Journal of Biosciences最新文献_第4页

Integrative analysis of coding and non-coding RNAs in rice reveals conserved molecular response signatures to heat, drought, and salt stresses. 水稻编码和非编码rna的综合分析揭示了对热、干旱和盐胁迫的保守分子响应特征。

IF 2.1 4区生物学

Journal of Biosciences Pub Date : 2025-01-01

Ananya Gogoi, Prangan Nath, Visakha Pradhan, Pankaj Barah

{"title":"Integrative analysis of coding and non-coding RNAs in rice reveals conserved molecular response signatures to heat, drought, and salt stresses.","authors":"Ananya Gogoi, Prangan Nath, Visakha Pradhan, Pankaj Barah","doi":"","DOIUrl":"","url":null,"abstract":"Abiotic stresses such as heat, drought, and salinity significantly impact rice cultivation by affecting its yield and quality. Identifying molecular candidates that confer resistance or tolerance to these stresses is crucial. This study identifies unique and overlapping molecular signatures mediated by coding and non-coding RNAs during heat, drought, and salt stresses in rice. It uses RNA-Seq data from 66 rice samples, including those treated with heat, drought, and salt stresses, to identify both unique and shared differentially expressed mRNAs and long non-coding RNAs (lncRNAs). Analyses reveal key regulatory hubs in transcriptional networks, particularly the ERF, DOF, and MYB family transcription factors, which are central to abiotic stress responses. Stress-specific competing endogenous RNA networks reveal conserved regulatory elements that coordinate these responses. Overlap analysis identifies 637 shared mRNAs and 76 lncRNAs among the three stresses. These findings enhance our understanding of the molecular mechanisms underlying stress resilience in rice and provide a foundation for developing stress-resistant cultivars.","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":"144674893","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

Origin of homochirality in terrestrial biology. 陆生生物中同种异性的起源。

IF 2.1 4区生物学

Journal of Biosciences Pub Date : 2025-01-01

Koji Tamura

引用次数: 0

Meta-analysis of QTLs for drought, heat, and salinity tolerance identifies high-confidence MQTLs and candidate genes in chickpea (Cicer arietinum L.). 鹰嘴豆（Cicer arietinum L.）耐干旱、耐热和耐盐qtl的meta分析确定了高置信度的mqtl和候选基因。

IF 2.1 4区生物学

Journal of Biosciences Pub Date : 2025-01-01

Shubham Sharma, Jatin Sharma, Shayla Bindra, Amool Singh Vadithya, O M Prakash Raigar, Dinesh Kumar Saini, Priyanka Anand, Sushil Kumar, Inderjit Singh, Chellapilla Bharadwaj

{"title":"Meta-analysis of QTLs for drought, heat, and salinity tolerance identifies high-confidence MQTLs and candidate genes in chickpea (Cicer arietinum L.).","authors":"Shubham Sharma, Jatin Sharma, Shayla Bindra, Amool Singh Vadithya, O M Prakash Raigar, Dinesh Kumar Saini, Priyanka Anand, Sushil Kumar, Inderjit Singh, Chellapilla Bharadwaj","doi":"","DOIUrl":"","url":null,"abstract":"A meta-analysis of 712 quantitative trait loci (QTLs) associated with traits conferring tolerance to drought, heat, and salinity stress was conducted in chickpea. Of these, 588 QTLs were successfully projected onto a high-density consensus map saturated with 14,246 markers. The resulting meta-QTLs (MQTLs) (54) had an average confidence interval (CI) of 1.01 cM, which was 3.49 times narrower than the CI of the original QTLs (3.53 cM) used in the meta-analysis. Significant single-nucleotide polymorphisms (SNPs) or marker-trait associations identified in previous genome-wide association studies were found to coincide with 36 of these MQTLs. Eleven MQTLs were identified as breeder's MQTLs due to their significant contribution to phenotypic variance (>10%), modest CI (<0.5 cM), and the inclusion of more than 10 QTLs. Candidate gene mining within MQTL regions revealed 49 high-confidence candidate genes associated with various abiotic stresses. Additionally, synteny and ortho-MQTL analyses among chickpea and two other legume crops, pigeon pea and pea, identified 23 ortho-MQTL regions. The markers associated with MQTLs can be utilized for MQTL-assisted breeding and to enhance the prediction accuracy of genomic selection in chickpea.","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":"143811403","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 interplay of tuberculosis and COVID-19: Insights into global health challenges. 结核病和COVID-19的相互作用：洞察全球卫生挑战。

IF 2.1 4区生物学

Journal of Biosciences Pub Date : 2025-01-01

Kirtimaan Syal

{"title":"The interplay of tuberculosis and COVID-19: Insights into global health challenges.","authors":"Kirtimaan Syal","doi":"","DOIUrl":"","url":null,"abstract":"Tuberculosis (TB), an ancient disease, has plagued humankind for centuries, and the coronavirus disease 2019 (COVID-19) pandemic has worsened the crisis. This article discusses various intersecting aspects of TB and COVID-19, including transmission, co-infection, progression, and resurgence, which underline the necessity of a coordinated response. The respiratory transmission routes shared by both diseases, coupled with overlapping symptoms, complicate their diagnosis. The relationship between COVID-19 and TB is complex, where TB patients could be predisposed to severe COVID-19 due to potential lung damage inflicted by Mycobacterium tuberculosis infection. Also, the disrupted healthcare services and quarantine practices attributed to COVID-19 pandemic could delay treatment and enable the spread of TB, highlighting their complex interplay. The sustenance of TB services amid the pandemic involving improvised diagnosis and access to treatment remains vital. The COVID-19 pandemic has highlighted the importance of coordination between policymakers, healthcare providers, and researchers for developing comprehensive plans for transparent global surveillance systems, treatment regimens, and providing equitable access to healthcare resources, which constitute the key steps for alleviating the dual threat of TB and COVID-19.","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":"143648622","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

Optimal endogenous controls for microRNA analysis of visceral adipose tissue in the NAFLD mouse model. NAFLD小鼠模型中内脏脂肪组织microRNA分析的最佳内源性对照。

IF 2.1 4区生物学

Journal of Biosciences Pub Date : 2025-01-01

Veronika Uhrova, Helena Parova, Zuzana Cervinkova, Otto Kucera, Vladimir Palicka

{"title":"Optimal endogenous controls for microRNA analysis of visceral adipose tissue in the NAFLD mouse model.","authors":"Veronika Uhrova, Helena Parova, Zuzana Cervinkova, Otto Kucera, Vladimir Palicka","doi":"","DOIUrl":"","url":null,"abstract":"The selection of proper reference genes and materials is critical in the design of PCR experiments, especially for differential expression studies. In this study, we propose a method to identify robust endogenous control miRNAs in the visceral adipose tissue of C57BL/6J mice with non-alcoholic fatty liver disease induced by alternating Western and control diets. This study outlines a comprehensive methodology for the analysis of microRNA endogenous controls using microfluidic cards in conjunction with miRNA profiling through small RNA sequencing and subsequent validation by quantitative PCR and the RefFinder algorithm. Criteria included were fold change, p-value, reads per million, and gene stability assessment. A set of six putative endogenous microRNAs was identified (miR-331-3p, let-7a-5p, miR-1839-5p, miR-151a-5p, let-7d-5p, and let-7c-5p). Subsequent validation and analysis using the RefFinder algorithm assessed the stability of the selected genes, and a combination of the three most stable endogenous miRNA controls (miR-331-3p, let-7a- 5p, and miR-1839-5p) exhibiting consistent expression patterns with minimal variability was set. Given the absence of universal endogenous controls, individual evaluation of normalizers for each experiment is imperative for accurate miRNA expression measurements. This approach, which combines multiple techniques and assessments, provides a reliable strategy for identifying and validating endogenous controls in miRNA studies.","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":"143648542","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

O-GlcNAc transferase promotes synaptic assembly independent of catalytic activity in C. elegans. O-GlcNAc转移酶在秀丽隐杆线虫中独立于催化活性促进突触组装。

IF 2.1 4区生物学

Journal of Biosciences Pub Date : 2025-01-01

Mengting Wu, Huihui Jiang, Qian Li, Yunhe Liu, Hongjun Zhang, Zhiyong Shao

引用次数: 0

Human adipose-derived stem cell exosomes alleviate human respiratory system-related cells damaged by exposure to SO₂ derivatives. 人类脂肪来源的干细胞外泌体减轻暴露于二氧化硫衍生物的人类呼吸系统相关细胞的损伤。

IF 2.1 4区生物学

Journal of Biosciences Pub Date : 2025-01-01

Ji-Seon Lee, You-Rin Kim, Dogeon Yoon, Ji Hye Park, Ga Eun You, Wook Chun

{"title":"Human adipose-derived stem cell exosomes alleviate human respiratory system-related cells damaged by exposure to SO2 derivatives.","authors":"Ji-Seon Lee, You-Rin Kim, Dogeon Yoon, Ji Hye Park, Ga Eun You, Wook Chun","doi":"","DOIUrl":"","url":null,"abstract":"Inhalation burns, especially when combined with thermal burns, can be fatal and significantly increase mortality rate through inhaling hazardous gas. However, there is no specific treatment for inhalation burns except for relieving bronchospasm and cleaning the airways. In particular, inhaled sulfur dioxide (SO2), a major component of inhalation burns, can easily be hydrated in the respiratory tract to produce sulfurous acid, which subsequently dissociates to form bisulfite and sulfite derivatives. In this study, we intend to assess whether human adipose-derived stem cell (ASC) exosomes rescue respiratory system-related cells damaged by exposure to SO2 derivatives. We found that the uptake of ASC exosomes was high in human respiratory systemrelated cells and they rescue decreased proliferation of cells damaged by treatment with SO2 derivatives. In human pulmonary endothelial cells (HPMECs), total tubule length was increased by pre-treatment of ASC exosomes through an in vitro angiogenesis assay. Besides, we confirmed that ASC exosomes alleviate increased expression of inflammation-related genes by treatment of SO2 derivatives in primary respiratory epithelial cells. Taken together, these results suggest that ASC exosomes have potential in regeneration of human respiratory system-related cells damaged by inhalation burns, which currently lack specific treatment methods.","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":"144325831","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

Respiratory viruses and systemic lupus erythematosus: Biomarkers and mechanisms leading to autoimmunity. 呼吸道病毒和系统性红斑狼疮：导致自身免疫的生物标志物和机制。

IF 2.1 4区生物学

Journal of Biosciences Pub Date : 2025-01-01

Aruna Rajalingam, Sekar Kanagaraj, Anjali Ganjiwale

{"title":"Respiratory viruses and systemic lupus erythematosus: Biomarkers and mechanisms leading to autoimmunity.","authors":"Aruna Rajalingam, Sekar Kanagaraj, Anjali Ganjiwale","doi":"","DOIUrl":"","url":null,"abstract":"Autoimmunity has been explored in various viral infections, and its relevance to respiratory viruses deserves more attention, especially its immune derangement during these infections, which could potentially trigger relapse and induction of many new cases. Our study aimed to utilize publicly available transcriptomic respiratory viral datasets of rhinovirus, influenza virus, respiratory syncytial virus, and COVID-19 to understand their autoimmune activation. Antibodies produced against the autoantigens associated with respiratory viruses resulted in the identification of three biomarker genes: TRIM21, ELANE, and CTSG. These genes are reported to be involved in the pathways of neuroactive ligand-receptor interaction, neutrophil extracellular trap formation, apoptosis, amebiasis, renin-angiotensin system, and lysosome, commonly triggering the systemic lupus erythematosus (SLE) pathway in genetically susceptible SLE patients. These results emphasize that the key genes are enriched mainly in the immune system process linking SLE pathogenesis. Literature sources suggest that the biomarkers induce autoreactivity through bystander activation and molecular mimicry which results in aberrant B-cell activation and the formation of neutrophil extracellular traps leading to autoimmunity. Thus, these key biomarkers indicate a new direction for early diagnosis, risk assessment, and treatment of respiratory virus infections and SLE pathogenesis.","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":"144674894","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

Analysis of downstream targets of PAX6 and LHX2, fundamental regulators of the developing mammalian neocortex. 哺乳动物新皮层发育的基本调控因子PAX6和LHX2的下游靶点分析。

IF 2.1 4区生物学

Journal of Biosciences Pub Date : 2025-01-01

Mansi Srivastava, Varun Suresh, Shubha Tole

{"title":"Analysis of downstream targets of PAX6 and LHX2, fundamental regulators of the developing mammalian neocortex.","authors":"Mansi Srivastava, Varun Suresh, Shubha Tole","doi":"","DOIUrl":"","url":null,"abstract":"The transcription factors PAX6 and LHX2 play fundamental roles in mammalian cerebral cortical development. Loss of either factor causes depletion of the cortical progenitor pool and reduction of neurogenesis of later-born cortical neurons. We compared the chromatin occupancy of PAX6 and LHX2 and transcriptional dysregulation upon loss of each factor to analyze whether they function via common gene regulatory networks. We identified common direct and indirect targets that were dysregulated either concordantly or discordantly, based on whether their expression showed similar up- or downregulation upon loss of either factor. Finally, we examined single-cell RNA-seq datasets from neocortical progenitors to identify the cell types within which each common direct/indirect and concordantly/discordantly regulated target gene is expressed as cortical progenitors undergo neurogenesis. Our analysis shows that PAX6 and LHX2 have several common targets that suggest similar pathways for progenitor maintenance, but the regulation of neurogenesis may occur via at least partially non-overlapping pathways. Furthermore, each factor functions to suppress the expression of a set of common Cajal-Retzius cell-specific and interneuron-specific genes which are not normally expressed by cortical progenitors. Together, our analysis offers experimentally testable hypotheses for how PAX6 and LHX2 may execute their critical roles.","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":"143255552","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

A jack of all trades: Hermaphrodite-specific serotonergic neuron in C. elegans. 多面手：秀丽隐杆线虫的雌雄同体特异性血清素能神经元。

IF 2.1 4区生物学

Journal of Biosciences Pub Date : 2025-01-01

Patrick Laurent

{"title":"A jack of all trades: Hermaphrodite-specific serotonergic neuron in C. elegans.","authors":"Patrick Laurent","doi":"","DOIUrl":"","url":null,"abstract":"How does a single neuron type shape both short- and long-term behavior? A study reveals how co-transmission by two hermaphrodite-specific neurons (HSNs) of Caenorhabditis elegans produces both transient and long-lasting effects on its egg-laying behavior. A key question in neuroscience is how neurons and circuits integrate information to drive behavior. In the nematode C. elegans, locomotion, feeding, defecation and egg-laying motor programs are all generated by a simple nervous system consisting of 302 neurons whose connectivity patterns are fully described (White et al. 1986). Egg-laying behavior allows dispersal of eggs in the most appropriate locations. The egg-laying circuit consists of two hermaphrodite-specific serotonergic neurons (HSNs) and six ventral cholinergic C-neurons (VCs) connected to the vulval muscle. In addition, uv1 neuroendocrine cells mechanically respond to egg laying by the release of tyramine and neuropeptides. Together, they produce a rhythmic behavior modulated by environmental cues that alternates between egg-laying phases and resting periods (Hardaker et al. 2001; Ringstad and Horvitz 2008; Fenk and de Bono 2015). How can such a simple circuit generate rhythmic and regulated behavior?","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":"144000971","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