Journal of Biosciences最新文献_第2页

Role of public DNA-Seq data in mitogenomics research: A case study on the flying fish family (Beloniformes: Exocoetidae).

IF 2.1 4区生物学

Journal of Biosciences Pub Date : 2025-01-01

Iuri Batista DA Silva, Igor Henrique Rodrigues-Oliveira, Karine Frehner Kavalco, Fabiano Bezerra Menegidio, Rubens Pasa

{"title":"Role of public DNA-Seq data in mitogenomics research: A case study on the flying fish family (Beloniformes: Exocoetidae).","authors":"Iuri Batista DA Silva, Igor Henrique Rodrigues-Oliveira, Karine Frehner Kavalco, Fabiano Bezerra Menegidio, Rubens Pasa","doi":"","DOIUrl":"","url":null,"abstract":"Flying fishes (Exocoetidae) are a highly specialized group of Beloniformes, with 4 subfamilies, 7 genera, and 78 species. However,only a small number of species of flying fishes have the mitochondrial genome described sof ar. Considering the importance of mitogenomes in evolution, in this study we aimed to expand the description of mitochondrial genomes and the phylogenetic relationships of Exocoetidae. We used publicly available DNA-Seq libraries to assemble the mitochondrial genomes of 7 species of flying fishes. The mitochondrial genomes of Exocoetidae showed conserved features among all species. With 22 tRNAs, 2 rRNAs, and 13 protein-coding genes, they share common features among vertebrates.Cheilopogon was reconstructedaspolyphyletic, with four clades, which reinforces previous studies that recovered Cheilopogon as non-monophyletic.Werecoveredallfour subfamilies as monophyletic,with Parexocoetinae as the sister group of all other subfamilies.The genetic distance between Exocoetidae species was two times smaller than the genetic distance among the Hyporhamphus species, indicating a low genetic divergence in the family. Hereby, this study expanded the knowledge of mitochondrial genome features and presented one of the most comprehensive mitochondrial genome datasets used for studying flying fishestodate. This was achievable using publicly available data, reinforcing the importanceof the re-use of such data in the fields of mitogenomics and phylogenetics.","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":"143709860","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.

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

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

Optimal endogenous controls for microRNA analysis of visceral adipose tissue in the NAFLD mouse model.

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

The interplay of tuberculosis and COVID-19: Insights into global health challenges.

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

Meta-analysis of QTLs for drought, heat, and salinity tolerance identifies high-confidence MQTLs and candidate genes in chickpea (Cicer arietinum L.).

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

Analysis of downstream targets of PAX6 and LHX2, fundamental regulators of the developing mammalian neocortex.

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

Caenorhabditis elegans as a model for studying intercellular communication via extracellular vesicles.

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

Role of EhLINE1_ORF1p outside retrotransposition: Downregulation causes growth defects in Entamoeba histolytica.

IF 2.1 4区生物学

Journal of Biosciences Pub Date : 2025-01-01

Devinder Kaur, Shashi Shekhar Singh, Shraddha Sharma, Sudha Bhattacharya

引用次数: 0

Independent control of functional rewiring after axon injury by let-7 miRNA and insulin/insulin-like growth factor signaling pathways.

IF 2.1 4区生物学

Journal of Biosciences Pub Date : 2025-01-01

Sruthy Ravivarma, Sibaram Behera, Dipanjan Roy, Anindya Ghosh-Roy

{"title":"Independent control of functional rewiring after axon injury by let-7 miRNA and insulin/insulin-like growth factor signaling pathways.","authors":"Sruthy Ravivarma, Sibaram Behera, Dipanjan Roy, Anindya Ghosh-Roy","doi":"","DOIUrl":"","url":null,"abstract":"The capability of neurons to regenerate after injury becomes poor in adulthood. Previous studies indicated that loss of either let-7 miRNA or components of insulin/insulin-like growth factor signaling (IIS) can overcome age-related decline in axon regeneration in Caenorhabditis elegans. In this study, we wanted to understand the relationship between these two pathways in axon regeneration. We found that the simultaneous removal of let-7 and the gene for insulin receptor daf-2 in parallel increased functional recovery involving posterior touch sensation following axotomy of posterior lateral microtubule (PLM) neurons in adulthood. Conversely, the loss of let-7 could bypass the regeneration block due to the loss of DAF-16, a transcriptional mediator of DAF-2. Similarly, the loss of daf-2 could bypass the requirement of LIN-41, a transcriptional co-factor of the let-7 pathway. Our analysis revealed that these two pathways independently control the targeting of the regenerating axon to the ventral nerve cord (VNC), which leads to functional recovery. The computational analysis of the gene expression data revealed that a large number of genes, their interacting modules, and hub genes under the let-7 and IIS pathways are exclusive in nature. Our study highlights a potential to promote neurite regeneration by harnessing the independent gene expression program involving the let-7 and IIS pathways.","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":"143811363","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