Journal of Biosciences最新文献_第4页

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

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

Enhanced whole-brain calcium imaging and cell identification in C. elegans reveal AWC^OFF neuronal responses to 2-nonanone. 秀丽隐杆线虫全脑钙成像和细胞鉴定显示AWCOFF神经元对2-壬烷酮的反应。

IF 2.1 4区生物学

Journal of Biosciences Pub Date : 2025-01-01

Yuto Endo, Ryoga Suzuki, Taira Ito, Reina E Itoh, Ryota Kawaguchi, Koutarou D Kimura

{"title":"Enhanced whole-brain calcium imaging and cell identification in C. elegans reveal AWCOFF neuronal responses to 2-nonanone.","authors":"Yuto Endo, Ryoga Suzuki, Taira Ito, Reina E Itoh, Ryota Kawaguchi, Koutarou D Kimura","doi":"","DOIUrl":"","url":null,"abstract":"Whole-brain calcium imaging combined with multicolor cell identification is a revolutionary technique for elucidating structure-function relationships in the neural network of the nematode Caenorhabditis elegans. Existing genetically encoded calcium indicator (GCaMP) (for calcium imaging) + neuronal polychromatic atlas of landmarks for whole-brain imaging (NeuroPAL) (for cell identification) strains, however, exhibit suboptimal behavioral and neural responses to external stimuli, at least under certain conditions. To address this, we established a new strain of GCaMP + NeuroPAL, KDK94, and found that this new strain showed improved behavioral and/or neural responses to the repulsive odor 2-nonanone and electric stimuli compared with existing strains. Whole-brain calcium and NeuroPAL imaging using the new strain with several technical improvements revealed that in addition to the previously known amphid sensory neuron (ASH) and amphid wing 'B' cells (AWB) sensory neurons, the AWCOFF neuron responds to both stepwise increases in the water phase and subtle gradual increases in the air phase of 2-nonanone concentration. The improvement of the whole-brain imaging system with cell identification and the transgenic strain for the system may provide new insights into the neural circuit dynamics underlying the basic brain functions, such as learning, decisionmaking, and emotion, of C. elegans.","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":"144575509","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

Isolation of a novel marine Aspergillus fumigatus strain AFK11 and inhibition of inflammatory mediators. 新型海洋烟曲霉AFK11菌株的分离及对炎症介质的抑制作用。

IF 2.1 4区生物学

Journal of Biosciences Pub Date : 2025-01-01

Kranti Kiran Reddy Ealla, Neema Kumari, Se-Kwon Kim, Nimisha Rawat, Anuradha Mokkapati, Ira Bhatnagar

{"title":"Isolation of a novel marine Aspergillus fumigatus strain AFK11 and inhibition of inflammatory mediators.","authors":"Kranti Kiran Reddy Ealla, Neema Kumari, Se-Kwon Kim, Nimisha Rawat, Anuradha Mokkapati, Ira Bhatnagar","doi":"","DOIUrl":"","url":null,"abstract":"Marine fungi are the leading producers of bioactive metabolites with medicinal properties against several diseases. However, since marine species survive in diverse climates, they are usually difficult to culture in laboratory setups, making them challenging to study. This study aimed to optimize culture conditions for marine fungi and evaluate the inhibitory action of the marine extract on primary pro-inflammatory cytokines. Culture conditions for marine fungi were optimized using biomass production, hyphal density, and radial extension, considering temperature and humidity. The study isolated a new Aspergillus fumigatus variant, AFK11 (GenBank accession no. JX022941), showing 96% similarity to reported strains. Ethyl acetate extracts of AFK11 significantly inhibited primary pro-inflammatory cytokines, tumor necrosis factor-α, and interleukin-6, in a dose-dependent manner. This research highlights the successful laboratory culture and anti-inflammatory potential of the new strain of Aspergillus, AFK11, emphasizing the need for further research for its potential in various other diseases such as cancer.","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":"144275034","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

Localization of mitochondria along axons and at synapses in C. elegans touch receptor neurons is necessary for touch habituation. 线虫触摸受体神经元沿轴突和突触的线粒体定位是触摸习惯化的必要条件。

IF 1.9 4区生物学

Journal of Biosciences Pub Date : 2025-01-01

Sneha Hegde, Nayantara Varma, Parul Sood, Sandhya P Koushika

{"title":"Localization of mitochondria along axons and at synapses in C. elegans touch receptor neurons is necessary for touch habituation.","authors":"Sneha Hegde, Nayantara Varma, Parul Sood, Sandhya P Koushika","doi":"","DOIUrl":"","url":null,"abstract":"Neuronal mitochondria are important for neuronal survival and function. Mitochondria buffer calcium, produce ATP, and contribute to reactive oxygen species (ROS) homeostasis, processes that help in neuronal outgrowth and synaptic transmission. Caenorhabditis elegans touch receptor neurons (TRNs) are essential for gentletouch perception and are also used as a model to study axon regeneration. We set up a localized touch habituation assay and investigated the role of the localization of mitochondria along axons and at synapses in the touch circuit for touch habituation behaviour. Mitochondrial transport mutant ric-7 and the metaxin-2;miro- 1 double mutant, which lack mitochondria in axons and at synapses, habituate faster to gentle touch compared with wild-type animals. The faster habituation phenotype is reversed upon restoration of mitochondria along axons and at synapses of only TRNs. Since mitochondria are shown to control actin dynamics, we asked two questions: (i) Can actin dynamics bypass the requirement of axonal mitochondria for touch habituation, and (ii) can upregulation of actin dynamics in injured axons occur independent of axonal mitochondria? Restoring axonal actin dynamics in the absence of axonal mitochondria did not restore defects in gentle-touch habituation of ric-7 animals. Axotomized TRNs in ric-7 animals show upregulation of axonal actin dynamics but do not show filopodial protrusions at the growth cone. Our study suggests that axonal mitochondria play key roles in habituation and axon regeneration independent of dynamic axonal actin.","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":"145137682","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