Pub Date : 2024-10-09DOI: 10.1038/s41592-024-02433-0
Andrew H. Bass, Jonathan T. Perelmuter
Miniature, transparent Danionella fishes, which are among the smallest living adult vertebrates, allow investigation of general principles of brain-wide neural circuits and evolutionary and developmental mechanisms for neurobehavioral innovations.
{"title":"Danionella fishes","authors":"Andrew H. Bass, Jonathan T. Perelmuter","doi":"10.1038/s41592-024-02433-0","DOIUrl":"10.1038/s41592-024-02433-0","url":null,"abstract":"Miniature, transparent Danionella fishes, which are among the smallest living adult vertebrates, allow investigation of general principles of brain-wide neural circuits and evolutionary and developmental mechanisms for neurobehavioral innovations.","PeriodicalId":18981,"journal":{"name":"Nature Methods","volume":"21 10","pages":"1767-1769"},"PeriodicalIF":36.1,"publicationDate":"2024-10-09","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142391939","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}
Pub Date : 2024-10-09DOI: 10.1038/s41592-024-02431-2
Rita Strack
For Nature Methods’ 20th anniversary, our current and past editors reminisce about their favorite papers, initiatives and projects at the journal.
在《自然-方法》创刊 20 周年之际，我们的现任和前任编辑回顾了他们最喜爱的论文、活动和项目。
{"title":"Making an impact with fluorescent probes","authors":"Rita Strack","doi":"10.1038/s41592-024-02431-2","DOIUrl":"10.1038/s41592-024-02431-2","url":null,"abstract":"For Nature Methods’ 20th anniversary, our current and past editors reminisce about their favorite papers, initiatives and projects at the journal.","PeriodicalId":18981,"journal":{"name":"Nature Methods","volume":"21 10","pages":"1781-1782"},"PeriodicalIF":36.1,"publicationDate":"2024-10-09","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.nature.com/articles/s41592-024-02431-2.pdf","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142391947","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}
Pub Date : 2024-10-09DOI: 10.1038/s41592-024-02451-y
Madhura Mukhopadhyay
For Nature Methods’ 20th anniversary, our current and past editors reminisce about their favorite papers, initiatives and projects at the journal.
在《自然-方法》创刊 20 周年之际，我们的现任和前任编辑回顾了他们最喜爱的论文、活动和项目。
{"title":"Ringside seats to a pandemic","authors":"Madhura Mukhopadhyay","doi":"10.1038/s41592-024-02451-y","DOIUrl":"10.1038/s41592-024-02451-y","url":null,"abstract":"For Nature Methods’ 20th anniversary, our current and past editors reminisce about their favorite papers, initiatives and projects at the journal.","PeriodicalId":18981,"journal":{"name":"Nature Methods","volume":"21 10","pages":"1783-1783"},"PeriodicalIF":36.1,"publicationDate":"2024-10-09","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.nature.com/articles/s41592-024-02451-y.pdf","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142391952","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}
Pub Date : 2024-10-08DOI: 10.1038/s41592-024-02458-5
Lu Bai, Lin Cong, Ziqi Shi, Yuchen Zhao, Yujie Zhang, Bin Lu, Jing Zhang, Zhi-Qi Xiong, Ninglong Xu, Yu Mu, Kai Wang
Voltage imaging measures neuronal activity directly and holds promise for understanding information processing within individual neurons and across populations. However, imaging voltage over large neuronal populations has been challenging owing to the simultaneous requirements of high imaging speed and signal-to-noise ratio, large volume coverage and low photobleaching rate. Here, to overcome this challenge, we developed a confocal light-field microscope that surpassed the traditional limits in speed and noise performance by incorporating a speed-enhanced camera, a fast and robust scanning mechanism, laser-speckle-noise elimination and optimized light efficiency. With this method, we achieved simultaneous recording from more than 300 spiking neurons within an 800-µm-diameter and 180-µm-thick volume in the mouse cortex, for more than 20 min. By integrating the spatial and voltage activity profiles, we have mapped three-dimensional neural coordination patterns in awake mouse brains. Our method is robust for routine application in volumetric voltage imaging. Confocal light-field microscopy allows volumetric voltage imaging in the mouse brain at speeds sufficiently high to extract the spiking activity of hundreds of neurons.
{"title":"Volumetric voltage imaging of neuronal populations in the mouse brain by confocal light-field microscopy","authors":"Lu Bai, Lin Cong, Ziqi Shi, Yuchen Zhao, Yujie Zhang, Bin Lu, Jing Zhang, Zhi-Qi Xiong, Ninglong Xu, Yu Mu, Kai Wang","doi":"10.1038/s41592-024-02458-5","DOIUrl":"10.1038/s41592-024-02458-5","url":null,"abstract":"Voltage imaging measures neuronal activity directly and holds promise for understanding information processing within individual neurons and across populations. However, imaging voltage over large neuronal populations has been challenging owing to the simultaneous requirements of high imaging speed and signal-to-noise ratio, large volume coverage and low photobleaching rate. Here, to overcome this challenge, we developed a confocal light-field microscope that surpassed the traditional limits in speed and noise performance by incorporating a speed-enhanced camera, a fast and robust scanning mechanism, laser-speckle-noise elimination and optimized light efficiency. With this method, we achieved simultaneous recording from more than 300 spiking neurons within an 800-µm-diameter and 180-µm-thick volume in the mouse cortex, for more than 20 min. By integrating the spatial and voltage activity profiles, we have mapped three-dimensional neural coordination patterns in awake mouse brains. Our method is robust for routine application in volumetric voltage imaging. Confocal light-field microscopy allows volumetric voltage imaging in the mouse brain at speeds sufficiently high to extract the spiking activity of hundreds of neurons.","PeriodicalId":18981,"journal":{"name":"Nature Methods","volume":"21 11","pages":"2160-2170"},"PeriodicalIF":36.1,"publicationDate":"2024-10-08","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142391957","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}
Pub Date : 2024-10-08DOI: 10.1038/s41592-024-02459-4
Voltage imaging, a promising technique for directly recording neuronal activity, faces barriers to broad application due to current limitations in compatible imaging modalities. Our team introduces an advanced confocal light field microscopy method enabling high-throughput, rapid and low-noise 3D voltage imaging in awake mice.
{"title":"Mapping voltage activity in a live mouse brain in 3D using confocal light field microscopy","authors":"","doi":"10.1038/s41592-024-02459-4","DOIUrl":"10.1038/s41592-024-02459-4","url":null,"abstract":"Voltage imaging, a promising technique for directly recording neuronal activity, faces barriers to broad application due to current limitations in compatible imaging modalities. Our team introduces an advanced confocal light field microscopy method enabling high-throughput, rapid and low-noise 3D voltage imaging in awake mice.","PeriodicalId":18981,"journal":{"name":"Nature Methods","volume":"21 11","pages":"1992-1993"},"PeriodicalIF":36.1,"publicationDate":"2024-10-08","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142391949","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}
Pub Date : 2024-10-07DOI: 10.1038/s41592-024-02382-8
Ezra Bruggeman, Oumeng Zhang, Lisa-Maria Needham, Markus Körbel, Sam Daly, Matthew Cheetham, Ruby Peters, Tingting Wu, Andrey S. Klymchenko, Simon J. Davis, Ewa K. Paluch, David Klenerman, Matthew D. Lew, Kevin O’Holleran, Steven F. Lee
Current methods for single-molecule orientation localization microscopy (SMOLM) require optical setups and algorithms that can be prohibitively slow and complex, limiting widespread adoption for biological applications. We present POLCAM, a simplified SMOLM method based on polarized detection using a polarization camera, which can be easily implemented on any wide-field fluorescence microscope. To make polarization cameras compatible with single-molecule detection, we developed theory to minimize field-of-view errors, used simulations to optimize experimental design and developed a fast algorithm based on Stokes parameter estimation that can operate over 1,000-fold faster than the state of the art, enabling near-instant determination of molecular anisotropy. To aid in the adoption of POLCAM, we developed open-source image analysis software and a website detailing hardware installation and software use. To illustrate the potential of POLCAM in the life sciences, we applied our method to study α-synuclein fibrils, the actin cytoskeleton of mammalian cells, fibroblast-like cells and the plasma membrane of live human T cells. Combining localization and polarization microscopy can yield detailed insights into subcellular structures. POLCAM uses a polarization camera and wide-field microscopy for rapid measurement of super-resolution orientation imaging in live cells.
{"title":"POLCAM: instant molecular orientation microscopy for the life sciences","authors":"Ezra Bruggeman, Oumeng Zhang, Lisa-Maria Needham, Markus Körbel, Sam Daly, Matthew Cheetham, Ruby Peters, Tingting Wu, Andrey S. Klymchenko, Simon J. Davis, Ewa K. Paluch, David Klenerman, Matthew D. Lew, Kevin O’Holleran, Steven F. Lee","doi":"10.1038/s41592-024-02382-8","DOIUrl":"10.1038/s41592-024-02382-8","url":null,"abstract":"Current methods for single-molecule orientation localization microscopy (SMOLM) require optical setups and algorithms that can be prohibitively slow and complex, limiting widespread adoption for biological applications. We present POLCAM, a simplified SMOLM method based on polarized detection using a polarization camera, which can be easily implemented on any wide-field fluorescence microscope. To make polarization cameras compatible with single-molecule detection, we developed theory to minimize field-of-view errors, used simulations to optimize experimental design and developed a fast algorithm based on Stokes parameter estimation that can operate over 1,000-fold faster than the state of the art, enabling near-instant determination of molecular anisotropy. To aid in the adoption of POLCAM, we developed open-source image analysis software and a website detailing hardware installation and software use. To illustrate the potential of POLCAM in the life sciences, we applied our method to study α-synuclein fibrils, the actin cytoskeleton of mammalian cells, fibroblast-like cells and the plasma membrane of live human T cells. Combining localization and polarization microscopy can yield detailed insights into subcellular structures. POLCAM uses a polarization camera and wide-field microscopy for rapid measurement of super-resolution orientation imaging in live cells.","PeriodicalId":18981,"journal":{"name":"Nature Methods","volume":"21 10","pages":"1873-1883"},"PeriodicalIF":36.1,"publicationDate":"2024-10-07","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.nature.com/articles/s41592-024-02382-8.pdf","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142391951","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}
Pub Date : 2024-10-07DOI: 10.1038/s41592-024-02435-y
A robotic neural recording system can sense the intended motion of the mouse that it is connected to, and it moves with the animal as it explores physical spaces. The robot can support recording interfaces that are much heavier and larger than mice and provide new capabilities for brain-wide recordings in locomoting mice.
{"title":"Exoskeleton empowers large-scale neural recordings in freely roaming mice","authors":"","doi":"10.1038/s41592-024-02435-y","DOIUrl":"10.1038/s41592-024-02435-y","url":null,"abstract":"A robotic neural recording system can sense the intended motion of the mouse that it is connected to, and it moves with the animal as it explores physical spaces. The robot can support recording interfaces that are much heavier and larger than mice and provide new capabilities for brain-wide recordings in locomoting mice.","PeriodicalId":18981,"journal":{"name":"Nature Methods","volume":"21 11","pages":"1994-1995"},"PeriodicalIF":36.1,"publicationDate":"2024-10-07","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142391942","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}
Pub Date : 2024-10-07DOI: 10.1038/s41592-024-02434-z
James Hope, Travis M. Beckerle, Pin-Hao Cheng, Zoey Viavattine, Michael Feldkamp, Skylar M. L. Fausner, Kapil Saxena, Eunsong Ko, Ihor Hryb, Russell E. Carter, Timothy J. Ebner, Suhasa B. Kodandaramaiah
Technologies that can record neural activity at cellular resolution at multiple spatial and temporal scales are typically much larger than the animals that are being recorded from and are thus limited to recording from head-fixed subjects. Here we have engineered robotic neural recording devices—‘cranial exoskeletons’—that assist mice in maneuvering recording headstages that are orders of magnitude larger and heavier than the mice, while they navigate physical behavioral environments. We discovered optimal controller parameters that enable mice to locomote at physiologically realistic velocities while maintaining natural walking gaits. We show that mice learn to work with the robot to make turns and perform decision-making tasks. Robotic imaging and electrophysiology headstages were used to record recordings of Ca2+ activity of thousands of neurons distributed across the dorsal cortex and spiking activity of hundreds of neurons across multiple brain regions and multiple days, respectively. To avoid head fixation or drawbacks of miniaturized devices for freely moving rodents, a robotic device can move a headstage for microscopy or electrophysiology with the animal, thereby enabling naturalistic behavior.
{"title":"Brain-wide neural recordings in mice navigating physical spaces enabled by robotic neural recording headstages","authors":"James Hope, Travis M. Beckerle, Pin-Hao Cheng, Zoey Viavattine, Michael Feldkamp, Skylar M. L. Fausner, Kapil Saxena, Eunsong Ko, Ihor Hryb, Russell E. Carter, Timothy J. Ebner, Suhasa B. Kodandaramaiah","doi":"10.1038/s41592-024-02434-z","DOIUrl":"10.1038/s41592-024-02434-z","url":null,"abstract":"Technologies that can record neural activity at cellular resolution at multiple spatial and temporal scales are typically much larger than the animals that are being recorded from and are thus limited to recording from head-fixed subjects. Here we have engineered robotic neural recording devices—‘cranial exoskeletons’—that assist mice in maneuvering recording headstages that are orders of magnitude larger and heavier than the mice, while they navigate physical behavioral environments. We discovered optimal controller parameters that enable mice to locomote at physiologically realistic velocities while maintaining natural walking gaits. We show that mice learn to work with the robot to make turns and perform decision-making tasks. Robotic imaging and electrophysiology headstages were used to record recordings of Ca2+ activity of thousands of neurons distributed across the dorsal cortex and spiking activity of hundreds of neurons across multiple brain regions and multiple days, respectively. To avoid head fixation or drawbacks of miniaturized devices for freely moving rodents, a robotic device can move a headstage for microscopy or electrophysiology with the animal, thereby enabling naturalistic behavior.","PeriodicalId":18981,"journal":{"name":"Nature Methods","volume":"21 11","pages":"2171-2181"},"PeriodicalIF":36.1,"publicationDate":"2024-10-07","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142391936","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}
Chromatin modifications are fundamental epigenetic marks that determine genome functions, but it remains challenging to profile those of repetitive elements and complex genomic regions. Here, we develop scNanoSeq-CUT&Tag, a streamlined method, by adapting modified cleavage under targets and tagmentation (CUT&Tag) to the nanopore sequencing platform for genome-wide chromatin modification profiling within individual cells. We show that scNanoSeq-CUT&Tag can accurately profile histone marks and transcription factor occupancy patterns at single-cell resolution as well as distinguish different cell types. scNanoSeq-CUT&Tag efficiently maps the allele-specific chromatin modifications and allows analysis of their neighboring region co-occupancy patterns within individual cells. Moreover, scNanoSeq-CUT&Tag can accurately detect chromatin modifications for individual copies of repetitive elements in both human and mouse genomes. Overall, we prove that scNanoSeq-CUT&Tag is a valuable single-cell tool for efficiently profiling histone marks and transcription factor occupancies, especially for previously poorly studied complex genomic regions and blacklist genomic regions. This work presents scNanoSeq-CUT&Tag, using long-read sequencing to profile histone modifications and DNA-binding proteins at the single-cell level.
{"title":"scNanoSeq-CUT&Tag: a single-cell long-read CUT&Tag sequencing method for efficient chromatin modification profiling within individual cells","authors":"Qingqing Li, Yuqing Guo, Zixin Wu, Xueqiang Xu, Zhenhuan Jiang, Shuyue Qi, Zhenyu Liu, Lu Wen, Fuchou Tang","doi":"10.1038/s41592-024-02453-w","DOIUrl":"10.1038/s41592-024-02453-w","url":null,"abstract":"Chromatin modifications are fundamental epigenetic marks that determine genome functions, but it remains challenging to profile those of repetitive elements and complex genomic regions. Here, we develop scNanoSeq-CUT&Tag, a streamlined method, by adapting modified cleavage under targets and tagmentation (CUT&Tag) to the nanopore sequencing platform for genome-wide chromatin modification profiling within individual cells. We show that scNanoSeq-CUT&Tag can accurately profile histone marks and transcription factor occupancy patterns at single-cell resolution as well as distinguish different cell types. scNanoSeq-CUT&Tag efficiently maps the allele-specific chromatin modifications and allows analysis of their neighboring region co-occupancy patterns within individual cells. Moreover, scNanoSeq-CUT&Tag can accurately detect chromatin modifications for individual copies of repetitive elements in both human and mouse genomes. Overall, we prove that scNanoSeq-CUT&Tag is a valuable single-cell tool for efficiently profiling histone marks and transcription factor occupancies, especially for previously poorly studied complex genomic regions and blacklist genomic regions. This work presents scNanoSeq-CUT&Tag, using long-read sequencing to profile histone modifications and DNA-binding proteins at the single-cell level.","PeriodicalId":18981,"journal":{"name":"Nature Methods","volume":"21 11","pages":"2044-2057"},"PeriodicalIF":36.1,"publicationDate":"2024-10-07","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142391953","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}
Pub Date : 2024-09-30DOI: 10.1038/s41592-024-02466-5
Quantitative and sensitive methods for the detection of pseudouridine (Ψ) have been lacking. Now, a method termed 2-bromoacrylamide-assisted cyclization sequencing (BACS) has been developed that enables the accurate quantification of Ψ stoichiometry, precise identification of Ψ positions and robust detection of densely modified Ψ sites.
{"title":"A method for quantitative and base-resolution sequencing of pseudouridine","authors":"","doi":"10.1038/s41592-024-02466-5","DOIUrl":"10.1038/s41592-024-02466-5","url":null,"abstract":"Quantitative and sensitive methods for the detection of pseudouridine (Ψ) have been lacking. Now, a method termed 2-bromoacrylamide-assisted cyclization sequencing (BACS) has been developed that enables the accurate quantification of Ψ stoichiometry, precise identification of Ψ positions and robust detection of densely modified Ψ sites.","PeriodicalId":18981,"journal":{"name":"Nature Methods","volume":"21 11","pages":"1984-1985"},"PeriodicalIF":36.1,"publicationDate":"2024-09-30","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142350509","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}
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