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Embedding AI in biology 将人工智能嵌入生物学。
IF 36.1 1区 生物学 Q1 BIOCHEMICAL RESEARCH METHODS Pub Date : 2024-08-09 DOI: 10.1038/s41592-024-02391-7
Advanced artificial intelligence approaches are rapidly transforming how biological data are acquired and analyzed.
先进的人工智能方法正在迅速改变生物数据的获取和分析方式。
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引用次数: 0
Proximity-triggered protein trans-splicing 近端触发的蛋白质转接。
IF 36.1 1区 生物学 Q1 BIOCHEMICAL RESEARCH METHODS Pub Date : 2024-08-09 DOI: 10.1038/s41592-024-02385-5
Arunima Singh
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引用次数: 0
Visual interpretability of bioimaging deep learning models 生物成像深度学习模型的可视化可解释性。
IF 36.1 1区 生物学 Q1 BIOCHEMICAL RESEARCH METHODS Pub Date : 2024-08-09 DOI: 10.1038/s41592-024-02322-6
Oded Rotem, Assaf Zaritsky
The success of deep learning in analyzing bioimages comes at the expense of biologically meaningful interpretations. We review the state of the art of explainable artificial intelligence (XAI) in bioimaging and discuss its potential in hypothesis generation and data-driven discovery.
深度学习在分析生物图像方面的成功是以牺牲具有生物学意义的解释为代价的。我们回顾了可解释人工智能(XAI)在生物成像中的应用现状,并讨论了它在假设生成和数据驱动发现方面的潜力。
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引用次数: 0
Smart parallel automated cryo-electron tomography 智能并行自动低温电子断层扫描。
IF 36.1 1区 生物学 Q1 BIOCHEMICAL RESEARCH METHODS Pub Date : 2024-08-08 DOI: 10.1038/s41592-024-02373-9
Fabian Eisenstein, Yoshiyuki Fukuda, Radostin Danev
In situ cryo-electron tomography enables investigation of macromolecules in their native cellular environment. Samples have become more readily available owing to recent software and hardware advancements. Data collection, however, still requires an experienced operator and appreciable microscope time to carefully select targets for high-throughput tilt series acquisition. Here, we developed smart parallel automated cryo-electron tomography (SPACEtomo), a workflow using machine learning approaches to fully automate the entire cryo-electron tomography process, including lamella detection, biological feature segmentation, target selection and parallel tilt series acquisition, all without the need for human intervention. This degree of automation will be essential for obtaining statistically relevant datasets and high-resolution structures of macromolecules in their native context. Smart parallel automated cryo-electron tomography (SPACEtomo) uses deep learning to fully automate data collection from lamella detection to tilt series acquisition, driving the future of cryo-ET through improved throughput and statistics.
原位低温电子断层扫描技术可以研究原生细胞环境中的大分子。由于最近软件和硬件的进步,样品变得更容易获得。然而,数据采集仍然需要经验丰富的操作人员和相当长的显微镜时间,以仔细选择目标进行高通量倾斜系列采集。在这里,我们开发了智能并行自动冷冻电子断层成像(SPACEtomo),这是一种利用机器学习方法实现整个冷冻电子断层成像过程完全自动化的工作流程,包括薄片检测、生物特征分割、目标选择和并行倾斜序列采集,所有这些都无需人工干预。这种自动化程度对于获得统计相关数据集和大分子在其原生环境中的高分辨率结构至关重要。
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引用次数: 0
ProDOL: a general method to determine the degree of labeling for staining optimization and molecular counting ProDOL:确定标记程度的通用方法,用于染色优化和分子计数。
IF 36.1 1区 生物学 Q1 BIOCHEMICAL RESEARCH METHODS Pub Date : 2024-08-08 DOI: 10.1038/s41592-024-02376-6
Stanimir Asenov Tashev, Jonas Euchner, Klaus Yserentant, Siegfried Hänselmann, Felix Hild, Wioleta Chmielewicz, Johan Hummert, Florian Schwörer, Nikolaos Tsopoulidis, Stefan Germer, Zoe Saßmannshausen, Oliver T. Fackler, Ursula Klingmüller, Dirk-Peter Herten
Determining the label to target ratio, also known as the degree of labeling (DOL), is crucial for quantitative fluorescence microscopy and a high DOL with minimal unspecific labeling is beneficial for fluorescence microscopy in general. Yet robust, versatile and easy-to-use tools for measuring cell-specific labeling efficiencies are not available. Here we present a DOL determination technique named protein-tag DOL (ProDOL), which enables fast quantification and optimization of protein-tag labeling. With ProDOL various factors affecting labeling efficiency, including substrate type, incubation time and concentration, as well as sample fixation and cell type can be easily assessed. We applied ProDOL to investigate how human immunodeficiency virus-1 pathogenesis factor Nef modulates CD4 T cell activation measuring total and activated copy numbers of the adapter protein SLP-76 in signaling microclusters. ProDOL proved to be a versatile and robust tool for labeling calibration, enabling determination of labeling efficiencies, optimization of strategies and quantification of protein stoichiometry. Protein-tag degree of labeling (ProDOL) is a versatile reference-based approach for experimentally determining the degree of target labeling for improved protein counting and quantification and for optimizing labeling protocols in fixed and live cells.
确定标记与目标的比率,也称为标记度(DOL),对于荧光显微镜定量分析至关重要。然而,目前还没有稳健、多功能且易于使用的工具来测量细胞特异性标记效率。在这里,我们介绍一种名为蛋白质标记 DOL(ProDOL)的 DOL 测定技术,它可以快速量化和优化蛋白质标记。使用 ProDOL 可以轻松评估影响标记效率的各种因素,包括底物类型、孵育时间和浓度以及样品固定和细胞类型。我们应用 ProDOL 研究了人类免疫缺陷病毒-1 致病因子 Nef 如何调节 CD4 T 细胞的活化,测量了信号微簇中适配蛋白 SLP-76 的总拷贝数和活化拷贝数。事实证明,ProDOL 是一种多功能、稳健的标记校准工具,可用于确定标记效率、优化策略和量化蛋白质的化学计量。
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引用次数: 0
A Cell Observatory to reveal the subcellular foundations of life. 细胞观测站揭示生命的亚细胞基础。
IF 36.1 1区 生物学 Q1 BIOCHEMICAL RESEARCH METHODS Pub Date : 2024-08-07 DOI: 10.1038/s41592-024-02379-3
Eric Betzig
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引用次数: 0
The DNA-PAINT palette: a comprehensive performance analysis of fluorescent dyes DNA-PAINT 调色板:荧光染料的综合性能分析。
IF 36.1 1区 生物学 Q1 BIOCHEMICAL RESEARCH METHODS Pub Date : 2024-08-07 DOI: 10.1038/s41592-024-02374-8
Philipp R. Steen, Eduard M. Unterauer, Luciano A. Masullo, Jisoo Kwon, Ana Perovic, Kristina Jevdokimenko, Felipe Opazo, Eugenio F. Fornasiero, Ralf Jungmann
DNA points accumulation for imaging in nanoscale topography (DNA-PAINT) is a super-resolution fluorescence microscopy technique that achieves single-molecule ‘blinking’ by transient DNA hybridization. Despite blinking kinetics being largely independent of fluorescent dye choice, the dye employed substantially affects measurement quality. Thus far, there has been no systematic overview of dye performance for DNA-PAINT. Here we defined four key parameters characterizing performance: brightness, signal-to-background ratio, DNA-PAINT docking site damage and off-target signal. We then analyzed 18 fluorescent dyes in three spectral regions and examined them both in DNA origami nanostructures, establishing a reference standard, and in a cellular environment, targeting the nuclear pore complex protein Nup96. Finally, having identified several well-performing dyes for each excitation wavelength, we conducted simultaneous three-color DNA-PAINT combined with Exchange-PAINT to image six protein targets in neurons at ~16 nm resolution in less than 2 h. We thus provide guidelines for DNA-PAINT dye selection and evaluation and an overview of performances of commonly used dyes. The dyes chosen for DNA-PAINT microscopy are pivotal for data quality. This Analysis shows a comprehensive comparison of 18 fluorescent dyes in DNA-PAINT and offers guidance for optimum dye selection in single-color and multiplexed imaging.
用于纳米尺度形貌成像的 DNA 点积累(DNA-PAINT)是一种超分辨率荧光显微镜技术,通过瞬时 DNA 杂交实现单分子 "闪烁"。尽管闪烁动力学在很大程度上与荧光染料的选择无关,但所使用的染料会对测量质量产生重大影响。迄今为止,还没有对 DNA-PAINT 染色剂性能的系统概述。在此,我们定义了表征性能的四个关键参数:亮度、信号-背景比、DNA-PAINT对接位点损伤和脱靶信号。然后,我们分析了三个光谱区域的 18 种荧光染料,并在 DNA 折纸纳米结构和细胞环境中对它们进行了检测,前者建立了参考标准,后者则以核孔复合体蛋白 Nup96 为目标。最后,在为每个激发波长确定了几种性能良好的染料后,我们同时进行了三色 DNA-PAINT 和 Exchange-PAINT,在不到 2 小时的时间内以 ~16 nm 的分辨率对神经元中的六个蛋白质靶点进行了成像。
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引用次数: 0
Studying RNA dynamics from single-cell RNA sequencing snapshots 从单细胞 RNA 测序快照中研究 RNA 动态。
IF 36.1 1区 生物学 Q1 BIOCHEMICAL RESEARCH METHODS Pub Date : 2024-08-05 DOI: 10.1038/s41592-024-02366-8
Rapid advancements in transcriptomics have enabled the quantification of individual transcripts for thousands of genes in millions of single cells. By coupling a machine learning inference framework with biophysical models describing the RNA life cycle, we can explore the dynamics driving RNA production, processing and degradation across cell types.
转录组学的飞速发展使得对数百万个单细胞中成千上万个基因的单个转录本进行量化成为可能。通过将机器学习推理框架与描述 RNA 生命周期的生物物理模型相结合,我们可以探索驱动跨细胞类型 RNA 生产、加工和降解的动力学。
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引用次数: 0
Geometric deep learning of protein–DNA binding specificity 蛋白质-DNA 结合特异性的几何深度学习。
IF 36.1 1区 生物学 Q1 BIOCHEMICAL RESEARCH METHODS Pub Date : 2024-08-05 DOI: 10.1038/s41592-024-02372-w
Raktim Mitra, Jinsen Li, Jared M. Sagendorf, Yibei Jiang, Ari S. Cohen, Tsu-Pei Chiu, Cameron J. Glasscock, Remo Rohs
Predicting protein–DNA binding specificity is a challenging yet essential task for understanding gene regulation. Protein–DNA complexes usually exhibit binding to a selected DNA target site, whereas a protein binds, with varying degrees of binding specificity, to a wide range of DNA sequences. This information is not directly accessible in a single structure. Here, to access this information, we present Deep Predictor of Binding Specificity (DeepPBS), a geometric deep-learning model designed to predict binding specificity from protein–DNA structure. DeepPBS can be applied to experimental or predicted structures. Interpretable protein heavy atom importance scores for interface residues can be extracted. When aggregated at the protein residue level, these scores are validated through mutagenesis experiments. Applied to designed proteins targeting specific DNA sequences, DeepPBS was demonstrated to predict experimentally measured binding specificity. DeepPBS offers a foundation for machine-aided studies that advance our understanding of molecular interactions and guide experimental designs and synthetic biology. DeepPBS is a deep-learning model designed to predict the binding specificity of protein–DNA interactions using physicochemical and geometric contexts. DeepPBS functions across protein families and on experimentally determined as well as predicted protein–DNA complex structures.
预测蛋白质-DNA 结合的特异性是了解基因调控的一项具有挑战性但又必不可少的任务。蛋白质-DNA 复合物通常表现为与选定的 DNA 目标位点结合,而蛋白质则以不同程度的结合特异性与多种 DNA 序列结合。单个结构无法直接获取这些信息。为了获取这些信息,我们提出了结合特异性深度预测模型(DeepPBS),这是一种几何深度学习模型,旨在从蛋白质-DNA 结构中预测结合特异性。DeepPBS 可应用于实验结构或预测结构。可以为界面残基提取可解释的蛋白质重原子重要性分数。在蛋白质残基水平上汇总后,这些分数可通过诱变实验进行验证。将 DeepPBS 应用于以特定 DNA 序列为靶标的设计蛋白质,证明它可以预测实验测定的结合特异性。DeepPBS 为机器辅助研究奠定了基础,这些研究可促进我们对分子相互作用的理解,并为实验设计和合成生物学提供指导。
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引用次数: 0
Rapid, biochemical tagging of cellular activity history in vivo 对体内细胞活动历史进行快速生化标记。
IF 36.1 1区 生物学 Q1 BIOCHEMICAL RESEARCH METHODS Pub Date : 2024-08-05 DOI: 10.1038/s41592-024-02375-7
Run Zhang, Maribel Anguiano, Isak K. Aarrestad, Sophia Lin, Joshua Chandra, Sruti S. Vadde, David E. Olson, Christina K. Kim
Intracellular calcium (Ca2+) is ubiquitous to cell signaling across biology. While existing fluorescent sensors and reporters can detect activated cells with elevated Ca2+ levels, these approaches require implants to deliver light to deep tissue, precluding their noninvasive use in freely behaving animals. Here we engineered an enzyme-catalyzed approach that rapidly and biochemically tags cells with elevated Ca2+ in vivo. Ca2+-activated split-TurboID (CaST) labels activated cells within 10 min with an exogenously delivered biotin molecule. The enzymatic signal increases with Ca2+ concentration and biotin labeling time, demonstrating that CaST is a time-gated integrator of total Ca2+ activity. Furthermore, the CaST readout can be performed immediately after activity labeling, in contrast to transcriptional reporters that require hours to produce signal. These capabilities allowed us to apply CaST to tag prefrontal cortex neurons activated by psilocybin, and to correlate the CaST signal with psilocybin-induced head-twitch responses in untethered mice. CaST is a Ca2+-activated version of split-TurboID. The tool allows labeling active neurons quickly, simply by administration of exogenous biotin, thus enabling the study of behaviors that would be impaired by hardware required for the use of other, light-dependent tools.
细胞内钙(Ca2+)在整个生物学的细胞信号传导中无处不在。虽然现有的荧光传感器和报告器可以检测 Ca2+ 水平升高的活化细胞,但这些方法需要植入物将光传递到深层组织,因此无法在自由活动的动物中进行非侵入性使用。在这里,我们设计了一种酶催化方法,可在体内快速对 Ca2+ 升高的细胞进行生化标记。Ca2+ 激活的分裂-TurboID(CaST)能在 10 分钟内用外源性生物素分子标记激活的细胞。酶信号随 Ca2+ 浓度和生物素标记时间的增加而增加,这表明 CaST 是总 Ca2+ 活性的时间门控积分器。此外,与需要数小时才能产生信号的转录报告器相比,CaST 可以在活性标记后立即读出信号。这些功能使我们能够应用 CaST 标记被迷幻剂激活的前额叶皮层神经元,并将 CaST 信号与迷幻剂诱导的无系小鼠头部抽动反应相关联。
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Nature Methods
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