal cord-transected rats by external magnetic fields.","authors":"Sajeev Kaur, Suman Jain, Ritika Bhardwaj, Senthil S Kumaran, Kanwal Preet Kochhar","doi":"","DOIUrl":"","url":null,"abstract":"A biphasic pattern of reorganization in the somatosensory cortical area, representing the hindlimb or forelimb, has been shown after complete spinal cord injury (cSCI) in rats. The present study hypothesized that extremely low-frequency magnetic fields (ELF-MF) would favourably modulate this biphasic pattern of cortical plasticity by altering brain-derived neurotrophic factor (BDNF) and neurite outgrowth inhibitor A (isoform of reticulon- 4) (Nogo-A) levels, leading to functional and electrophysiological recovery in cSCI rats. Adult male Wistar rats underwent cSCI at the T-13 spinal level, followed by ELF-MF exposure for either 5, 12, or 32 days, for analysis of the biphasic pattern. A set of motor and sensorimotor behavioural tests, spinal cord lesion volume, cortical electroencephalography (EEG), expression of neurotrophic factor (BDNF), and inhibitory molecule (Nogo-A) were recorded at each time period. Significant (p≤0.01) recovery was evident in the Basso-Beattie- Bresnahan (BBB) locomotor score, allodynia, grip strength, power spectrum of EEG waves, and lesion volume after 32 days of ELF-MF. Although both SCI and SCI+MF rats exhibited characteristic biphasic patterns in the expression of Nogo-A and BDNF, the SCI+MF group showed a significant increase in BDNF levels along with a decrease in Nogo-A. These findings suggest that ELF-MF enhances functional recovery after cSCI by moderating molecular and electrophysiological markers of cortical plasticity, without disrupting the inherent biphasic expression dynamics.","PeriodicalId":15171,"journal":{"name":"Journal of Biosciences","volume":"50 ","pages":""},"PeriodicalIF":1.9,"publicationDate":"2025-01-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145137706","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}

引用次数: 0

Caenorhabditis elegans as a model for studying intercellular communication via extracellular vesicles. 秀丽隐杆线虫作为研究细胞外囊泡细胞间通讯的模型。

IF 2.1 4区生物学

Journal of Biosciences Pub Date : 2025-01-01

Tingting Li, Yunpeng Zhao, Yan Zou, Yue Wang

引用次数: 0

Impact of HIV-1 TAT activation on retinal Müller glia: Implications for barrier properties. HIV-1 TAT激活对视网膜<s:1>神经胶质细胞的影响：对屏障特性的影响。

IF 2.1 4区生物学

Journal of Biosciences Pub Date : 2025-01-01

Kamini Khatak, Kavitha Sankaranarayanan, Nivedita Chatterjee

{"title":"Impact of HIV-1 TAT activation on retinal Müller glia: Implications for barrier properties.","authors":"Kamini Khatak, Kavitha Sankaranarayanan, Nivedita Chatterjee","doi":"","DOIUrl":"","url":null,"abstract":"HIV-associated immune activation is characterized by an increase in pro-inflammatory mediators and dysfunctional T-cells with senescent phenotypes. This persistent activation predisposes HIV-infected persons to non-AIDS-defining co-morbid conditions. At the retina, Müller glia undertake innate immune functions. Evidence from our microarray data shows changes in pathways which include cytokines, their receptors, and focal adhesion genes, suggesting inflammatory changes which could affect the blood-retinal barrier. Using a bioinformatics approach, we analyzed our dataset to identify changes in reactive Müller glia. Abnormalities in Müller glia signaling involve phosphatidylinositol 3-kinase (PI3K) and protein kinase B (AKT). In silico analysis was validated by quantitative RT-PCR. PKB/AKT is increased in reactive Müller glia. Inhibition of PI3K/AKT affected transendothelial resistance in TAT-exposed Müller glia. Identification of a cluster of gene expression suggests underlying changes in the functions of Müller glia in maintaining barrier permeability through the PI3K/AKT signaling network. Activation of retinal Müller cells can therefore lead to proinflammatory molecular cascades that promote widespread physiological changes. Alterations in these pathways may affect vascular permeability, retinal and corneal angiogenesis, and disruption of the blood-ocular barrier.","PeriodicalId":15171,"journal":{"name":"Journal of Biosciences","volume":"50 ","pages":""},"PeriodicalIF":2.1,"publicationDate":"2025-01-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144608428","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}

引用次数: 0

CroPCS: Crop Plants Combined Stress Knowledgebase. 农作物综合胁迫知识库。

IF 1.9 4区生物学

Journal of Biosciences Pub Date : 2025-01-01

Akash DAS, Drishtee Barua, Souvik Pal, Ananya Gogoi, Pankaj Barah

{"title":"CroPCS: Crop Plants Combined Stress Knowledgebase.","authors":"Akash DAS, Drishtee Barua, Souvik Pal, Ananya Gogoi, Pankaj Barah","doi":"","DOIUrl":"","url":null,"abstract":"Plants, being sessile organisms, are continually exposed to diverse combinations of biotic and abiotic stresses in their natural habitats. Combined stresses are considered significant threats to plants, particularly in the context of today's climate change. Despite the vast amount of data generated by OMICS experiments, information remains widely dispersed and inaccessible within the literature. Attempts to collect, integrate, store, and generate such data and information that are easily accessible to the public are the need of the hour. Crop Plants Combined Stress Knowledgebase (CroPCS) is a manually curated repository, created through the biocuration of OMICS literature, storing valuable data on crop plant responses to combined stresses. It offers a user-friendly interface for exploring, querying, and downloading molecular data [genes, proteins, metabolites, and non-coding RNAs (ncRNAs)] under various stress combinations. The literature on all OMICS (transcriptomics, proteomics and metabolomics) are listed with cross-referenced data. The current version of CroPCS encompasses 13 crop plants and 16 stress combinations, and contains a total of 266,417 molecules, including 262,220 genes, 1709 proteins, 274 metabolites, and 2214 ncRNAs. Additionally, it supports community curation by allowing users to submit their own data. CroPCS stands out as a unique online resource and is available at https://www2.tezu.ernet.in/cropcs.","PeriodicalId":15171,"journal":{"name":"Journal of Biosciences","volume":"50 ","pages":""},"PeriodicalIF":1.9,"publicationDate":"2025-01-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144955410","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}

引用次数: 0

Computational exploration of Arabidopsis thaliana N-Myc downregulated-like-1 for protein-protein interaction and phylogenetic conservation. 拟南芥N-Myc下调样-1蛋白相互作用和系统发育保护的计算探索。

IF 2.1 4区生物学

Journal of Biosciences Pub Date : 2025-01-01

Abhishek Kanojia, Asani Bhaduri, Soumya Nayak, R Sowdhamini, Yashwanti Mudgil

{"title":"Computational exploration of Arabidopsis thaliana N-Myc downregulated-like-1 for protein-protein interaction and phylogenetic conservation.","authors":"Abhishek Kanojia, Asani Bhaduri, Soumya Nayak, R Sowdhamini, Yashwanti Mudgil","doi":"","DOIUrl":"","url":null,"abstract":"N-Myc downregulated-like (NDL) proteins belong to the α/ꞵ-hydrolase-fold-containing protein family. NDLs are interacting partners of G-protein subunits which are involved in abiotic and biotic stress signaling mechanisms in plants. Three NDLs (NDL1, NDL2, and NDL3) have been identified in Arabidopsis thaliana. The NDL1 interactome reveals its interaction with numerous proteins involved in diverse plant functions, suggesting its role in various signaling mechanisms. The current study was designed to explore the level of conservation of NDL proteins across the plant kingdom to analyze protein structure for the conserved sites involved in protein-protein interactions. We analyzed NDL proteins from different plant groups for sequence conservation patterns through phylogenetic and motif analyses. Subsequently, homology-based models were built for NDLs and their selected interactors using MODELLER, and interaction sites were also analyzed using molecular docking. Overall, our study revealed sequence conservation within the NDL family and the presence of several conserved motifs across diverse plant groups. Additionally, docking analysis suggests that two specific regions, spanning positions 40-50 and 135-170 in the NDL1 structure, may serve as hotspots for various protein-protein interactions.","PeriodicalId":15171,"journal":{"name":"Journal of Biosciences","volume":"50 ","pages":""},"PeriodicalIF":2.1,"publicationDate":"2025-01-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144275024","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}

引用次数: 0

Stonebrood in Argentinian wild bees: A neglected disease? 阿根廷野蜂中的石窝：一种被忽视的疾病？

IF 2.1 4区生物学

Journal of Biosciences Pub Date : 2025-01-01

Leopoldo Jesús Alvarez, Marcos Daniel Salina, María Cecilia Estravis-Barcala, Ailen Alejandra Solis, Marco Antonio Tizzano, Valentín Almada, Guillermo Hernán Sguazza, Mariano Lucia, Francisco José Reynaldi

{"title":"Stonebrood in Argentinian wild bees: A neglected disease?","authors":"Leopoldo Jesús Alvarez, Marcos Daniel Salina, María Cecilia Estravis-Barcala, Ailen Alejandra Solis, Marco Antonio Tizzano, Valentín Almada, Guillermo Hernán Sguazza, Mariano Lucia, Francisco José Reynaldi","doi":"","DOIUrl":"","url":null,"abstract":"Wild bees are crucial for pollinating flowering plants, with about 1,200 species found in Argentina. While the complex of pests and pathogens that attack honey bees are widely known, few studies have investigated fungal pathogens such as Aspergillus in wild bee fauna. This study focuses on understanding the nesting biology of two solitary ground-nesting wild bees and sheds light on the impact of fungal infections caused by Aspergillus flavus on larval mortality in these bees. Brood cells were excavated from two aggregations of nests from two localities in Buenos Aires, Argentina. Cells were isolated in plates and monitored daily until adult emergence. Data on species, date, sex, and presence of parasitoids and cleptoparasites were recorded, and the total mortality due to insects and fungal pathogens was estimated. Pollen masses, larvae, and dead pupae were photographed and stored for microbiological analysis. Samples were cultured on yeast-glucose-starch-agar (YGPSA) in media plates. In positive samples, DNA was extracted using a specific commercial kit. Molecular analysis involved PCR amplification and sequencing, utilizing specific primers. Data on the nesting biology of Melitoma segmentaria and Ancyloscelis halictoides were presented. We identified three causes of mortality: Aspergillus flavus, Leiopodus lacertinus, and Melittobia hawaiiensis. The most prevalent cause of mortality in both study sites was A. flavus, the first record of this fungus causing stonebrood in wild bees of South America. Our findings open up discussions on the importance of this fungal pathogen for the health of wild bees.","PeriodicalId":15171,"journal":{"name":"Journal of Biosciences","volume":"50 ","pages":""},"PeriodicalIF":2.1,"publicationDate":"2025-01-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144275036","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}

引用次数: 0

The many roads to C. elegans dauer arrest: A review and perspective. 秀丽隐杆线虫的许多途径：回顾与展望。

IF 2.1 4区生物学

Journal of Biosciences Pub Date : 2025-01-01

Kavinila Selvarasu, Abhishiktha Godthi, Veena Prahlad

引用次数: 0