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Sequencing of historical plastid genomes reveal exceptional genetic diversity in early domesticated rye plants 历史质体基因组测序揭示了早期驯化黑麦植株的特殊遗传多样性

IF 4.6 2区综合性期刊

iScience Pub Date : 2025-06-06 DOI: 10.1016/j.isci.2025.112716

Jovan Komluski , Sofia Filatova , Frank Schlütz , Benjamin Claaßen , Manfred Rösch , Ben Krause-Kyora , Wiebke Kirleis , Eva H. Stukenbrock

{"title":"Sequencing of historical plastid genomes reveal exceptional genetic diversity in early domesticated rye plants","authors":"Jovan Komluski , Sofia Filatova , Frank Schlütz , Benjamin Claaßen , Manfred Rösch , Ben Krause-Kyora , Wiebke Kirleis , Eva H. Stukenbrock","doi":"10.1016/j.isci.2025.112716","DOIUrl":"10.1016/j.isci.2025.112716","url":null,"abstract":"<div><div>In medieval central Europe, rye was one of the most important agricultural crops. We combined archaeobotanical methods and ancient DNA sequencing of historical rye material to study patterns of genetic diversity across four centuries. We applied archaeobotanical methods to characterize rye material acquired from construction material ranging from the 14th to 18th centuries from different locations in Germany. Next, we extracted DNA to sequence complete chloroplast genomes of six individual samples and compared sequences of historical rye samples to chloroplast genomes of other cereal crops, including a modern rye cultivar. Comparing the aDNA chloroplast samples with modern and non-domesticated rye chloroplast, we show that genetic variation in the historical German rye population was considerably higher. The exceptional difference in levels of genetic variation likely reflects the consequences of late domestication and selective breeding on genetic variation in this important crop in the last few centuries.</div></div>","PeriodicalId":342,"journal":{"name":"iScience","volume":"28 7","pages":"Article 112716"},"PeriodicalIF":4.6,"publicationDate":"2025-06-06","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144501121","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

BMSC exosomes deliver JKAP to restore Th17/Treg balance via AKT/ERK, alleviating rheumatoid arthritis BMSC外泌体传递JKAP，通过AKT/ERK恢复Th17/Treg平衡，缓解类风湿关节炎

IF 4.6 2区综合性期刊

iScience Pub Date : 2025-06-06 DOI: 10.1016/j.isci.2025.112832

Fang-Tian Xu , Yu Ling , Hui-Xian Wei , Lingzhang Meng , Dong Yin , Zhong-Hong Lai , Yu Huang , Xiao Huang , Hai-Ye Li , Qin-Wen Luo , Jian Song , Qiang Tang , Hong-Mian Li

{"title":"BMSC exosomes deliver JKAP to restore Th17/Treg balance via AKT/ERK, alleviating rheumatoid arthritis","authors":"Fang-Tian Xu , Yu Ling , Hui-Xian Wei , Lingzhang Meng , Dong Yin , Zhong-Hong Lai , Yu Huang , Xiao Huang , Hai-Ye Li , Qin-Wen Luo , Jian Song , Qiang Tang , Hong-Mian Li","doi":"10.1016/j.isci.2025.112832","DOIUrl":"10.1016/j.isci.2025.112832","url":null,"abstract":"<div><div>JKAP regulates T cell immunity and inflammation in autoimmune diseases. This study investigates how bone marrow mesenchymal stem cell (BMSC)-derived exosomes deliver JKAP to restore Th17/Treg balance in rheumatoid arthritis (RA). RA CD4<sup>+</sup> T-cells and fibroblast-like synoviocytes (RA-FLS) were treated with BMSC, exosomes, or JKAP-modified exosomes ± AKT/ERK inhibitors. BMSC/exosomes suppressed Th17 and promoted Treg differentiation, effects diminished without exosomes. JKAP knockdown impaired exosome-mediated Th17/Treg regulation and AKT/ERK activation, while overexpression enhanced these effects. JKAP-deficient exosomes increased CD4<sup>+</sup> T cell proliferation and RA-FLS inflammation, reversed by AKT/ERK inhibition. In collagen-induced arthritis mice, exosomes alleviated symptoms and restored Th17/Treg balance, whereas JKAP knockdown exacerbated arthritis and disrupted balance. JKAP-overexpressing exosomes showed opposite effects. Thus, BMSC exosomes mitigate RA by delivering JKAP to restore immune balance via AKT/ERK pathways.</div></div>","PeriodicalId":342,"journal":{"name":"iScience","volume":"28 7","pages":"Article 112832"},"PeriodicalIF":4.6,"publicationDate":"2025-06-06","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144522812","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

Interdisciplinarity at the nexus of biomedical science training: The R3 Center for Innovation in Science Education 生物医学科学培训的交叉学科：R3科学教育创新中心

IF 4.6 2区综合性期刊

iScience Pub Date : 2025-06-05 DOI: 10.1016/j.isci.2025.112735

Ilinca I. Ciubotariu , Tamaki Kobayashi , Crystal J. Neely , Daniel Fiifi Tawia Hagan , David Ewusi-Mensah , David Van Vactor , Elizabeth C. Whipple , Emma Camacho , Gautam Ghosh , Heather M. Lamb , Isaac Owusu-Frimpong , James Alltop , Julia D. Romano , Kristen Kelly , Lindsay Smith Rogers , Lymari Morales , Matthew Seibel , Roshni Rao , Soumia Bekka , William T. Mills IV , Gundula Bosch

{"title":"Interdisciplinarity at the nexus of biomedical science training: The R3 Center for Innovation in Science Education","authors":"Ilinca I. Ciubotariu , Tamaki Kobayashi , Crystal J. Neely , Daniel Fiifi Tawia Hagan , David Ewusi-Mensah , David Van Vactor , Elizabeth C. Whipple , Emma Camacho , Gautam Ghosh , Heather M. Lamb , Isaac Owusu-Frimpong , James Alltop , Julia D. Romano , Kristen Kelly , Lindsay Smith Rogers , Lymari Morales , Matthew Seibel , Roshni Rao , Soumia Bekka , William T. Mills IV , Gundula Bosch","doi":"10.1016/j.isci.2025.112735","DOIUrl":"10.1016/j.isci.2025.112735","url":null,"abstract":"<div><div>The R<sup>3</sup> Center for Innovation in Science Education (R<sup>3</sup>ISE), established at Johns Hopkins Bloomberg School of Public Health, addresses critical gaps in scientific education by instilling the core values of rigorous research, reproducible methods, and scientific responsibility in our students. Through graduate- and professional-level courses, certificate programs, workshops, and open-access resources, R<sup>3</sup>ISE fosters critical thinking, communication, leadership, and other skills essential for scientists.</div><div>In this Backstory piece, faculty, students, alumni, and network partners reflect on their experiences with R<sup>3</sup>ISE, which were highlighted in the past year’s annual symposium. In this symposium, themes such as ethical leadership, translating classroom theory into practice, and strategies to combat misinformation highlighted R<sup>3</sup>ISE sustained efforts and proposed further directions. These reflections exemplify how the R<sup>3</sup>ISE community continues to grow—fostering scientific integrity, resilience, and empathy within a global network committed to excellence and responsibility in the biomedical sciences.</div></div>","PeriodicalId":342,"journal":{"name":"iScience","volume":"28 6","pages":"Article 112735"},"PeriodicalIF":4.6,"publicationDate":"2025-06-05","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144223107","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

Erratum: Rapid hydrolysis rates of thio- and phosphate esters constrain the origin of metabolism to cool, acidic to neutral environments. 更正：快速水解速率的硫和磷酸酯限制了代谢的起源，以凉爽，酸性到中性的环境。

IF 4.6 2区综合性期刊

iScience Pub Date : 2025-06-05 eCollection Date: 2025-06-20 DOI: 10.1016/j.isci.2025.112790

Sebastian A Sanden, Christopher J Butch, Stuart Bartlett, Nathaniel Virgo, Yasuhito Sekine, Shawn Erin McGlynn

引用次数: 0

Microbial responses to ocean deoxygenation: Revisiting the impacts on organic carbon cycling 微生物对海洋脱氧的响应：重新审视对有机碳循环的影响

IF 4.6 2区综合性期刊

iScience Pub Date : 2025-06-05 DOI: 10.1016/j.isci.2025.112826

Quanrui Chen , Kai Tang , Weidong Zhai , Zhuoyi Zhu , Jin-Yu Terence Yang , Zhili He , Meng Li , Shuh-Ji Kao , Jun Yang , Qiang Zheng , Christian Lønborg , Helmuth Thomas , Nianzhi Jiao

{"title":"Microbial responses to ocean deoxygenation: Revisiting the impacts on organic carbon cycling","authors":"Quanrui Chen , Kai Tang , Weidong Zhai , Zhuoyi Zhu , Jin-Yu Terence Yang , Zhili He , Meng Li , Shuh-Ji Kao , Jun Yang , Qiang Zheng , Christian Lønborg , Helmuth Thomas , Nianzhi Jiao","doi":"10.1016/j.isci.2025.112826","DOIUrl":"10.1016/j.isci.2025.112826","url":null,"abstract":"<div><div>Ocean deoxygenation is impacting and will also in the future impact fundamental biogeochemical cycles. This review explores the ecological functions of microbes under hypoxic and anoxic conditions, emphasizing their critical roles in carbon source-sink dynamics. We examine microbial ecosystems in both open-ocean oxygen minimum zones and China’s coastal hypoxic areas, highlighting the microbial contributions to deoxygenation driven processes. We also explore how organic carbon cycling driven by microbial heterotrophic and autotrophic metabolisms change across oxygen gradients. Furthermore, this review elucidates the interconnected cycling of carbon, nitrogen, sulfur, and phosphorus, which regulate organic matter consumption and/or storage under deoxygenation, and alters the elemental composition of organic matter. Our study highlights the importance of microbial processes in regulating carbon cycle under ocean deoxygenation, emphasizing the dual role of hypoxic zones as transient sources and long-term sinks of organic carbon. Lastly, we highlight current challenges in addressing ocean deoxygenation and provide avenues for future research.</div></div>","PeriodicalId":342,"journal":{"name":"iScience","volume":"28 7","pages":"Article 112826"},"PeriodicalIF":4.6,"publicationDate":"2025-06-05","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144470790","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

Photoconverted cells allow rapid assessment of vaccine adjuvant potency in mice 光转化细胞允许在小鼠中快速评估疫苗佐剂效力

IF 4.6 2区综合性期刊

iScience Pub Date : 2025-06-05 DOI: 10.1016/j.isci.2025.112774

Yiwei Zhong , Mingyue Chen , Hongzhe Lin , Cheng Zu , Yue He , Bin Wang

引用次数: 0

Olink proteomics reveals TNFRSF9 as a biomarker for abdominal aortic aneurysms 链接蛋白质组学显示TNFRSF9是腹主动脉瘤的生物标志物

IF 4.6 2区综合性期刊

iScience Pub Date : 2025-06-05 DOI: 10.1016/j.isci.2025.112828

Runze Chang , Heng Wang , Chuanlong Lu , Jinshan Chen , Yaling Li , Maolin Qiao , Siqi Gao , Lizheng Li , Keyi Fan , Ruijing Zhang , Honglin Dong

{"title":"Olink proteomics reveals TNFRSF9 as a biomarker for abdominal aortic aneurysms","authors":"Runze Chang , Heng Wang , Chuanlong Lu , Jinshan Chen , Yaling Li , Maolin Qiao , Siqi Gao , Lizheng Li , Keyi Fan , Ruijing Zhang , Honglin Dong","doi":"10.1016/j.isci.2025.112828","DOIUrl":"10.1016/j.isci.2025.112828","url":null,"abstract":"<div><div>Abdominal aortic aneurysm (AAA) is a serious cardiovascular disease associated with chronic inflammation. The purpose of this study was to use the Olink proteomics to reveal serum inflammatory markers in AAA. We examined the expression levels of 92 inflammation-related proteins in patients with AAA (<em>n</em> = 18) and healthy individuals (<em>n</em> = 10) using the Olink proximity extension assay (PEA) inflammatory plate. Olink proteomics identified 38 differential proteins. Combined analysis of Olink proteomics and <span><span>GSE183464</span><svg><path></path></svg></span> showed interleukin-6 (IL-6) and tumor necrosis factor receptor superfamily member 9 (TNFRSF9) were upregulated at both gene and protein levels in AAA patients. The ELISA results were consistent with the Olink proteomics results, and the receiver operating characteristic (ROC) curve analysis revealed that the binding of TNFRSF9 and IL-6 has high diagnostic value (Olink AUC = 0.9056; ELISA AUC = 0.950). Subsequently, elevated TNFRSF9 expression in AAA was confirmed by animal models, suggesting that TNFRSF9 may serve as a potential biomarker for AAA.</div></div>","PeriodicalId":342,"journal":{"name":"iScience","volume":"28 7","pages":"Article 112828"},"PeriodicalIF":4.6,"publicationDate":"2025-06-05","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144297195","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

A framework for assessing and managing dependencies in corporate transition plans 用于评估和管理公司过渡计划中的依赖关系的框架

IF 4.6 2区综合性期刊

iScience Pub Date : 2025-06-05 DOI: 10.1016/j.isci.2025.112811

Adrien Rose , Gireesh Shrimali , Krista Halttunen

引用次数: 0

Proteome-wide prediction of the mode of inheritance and molecular mechanisms underlying genetic diseases using structural interactomics 利用结构相互作用组学预测遗传模式和遗传疾病的分子机制

IF 4.6 2区综合性期刊

iScience Pub Date : 2025-06-04 DOI: 10.1016/j.isci.2025.112812

Ali Saadat , Jacques Fellay

引用次数: 0

Chemical and mechanical patterning of tortoise skin scales occur in different regions of the head. 乌龟皮肤鳞片的化学和机械图案发生在头部的不同区域。

IF 4.6 2区综合性期刊

iScience Pub Date : 2025-06-04 eCollection Date: 2025-06-20 DOI: 10.1016/j.isci.2025.112684

Rory L Cooper, Ebrahim Jahanbakhsh, Michel C Milinkovitch

{"title":"Chemical and mechanical patterning of tortoise skin scales occur in different regions of the head.","authors":"Rory L Cooper, Ebrahim Jahanbakhsh, Michel C Milinkovitch","doi":"10.1016/j.isci.2025.112684","DOIUrl":"10.1016/j.isci.2025.112684","url":null,"abstract":"<p><p>Vertebrate skin appendages are diverse micro-organs such as scales, feathers, and hair. These units typically develop from placodes, whose spatial patterning involves conserved chemical reaction-diffusion dynamics. Crocodile head scales are a spectacular exception to this paradigm, as they instead arise from a mechanically dominated process of compressive folding driven by constrained skin growth. Here, we reveal that chemical versus mechanical processes pattern tortoise scales in different regions of their head. Indeed, we show that placode-derived scales emerge across the peripheral head surfaces while remaining absent from the central dorsal region where scales subsequently form through a mechanical folding process. Using light sheet microscopy, we build a three-dimensional mechanical model that qualitatively recapitulates the diversity of scale patterns observed in this central head region in different tortoise species. Overall, our analyses indicate that mechanical head-scale patterning likely arose before the divergence between Testudinata and Archosauria, and was subsequently lost in birds.</p>","PeriodicalId":342,"journal":{"name":"iScience","volume":"28 6","pages":"112684"},"PeriodicalIF":4.6,"publicationDate":"2025-06-04","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC12225933/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144558706","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"综合性期刊","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

引用次数: 0