Pub Date : 2025-12-02DOI: 10.1016/j.isci.2025.114071
Klaus Spiess
This immersive performance explores speech as a biological environment for oral microbiota, merging art and science to promote ecological awareness. Using scientific data, recursive echo, and tactile feedback, it encourages visitors to engage directly with microbial processes through vocalizations and vibrations, blurring boundaries between human and non-human elements. Here an art-science collaboration turns laboratory research into a public, sensory experience that supports reflection on our shared biological environments, fostering sensory, evocative, and scientific engagement with microbiome ecology.
{"title":"Sensing the good vibes: Audience vocal engagement with the oral microbiota","authors":"Klaus Spiess","doi":"10.1016/j.isci.2025.114071","DOIUrl":"10.1016/j.isci.2025.114071","url":null,"abstract":"<div><div>This immersive performance explores speech as a biological environment for oral microbiota, merging art and science to promote ecological awareness. Using scientific data, recursive echo, and tactile feedback, it encourages visitors to engage directly with microbial processes through vocalizations and vibrations, blurring boundaries between human and non-human elements. Here an art-science collaboration turns laboratory research into a public, sensory experience that supports reflection on our shared biological environments, fostering sensory, evocative, and scientific engagement with microbiome ecology.</div></div>","PeriodicalId":342,"journal":{"name":"iScience","volume":"28 12","pages":"Article 114071"},"PeriodicalIF":4.1,"publicationDate":"2025-12-02","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145681681","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}
Pub Date : 2025-12-02DOI: 10.1016/j.isci.2025.114312
Yibin Zhang , Nan Qiao , Yihang Jiang , Miaozhuang Fan , Wenguang Zhang , Yue Jiao , Zhengzheng Li , Gang Feng , Wing-Cheung Law , Zhourui Xu , Gaixia Xu
Luminogens with aggregation-induced emission (AIEgens) have attracted increasing attention for biomedical applications, prompting concerns regarding their potential toxicity. Although some studies have reported the in vivo toxicity of AIEgens, their reproductive effects remain insufficiently characterized. In this study, we investigated the reproductive toxicity of a representative AIEgen, TPA-BT, encapsulated into nanoparticles (NPs), with a particular focus on ovarian function in mice. Oocyte maturation rates in vitro, body weight, and organ coefficients were evaluated following TPA-BT NPs exposure. Furthermore, oocyte apoptosis and serum hormone levels were examined. TPA-BT NPs significantly reduced oocyte maturation in a concentration-dependent manner. In vivo, high concentrations induced ovarian cell apoptosis, suppressed estrogen receptor (ERα and ERβ) expression, and disrupted anti-Müllerian hormone secretion, ultimately impairing reproductive function. These findings provide critical insights into the reproductive toxicity of AIEgens and establish a foundation for further mechanistic investigations to ensure their safe application in the biomedical field.
{"title":"The reproductive toxicity of aggregation-induced emission nanoparticles on mouse ovarian function","authors":"Yibin Zhang , Nan Qiao , Yihang Jiang , Miaozhuang Fan , Wenguang Zhang , Yue Jiao , Zhengzheng Li , Gang Feng , Wing-Cheung Law , Zhourui Xu , Gaixia Xu","doi":"10.1016/j.isci.2025.114312","DOIUrl":"10.1016/j.isci.2025.114312","url":null,"abstract":"<div><div>Luminogens with aggregation-induced emission (AIEgens) have attracted increasing attention for biomedical applications, prompting concerns regarding their potential toxicity. Although some studies have reported the <em>in vivo</em> toxicity of AIEgens, their reproductive effects remain insufficiently characterized. In this study, we investigated the reproductive toxicity of a representative AIEgen, TPA-BT, encapsulated into nanoparticles (NPs), with a particular focus on ovarian function in mice. Oocyte maturation rates <em>in vitro</em>, body weight, and organ coefficients were evaluated following TPA-BT NPs exposure. Furthermore, oocyte apoptosis and serum hormone levels were examined. TPA-BT NPs significantly reduced oocyte maturation in a concentration-dependent manner. <em>In vivo</em>, high concentrations induced ovarian cell apoptosis, suppressed estrogen receptor (ERα and ERβ) expression, and disrupted anti-Müllerian hormone secretion, ultimately impairing reproductive function. These findings provide critical insights into the reproductive toxicity of AIEgens and establish a foundation for further mechanistic investigations to ensure their safe application in the biomedical field.</div></div>","PeriodicalId":342,"journal":{"name":"iScience","volume":"29 1","pages":"Article 114312"},"PeriodicalIF":4.1,"publicationDate":"2025-12-02","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145735648","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}
Pub Date : 2025-12-02DOI: 10.1016/j.isci.2025.114308
Harpreet Kaur , Julie A. Talbert , Syed Azmal Ali , M. Kay Washington , Daniel P. Barry , Keith T. Wilson , Richard M. Peek Jr. , Sari A. Acra , Steven D. Townsend , Fang Yan
Human milk oligosaccharides (HMOs) benefit growth in infancy. However, mechanisms underlying regulation of host cellular responses by HMOs remain largely unknown. We report that 2′-fucosyllactose (2′-FL), an abundant oligosaccharide in human milk, interacts with a metalloproteinase, ADAM17, on the cell surface and stimulates its catalytic activity for releasing membrane-bound heparin-binding (HB)-EGF, leading to transactivation of epidermal growth factor receptor (EGFR) in intestinal epithelial cells (IECs). Further, this direct effect of 2′-FL on IECs contributed to preserving tight junctions and attenuating apoptosis in response to proinflammatory cytokine and oxidative stress. Remarkably, 2′-FL treatment prevented colitis and maintained intestinal epithelial integrity during colonic injury and colitis in wild-type adult mice, which was mitigated in mice with deletion of EGFR in IECs. These findings reveal a molecular mechanism of the direct protection of intestinal epithelium by 2′-FL and discern this effect as an approach for the prevention of intestinal inflammation beyond the early life.
{"title":"2′-Fucosyllactose transactivates EGF receptor in intestinal epithelial cells for prevention of colitis in adulthood","authors":"Harpreet Kaur , Julie A. Talbert , Syed Azmal Ali , M. Kay Washington , Daniel P. Barry , Keith T. Wilson , Richard M. Peek Jr. , Sari A. Acra , Steven D. Townsend , Fang Yan","doi":"10.1016/j.isci.2025.114308","DOIUrl":"10.1016/j.isci.2025.114308","url":null,"abstract":"<div><div>Human milk oligosaccharides (HMOs) benefit growth in infancy. However, mechanisms underlying regulation of host cellular responses by HMOs remain largely unknown. We report that 2′-fucosyllactose (2′-FL), an abundant oligosaccharide in human milk, interacts with a metalloproteinase, ADAM17, on the cell surface and stimulates its catalytic activity for releasing membrane-bound heparin-binding (HB)-EGF, leading to transactivation of epidermal growth factor receptor (EGFR) in intestinal epithelial cells (IECs). Further, this direct effect of 2′-FL on IECs contributed to preserving tight junctions and attenuating apoptosis in response to proinflammatory cytokine and oxidative stress. Remarkably, 2′-FL treatment prevented colitis and maintained intestinal epithelial integrity during colonic injury and colitis in wild-type adult mice, which was mitigated in mice with deletion of EGFR in IECs. These findings reveal a molecular mechanism of the direct protection of intestinal epithelium by 2′-FL and discern this effect as an approach for the prevention of intestinal inflammation beyond the early life.</div></div>","PeriodicalId":342,"journal":{"name":"iScience","volume":"29 1","pages":"Article 114308"},"PeriodicalIF":4.1,"publicationDate":"2025-12-02","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145736039","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}
The accurate identification of individuals from functional connectomes (FCs) is central to individualized neuro/psychiatric assessment. Traditional metrics (Pearson and Euclidean) fail to capture the non-Euclidean geometry of FCs, and geodesic metrics (affine-invariant and Log-Euclidean) require task- and scale-specific regularization and degrade in high-dimensional settings. To address these challenges, we propose the Alpha-Z Bures-Wasserstein divergence, a geometry-aware divergence for FC comparison that operates effectively without meticulous parameter tuning. Across Human Connectome Project tasks, scan lengths, and spatial resolutions, we benchmark Alpha-Z against classical and state-of-the-art manifold-based distances and quantify how varying regularization influences geodesic performance. Alpha-Z yields consistently higher identification rates, with pronounced advantages in rank-deficient regimes, and preserves performance across parcellations and conditions. We further verify generalization across resting-state and task fMRI under multiple parcellation schemes. These results position Alpha-Z as a reliable, robust, and scalable framework for functional connectivity analysis, improving sensitivity to cognitive and behavioral patterns and offering strong potential for individualized clinical neuroscience.
{"title":"Divergence unveils further distinct phenotypic traits of human brain connectomics fingerprint","authors":"Md Kaosar Uddin , Nghi Nguyen , Huajun Huang , Duy Duong-Tran , Jingyi Zheng","doi":"10.1016/j.isci.2025.114282","DOIUrl":"10.1016/j.isci.2025.114282","url":null,"abstract":"<div><div>The accurate identification of individuals from functional connectomes (FCs) is central to individualized neuro/psychiatric assessment. Traditional metrics (Pearson and Euclidean) fail to capture the non-Euclidean geometry of FCs, and geodesic metrics (affine-invariant and Log-Euclidean) require task- and scale-specific regularization and degrade in high-dimensional settings. To address these challenges, we propose the Alpha-Z Bures-Wasserstein divergence, a geometry-aware divergence for FC comparison that operates effectively without meticulous parameter tuning. Across Human Connectome Project tasks, scan lengths, and spatial resolutions, we benchmark Alpha-Z against classical and state-of-the-art manifold-based distances and quantify how varying regularization influences geodesic performance. Alpha-Z yields consistently higher identification rates, with pronounced advantages in rank-deficient regimes, and preserves performance across parcellations and conditions. We further verify generalization across resting-state and task fMRI under multiple parcellation schemes. These results position Alpha-Z as a reliable, robust, and scalable framework for functional connectivity analysis, improving sensitivity to cognitive and behavioral patterns and offering strong potential for individualized clinical neuroscience.</div></div>","PeriodicalId":342,"journal":{"name":"iScience","volume":"29 1","pages":"Article 114282"},"PeriodicalIF":4.1,"publicationDate":"2025-12-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145735647","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}
Pub Date : 2025-12-01DOI: 10.1016/j.isci.2025.114275
Jiangchen Yao , Dingfa Deng , Han Yu , Junxia Duan , Shuyun Xia , Xunyu Cao , Yafeng Xie , Bibo Xie , Peng Ling , Feijun Zhao
As the reliability of nontreponemal tests for evaluating syphilis treatment efficacy is increasingly questioned, we propose an optimized approach using Treponema pallidum (Tp) antigens (Tp0134, Tp0768, Tp0971, Tp0462, and Tp92) combined with a machine learning (ML) model. Analysis of 509 serum samples (including paired pre- and post-treatment samples) employed an established ELISA assay to dynamically monitor antibody changes. Results demonstrated that post-treatment antibody reduction for potential infection-stage-dependent antigens (pIDAs) (especially Tp0134 and Tp0768) was markedly higher than for the non-infection-stage-dependent antigen Tp92 and traditional methods. Utilizing nested cross-validation to train an array of ML models, ultimately chosen random forest model (AUC = 0.815) demonstrated enhanced efficacy in accurately distinguishing between infection and cure. Specifically, Tp0768, Tp92, and Tp0134 were identified as the pivotal features. Combining Tp antigens with ML provides a more accurate and dynamic tool for treatment efficacy assessment, enabling a more effective evaluation of syphilis treatment outcomes in the future.
{"title":"A pilot study: Incorporating Treponema pallidum antigens into machine learning models for accurate syphilis treatment outcome assessment","authors":"Jiangchen Yao , Dingfa Deng , Han Yu , Junxia Duan , Shuyun Xia , Xunyu Cao , Yafeng Xie , Bibo Xie , Peng Ling , Feijun Zhao","doi":"10.1016/j.isci.2025.114275","DOIUrl":"10.1016/j.isci.2025.114275","url":null,"abstract":"<div><div>As the reliability of nontreponemal tests for evaluating syphilis treatment efficacy is increasingly questioned, we propose an optimized approach using <em>Treponema pallidum</em> (Tp) antigens (Tp0134, Tp0768, Tp0971, Tp0462, and Tp92) combined with a machine learning (ML) model. Analysis of 509 serum samples (including paired pre- and post-treatment samples) employed an established ELISA assay to dynamically monitor antibody changes. Results demonstrated that post-treatment antibody reduction for potential infection-stage-dependent antigens (pIDAs) (especially Tp0134 and Tp0768) was markedly higher than for the non-infection-stage-dependent antigen Tp92 and traditional methods. Utilizing nested cross-validation to train an array of ML models, ultimately chosen random forest model (AUC = 0.815) demonstrated enhanced efficacy in accurately distinguishing between infection and cure. Specifically, Tp0768, Tp92, and Tp0134 were identified as the pivotal features. Combining Tp antigens with ML provides a more accurate and dynamic tool for treatment efficacy assessment, enabling a more effective evaluation of syphilis treatment outcomes in the future.</div></div>","PeriodicalId":342,"journal":{"name":"iScience","volume":"29 1","pages":"Article 114275"},"PeriodicalIF":4.1,"publicationDate":"2025-12-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145735576","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}
Pub Date : 2025-12-01DOI: 10.1016/j.isci.2025.114295
Hongjuan Zhang , Haibing Liu , Rongkai Chen
Innovation networks drive technological progress, yet their multilayer structures remain poorly understood in digital economy vulnerability contexts. This study develops a comprehensive framework for assessing multilayer innovation network resilience, analyzing interdependencies and disruption scenarios using China’s digital economy as a representative empirical context. We construct coupled multilayer networks implementing four integrated attack strategies to identify cascading vulnerability mechanisms. Results reveal asymmetric patterns: collaboration networks show significant fragility to targeted attacks, while knowledge networks demonstrate higher resilience, especially during mature stages. Cascade failure analysis establishes that knowledge network disruptions propagate severe ecosystem-wide effects, whereas collaboration network perturbations generate limited cross-layer impacts. This asymmetry advances multilayer innovation network theory and provides practical insights for vulnerability assessment. The framework indicates that protecting critical technological knowledge should prioritize over maintaining collaborative arrangements when resources are limited, as knowledge networks constitute the essential integrative mechanism within innovation systems.
{"title":"Multilayer innovation network resilience: A framework for digital economy vulnerability assessment","authors":"Hongjuan Zhang , Haibing Liu , Rongkai Chen","doi":"10.1016/j.isci.2025.114295","DOIUrl":"10.1016/j.isci.2025.114295","url":null,"abstract":"<div><div>Innovation networks drive technological progress, yet their multilayer structures remain poorly understood in digital economy vulnerability contexts. This study develops a comprehensive framework for assessing multilayer innovation network resilience, analyzing interdependencies and disruption scenarios using China’s digital economy as a representative empirical context. We construct coupled multilayer networks implementing four integrated attack strategies to identify cascading vulnerability mechanisms. Results reveal asymmetric patterns: collaboration networks show significant fragility to targeted attacks, while knowledge networks demonstrate higher resilience, especially during mature stages. Cascade failure analysis establishes that knowledge network disruptions propagate severe ecosystem-wide effects, whereas collaboration network perturbations generate limited cross-layer impacts. This asymmetry advances multilayer innovation network theory and provides practical insights for vulnerability assessment. The framework indicates that protecting critical technological knowledge should prioritize over maintaining collaborative arrangements when resources are limited, as knowledge networks constitute the essential integrative mechanism within innovation systems.</div></div>","PeriodicalId":342,"journal":{"name":"iScience","volume":"29 1","pages":"Article 114295"},"PeriodicalIF":4.1,"publicationDate":"2025-12-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145736037","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}
Spatial patterning in multicellular organisms is commonly explained by Turing-type reaction-diffusion systems, but the maturation of diffusible inhibitors remains poorly understood. In the cyanobacterium Nostoc PCC 7120, nitrogen deprivation triggers a pattern of nitrogen-fixing heterocysts regulated by HetR and inhibitory peptides, including PatX. We uncover the post-translational mechanism controlling PatX maturation, demonstrating its export and subsequent processing by the peptidase PatP. We identify HRGTGR, a PatX-derived hexapeptide, as the direct inhibitor of HetR, linking maturation to suppressed differentiation. Genomic analyses reveal that patP is ancient and conserved across all cyanobacteria, predating the patX-hetR module found only in filamentous clades. We therefore propose that this ancient peptidase was co-opted to process a new ligand, transforming a proteolytic event into a spatial patterning mechanism. This repurposing parallels eukaryotic signaling, underscoring a universal principle in the emergence of multicellular organization and providing a model for how complex patterns evolve from “simple” components.
{"title":"Co-option of an ancestral peptidase controls developmental patterning in multicellular cyanobacteria","authors":"Xiaomei Xu , Anaïs Scholivet , Stéphanie Champ , Matthieu Bergé , Zulihumaer Yeerkenjiang , Jonas Desjardins , Yann Denis , Badreddine Douzi , Deborah Byrne , Emmanuel Talla , Amel Latifi","doi":"10.1016/j.isci.2025.114265","DOIUrl":"10.1016/j.isci.2025.114265","url":null,"abstract":"<div><div>Spatial patterning in multicellular organisms is commonly explained by Turing-type reaction-diffusion systems, but the maturation of diffusible inhibitors remains poorly understood. In the cyanobacterium <em>Nostoc</em> PCC 7120, nitrogen deprivation triggers a pattern of nitrogen-fixing heterocysts regulated by HetR and inhibitory peptides, including PatX. We uncover the post-translational mechanism controlling PatX maturation, demonstrating its export and subsequent processing by the peptidase PatP. We identify HRGTGR, a PatX-derived hexapeptide, as the direct inhibitor of HetR, linking maturation to suppressed differentiation. Genomic analyses reveal that <em>patP</em> is ancient and conserved across all cyanobacteria, predating the <em>patX-hetR</em> module found only in filamentous clades. We therefore propose that this ancient peptidase was co-opted to process a new ligand, transforming a proteolytic event into a spatial patterning mechanism. This repurposing parallels eukaryotic signaling, underscoring a universal principle in the emergence of multicellular organization and providing a model for how complex patterns evolve from “simple” components.</div></div>","PeriodicalId":342,"journal":{"name":"iScience","volume":"29 1","pages":"Article 114265"},"PeriodicalIF":4.1,"publicationDate":"2025-11-28","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145712199","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}
Pub Date : 2025-11-28DOI: 10.1016/j.isci.2025.114273
Chiara De Gregorio , Adriano R. Lameira
Rhythmic pulse, the division of a beat into subordinate patterns, is the backbone of music. Across the world’s musical traditions, the division of the primary beat into two equal parts – “double meter” – represents a prototypical pulse, also found in singing nonhuman primates. The last great ape common ancestor was, however, a non-singing species. How rhythmic pulse evolved in human song and music is, thus, enigmatic. Here, we analyze wild male orangutan long calls, which are structurally isochronous (i.e., with a steady of 1:1 rhythm). Males divided the primary rhythm into 1:2 and 2:1 subordinate patterns and did so by two distinct mechanisms: tempo changes as used by other primates and voiced in-exhale alternations as still used today by some human song traditions. Findings confirm double-meter in a non-singing great ape and suggest the two-phase cycle of the phonatory-respiratory system may have been leveraged for the evolution of human song and music.
{"title":"Twice times two: Dual mechanism for double rhythmic meter in orangutans and the evolution of human song","authors":"Chiara De Gregorio , Adriano R. Lameira","doi":"10.1016/j.isci.2025.114273","DOIUrl":"10.1016/j.isci.2025.114273","url":null,"abstract":"<div><div>Rhythmic pulse, the division of a beat into subordinate patterns, is the backbone of music. Across the world’s musical traditions, the division of the primary beat into two equal parts – “double meter” – represents a prototypical pulse, also found in singing nonhuman primates. The last great ape common ancestor was, however, a non-singing species. How rhythmic pulse evolved in human song and music is, thus, enigmatic. Here, we analyze wild male orangutan long calls, which are structurally isochronous (i.e., with a steady of 1:1 rhythm). Males divided the primary rhythm into 1:2 and 2:1 subordinate patterns and did so by two distinct mechanisms: tempo changes as used by other primates and voiced in-exhale alternations as still used today by some human song traditions. Findings confirm double-meter in a non-singing great ape and suggest the two-phase cycle of the phonatory-respiratory system may have been leveraged for the evolution of human song and music.</div></div>","PeriodicalId":342,"journal":{"name":"iScience","volume":"29 1","pages":"Article 114273"},"PeriodicalIF":4.1,"publicationDate":"2025-11-28","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145736038","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}
Pub Date : 2025-11-28DOI: 10.1016/j.isci.2025.114261
Sally W. Yousief , Nader Abdelmalek , Martin S. Bojer , Yibing Ma , Priscila R. Guerra , Sajid Nisar , John E. Olsen , Bianca Paglietti
Staphylococcus aureus must dynamically rewire its metabolism to persist within distinct host tissues during infection. We applied in vivo transposon-directed insertion site sequencing (TraDIS) in murine models of skin, kidney, and spleen infections to define tissue-specific fitness landscapes for the epidemic USA300 lineage. We identified 46, 76, and 69 fitness genes in the skin, kidney, and spleen, respectively. The core gluconeogenesis gene fbp was essential across all tissues, whereas pckA and gapB showed organ-specific essentiality in the kidney and spleen. Skin infection required oxidative stress and DNA repair genes (ahpC, ahpF, dps, uvrC, and xseA), consistent with elevated genotoxic pressure. In contrast, kidney and spleen relied on branched-chain amino acid catabolism (bkdAB), lipid metabolism (SAUSA300_0355), and putative polyamine biosynthesis (SAUSA300_0458). Competition assays in vivo and under oxidative (H2O2) and gluconeogenic (M9) conditions validated these tissue-specific dependencies. These results reveal how S. aureus remodels metabolic networks and identifies context-specific vulnerabilities for therapeutic targeting.
{"title":"Genome-wide identification of tissue-specific fitness genes in murine models of Staphylococcus aureus infection","authors":"Sally W. Yousief , Nader Abdelmalek , Martin S. Bojer , Yibing Ma , Priscila R. Guerra , Sajid Nisar , John E. Olsen , Bianca Paglietti","doi":"10.1016/j.isci.2025.114261","DOIUrl":"10.1016/j.isci.2025.114261","url":null,"abstract":"<div><div><em>Staphylococcus aureus</em> must dynamically rewire its metabolism to persist within distinct host tissues during infection. We applied <em>in vivo</em> transposon-directed insertion site sequencing (TraDIS) in murine models of skin, kidney, and spleen infections to define tissue-specific fitness landscapes for the epidemic USA300 lineage. We identified 46, 76, and 69 fitness genes in the skin, kidney, and spleen, respectively. The core gluconeogenesis gene <em>fbp</em> was essential across all tissues, whereas <em>pckA</em> and <em>gapB</em> showed organ-specific essentiality in the kidney and spleen. Skin infection required oxidative stress and DNA repair genes (<em>ahpC</em>, <em>ahpF</em>, <em>dps</em>, <em>uvrC</em>, and <em>xseA</em>), consistent with elevated genotoxic pressure. In contrast, kidney and spleen relied on branched-chain amino acid catabolism (<em>bkdAB</em>), lipid metabolism (<em>SAUSA300_0355</em>), and putative polyamine biosynthesis (<em>SAUSA300_0458</em>). Competition assays <em>in vivo</em> and under oxidative (H<sub>2</sub>O<sub>2</sub>) and gluconeogenic (M9) conditions validated these tissue-specific dependencies. These results reveal how <em>S. aureus</em> remodels metabolic networks and identifies context-specific vulnerabilities for therapeutic targeting.</div></div>","PeriodicalId":342,"journal":{"name":"iScience","volume":"29 1","pages":"Article 114261"},"PeriodicalIF":4.1,"publicationDate":"2025-11-28","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145735578","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}
Pub Date : 2025-11-28DOI: 10.1016/j.isci.2025.114286
Enhui Shen , Yifan Yu , Xiaoya Ma , Zhicheng Shen , Yuxuan Ye
Tracking parental genome contributions in segregating populations is crucial for accelerating genetic gain in plant breeding. We introduce GCCVision (Genome Contribution Calculator and Visualizer), an integrated bioinformatics toolkit to simplify this process. GCCVision uses an efficient Python-based backend and a user-friendly web-based frontend to analyze Variant Call Format (VCF) files from biparental crosses. The software identifies informative single-nucleotide polymorphisms (SNPs), calculates parental contribution rates, and generates clear, customizable graphical genotype maps where chromosome segments are color-coded by parental origin. By providing clear visualizations of genomic composition, GCCVision assists breeders in selection decisions for backcrossing, F2 analysis, quality control of hybrid seeds, and other breeding programs. This streamlined workflow shortens breeding cycles and accelerates the development of improved crop varieties.
{"title":"GCCVision: An integrated toolkit for calculating and visualizing parental genome contribution in breeding populations","authors":"Enhui Shen , Yifan Yu , Xiaoya Ma , Zhicheng Shen , Yuxuan Ye","doi":"10.1016/j.isci.2025.114286","DOIUrl":"10.1016/j.isci.2025.114286","url":null,"abstract":"<div><div>Tracking parental genome contributions in segregating populations is crucial for accelerating genetic gain in plant breeding. We introduce GCCVision (Genome Contribution Calculator and Visualizer), an integrated bioinformatics toolkit to simplify this process. GCCVision uses an efficient Python-based backend and a user-friendly web-based frontend to analyze Variant Call Format (VCF) files from biparental crosses. The software identifies informative single-nucleotide polymorphisms (SNPs), calculates parental contribution rates, and generates clear, customizable graphical genotype maps where chromosome segments are color-coded by parental origin. By providing clear visualizations of genomic composition, GCCVision assists breeders in selection decisions for backcrossing, F<sub>2</sub> analysis, quality control of hybrid seeds, and other breeding programs. This streamlined workflow shortens breeding cycles and accelerates the development of improved crop varieties.</div></div>","PeriodicalId":342,"journal":{"name":"iScience","volume":"29 1","pages":"Article 114286"},"PeriodicalIF":4.1,"publicationDate":"2025-11-28","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145735582","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}
扫码关注我们
求助内容：
应助结果提醒方式：
京公网安备 11010802042870号