Nature MethodsPub Date : 2025-08-25DOI: 10.1038/s41592-025-02777-1
Teun A P M Huijben, Ashley G Anderson, Andrew Sweet, Erin Hoops, Connor Larsen, Kyle Awayan, Jordão Bragantini, Merlin Lange, Chi-Li Chiu, Loïc A Royer
{"title":"inTRACKtive: a web-based tool for interactive cell tracking visualization.","authors":"Teun A P M Huijben, Ashley G Anderson, Andrew Sweet, Erin Hoops, Connor Larsen, Kyle Awayan, Jordão Bragantini, Merlin Lange, Chi-Li Chiu, Loïc A Royer","doi":"10.1038/s41592-025-02777-1","DOIUrl":"https://doi.org/10.1038/s41592-025-02777-1","url":null,"abstract":"","PeriodicalId":18981,"journal":{"name":"Nature Methods","volume":" ","pages":""},"PeriodicalIF":32.1,"publicationDate":"2025-08-25","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144962096","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":1,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
{"title":"A versatile miniature two-photon microscope enabling multicolor deep-brain imaging","authors":"Runlong Wu, Chunzhu Zhao, Shan Qiu, Yufei Zhu, Lifeng Zhang, Qiang Fu, Yanhui Hu, Dakun Wu, Fei Yu, Fangxu Zhou, Haipeng Huang, Yunfeng Zhang, Xianhua Wang, Aimin Wang, Heping Cheng","doi":"10.1038/s41592-025-02780-6","DOIUrl":"10.1038/s41592-025-02780-6","url":null,"abstract":"Here we present FHIRM-TPM 3.0, a 2.6 g miniature two-photon microscope capable of multicolor deep-brain imaging in freely behaving mice. The system was integrated with a broadband anti-resonant hollow-core fiber featuring low transmission loss, minimal dispersion from 700 nm to 1,060 nm and high tolerance of laser power. By correcting chromatic and spherical aberrations and optimizing the fluorescence collection aperture, we achieved cortical neuronal imaging at depths exceeding 820 μm and, using a GRIN lens, hippocampal Ca2+ imaging at single dendritic spine resolution. Moreover, we engineered three interchangeable parfocal objectives, allowing for a tenfold scalable field of view up to 1 × 0.8 mm², with lateral resolutions ranging from 0.68 μm to 1.46 μm. By multicolor imaging at excitation wavelengths of 780 nm, 920 nm and 1,030 nm, we investigated mitochondrial and cytosolic Ca2+ activities relative to the deposition of amyloid plaques in the cortex of awake APP/PS1 transgenic mice. Thus, FHIRM-TPM 3.0 provides a versatile imaging system suitable for diverse brain imaging scenarios. FHIRM-TPM 3.0 is a miniature microscope for multicolor two-photon imaging in freely moving mice. In addition to the multicolor imaging abilities achieved with the help of a specially designed optical fiber, the microscope is also compatible with multiple lenses for a choice of field of view and resolution.","PeriodicalId":18981,"journal":{"name":"Nature Methods","volume":"22 9","pages":"1935-1943"},"PeriodicalIF":32.1,"publicationDate":"2025-08-21","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144962093","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":1,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Nature MethodsPub Date : 2025-08-21DOI: 10.1038/s41592-025-02779-z
{"title":"A miniature two-photon microscope detects multiple signals deep in the brains of moving mice","authors":"","doi":"10.1038/s41592-025-02779-z","DOIUrl":"10.1038/s41592-025-02779-z","url":null,"abstract":"A lightweight miniature two-photon microscope features multi-wavelength excitation, correction of aberrations, and interchangeable objectives for scalable fields of view. It enables multicolor, deep-brain and scalable neural imaging in freely moving mice.","PeriodicalId":18981,"journal":{"name":"Nature Methods","volume":"22 9","pages":"1772-1773"},"PeriodicalIF":32.1,"publicationDate":"2025-08-21","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144961828","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":1,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Nature MethodsPub Date : 2025-08-18DOI: 10.1038/s41592-025-02801-4
Vivien Marx
{"title":"Road trip home to start a lab","authors":"Vivien Marx","doi":"10.1038/s41592-025-02801-4","DOIUrl":"10.1038/s41592-025-02801-4","url":null,"abstract":"As a postdoctoral fellowship ends, for some, next is a trek to their new lab.","PeriodicalId":18981,"journal":{"name":"Nature Methods","volume":"22 9","pages":"1754-1754"},"PeriodicalIF":32.1,"publicationDate":"2025-08-18","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144874142","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":1,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Nature MethodsPub Date : 2025-08-18DOI: 10.1038/s41592-025-02781-5
Lei Xiang, Yumei Wang, Wei Shao, Qingzhou Li, Xiankuo Yu, Mingming Wei, Yu Gui, Shengrong Li, Pan Qin, Chao Hu, Guochen Zhang, Xianwen Zhang, Jiawen Wang, Yingying Li, Jun An, Yan Luo, Yile Liao, Jinghong Deng, Xinran Tai, Richard Y. Xu, Lijun Huang, Dale Guo, Guanbin Zhang, Zhi Xie, Yun Deng, Junquan Xu, Dong Wang
{"title":"High-throughput profiling of chemical-induced gene expression across 93,644 perturbations","authors":"Lei Xiang, Yumei Wang, Wei Shao, Qingzhou Li, Xiankuo Yu, Mingming Wei, Yu Gui, Shengrong Li, Pan Qin, Chao Hu, Guochen Zhang, Xianwen Zhang, Jiawen Wang, Yingying Li, Jun An, Yan Luo, Yile Liao, Jinghong Deng, Xinran Tai, Richard Y. Xu, Lijun Huang, Dale Guo, Guanbin Zhang, Zhi Xie, Yun Deng, Junquan Xu, Dong Wang","doi":"10.1038/s41592-025-02781-5","DOIUrl":"10.1038/s41592-025-02781-5","url":null,"abstract":"In this Resource, we present an extensive dataset of chemical-induced gene signatures (CIGS), encompassing expression patterns of 3,407 genes regulating key biological processes in 2 human cell lines exposed to 13,221 compounds across 93,664 perturbations. This dataset encompasses 319,045,108 gene expression events, generated through 2 high-throughput technologies: the previously documented high-throughput sequencing-based high-throughput screening (HTS2) and the newly developed highly multiplexed and parallel sequencing (HiMAP-seq). Our results show that HiMAP-seq is comparable to RNA sequencing, but can profile the expression of thousands of genes across thousands of samples in one single test by utilizing a pooled-sample strategy. We further illustrate CIGS’s utility in elucidating the mechanism of action of unannotated small molecules, like ligustroflavone and 2,4-dihydroxybenzaldehyde, and to identify perturbation-induced cell states, such as those resistant to ferroptosis. The full dataset is publicly accessible at https://cigs.iomicscloud.com/ . CIGS is a high-resolution dataset comprising chemical perturbation-induced 319,045,108 gene expression events.","PeriodicalId":18981,"journal":{"name":"Nature Methods","volume":"22 9","pages":"1954-1963"},"PeriodicalIF":32.1,"publicationDate":"2025-08-18","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144874141","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":1,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Nature MethodsPub Date : 2025-08-11DOI: 10.1038/s41592-025-02774-4
Qi-Xuan Cheng, Gang Xie, Xiangyu Zhang, Jie Wang, Shuangjin Ding, Yi-Xia Wu, Ming Shi, Fei-Fei Duan, Zi-Li Wan, Jing-Jia Wei, Junyu Xiao, Yangming Wang
{"title":"Co-profiling of in situ RNA-protein interactions and transcriptome in single cells and tissues","authors":"Qi-Xuan Cheng, Gang Xie, Xiangyu Zhang, Jie Wang, Shuangjin Ding, Yi-Xia Wu, Ming Shi, Fei-Fei Duan, Zi-Li Wan, Jing-Jia Wei, Junyu Xiao, Yangming Wang","doi":"10.1038/s41592-025-02774-4","DOIUrl":"10.1038/s41592-025-02774-4","url":null,"abstract":"RNA-binding proteins (RBPs) are essential regulators of RNA fate and function. A long-standing challenge in studying RBP regulation has been mapping RNA interactomes within the dynamic transcriptomic landscape, especially in single-cell contexts and primary tissues. Here we introduce MAPIT-seq (modification added to RBP interacting transcript-sequencing), which uses an antibody-directed editing strategy to map genome-wide in situ RBP–RNA interactions and gene expression concurrently. We demonstrate MAPIT-seq’s robustness across multiple RBPs and systematically analyze RNA substrates associated with core polycomb repressive complex 2 (PRC2) components. MAPIT-seq is also applicable to frozen tissue sections, enabling the mapping of RBP roles during brain development. Importantly, we develop high-throughput single-cell MAPIT-seq (scMAPIT-seq) to reveal cell stage-specific RBP regulation. In summary, MAPIT-seq expands multi-omics profiling, providing an effective framework to study post-transcriptional regulation in dynamic biological processes and clinically relevant scenarios. This work presents MAPIT-seq, an antibody-guided RNA editing method that enables co-profiling of RBP-RNA interactions and gene expression at single-cell resolution and in tissue contexts.","PeriodicalId":18981,"journal":{"name":"Nature Methods","volume":"22 9","pages":"1824-1835"},"PeriodicalIF":32.1,"publicationDate":"2025-08-11","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC12446063/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144817186","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":1,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Nature MethodsPub Date : 2025-08-11DOI: 10.1038/s41592-025-02775-3
{"title":"MAPIT-seq reveals both RBP targets and transcriptome-wide gene expression profiles","authors":"","doi":"10.1038/s41592-025-02775-3","DOIUrl":"10.1038/s41592-025-02775-3","url":null,"abstract":"We present MAPIT-seq, a method that uses antibody-directed RNA editing to concurrently profile in situ RNA-binding protein (RBP)–RNA interactions and transcriptome-wide gene expression in limited input material, including single cells and frozen tissues. This dual-omic strategy streamlines mechanistic analyses of post-transcriptional regulation in dynamic biological processes and clinically relevant samples.","PeriodicalId":18981,"journal":{"name":"Nature Methods","volume":"22 9","pages":"1768-1769"},"PeriodicalIF":32.1,"publicationDate":"2025-08-11","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144822090","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":1,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Nature MethodsPub Date : 2025-08-08DOI: 10.1038/s41592-025-02785-1
Tito Damiani, Alan K. Jarmusch, Allegra T. Aron, Daniel Petras, Vanessa V. Phelan, Haoqi Nina Zhao, Wout Bittremieux, Deepa D. Acharya, Mohammed M. A. Ahmed, Anelize Bauermeister, Matthew J. Bertin, Paul D. Boudreau, Ricardo M. Borges, Benjamin P. Bowen, Christopher J. Brown, Fernanda O. Chagas, Kenneth D. Clevenger, Mario S. P. Correia, William J. Crandall, Max Crüsemann, Eoin Fahy, Oliver Fiehn, Neha Garg, William H. Gerwick, Jeffrey R. Gilbert, Daniel Globisch, Paulo Wender P. Gomes, Steffen Heuckeroth, C. Andrew James, Scott A. Jarmusch, Sarvar A. Kakhkhorov, Kyo Bin Kang, Nikolas Kessler, Roland D. Kersten, Hyunwoo Kim, Riley D. Kirk, Oliver Kohlbacher, Eftychia E. Kontou, Ken Liu, Itzel Lizama-Chamu, Gordon T. Luu, Tal Luzzatto Knaan, Helena Mannochio-Russo, Michael T. Marty, Yuki Matsuzawa, Andrew C. McAvoy, Laura-Isobel McCall, Osama G. Mohamed, Omri Nahor, Heiko Neuweger, Timo H. J. Niedermeyer, Kozo Nishida, Trent R. Northen, Kirsten E. Overdahl, Johannes Rainer, Raphael Reher, Elys Rodriguez, Timo T. Sachsenberg, Laura M. Sanchez, Robin Schmid, Cole Stevens, Shankar Subramaniam, Zhenyu Tian, Ashootosh Tripathi, Hiroshi Tsugawa, Justin J. J. van der Hooft, Andrea Vicini, Axel Walter, Tilmann Weber, Quanbo Xiong, Tao Xu, Tomáš Pluskal, Pieter C. Dorrestein, Mingxun Wang
{"title":"Author Correction: A universal language for finding mass spectrometry data patterns","authors":"Tito Damiani, Alan K. Jarmusch, Allegra T. Aron, Daniel Petras, Vanessa V. Phelan, Haoqi Nina Zhao, Wout Bittremieux, Deepa D. Acharya, Mohammed M. A. Ahmed, Anelize Bauermeister, Matthew J. Bertin, Paul D. Boudreau, Ricardo M. Borges, Benjamin P. Bowen, Christopher J. Brown, Fernanda O. Chagas, Kenneth D. Clevenger, Mario S. P. Correia, William J. Crandall, Max Crüsemann, Eoin Fahy, Oliver Fiehn, Neha Garg, William H. Gerwick, Jeffrey R. Gilbert, Daniel Globisch, Paulo Wender P. Gomes, Steffen Heuckeroth, C. Andrew James, Scott A. Jarmusch, Sarvar A. Kakhkhorov, Kyo Bin Kang, Nikolas Kessler, Roland D. Kersten, Hyunwoo Kim, Riley D. Kirk, Oliver Kohlbacher, Eftychia E. Kontou, Ken Liu, Itzel Lizama-Chamu, Gordon T. Luu, Tal Luzzatto Knaan, Helena Mannochio-Russo, Michael T. Marty, Yuki Matsuzawa, Andrew C. McAvoy, Laura-Isobel McCall, Osama G. Mohamed, Omri Nahor, Heiko Neuweger, Timo H. J. Niedermeyer, Kozo Nishida, Trent R. Northen, Kirsten E. Overdahl, Johannes Rainer, Raphael Reher, Elys Rodriguez, Timo T. Sachsenberg, Laura M. Sanchez, Robin Schmid, Cole Stevens, Shankar Subramaniam, Zhenyu Tian, Ashootosh Tripathi, Hiroshi Tsugawa, Justin J. J. van der Hooft, Andrea Vicini, Axel Walter, Tilmann Weber, Quanbo Xiong, Tao Xu, Tomáš Pluskal, Pieter C. Dorrestein, Mingxun Wang","doi":"10.1038/s41592-025-02785-1","DOIUrl":"10.1038/s41592-025-02785-1","url":null,"abstract":"","PeriodicalId":18981,"journal":{"name":"Nature Methods","volume":"22 9","pages":"1995-1995"},"PeriodicalIF":32.1,"publicationDate":"2025-08-08","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC12446056/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144804455","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":1,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
求助内容：
应助结果提醒方式：
京公网安备 11010802042870号
