Nature Communications最新文献

{"title":"Author Correction: In vivo imaging in mouse spinal cord reveals that microglia prevent degeneration of injured axons","authors":"Wanjie Wu, Yingzhu He, Yujun Chen, Yiming Fu, Sicong He, Kai Liu, Jianan Y. Qu","doi":"10.1038/s41467-024-55357-w","DOIUrl":"https://doi.org/10.1038/s41467-024-55357-w","url":null,"abstract":"<p>Correction to: <i>Nature Communications</i> https://doi.org/10.1038/s41467-024-53218-0, published online 13 October 2024</p>","PeriodicalId":19066,"journal":{"name":"Nature Communications","volume":"13 1","pages":""},"PeriodicalIF":16.6,"publicationDate":"2024-12-20","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142857866","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":1,"RegionCategory":"综合性期刊","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Role of anthropogenic forcing in Antarctic sea ice variability simulated in climate models","authors":"Yushi Morioka, Liping Zhang, William Cooke, Masami Nonaka, Swadhin K. Behera, Syukuro Manabe","doi":"10.1038/s41467-024-54485-7","DOIUrl":"https://doi.org/10.1038/s41467-024-54485-7","url":null,"abstract":"<p>Antarctic sea ice extent has seen a slight increase over recent decades, yet since 2016, it has undergone a sharp decline, reaching record lows. While the precise impact of anthropogenic forcing remains uncertain, natural fluctuations have been shown to be important for this variability. Our study employs a series of coupled model experiments, revealing that with constant anthropogenic forcing, the primary driver of interannual sea ice variability lies in deep convection within the Southern Ocean, although it is model dependent. However, as anthropogenic forcing increases, the influence of deep convection weakens, and the Southern Annular Mode, an atmospheric intrinsic variability, plays a more significant role in the sea ice fluctuations owing to the shift from a zonal wavenumber-three pattern observed in the historical period. These model results indicate that surface air-sea interaction will play a more prominent role in Antarctic sea ice variability in the future.</p>","PeriodicalId":19066,"journal":{"name":"Nature Communications","volume":"83 1","pages":""},"PeriodicalIF":16.6,"publicationDate":"2024-12-20","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142857871","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":1,"RegionCategory":"综合性期刊","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Nuclear microRNA 9 mediates G-quadruplex formation and 3D genome organization during TGF-β-induced transcription","authors":"Julio Cordero, Guruprasadh Swaminathan, Diana G. Rogel-Ayala, Karla Rubio, Adel Elsherbiny, Samina Mahmood, Witold Szymanski, Johannes Graumann, Thomas Braun, Stefan Günther, Gergana Dobreva, Guillermo Barreto","doi":"10.1038/s41467-024-54740-x","DOIUrl":"https://doi.org/10.1038/s41467-024-54740-x","url":null,"abstract":"<p>The dynamics of three-dimensional (3D) genome organization are essential to transcriptional regulation. While enhancers regulate spatiotemporal gene expression, chromatin looping is a means for enhancer-promoter interactions yielding cell-type-specific gene expression. Further, non-canonical DNA secondary structures, such as G-quadruplexes (G4s), are related to increased gene expression. However, the role of G4s in promoter-distal regulatory elements, such as super-enhancers (SE), and in chromatin looping has remained elusive. Here we show that mature microRNA 9 (<i>miR-9</i>) is enriched at promoters and SE of genes that are inducible by transforming growth factor beta 1 (TGFB1) signaling. Moreover, we find that <i>miR-9</i> is required for formation of G4s, promoter-super-enhancer looping and broad domains of the euchromatin histone mark H3K4me3 at TGFB1-responsive genes. Our study places <i>miR-9</i> in the same functional context with G4s and promoter-enhancer interactions during 3D genome organization and transcriptional activation induced by TGFB1 signaling, a critical signaling pathway in cancer and fibrosis.</p>","PeriodicalId":19066,"journal":{"name":"Nature Communications","volume":"31 1","pages":""},"PeriodicalIF":16.6,"publicationDate":"2024-12-20","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142857868","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":1,"RegionCategory":"综合性期刊","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Author Correction: Breakdown of the scaling relation of anomalous Hall effect in Kondo lattice ferromagnet USbTe","authors":"Hasan Siddiquee, Christopher Broyles, Erica Kotta, Shouzheng Liu, Shiyu Peng, Tai Kong, Byungkyun Kang, Qiang Zhu, Yongbin Lee, Liqin Ke, Hongming Weng, Jonathan D. Denlinger, L. Andrew Wray, Sheng Ran","doi":"10.1038/s41467-024-55351-2","DOIUrl":"https://doi.org/10.1038/s41467-024-55351-2","url":null,"abstract":"<p>Correction to: <i>Nature Communications</i> https://doi.org/10.1038/s41467-023-36221-9, published online 01 February 2023</p>","PeriodicalId":19066,"journal":{"name":"Nature Communications","volume":"22 1","pages":""},"PeriodicalIF":16.6,"publicationDate":"2024-12-20","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142857872","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":1,"RegionCategory":"综合性期刊","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Author Correction: Effectiveness of mRNA COVID-19 vaccine booster doses against Omicron severe outcomes","authors":"Ramandip Grewal, Lena Nguyen, Sarah A. Buchan, Sarah E. Wilson, Sharifa Nasreen, Peter C. Austin, Kevin A. Brown, Deshayne B. Fell, Jonathan B. Gubbay, Kevin L. Schwartz, Mina Tadrous, Kumanan Wilson, Jeffrey C. Kwong","doi":"10.1038/s41467-024-55350-3","DOIUrl":"https://doi.org/10.1038/s41467-024-55350-3","url":null,"abstract":"<p>Correction to: <i>Nature Communications</i> https://doi.org/10.1038/s41467-023-36566-1, published online 07 March 2023</p>","PeriodicalId":19066,"journal":{"name":"Nature Communications","volume":"23 1","pages":""},"PeriodicalIF":16.6,"publicationDate":"2024-12-20","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142857867","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":1,"RegionCategory":"综合性期刊","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Unveiling the power of high-dimensional cytometry data with cyCONDOR","authors":"Charlotte Kröger, Sophie Müller, Jacqueline Leidner, Theresa Kröber, Stefanie Warnat-Herresthal, Jannis Bastian Spintge, Timo Zajac, Anna Neubauer, Aleksej Frolov, Caterina Carraro, Frank Jessen, Simone Puccio, Anna C. Aschenbrenner, Joachim L. Schultze, Tal Pecht, Marc D. Beyer, Lorenzo Bonaguro","doi":"10.1038/s41467-024-55179-w","DOIUrl":"https://doi.org/10.1038/s41467-024-55179-w","url":null,"abstract":"<p>High-dimensional cytometry (HDC) is a powerful technology for studying single-cell phenotypes in complex biological systems. Although technological developments and affordability have made HDC broadly available in recent years, technological advances were not coupled with an adequate development of analytical methods that can take full advantage of the complex data generated. While several analytical platforms and bioinformatics tools have become available for the analysis of HDC data, these are either web-hosted with limited scalability or designed for expert computational biologists, making their use unapproachable for wet lab scientists. Additionally, end-to-end HDC data analysis is further hampered due to missing unified analytical ecosystems, requiring researchers to navigate multiple platforms and software packages to complete the analysis. To bridge this data analysis gap in HDC we develop <i>cyCONDOR</i>, an easy-to-use computational framework covering not only all essential steps of cytometry data analysis but also including an array of downstream functions and tools to expand the biological interpretation of the data. The comprehensive suite of features of <i>cyCONDOR</i>, including guided pre-processing, clustering, dimensionality reduction, and machine learning algorithms, facilitates the seamless integration of <i>cyCONDOR</i> into clinically relevant settings, where scalability and disease classification are paramount for the widespread adoption of HDC in clinical practice. Additionally, the advanced analytical features of <i>cyCONDOR</i>, such as pseudotime analysis and batch integration, provide researchers with the tools to extract deeper insights from their data. We use <i>cyCONDOR</i> on a variety of data from different tissues and technologies demonstrating its versatility to assist the analysis of high-dimensional data from preprocessing to biological interpretation.</p>","PeriodicalId":19066,"journal":{"name":"Nature Communications","volume":"31 1","pages":""},"PeriodicalIF":16.6,"publicationDate":"2024-12-19","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142849004","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":1,"RegionCategory":"综合性期刊","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"The need for adaptability in detection, characterization, and attribution of biosecurity threats","authors":"William Mo, Christopher A. Vaiana, Chris J. Myers","doi":"10.1038/s41467-024-55436-y","DOIUrl":"https://doi.org/10.1038/s41467-024-55436-y","url":null,"abstract":"<p>Modern biotechnology necessitates robust biosecurity protocols to address the risk of engineered biological threats. Current efforts focus on screening DNA and rejecting the synthesis of dangerous elements but face technical and logistical barriers. Screening should integrate into a broader strategy that addresses threats at multiple stages of development and deployment. The success of this approach hinges upon reliable detection, characterization, and attribution of engineered DNA. Recent advances notably aid the potential to both develop threats and analyze them. However, further work is needed to translate developments into biosecurity applications. This work reviews cutting-edge methods for DNA analysis and recommends avenues to improve biosecurity in an adaptable manner.</p>","PeriodicalId":19066,"journal":{"name":"Nature Communications","volume":"60 1","pages":""},"PeriodicalIF":16.6,"publicationDate":"2024-12-19","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142848999","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":1,"RegionCategory":"综合性期刊","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Author Correction: Making sense of eastern Asian Late Quaternary hominin variability","authors":"Christopher J. Bae, Xiujie Wu","doi":"10.1038/s41467-024-55313-8","DOIUrl":"https://doi.org/10.1038/s41467-024-55313-8","url":null,"abstract":"<p>Correction to: <i>Nature Communications</i> https://doi.org/10.1038/s41467-024-53918-7, published online 02 November 2024</p>","PeriodicalId":19066,"journal":{"name":"Nature Communications","volume":"23 1","pages":""},"PeriodicalIF":16.6,"publicationDate":"2024-12-19","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142848811","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":1,"RegionCategory":"综合性期刊","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"A family of NADPH/NADP+ biosensors reveals in vivo dynamics of central redox metabolism across eukaryotes","authors":"Marie Scherschel, Jan-Ole Niemeier, Lianne J. H. C. Jacobs, Markus D. A. Hoffmann, Anika Diederich, Christopher Bell, Pascal Höhne, Sonja Raetz, Johanna B. Kroll, Janina Steinbeck, Sophie Lichtenauer, Jan Multhoff, Jannik Zimmermann, Tanmay Sadhanasatish, R. Alexander Rothemann, Carsten Grashoff, Joris Messens, Emmanuel Ampofo, Matthias W. Laschke, Jan Riemer, Leticia Prates Roma, Markus Schwarzländer, Bruce Morgan","doi":"10.1038/s41467-024-55302-x","DOIUrl":"https://doi.org/10.1038/s41467-024-55302-x","url":null,"abstract":"<p>The NADPH/NADP⁺ redox couple is central to metabolism and redox signalling. NADP redox state is differentially regulated by distinct enzymatic machineries at the subcellular compartment level. Nonetheless, a detailed understanding of subcellular NADP redox dynamics is limited by the availability of appropriate tools. Here, we introduce NAPstars, a family of genetically encoded, fluorescent protein-based NADP redox state biosensors. NAPstars offer real-time, specific measurements, across a broad-range of NADP redox states, with subcellular resolution. NAPstar measurements in yeast, plants, and mammalian cell models, reveal a conserved robustness of cytosolic NADP redox homoeostasis. NAPstars uncover cell cycle-linked NADP redox oscillations in yeast and illumination- and hypoxia-dependent NADP redox changes in plant leaves. By applying NAPstars in combination with selective impairment of the glutathione and thioredoxin antioxidative pathways under acute oxidative challenge, we find an unexpected and conserved role for the glutathione system as the primary mediator of antioxidative electron flux.</p>","PeriodicalId":19066,"journal":{"name":"Nature Communications","volume":"23 1","pages":""},"PeriodicalIF":16.6,"publicationDate":"2024-12-19","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142849000","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":1,"RegionCategory":"综合性期刊","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Author Correction: Octyl itaconate enhances VSVΔ51 oncolytic virotherapy by multitarget inhibition of antiviral and inflammatory pathways","authors":"Naziia Kurmasheva, Aida Said, Boaz Wong, Priscilla Kinderman, Xiaoying Han, Anna H. F. Rahimic, Alena Kress, Madalina E. Carter-Timofte, Emilia Holm, Demi van der Horst, Christoph F. Kollmann, Zhenlong Liu, Chen Wang, Huy-Dung Hoang, Elina Kovalenko, Maria Chrysopoulou, Krishna Sundar Twayana, Rasmus N. Ottosen, Esben B. Svenningsen, Fabio Begnini, Anders E. Kiib, Florian E. H. Kromm, Hauke J. Weiss, Daniele Di Carlo, Michela Muscolini, Maureen Higgins, Mirte van der Heijden, Rozanne Arulanandam, Angelina Bardoul, Tong Tong, Attila Ozsvar, Wen-Hsien Hou, Vivien R. Schack, Christian K. Holm, Yunan Zheng, Melanie Ruzek, Joanna Kalucka, Laureano de la Vega, Walid A. M. Elgaher, Anders R. Korshoej, Rongtuan Lin, John Hiscott, Thomas B. Poulsen, Luke A. O’Neill, Dominic G. Roy, Markus M. Rinschen, Nadine van Montfoort, Jean-Simon Diallo, Henner F. Farin, Tommy Alain, David Olagnier","doi":"10.1038/s41467-024-55044-w","DOIUrl":"https://doi.org/10.1038/s41467-024-55044-w","url":null,"abstract":"<p>Correction to: <i>Nature Communications</i> https://doi.org/10.1038/s41467-024-48422-x, published online 15 May 2024</p>","PeriodicalId":19066,"journal":{"name":"Nature Communications","volume":"8 1","pages":""},"PeriodicalIF":16.6,"publicationDate":"2024-12-19","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142849007","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":1,"RegionCategory":"综合性期刊","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}