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Metagenomics identification of genetically distinct tick virome in India unveils signs of purifying selection, and APOBEC and ADAR editing 印度遗传上不同的蜱虫病毒的宏基因组鉴定揭示了纯化选择、APOBEC和ADAR编辑的迹象

IF 4.6 2区综合性期刊

iScience Pub Date : 2025-06-11 DOI: 10.1016/j.isci.2025.112873

Perumal Arumugam Desingu , Selvarayar Arunkumar , Kumaresan Nagarajan , G. Saikumar

{"title":"Metagenomics identification of genetically distinct tick virome in India unveils signs of purifying selection, and APOBEC and ADAR editing","authors":"Perumal Arumugam Desingu , Selvarayar Arunkumar , Kumaresan Nagarajan , G. Saikumar","doi":"10.1016/j.isci.2025.112873","DOIUrl":"10.1016/j.isci.2025.112873","url":null,"abstract":"<div><div>Recently, several tick-borne zoonotic viruses have been identified through the application of virus metagenomics. However, the tick virome in South Asia and the factors driving the evolution of these viruses remain largely unknown. In this study, we report the complete genomes of the genetically distinct Nairobi sheep disease virus (NSDV), Jingmen tick virus (JMTV), Lihan tick virus (LTV), and Mivirus, along with nearly complete genomes of turnip mosaic virus (TMV) and turnip yellows virus (TYV). We also present partial genomes of Tamdy orthonairovirus, Nayun tick nairoviruses (NTNV), PTV-like viruses, Xinjiang tick-associated virus-1 (XTAV1), Totivirus, Kismayo viruses, Quaranjavirus, and Brown dog tick phlebovirus-2 (BDTPV-2), identified from Indian ticks through virus metagenomics. The diversity was categorized into distinct groups specific to particular host organisms and/or geographical regions. Our findings also indicated that selection pressure for codon usage in these viruses was influenced by purifying selection, which induces transition mutations potentially through apolipoprotein B mRNA editing enzyme, catalytic polypeptide (APOBEC) and adenosine deaminases acting on RNA (ADAR) editing.</div></div>","PeriodicalId":342,"journal":{"name":"iScience","volume":"28 7","pages":"Article 112873"},"PeriodicalIF":4.6,"publicationDate":"2025-06-11","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144338632","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"综合性期刊","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

引用次数: 0

Altered immunometabolic response to fasting in humans living with obesity 肥胖患者禁食后免疫代谢反应的改变

IF 4.6 2区综合性期刊

iScience Pub Date : 2025-06-11 DOI: 10.1016/j.isci.2025.112872

Helena Neudorf , Roderick E. Sandilands , Spencer Ursel , Hillary Shaba , Darren Barg , Takeshi Tsusaka , María Dolores Moya-Garzón , Erica Vaz , Patricia Schimweg , Emily L. Goldberg , Jonathan Z. Long , Karsten Krüger , Hashim Islam , Jonathan P. Little

{"title":"Altered immunometabolic response to fasting in humans living with obesity","authors":"Helena Neudorf , Roderick E. Sandilands , Spencer Ursel , Hillary Shaba , Darren Barg , Takeshi Tsusaka , María Dolores Moya-Garzón , Erica Vaz , Patricia Schimweg , Emily L. Goldberg , Jonathan Z. Long , Karsten Krüger , Hashim Islam , Jonathan P. Little","doi":"10.1016/j.isci.2025.112872","DOIUrl":"10.1016/j.isci.2025.112872","url":null,"abstract":"<div><div>Fasting and ketosis are gaining interest for treating obesity-related immunometabolic dysfunction. We aimed to (1) characterize systemic and T cell immunometabolic responses to a 48-h fast in humans and (2) determine if responses differed between individuals with (O-BMI) and without (L-BMI) obesity (n = 16 per group). Despite similar increases in systemic fat oxidation, increases in blood β-hydroxybutyrate (BHB), BHB-amino acid conjugates, and lysine β-hydroxybutyrylation were blunted in obesity. T cells from the L-BMI group upregulated their relative capacity for fat oxidation while the O-BMI group did not. The O-BMI group had a greater proportion of Th17 cells and secreted more interleukin-17 (IL-17), even after fasting. CD8 expression decreased in both groups and CD4 expression only decreased in the L-BMI group. The balance of anti-to pro-inflammatory cytokines increased less in the O-BMI group. Collectively, these findings show that humans living with obesity have a blunted systemic and T cell immunometabolic response to fasting. <span><span>NCT05886738</span><svg><path></path></svg></span>.</div></div>","PeriodicalId":342,"journal":{"name":"iScience","volume":"28 7","pages":"Article 112872"},"PeriodicalIF":4.6,"publicationDate":"2025-06-11","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144471291","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"综合性期刊","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

引用次数: 0

Controlled liquid-liquid phase separation via the simulation-guided, targeted engineering of the RNA-binding protein PARCL 通过模拟引导的rna结合蛋白PARCL的靶向工程控制液-液相分离

IF 4.6 2区综合性期刊

iScience Pub Date : 2025-06-11 DOI: 10.1016/j.isci.2025.112852

Ruth Veevers , Steffen Ostendorp , Anna Ostendorp , Julia Kehr , Richard J. Morris

{"title":"Controlled liquid-liquid phase separation via the simulation-guided, targeted engineering of the RNA-binding protein PARCL","authors":"Ruth Veevers , Steffen Ostendorp , Anna Ostendorp , Julia Kehr , Richard J. Morris","doi":"10.1016/j.isci.2025.112852","DOIUrl":"10.1016/j.isci.2025.112852","url":null,"abstract":"<div><div>The Phloem-Associated RNA-Chaperone-Like (PARCL) protein is a plant-specific RNA-binding protein (RBP) that is highly abundant in the phloem. PARCL has been observed to form large biomolecular condensates that move within the phloem stream, potentially being involved in RNA transport. Here, we present results on unraveling drivers for PARCL’s phase separation. We used coarse-grained molecular dynamics simulations to compute a residue interaction map that identifies candidate residues involved in phase separation. Subsequent simulations with mutations of candidate residues resulted in disrupted condensation, supporting their involvement in phase separation. We performed <em>in vitro</em> and <em>in vivo</em> experiments to validate these predictions. To investigate the RNA-binding of PARCL, we added microRNA to the simulations and identified a short region of PARCL that consistently made contact with the miRNA in agreement with bioinformatics predictions and experiments. We discuss the implications of our findings in terms of model-guided engineering of biomolecular condensates.</div></div>","PeriodicalId":342,"journal":{"name":"iScience","volume":"28 7","pages":"Article 112852"},"PeriodicalIF":4.6,"publicationDate":"2025-06-11","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144471295","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"综合性期刊","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

引用次数: 0

Altered cofactor recruitment and nucleosome dynamics underlie bisphenol A’s impact on ERα-mediated transcriptional bursting 辅助因子募集和核小体动力学的改变是双酚A对er α介导的转录爆发影响的基础

IF 4.6 2区综合性期刊

iScience Pub Date : 2025-06-10 DOI: 10.1016/j.isci.2025.112864

Christopher R. Day , Pelin Yaşar , Gloria Adedoyin , Brian D. Bennett , Carson C. Chow , Joseph Rodriguez

{"title":"Altered cofactor recruitment and nucleosome dynamics underlie bisphenol A’s impact on ERα-mediated transcriptional bursting","authors":"Christopher R. Day , Pelin Yaşar , Gloria Adedoyin , Brian D. Bennett , Carson C. Chow , Joseph Rodriguez","doi":"10.1016/j.isci.2025.112864","DOIUrl":"10.1016/j.isci.2025.112864","url":null,"abstract":"<div><div>Transcription initiation at hormone-responsive gene promoters involves recruitment of numerous proteins that initiate stochastic events known as transcriptional bursts. Estrogen responsive genes are regulated by Estradiol (E2) that binds to the Estrogen Receptor-α (ERα), allowing ERα to interact with DNA regulatory elements, recruit cofactors, and initiate transcription. Here, we utilized single-molecule imaging to determine how ERα mediated transcription is altered by non-canonical ligands such as Bisphenol A (BPA). Our analysis showed that the <em>TFF1</em> gene exhibited similar burst initiation kinetics in BPA-treated cells compared to cells treated with E2. However, there was a significant reduction in the number of active alleles in the BPA-treated cells. We show that while BPA bound ERα did induce chromatin remodeling, nucleosome positioning was altered and coincided with reduced transcription factor binding. Additionally, BPA treatment impaired enhancer mediated <em>TFF1</em> bursting. Together, this demonstrates that BPA disrupts transcriptional states by altering gene specific ERα cofactor recruitment.</div></div>","PeriodicalId":342,"journal":{"name":"iScience","volume":"28 7","pages":"Article 112864"},"PeriodicalIF":4.6,"publicationDate":"2025-06-10","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144481387","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"综合性期刊","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

引用次数: 0

DaapNLRSeek, prediction, and evolution of resistance genes in polyploid sugarcane genomes 多倍体甘蔗基因组中抗性基因的寻找、预测和进化

IF 4.6 2区综合性期刊

iScience Pub Date : 2025-06-10 DOI: 10.1016/j.isci.2025.112869

Yiting Huang , Yingfeng Luo , Xiao Lin

{"title":"DaapNLRSeek, prediction, and evolution of resistance genes in polyploid sugarcane genomes","authors":"Yiting Huang , Yingfeng Luo , Xiao Lin","doi":"10.1016/j.isci.2025.112869","DOIUrl":"10.1016/j.isci.2025.112869","url":null,"abstract":"<div><div>Sugarcane (<em>Saccharum</em> spp. hybrids) is an important crop for sugar and biofuel production. However, pathogens cause significant yield losses. Most plant resistance (R) proteins are nucleotide-binding leucine-rich repeat (NLR) proteins, which detect pathogen effectors and activate immune responses. Recent advances in polyploid sugarcane genomes will accelerate sugarcane resistance breeding, however, <em>NLR</em> gene prediction in the complex polyploid genomes remains challenging. To address this, we developed a diploidy-assisted annotation of polyploid NLRs (DaapNLRSeek) pipeline to accurately predict and annotate <em>NLR</em> genes from the complex polyploid sugarcane genomes. Using DaapNLRSeek, we annotated <em>NLR</em> genes in <em>Erianthus rufipilus</em> and five sugarcane cultivars (R570, ZZ1, XTT22, Np-X, and AP85-441), analyzing their architecture, collinearity, and evolution. We also identified paired NLRs, TIR-only, and <em>TPK</em> genes from these sugarcane genomes. Intriguingly, two sugarcane-paired <em>NLR</em>s induce immune responses in <em>Nicotiana benthamiana</em>. DaapNLRSeek bridges polyploid genome assembly with functional genomics and will accelerate sugarcane resistance breeding.</div></div>","PeriodicalId":342,"journal":{"name":"iScience","volume":"28 7","pages":"Article 112869"},"PeriodicalIF":4.6,"publicationDate":"2025-06-10","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144366121","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"综合性期刊","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

引用次数: 0

Photocuring CsA and bFGF-embedded hemostatic hydrogel promotes recovery from TBI by mitigating ferroptosis and neuroinflammation 光固化CsA和bfgf包埋止血水凝胶通过减轻铁下垂和神经炎症促进TBI恢复

IF 4.6 2区综合性期刊

iScience Pub Date : 2025-06-09 DOI: 10.1016/j.isci.2025.112865

Jianing Shen , Yong Li , Ning Bian , Lu Yang , Yangping Pan , Yuyu Niu , Lu Zhao , Lei Zhang , Jingkuan Wei

{"title":"Photocuring CsA and bFGF-embedded hemostatic hydrogel promotes recovery from TBI by mitigating ferroptosis and neuroinflammation","authors":"Jianing Shen , Yong Li , Ning Bian , Lu Yang , Yangping Pan , Yuyu Niu , Lu Zhao , Lei Zhang , Jingkuan Wei","doi":"10.1016/j.isci.2025.112865","DOIUrl":"10.1016/j.isci.2025.112865","url":null,"abstract":"<div><div>Traumatic brain injury (TBI) causes focal intracranial hemorrhage, neuroinflammation, and gliosis, which contribute to motor dysfunction. Therapies addressing singular aspects of TBI damage have demonstrated limited efficacy in mitigating its comprehensive impact. Here, we investigated the therapeutic efficacy of a combination therapy comprising cyclosporine A (CsA) and basic fibroblast growth factor (bFGF) during the acute phase of TBI, delivered in a hemostatic hyaluronan-based hydrogel (OCHAMA). The OCHAMA hydrogel substantially reduced iron deposition and inhibited key drivers within the ferroptotic pathway in focal mechanical brain injury. CsA and bFGF-embedded OCHAMA (OCHAMA/CF) treatment resulted in a significant reduction in CD8<sup>+</sup> T lymphocyte infiltration and interferon-γ (IFN-γ) secretion, which correlated with attenuated neuroinflammation. TBI rats treated with OCHAMA/CF exhibited enhanced neuronal preservation and reduced lesion volume, which was associated with significant recovery of motor function. This therapeutic approach reshaped the peritraumatic neuroinflammatory microenvironment and facilitated neuron survival, underscoring its potential for widespread clinical applicability.</div></div>","PeriodicalId":342,"journal":{"name":"iScience","volume":"28 7","pages":"Article 112865"},"PeriodicalIF":4.6,"publicationDate":"2025-06-09","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144329817","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"综合性期刊","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

引用次数: 0

Global mapping of freshwater contamination by pesticides and implications for agriculture and water resource protection 全球淡水农药污染制图及其对农业和水资源保护的影响

IF 4.6 2区综合性期刊

iScience Pub Date : 2025-06-09 DOI: 10.1016/j.isci.2025.112861

Yabi Huang , Zijian Li

{"title":"Global mapping of freshwater contamination by pesticides and implications for agriculture and water resource protection","authors":"Yabi Huang , Zijian Li","doi":"10.1016/j.isci.2025.112861","DOIUrl":"10.1016/j.isci.2025.112861","url":null,"abstract":"<div><div>Pesticide residues in freshwater threaten water sustainability, but the global discrepancies in freshwater pesticide contamination remain uncertain. This study collected pesticide concentration data from various countries around the world and adopted a flexible scoring approach to assess contamination within surface freshwater and groundwater. Results revealed significant disparities in contamination among countries. Africa was identified as a priority for freshwater pesticide control as most countries there showed relatively high scores in both surface freshwater and groundwater. Notably, robust pesticide regulations were associated with reduced surface freshwater pollution, whereas pesticide usage intensity showed no clear effect. Additionally, pesticide residues in freshwater pose challenges to drinking water safety, with over half of the water samples in many African and Asian countries exceeding aldrin and dieldrin limits. These findings provide insight into the pattern of global pesticide freshwater contamination, urging efforts on comprehensive water monitoring networks and joint pesticide management within freshwater.</div></div>","PeriodicalId":342,"journal":{"name":"iScience","volume":"28 7","pages":"Article 112861"},"PeriodicalIF":4.6,"publicationDate":"2025-06-09","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144471293","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"综合性期刊","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

引用次数: 0

Disturbance of gut microbiota in diabetes related macroangiopathy: Evidence from the gut bacteriome and mycobiome 糖尿病相关大血管病变的肠道微生物群紊乱：来自肠道细菌群和真菌群的证据

IF 4.6 2区综合性期刊

iScience Pub Date : 2025-06-09 DOI: 10.1016/j.isci.2025.112856

Xiaoling Gou , Yuqing Chen , Yi Zong , Xuemei Huang , Yihong Shen , Lijie Wang , Yifan Liu , Yuchi He , Jialong Jia , Xiyu Zhang , Sihan Peng , Xianhua Zhou , Ya Liu , Jing Zhang , Gang Fan

{"title":"Disturbance of gut microbiota in diabetes related macroangiopathy: Evidence from the gut bacteriome and mycobiome","authors":"Xiaoling Gou , Yuqing Chen , Yi Zong , Xuemei Huang , Yihong Shen , Lijie Wang , Yifan Liu , Yuchi He , Jialong Jia , Xiyu Zhang , Sihan Peng , Xianhua Zhou , Ya Liu , Jing Zhang , Gang Fan","doi":"10.1016/j.isci.2025.112856","DOIUrl":"10.1016/j.isci.2025.112856","url":null,"abstract":"<div><div>Diabetes related macroangiopathy (DMA) is a major complication of type 2 diabetes (T2D), impacting both morbidity and mortality. This study characterized the gut bacteriome and mycobiome in 179 adults, including 58 with DMA, 71 with T2D, and 50 healthy controls. The gut microbiome of DMA subjects exhibited reduced alpha diversity, and a distinct microbial composition compared with healthy control. Two bacterial families, six bacterial genera, and four bacterial species exhibited significant differences between DMA and T2D subjects. Additionally, in the mycobiome group, Xylariales was significantly decreased in DMA subjects compared with T2D subjects. Disruptions in transkingdom interactions between gut bacteria and fungi supported microbiota dysbiosis in DMA. A diagnostic model combining bacterial and fungal markers achieved an AUC of 94.20%. This work deepens our understanding of the microbial landscape associated with macroangiopathy in diabetes and highlights potential microbial targets for diagnostics and therapeutic intervention.</div></div>","PeriodicalId":342,"journal":{"name":"iScience","volume":"28 7","pages":"Article 112856"},"PeriodicalIF":4.6,"publicationDate":"2025-06-09","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144489394","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"综合性期刊","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

引用次数: 0

Merits of dietary patterns for China’s future food security satisfying socioeconomic development and climate change adaptation 膳食结构对中国未来粮食安全的好处，以满足社会经济发展和适应气候变化

IF 4.6 2区综合性期刊

iScience Pub Date : 2025-06-09 DOI: 10.1016/j.isci.2025.112859

Wencong Yue , Meirong Su , Yanpeng Cai , Qiangqiang Rong , Chao Xu , Yuanchao Hu , Jiajia Li , Shujie Yu , Donghan Chen , Zhongqi Liu , Zhenkun Tan , Zhifeng Yang

{"title":"Merits of dietary patterns for China’s future food security satisfying socioeconomic development and climate change adaptation","authors":"Wencong Yue , Meirong Su , Yanpeng Cai , Qiangqiang Rong , Chao Xu , Yuanchao Hu , Jiajia Li , Shujie Yu , Donghan Chen , Zhongqi Liu , Zhenkun Tan , Zhifeng Yang","doi":"10.1016/j.isci.2025.112859","DOIUrl":"10.1016/j.isci.2025.112859","url":null,"abstract":"<div><div>Food security depends on food production exceeding consumption, which are influenced, respectively, by climate change and socio-economic development. We adopted a hybrid approach for predicting features of future food security in China. Specifically, complex interactions in food security were examined using copula-based Markov Chain Monte Carlo simulation. Crop yields per unit area were simulated with a denitrification-decomposition (DNDC) model under four climate-change scenarios. A high shortage risk for soybean and lower shortage risks for maize and wheat were predicted. Compared with the extent of food security in China under other dietary patterns, the performance advantage of the Chinese dietary pattern was identified, which could mitigate crop shortage risks. The shortage risk of core crops would not be influenced greatly under the different dietary patterns. In the planning years 2025 and 2030, the shortage risks for soybean and rice would be pronounced (i.e., more than 50%), whereas those for maize and wheat would not be prominent.</div></div>","PeriodicalId":342,"journal":{"name":"iScience","volume":"28 7","pages":"Article 112859"},"PeriodicalIF":4.6,"publicationDate":"2025-06-09","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144548894","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"综合性期刊","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

引用次数: 0

Socially integrated female chimpanzees have lower offspring mortality 融入社会的雌性黑猩猩后代的死亡率较低

IF 4.6 2区综合性期刊

iScience Pub Date : 2025-06-09 DOI: 10.1016/j.isci.2025.112863

Joseph T. Feldblum , Kara K. Walker , Margaret A. Stanton , Elizabeth V. Lonsdorf , Deus C. Mjungu , Carson M. Murray , Anne E. Pusey

引用次数: 0