Journal of Biosciences最新文献_第2页

Kinome-wide RNAi screening in Caenorhabditis elegans reveals new modulators of insulin signaling and longevity. 秀丽隐杆线虫的全基因组RNAi筛选揭示了胰岛素信号传导和寿命的新调节剂。

IF 2.1 4区生物学

Journal of Biosciences Pub Date : 2025-01-01

Manish Chamoli, Anna Foulger, Prachi Singh, Gordon Lithgow, Arnab Mukhopadhyay

{"title":"Kinome-wide RNAi screening in Caenorhabditis elegans reveals new modulators of insulin signaling and longevity.","authors":"Manish Chamoli, Anna Foulger, Prachi Singh, Gordon Lithgow, Arnab Mukhopadhyay","doi":"","DOIUrl":"","url":null,"abstract":"The insulin/IGF-I-like signaling (IIS) pathway is a highly conserved signaling cascade that plays a crucial role in regulating longevity across species. Given its significance in aging, identifying novel kinases interacting with the IIS pathway can provide deeper insights into the mechanisms governing longevity. In this study, we performed a targeted RNAi screening of the Caenorhabditis elegans kinome, using dauer formation as a phenotypic readout. We identified several known and novel kinase modulators of the IIS pathway. These hits were enriched with both previously documented and undocumented lifespan regulators. Thermotolerance assays revealed mixed trends, with some kinase inhibitions increasing while others decreasing protection against thermal stress. We observed a positive correlation between thermotolerance and lifespan extension, as well as between dauer formation and lifespan extension, with thermotolerance proving to be a better predictor of longevity. Our findings offer a valuable resource for researchers exploring the IIS pathway and highlight novel, unannotated kinases as potential new therapeutic targets for aging interventions.","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":"143811388","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

What keeps Caenorhabditis elegans precise: The spatiotemporal regulation of defecation. 是什么让秀丽隐杆线虫保持精确：排便的时空调节。

IF 2.1 4区生物学

Journal of Biosciences Pub Date : 2025-01-01

Qiang Liu, Louis Tao

引用次数: 0

Contrasting sequence polymorphism and structural basis patterns of Plasmodium falciparum histidine-rich proteins 2/3 in Cameroon and India. 喀麦隆和印度恶性疟原虫富组氨酸蛋白2/3序列多态性和结构基谱对比

IF 2.1 4区生物学

Journal of Biosciences Pub Date : 2025-01-01

Loick Pradel Kojom Foko, Joseph Hawadak, Soumyananda Chakraborti, Veena Pande, Vineeta Singh

{"title":"Contrasting sequence polymorphism and structural basis patterns of Plasmodium falciparum histidine-rich proteins 2/3 in Cameroon and India.","authors":"Loick Pradel Kojom Foko, Joseph Hawadak, Soumyananda Chakraborti, Veena Pande, Vineeta Singh","doi":"","DOIUrl":"","url":null,"abstract":"The bulk of malaria rapid diagnostic tests (RDTs) target Plasmodium falciparum histidine-rich protein 2 (PfHRP2), but several reports have shown that sequence variations in this protein are associated with falsenegative RDT results. The polymorphism of PfHRP2/3 was analyzed from Cameroonian and Indian P. falciparum isolates. Cameroon and India are two of eleven countries with the highest malaria burden. Exon 2 of pfhrp 2/3 genes were PCR-amplified, and the amplicons were purified and sequenced. A total of 25 PfHRP2 and 12 PfHRP3 novel repeat type variants were found. The nature and organization of PfHRP3 sequences were quite similar between Cameroon and India. Some structurally unique PfHRP2/3 sequences, characterized by a high proportion of proline (5.8-10.3%) for PfHRP2, and two non-repeat regions for PfHRP3, were found in both countries. Most of the Cameroonian isolates belonged to group B (66.7%), while the Indian isolates belonged to group C (69.2%) (p=0.03). Three epitope motifs (AHHAHHA, HATDAHH, and YAHHAHHA) were found in all Cameroonian and Indian PfHRP2 sequences. Mutations observed in unique sequences were mainly associated with alterations of helical structures in the PfHRP2 C-terminal region. The high genetic diversity, epitope availability, and structural basis patterns found here could help develop the next generation of RDTs with improved quality.","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":"143255556","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

Why does community ecology need chemistry? Because keystone molecules can govern food webs. 为什么群落生态学需要化学？因为关键分子可以控制食物网。

IF 2.1 4区生物学

Journal of Biosciences Pub Date : 2025-01-01

Renee M Borges

{"title":"Why does community ecology need chemistry? Because keystone molecules can govern food webs.","authors":"Renee M Borges","doi":"","DOIUrl":"","url":null,"abstract":"In an earlier editorial (Borges 2022), I had talked about the keystone concept formulated by Robert Paine. This important concept (Paine 1966) emphasised the idea that biodiversity is maintained by a top-down process in which the removal of a keystone predator would allow the unchecked proliferation of herbivores; during this process a dominant herbivore might outcompete another herbivore species, resulting in the removal of the lesser competitor from the community and a reduction in overall species richness (i.e., the number of species present). The keystone predator concept is well-established in community ecology. Are there keystone molecules whose presence can influence the diversity of communities? At an extreme, of course, one may say that oxygen is a most important molecule whose presence has fuelled the diversification of autotrophs such as diatoms and plants, and hence the flowering of life. A key feature of Paine's keystone concept is that the species must exert an impact that is disproportionate to its abundance (Power et al. 1996). By this definition, oxygen, although vital to all life, would fail to be recognised as a keystone chemical or molecule in species communities. Are there chemical compounds that can govern species diversity within trophic levels of an ecological community, as defined by Paine's keystone concept?","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":"143997552","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

Role of public DNA-Seq data in mitogenomics research: A case study on the flying fish family (Beloniformes: Exocoetidae). 公开DNA-Seq数据在有丝分裂基因组学研究中的作用：以飞鱼科（飞鱼目：外鱼科）为例。

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

Assay medium composition affects Caenorhabditis elegans thermotaxis behaviours. 实验培养基组成影响秀丽隐杆线虫的趋热性行为。

IF 2.1 4区生物学

Journal of Biosciences Pub Date : 2025-01-01

Yanshu Zhang, Masami Shima, Yuki Aoki, Asuka Takeishi

{"title":"Assay medium composition affects Caenorhabditis elegans thermotaxis behaviours.","authors":"Yanshu Zhang, Masami Shima, Yuki Aoki, Asuka Takeishi","doi":"","DOIUrl":"","url":null,"abstract":"Animals exhibit behavioural responses to environmental stimuli. To date, various experimental assays have been conducted to investigate the molecular and neural mechanisms underlying behavioural responses in Caenorhabditis elegans. However, behavioural outcomes can vary even under the same stimulus due to factors such as past experience, individual circumstances, and modifications in behavioural assay procedures, which complicate the interpretation of results. In this study, we focussed on the composition of the behavioural assay media and compared the behaviours of C. elegans in response to temperature and odour stimuli using three commonly used media: nematode growth medium (NGM), thermotaxis (TTX), and chemotaxis (Chemo) assay media. Our results demonstrated that in thermotaxis, C. elegans exhibited stable behavioural decisions across all examined media. However, the population of worms reaching the preferable areas was smaller in Chemo and TTX media compared with NGM due to prolonged exploration period and reduced migration speed. By contrast, in chemotaxis, we did not observe significant differences across the tested media. This study provides insights into the significant effects on C. elegans behaviour caused by the modifications of the behavioural assay media and emphasises the importance of further studies to explore the detailed neural mechanisms that regulate animal behaviour under diverse environmental factors.","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":"144063953","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