Nature Methods最新文献_第2页

Challenges of microscopy technology dissemination to resource-constrained communities. 显微镜技术向资源受限社区传播的挑战。

IF 36.1 1区生物学

Nature Methods Pub Date : 2025-05-06 DOI: 10.1038/s41592-025-02690-7

Jesse S Aaron, Caron A Jacobs, Leonel Malacrida, Antje Keppler, Paul French, Daniel A Fletcher, Christopher Wood, Claire M Brown, Graham D Wright, Satoshi Ogawa, Mahmoud Maina, Teng-Leong Chew

引用次数: 0

Mild and ultrafast GLORI enables absolute quantification of m⁶A methylome from low-input samples. 温和和超快GLORI能够从低输入样品中绝对定量m6A甲基组。

IF 36.1 1区生物学

Nature Methods Pub Date : 2025-05-05 DOI: 10.1038/s41592-025-02680-9

Hanxiao Sun, Bo Lu, Zeyu Zhang, Ye Xiao, Zhe Zhou, Lin Xi, Zhichao Li, Zhe Jiang, Jiayi Zhang, Meng Wang, Cong Liu, Yichen Ma, Jinying Peng, Xiu-Jie Wang, Chengqi Yi

{"title":"Mild and ultrafast GLORI enables absolute quantification of m6A methylome from low-input samples.","authors":"Hanxiao Sun, Bo Lu, Zeyu Zhang, Ye Xiao, Zhe Zhou, Lin Xi, Zhichao Li, Zhe Jiang, Jiayi Zhang, Meng Wang, Cong Liu, Yichen Ma, Jinying Peng, Xiu-Jie Wang, Chengqi Yi","doi":"10.1038/s41592-025-02680-9","DOIUrl":"https://doi.org/10.1038/s41592-025-02680-9","url":null,"abstract":"Methods for absolute quantification of N6-methyladenosine (m6A) have emerged as powerful tools in epitranscriptomics. We previously reported GLORI, a chemical-assisted approach to achieve unbiased and precise m6A measurement. However, its lengthy reaction time and severe RNA degradation have limited its applicability, particularly for low-input samples. Here, we present two updated GLORI approaches that are ultrafast, mild and enable absolute m6A quantification from one to two orders of magnitude less than the RNA starting material: GLORI 2.0 is compatible with RNA from ~10,000 cells and enhances sensitivity for both transcriptome-wide and locus-specific m6A detection; GLORI 3.0 further utilizes a reverse transcription-silent carrier RNA to achieve m6A quantification from as low as 500-1,000 cells. Using limited RNA from mouse dorsal hippocampus, we reveal a high modification level in synapse-related gene sets. We envision that the updated GLORI methods will greatly expand the applicability of absolute quantification of m6A in biology.","PeriodicalId":18981,"journal":{"name":"Nature Methods","volume":" ","pages":""},"PeriodicalIF":36.1,"publicationDate":"2025-05-05","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143982104","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

Deep learning-assisted analysis of single-particle tracking for automated correlation between diffusion and function. 深度学习辅助的单粒子跟踪分析，用于扩散和函数之间的自动关联。

IF 36.1 1区生物学

Nature Methods Pub Date : 2025-05-01 Epub Date: 2025-05-08 DOI: 10.1038/s41592-025-02665-8

Jacob Kæstel-Hansen, Marilina de Sautu, Anand Saminathan, Gustavo Scanavachi, Ricardo F Bango Da Cunha Correia, Annette Juma Nielsen, Sara Vogt Bleshøy, Konstantinos Tsolakidis, Wouter Boomsma, Tomas Kirchhausen, Nikos S Hatzakis

{"title":"Deep learning-assisted analysis of single-particle tracking for automated correlation between diffusion and function.","authors":"Jacob Kæstel-Hansen, Marilina de Sautu, Anand Saminathan, Gustavo Scanavachi, Ricardo F Bango Da Cunha Correia, Annette Juma Nielsen, Sara Vogt Bleshøy, Konstantinos Tsolakidis, Wouter Boomsma, Tomas Kirchhausen, Nikos S Hatzakis","doi":"10.1038/s41592-025-02665-8","DOIUrl":"https://doi.org/10.1038/s41592-025-02665-8","url":null,"abstract":"Subcellular diffusion in living systems reflects cellular processes and interactions. Recent advances in optical microscopy allow the tracking of this nanoscale diffusion of individual objects with unprecedented precision. However, the agnostic and automated extraction of functional information from the diffusion of molecules and organelles within the subcellular environment is labor intensive and poses a significant challenge. Here we introduce DeepSPT, a deep learning framework integrated in an analysis software, to interpret the diffusional two- or three-dimensional temporal behavior of objects in a rapid and efficient manner, agnostically. Demonstrating its versatility, we have applied DeepSPT to automated mapping of the early events of viral infections, identifying endosomal organelles, clathrin-coated pits and vesicles among others with F1 scores of 81%, 82% and 95%, respectively, and within seconds instead of weeks. The fact that DeepSPT effectively extracts biological information from diffusion alone illustrates that besides structure, motion encodes function at the molecular and subcellular level.","PeriodicalId":18981,"journal":{"name":"Nature Methods","volume":"22 5","pages":"1091-1100"},"PeriodicalIF":36.1,"publicationDate":"2025-05-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144034068","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

scMultiSim: simulation of single-cell multi-omics and spatial data guided by gene regulatory networks and cell-cell interactions. scMultiSim：由基因调控网络和细胞-细胞相互作用引导的单细胞多组学和空间数据模拟。

IF 36.1 1区生物学

Nature Methods Pub Date : 2025-05-01 Epub Date: 2025-04-17 DOI: 10.1038/s41592-025-02651-0

Hechen Li, Ziqi Zhang, Michael Squires, Xi Chen, Xiuwei Zhang

{"title":"scMultiSim: simulation of single-cell multi-omics and spatial data guided by gene regulatory networks and cell-cell interactions.","authors":"Hechen Li, Ziqi Zhang, Michael Squires, Xi Chen, Xiuwei Zhang","doi":"10.1038/s41592-025-02651-0","DOIUrl":"https://doi.org/10.1038/s41592-025-02651-0","url":null,"abstract":"Simulated single-cell data are essential for designing and evaluating computational methods in the absence of experimental ground truth. Here we present scMultiSim, a comprehensive simulator that generates multimodal single-cell data encompassing gene expression, chromatin accessibility, RNA velocity and spatial cell locations while accounting for the relationships between modalities. Unlike existing tools that focus on limited biological factors, scMultiSim simultaneously models cell identity, gene regulatory networks, cell-cell interactions and chromatin accessibility while incorporating technical noise. Moreover, it allows users to adjust each factor's effect easily. Here we show that scMultiSim generates data with expected biological effects, and demonstrate its applications by benchmarking a wide range of computational tasks, including multimodal and multi-batch data integration, RNA velocity estimation, gene regulatory network inference and cell-cell interaction inference using spatially resolved gene expression data. Compared to existing simulators, scMultiSim can benchmark a much broader range of existing computational problems and even new potential tasks.","PeriodicalId":18981,"journal":{"name":"Nature Methods","volume":"22 5","pages":"982-993"},"PeriodicalIF":36.1,"publicationDate":"2025-05-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144028492","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

Illuminating life processes by vibrational probes. 用振动探测器照亮生命过程。

IF 36.1 1区生物学

Nature Methods Pub Date : 2025-05-01 Epub Date: 2025-05-13 DOI: 10.1038/s41592-025-02689-0

Naixin Qian, Zhilun Zhao, Elsy El Khoury, Xin Gao, Carli Canela, Yihui Shen, Lingyan Shi, Lixue Shi, Fanghao Hu, Lu Wei, Wei Min

引用次数: 0

Pooled CRISPR screening with optical sequencing reveals regulators of 3D chromatin organization. 光学测序的CRISPR筛选揭示了三维染色质组织的调节因子。

IF 36.1 1区生物学

Nature Methods Pub Date : 2025-05-01 DOI: 10.1038/s41592-025-02633-2

Mazhar Adli

引用次数: 0

Capturing more than meets the eye. 捕捉比表面更多的东西。

IF 36.1 1区生物学

Nature Methods Pub Date : 2025-05-01 DOI: 10.1038/s41592-025-02714-2

引用次数: 0

Unlocking in vivo metabolic insights with vibrational microscopy. 用振动显微镜解锁体内代谢的见解。

IF 36.1 1区生物学

Nature Methods Pub Date : 2025-05-01 DOI: 10.1038/s41592-025-02616-3

Tao Chen, Marzia Savini, Meng C Wang

引用次数: 0

25 years of 3D coherent Raman imaging for biomedicine. 25年的生物医学三维相干拉曼成像。

IF 36.1 1区生物学

Nature Methods Pub Date : 2025-05-01 DOI: 10.1038/s41592-025-02650-1

Xiaoliang Sunney Xie

引用次数: 0

Denoising Search doubles the number of metabolite and exposome annotations in human plasma using an Orbitrap Astral mass spectrometer. 使用Orbitrap星质谱计，降噪搜索使人类血浆中代谢物和暴露注释的数量加倍。

IF 36.1 1区生物学

Nature Methods Pub Date : 2025-05-01 Epub Date: 2025-03-28 DOI: 10.1038/s41592-025-02646-x

Fanzhou Kong, Tong Shen, Yuanyue Li, Amer Bashar, Susan S Bird, Oliver Fiehn

{"title":"Denoising Search doubles the number of metabolite and exposome annotations in human plasma using an Orbitrap Astral mass spectrometer.","authors":"Fanzhou Kong, Tong Shen, Yuanyue Li, Amer Bashar, Susan S Bird, Oliver Fiehn","doi":"10.1038/s41592-025-02646-x","DOIUrl":"10.1038/s41592-025-02646-x","url":null,"abstract":"Chemical exposures may affect human metabolism and contribute to the etiology of neurodegenerative disorders such as Alzheimer's disease. Identifying these small metabolites involves matching experimental spectra to reference spectra in databases. However, environmental chemicals or physiologically active metabolites are usually present at low concentrations in human specimens. The presence of noise ions can substantially degrade spectral quality, leading to false negatives and reduced identification rates. In response to this challenge, the Spectral Denoising algorithm removes both chemical and electronic noise. Spectral Denoising outperformed alternative methods in benchmarking studies on 240 tested metabolites. It improved high confident compound identifications at an average 35-fold lower concentrations than previously achievable. Spectral Denoising proved highly robust against varying levels of both chemical and electronic noise even with a greater than 150-fold higher intensity of noise ions than true fragment ions. For human plasma samples from patients with Alzheimer's disease that were analyzed on the Orbitrap Astral mass spectrometer, Denoising Search detected 2.5-fold more annotated compounds compared to the Exploris 240 Orbitrap instrument, including drug metabolites, household and industrial chemicals, and pesticides.","PeriodicalId":18981,"journal":{"name":"Nature Methods","volume":" ","pages":"1008-1016"},"PeriodicalIF":36.1,"publicationDate":"2025-05-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143742981","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