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Can stem cells save the animals? 干细胞能拯救动物吗？
IF 36.1 1区 生物学
Nature Methods Pub Date : 2025-01-13 DOI: 10.1038/s41592-024-02577-z
Vivien Marx
{"title":"Can stem cells save the animals?","authors":"Vivien Marx","doi":"10.1038/s41592-024-02577-z","DOIUrl":"10.1038/s41592-024-02577-z","url":null,"abstract":"Scientists in stem cell and conservation biology are exploring how they might rescue endangered species, and perhaps even de-extinct some. From cell to genetically diverse population is a trek.","PeriodicalId":18981,"journal":{"name":"Nature Methods","volume":"22 1","pages":"8-12"},"PeriodicalIF":36.1,"publicationDate":"2025-01-13","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.nature.com/articles/s41592-024-02577-z.pdf","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142976658","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}
引用次数: 0
Learning regulatory grammar 学习规则语法
IF 36.1 1区 生物学
Nature Methods Pub Date : 2025-01-13 DOI: 10.1038/s41592-024-02588-w
Lei Tang
{"title":"Learning regulatory grammar","authors":"Lei Tang","doi":"10.1038/s41592-024-02588-w","DOIUrl":"10.1038/s41592-024-02588-w","url":null,"abstract":"","PeriodicalId":18981,"journal":{"name":"Nature Methods","volume":"22 1","pages":"7-7"},"PeriodicalIF":36.1,"publicationDate":"2025-01-13","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142976679","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}
引用次数: 0
3D holograms of embryos 胚胎的3D全息图
IF 36.1 1区 生物学
Nature Methods Pub Date : 2025-01-13 DOI: 10.1038/s41592-024-02587-x
Madhura Mukhopadhyay
{"title":"3D holograms of embryos","authors":"Madhura Mukhopadhyay","doi":"10.1038/s41592-024-02587-x","DOIUrl":"10.1038/s41592-024-02587-x","url":null,"abstract":"Spateo reveals multiscale 3D spatiotemporal dynamics of mouse embryogenesis.","PeriodicalId":18981,"journal":{"name":"Nature Methods","volume":"22 1","pages":"6-6"},"PeriodicalIF":36.1,"publicationDate":"2025-01-13","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142976699","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}
引用次数: 0
Generative modeling of genomes 基因组的生成建模
IF 36.1 1区 生物学
Nature Methods Pub Date : 2025-01-13 DOI: 10.1038/s41592-024-02589-9
Lin Tang
{"title":"Generative modeling of genomes","authors":"Lin Tang","doi":"10.1038/s41592-024-02589-9","DOIUrl":"10.1038/s41592-024-02589-9","url":null,"abstract":"","PeriodicalId":18981,"journal":{"name":"Nature Methods","volume":"22 1","pages":"7-7"},"PeriodicalIF":36.1,"publicationDate":"2025-01-13","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142976691","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}
引用次数: 0
Orthology inference at scale with FastOMA 使用FastOMA进行大规模的正交推理。
IF 36.1 1区 生物学
Nature Methods Pub Date : 2025-01-03 DOI: 10.1038/s41592-024-02552-8
Sina Majidian, Yannis Nevers, Ali Yazdizadeh Kharrazi, Alex Warwick Vesztrocy, Stefano Pascarelli, David Moi, Natasha Glover, Adrian M. Altenhoff, Christophe Dessimoz
{"title":"Orthology inference at scale with FastOMA","authors":"Sina Majidian, Yannis Nevers, Ali Yazdizadeh Kharrazi, Alex Warwick Vesztrocy, Stefano Pascarelli, David Moi, Natasha Glover, Adrian M. Altenhoff, Christophe Dessimoz","doi":"10.1038/s41592-024-02552-8","DOIUrl":"10.1038/s41592-024-02552-8","url":null,"abstract":"The surge in genome data, with ongoing efforts aiming to sequence 1.5 M eukaryotes in a decade, could revolutionize genomics, revealing the origins, evolution and genetic innovations of biological processes. Yet, traditional genomics methods scale poorly with such large datasets. Here, addressing this, ‘FastOMA’ provides linear scalability for orthology inference, enabling the processing of thousands of eukaryotic genomes within a day. FastOMA maintains the high accuracy and resolution of the well-established Orthologous Matrix (OMA) approach in benchmarks. FastOMA is available via GitHub at https://github.com/DessimozLab/FastOMA/ . FastOMA achieves fast and accurate orthology inference, with linear scalability.","PeriodicalId":18981,"journal":{"name":"Nature Methods","volume":"22 2","pages":"269-272"},"PeriodicalIF":36.1,"publicationDate":"2025-01-03","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.nature.com/articles/s41592-024-02552-8.pdf","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142927640","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}
引用次数: 0
Efficiently accelerated bioimage analysis with NanoPyx, a Liquid Engine-powered Python framework 有效地加速生物图像分析与NanoPyx，一个液体引擎驱动的Python框架。
IF 36.1 1区 生物学
Nature Methods Pub Date : 2025-01-02 DOI: 10.1038/s41592-024-02562-6
Bruno M. Saraiva, Inês Cunha, António D. Brito, Gautier Follain, Raquel Portela, Robert Haase, Pedro M. Pereira, Guillaume Jacquemet, Ricardo Henriques
{"title":"Efficiently accelerated bioimage analysis with NanoPyx, a Liquid Engine-powered Python framework","authors":"Bruno M. Saraiva, Inês Cunha, António D. Brito, Gautier Follain, Raquel Portela, Robert Haase, Pedro M. Pereira, Guillaume Jacquemet, Ricardo Henriques","doi":"10.1038/s41592-024-02562-6","DOIUrl":"10.1038/s41592-024-02562-6","url":null,"abstract":"The expanding scale and complexity of microscopy image datasets require accelerated analytical workflows. NanoPyx meets this need through an adaptive framework enhanced for high-speed analysis. At the core of NanoPyx, the Liquid Engine dynamically generates optimized central processing unit and graphics processing unit code variations, learning and predicting the fastest based on input data and hardware. This data-driven optimization achieves considerably faster processing, becoming broadly relevant to reactive microscopy and computing fields requiring efficiency. NanoPyx optimizes bioimage analysis workflows by dynamically selecting code variations based on input data and hardware. This ensures maximum computational efficiency, enabling fast analysis of large datasets and real-time reactive microscopy.","PeriodicalId":18981,"journal":{"name":"Nature Methods","volume":"22 2","pages":"283-286"},"PeriodicalIF":36.1,"publicationDate":"2025-01-02","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.nature.com/articles/s41592-024-02562-6.pdf","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142922244","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}
引用次数: 0
Conference networking: posters, talks, conversations 会议网络：海报，演讲，对话。
IF 36.1 1区 生物学
Nature Methods Pub Date : 2025-01-02 DOI: 10.1038/s41592-024-02566-2
Vivien Marx
{"title":"Conference networking: posters, talks, conversations","authors":"Vivien Marx","doi":"10.1038/s41592-024-02566-2","DOIUrl":"10.1038/s41592-024-02566-2","url":null,"abstract":"At the American Society of Human Genetics’ annual meeting in Denver, some attendees shared how they network at conferences.","PeriodicalId":18981,"journal":{"name":"Nature Methods","volume":"22 1","pages":"2-2"},"PeriodicalIF":36.1,"publicationDate":"2025-01-02","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142922242","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}
引用次数: 0
Vibrational fiber photometry: label-free and reporter-free minimally invasive Raman spectroscopy deep in the mouse brain 振动纤维光度法：无标签和无报告的小鼠脑深部微创拉曼光谱。
IF 36.1 1区 生物学
Nature Methods Pub Date : 2024-12-31 DOI: 10.1038/s41592-024-02557-3
Filippo Pisano, Mariam Masmudi-Martín, Maria Samuela Andriani, Elena Cid, Mohammadrahim Kazemzadeh, Marco Pisanello, Antonio Balena, Liam Collard, Teresa Jurado Parras, Marco Bianco, Patricia Baena, Francesco Tantussi, Marco Grande, Leonardo Sileo, Francesco Gentile, Francesco De Angelis, Massimo De Vittorio, Liset Menendez de la Prida, Manuel Valiente, Ferruccio Pisanello
{"title":"Vibrational fiber photometry: label-free and reporter-free minimally invasive Raman spectroscopy deep in the mouse brain","authors":"Filippo Pisano, Mariam Masmudi-Martín, Maria Samuela Andriani, Elena Cid, Mohammadrahim Kazemzadeh, Marco Pisanello, Antonio Balena, Liam Collard, Teresa Jurado Parras, Marco Bianco, Patricia Baena, Francesco Tantussi, Marco Grande, Leonardo Sileo, Francesco Gentile, Francesco De Angelis, Massimo De Vittorio, Liset Menendez de la Prida, Manuel Valiente, Ferruccio Pisanello","doi":"10.1038/s41592-024-02557-3","DOIUrl":"10.1038/s41592-024-02557-3","url":null,"abstract":"Optical approaches to monitor neural activity are transforming neuroscience, owing to a fast-evolving palette of genetically encoded molecular reporters. However, the field still requires robust and label-free technologies to monitor the multifaceted biomolecular changes accompanying brain development, aging or disease. Here, we have developed vibrational fiber photometry as a low-invasive method for label-free monitoring of the biomolecular content of arbitrarily deep regions of the mouse brain in vivo through spontaneous Raman spectroscopy. Using a tapered fiber probe as thin as 1 µm at its tip, we elucidate the cytoarchitecture of the mouse brain, monitor molecular alterations caused by traumatic brain injury, as well as detect markers of brain metastasis with high accuracy. We view our approach, which introduces a deep learning algorithm to suppress probe background, as a promising complement to the existing palette of tools for the optical interrogation of neural function, with application to fundamental and preclinical investigations of the brain and other organs. Vibrational fiber photometry enables Raman spectroscopy in the mouse brain with low impact, owing to the use of tapered fibers.","PeriodicalId":18981,"journal":{"name":"Nature Methods","volume":"22 2","pages":"371-379"},"PeriodicalIF":36.1,"publicationDate":"2024-12-31","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142910033","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}
引用次数: 0
Isotropic 100-nm resolution live-cell imaging with 4Pi-SIM 使用4Pi-SIM进行各向同性100纳米分辨率活细胞成像。
IF 36.1 1区 生物学
Nature Methods Pub Date : 2024-12-30 DOI: 10.1038/s41592-024-02514-0
{"title":"Isotropic 100-nm resolution live-cell imaging with 4Pi-SIM","authors":"","doi":"10.1038/s41592-024-02514-0","DOIUrl":"10.1038/s41592-024-02514-0","url":null,"abstract":"We developed 4Pi-SIM, which integrates 4Pi microscopy with structured illumination microscopy to achieve isotropic optical resolution through interference in both illumination and detection. We demonstrate its capabilities by time-lapse volumetric imaging of various subcellular structures at 100-nm resolution.","PeriodicalId":18981,"journal":{"name":"Nature Methods","volume":"22 2","pages":"233-234"},"PeriodicalIF":36.1,"publicationDate":"2024-12-30","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142910031","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}
引用次数: 0
Elucidating subcellular architecture and dynamics at isotropic 100-nm resolution with 4Pi-SIM 利用4Pi-SIM在各向同性100纳米分辨率下阐明亚细胞结构和动力学。
IF 36.1 1区 生物学
Nature Methods Pub Date : 2024-12-23 DOI: 10.1038/s41592-024-02515-z
Zijing Ouyang, Qian Wang, Xiaoyu Li, Qiuyang Dai, Muyuan Tang, Lin Shao, Wen Gou, Zijing Yu, Yanqin Chen, Bei Zheng, Linlin Chen, Conghui Ping, Xiuli Bi, Bin Xiao, Xiaochun Yu, Changliang Liu, Liangyi Chen, Junchao Fan, Xiaoshuai Huang, Yongdeng Zhang
{"title":"Elucidating subcellular architecture and dynamics at isotropic 100-nm resolution with 4Pi-SIM","authors":"Zijing Ouyang, Qian Wang, Xiaoyu Li, Qiuyang Dai, Muyuan Tang, Lin Shao, Wen Gou, Zijing Yu, Yanqin Chen, Bei Zheng, Linlin Chen, Conghui Ping, Xiuli Bi, Bin Xiao, Xiaochun Yu, Changliang Liu, Liangyi Chen, Junchao Fan, Xiaoshuai Huang, Yongdeng Zhang","doi":"10.1038/s41592-024-02515-z","DOIUrl":"10.1038/s41592-024-02515-z","url":null,"abstract":"Three-dimensional structured illumination microscopy (3D-SIM) provides excellent optical sectioning and doubles the resolution in all dimensions compared with wide-field microscopy. However, its much lower axial resolution results in blurred fine details in that direction and overall image distortion. Here we present 4Pi-SIM, a substantial revamp of I5S that synergizes 3D-SIM with interferometric microscopy to achieve isotropic optical resolution through interference in both the illumination and detection wavefronts. We evaluate the performance of 4Pi-SIM by imaging various subcellular structures across different cell types with high fidelity. Furthermore, we demonstrate its capability by conducting time-lapse volumetric imaging over hundreds of time points, achieving a 3D resolution of approximately 100 nm. Additionally, we illustrate its ability to simultaneously image in two colors and capture the rapid interactions between closely positioned organelles in three dimensions. These results underscore the great potential of 4Pi-SIM for elucidating subcellular architecture and revealing dynamic behaviors at the nanoscale. The 4Pi-SIM microscope combines the benefits of structured illumination microscopy with 4Pi geometry for improved axial resolution, offering isotropic, multicolor super-resolution imaging of dynamic processes in living cells.","PeriodicalId":18981,"journal":{"name":"Nature Methods","volume":"22 2","pages":"335-347"},"PeriodicalIF":36.1,"publicationDate":"2024-12-23","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.nature.com/articles/s41592-024-02515-z.pdf","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142882306","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}
引用次数: 0
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