Nature MethodsPub Date : 2024-12-13DOI: 10.1038/s41592-024-02534-w
Irene Garcia-Gonzalez, Stefano Gambera, Susana F. Rocha, Alvaro Regano, Lourdes Garcia-Ortega, Mariya Lytvyn, Luis Diago-Domingo, Maria S. Sanchez-Muñoz, Aroa Garcia-Cabero, Ivana Zagorac, Wen Luo, Macarena De Andrés-Laguillo, Macarena Fernández-Chacón, Verónica Casquero-Garcia, Federica Francesca Lunella, Carlos Torroja, Fátima Sánchez-Cabo, Rui Benedito
{"title":"iFlpMosaics enable the multispectral barcoding and high-throughput comparative analysis of mutant and wild-type cells","authors":"Irene Garcia-Gonzalez, Stefano Gambera, Susana F. Rocha, Alvaro Regano, Lourdes Garcia-Ortega, Mariya Lytvyn, Luis Diago-Domingo, Maria S. Sanchez-Muñoz, Aroa Garcia-Cabero, Ivana Zagorac, Wen Luo, Macarena De Andrés-Laguillo, Macarena Fernández-Chacón, Verónica Casquero-Garcia, Federica Francesca Lunella, Carlos Torroja, Fátima Sánchez-Cabo, Rui Benedito","doi":"10.1038/s41592-024-02534-w","DOIUrl":"10.1038/s41592-024-02534-w","url":null,"abstract":"To understand gene function, it is necessary to compare cells carrying the mutated target gene with normal cells. In most biomedical studies, the cells being compared are in different mutant and control animals and, therefore, do not experience the same epigenetic changes and tissue microenvironment. The experimental induction of genetic mosaics is essential to determine a gene cell-autonomous function and to model the etiology of diseases caused by somatic mutations. Current technologies used to induce genetic mosaics in mice lack either accuracy, throughput or barcoding diversity. Here we present the iFlpMosaics toolkit comprising a large set of new genetic tools and mouse lines that enable recombinase-dependent ratiometric induction and single-cell clonal tracking of multiple fluorescently labeled wild-type and Cre-mutant cells within the same time window and tissue microenvironment. The labeled cells can be profiled by multispectral imaging or by fluorescence-activated flow cytometry and single-cell RNA sequencing. iFlpMosaics facilitate the induction and analysis of genetic mosaics in any quiescent or progenitor cell, and for any given single or combination of floxed genes, thus enabling a more accurate understanding of how induced genetic mutations affect the biology of single cells during tissue development, homeostasis and disease. iFlpMosaics are a compendium of mouse lines and genetic tools for tissue-agnostic generation and analysis of genetic mosaics.","PeriodicalId":18981,"journal":{"name":"Nature Methods","volume":"22 2","pages":"323-334"},"PeriodicalIF":36.1,"publicationDate":"2024-12-13","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.nature.com/articles/s41592-024-02534-w.pdf","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142822234","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 : 2024-12-12DOI: 10.1038/s41592-024-02578-y
Srijit Seal, Maria-Anna Trapotsi, Ola Spjuth, Shantanu Singh, Jordi Carreras-Puigvert, Nigel Greene, Andreas Bender, Anne E. Carpenter
{"title":"Author Correction: Cell Painting: a decade of discovery and innovation in cellular imaging","authors":"Srijit Seal, Maria-Anna Trapotsi, Ola Spjuth, Shantanu Singh, Jordi Carreras-Puigvert, Nigel Greene, Andreas Bender, Anne E. Carpenter","doi":"10.1038/s41592-024-02578-y","DOIUrl":"10.1038/s41592-024-02578-y","url":null,"abstract":"","PeriodicalId":18981,"journal":{"name":"Nature Methods","volume":"22 2","pages":"447-447"},"PeriodicalIF":36.1,"publicationDate":"2024-12-12","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.nature.com/articles/s41592-024-02578-y.pdf","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142818748","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 : 2024-12-12DOI: 10.1038/s41592-024-02540-y
Matthew Isaacson, Hongyu Chang, Laura Berkowitz, Rick Zirkel, Yusol Park, Danyu Hu, Ian Ellwood, Chris B. Schaffer
{"title":"MouseGoggles: an immersive virtual reality headset for mouse neuroscience and behavior","authors":"Matthew Isaacson, Hongyu Chang, Laura Berkowitz, Rick Zirkel, Yusol Park, Danyu Hu, Ian Ellwood, Chris B. Schaffer","doi":"10.1038/s41592-024-02540-y","DOIUrl":"10.1038/s41592-024-02540-y","url":null,"abstract":"Small-animal virtual reality (VR) systems have become invaluable tools in neuroscience for studying complex behavior during head-fixed neural recording, but they lag behind commercial human VR systems in terms of miniaturization, immersivity and advanced features such as eye tracking. Here we present MouseGoggles, a miniature VR headset for head-fixed mice that delivers independent, binocular visual stimulation over a wide field of view while enabling eye tracking and pupillometry in VR. Neural recordings in the visual cortex validate the quality of image presentation, while hippocampal recordings, associative reward learning and innate fear responses to virtual looming stimuli demonstrate an immersive VR experience. Our open-source system’s simplicity and compact size will enable the broader adoption of VR methods in neuroscience. MouseGoggles is a miniaturized virtual reality (VR) headset for mice that provides an improved immersive experience compared with existing VR equipment. MouseGoggles can also be combined with pupil tracking and has been applied in combination with calcium imaging or electrophysiological recordings.","PeriodicalId":18981,"journal":{"name":"Nature Methods","volume":"22 2","pages":"380-385"},"PeriodicalIF":36.1,"publicationDate":"2024-12-12","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.nature.com/articles/s41592-024-02540-y.pdf","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142818752","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 : 2024-12-12DOI: 10.1038/s41592-024-02554-6
Linda Judák, Gergely Dobos, Katalin Ócsai, Eszter Báthory, Huba Szebik, Balázs Tarján, Pál Maák, Zoltán Szadai, István Takács, Balázs Chiovini, Tibor Lőrincz, Áron Szepesi, Botond Roska, Gergely Szalay, Balázs Rózsa
{"title":"Moculus: an immersive virtual reality system for mice incorporating stereo vision","authors":"Linda Judák, Gergely Dobos, Katalin Ócsai, Eszter Báthory, Huba Szebik, Balázs Tarján, Pál Maák, Zoltán Szadai, István Takács, Balázs Chiovini, Tibor Lőrincz, Áron Szepesi, Botond Roska, Gergely Szalay, Balázs Rózsa","doi":"10.1038/s41592-024-02554-6","DOIUrl":"10.1038/s41592-024-02554-6","url":null,"abstract":"Due to technical roadblocks, it is unclear how visual circuits represent multiple features or how behaviorally relevant representations are selected for long-term memory. Here we developed Moculus, a head-mounted virtual reality platform for mice that covers the entire visual field, and allows binocular depth perception and full visual immersion. This controllable environment, with three-dimensional (3D) corridors and 3D objects, in combination with 3D acousto-optical imaging, affords rapid visual learning and the uncovering of circuit substrates in one measurement session. Both the control and reinforcement-associated visual cue coding neuronal assemblies are transiently expanded by reinforcement feedback to near-saturation levels. This increases computational capability and allows competition among assemblies that encode behaviorally relevant information. The coding assemblies form partially orthogonal and overlapping clusters centered around hub cells with higher and earlier ramp-like responses, as well as locally increased functional connectivity. Moculus is a virtual reality headset for mice that allows realistic display of three-dimensional environments. The system improves performance in visual-learning tasks and can be combined with various microscopes to study neural circuitry.","PeriodicalId":18981,"journal":{"name":"Nature Methods","volume":"22 2","pages":"386-398"},"PeriodicalIF":36.1,"publicationDate":"2024-12-12","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.nature.com/articles/s41592-024-02554-6.pdf","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142818750","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 : 2024-12-10DOI: 10.1038/s41592-024-02560-8
Pallav Kosuri
{"title":"Single-molecule DNA dynamics with graphene energy transfer","authors":"Pallav Kosuri","doi":"10.1038/s41592-024-02560-8","DOIUrl":"10.1038/s41592-024-02560-8","url":null,"abstract":"Graphene energy transfer (GET) can be used to measure the distance between a graphene surface and a fluorescent dye. A new strategy for attaching DNA in a controlled orientation onto graphene now makes it possible to use GET to track the dynamics of DNA and protein–DNA interactions with base-pair resolution.","PeriodicalId":18981,"journal":{"name":"Nature Methods","volume":"22 1","pages":"16-17"},"PeriodicalIF":36.1,"publicationDate":"2024-12-10","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142807732","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 peptide-centric local stability assay enables proteome-scale identification of the protein targets and binding regions of diverse ligands","authors":"Kejia Li, Shijie Chen, Keyun Wang, Yan Wang, Lianji Xue, Yuying Ye, Zheng Fang, Jiawen Lyu, Haiyang Zhu, Yanan Li, Ting Yu, Feng Yang, Xiaolei Zhang, Siqi Guo, Chengfei Ruan, Jiahua Zhou, Qi Wang, Mingming Dong, Cheng Luo, Mingliang Ye","doi":"10.1038/s41592-024-02553-7","DOIUrl":"10.1038/s41592-024-02553-7","url":null,"abstract":"By using a limited-proteolysis strategy that employs a large amount of trypsin to generate peptides directly from native proteins, we found that ligand-induced protein local stability shifts can be sensitively detected on a proteome-wide scale. This enabled us to develop the peptide-centric local stability assay, a modification-free approach that achieves unprecedented sensitivity in proteome-wide target identification and binding-region determination. We demonstrate the broad applications of the peptide-centric local stability assay by investigating interactions across various biological contexts. The peptide-centric local stability assay (PELSA) can be used to determine ligand-binding targets and binding regions on a proteome-wide scale with high sensitivity.","PeriodicalId":18981,"journal":{"name":"Nature Methods","volume":"22 2","pages":"278-282"},"PeriodicalIF":36.1,"publicationDate":"2024-12-10","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142807795","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 : 2024-12-09DOI: 10.1038/s41592-024-02506-0
Jakub Vašíček, Ksenia G. Kuznetsova, Dafni Skiadopoulou, Lucas Unger, Simona Chera, Luiza M. Ghila, Nuno Bandeira, Pål R. Njølstad, Stefan Johansson, Stefan Bruckner, Lukas Käll, Marc Vaudel
{"title":"ProHap enables human proteomic database generation accounting for population diversity","authors":"Jakub Vašíček, Ksenia G. Kuznetsova, Dafni Skiadopoulou, Lucas Unger, Simona Chera, Luiza M. Ghila, Nuno Bandeira, Pål R. Njølstad, Stefan Johansson, Stefan Bruckner, Lukas Käll, Marc Vaudel","doi":"10.1038/s41592-024-02506-0","DOIUrl":"10.1038/s41592-024-02506-0","url":null,"abstract":"Amid the advances in genomics, the availability of large reference panels of human haplotypes is key to account for human diversity within and across populations. However, mass spectrometry-based proteomics does not benefit from this information. To address this gap, we introduce ProHap, a Python-based tool that constructs protein sequence databases from phased genotypes of reference panels. ProHap enables researchers to account for haplotype diversity in proteomic searches. ProHap is a Python-based tool that constructs protein sequence databases from phased genotypes of reference panels to enable researchers to account for haplotype diversity in proteomic searches.","PeriodicalId":18981,"journal":{"name":"Nature Methods","volume":"22 2","pages":"273-277"},"PeriodicalIF":36.1,"publicationDate":"2024-12-09","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142801715","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 : 2024-12-09DOI: 10.1038/s41592-024-02555-5
Nicolò Caporale, Davide Castaldi, Marco Tullio Rigoli, Cristina Cheroni, Alessia Valenti, Sarah Stucchi, Manuel Lessi, Davide Bulgheresi, Sebastiano Trattaro, Martina Pezzali, Alessandro Vitriolo, Alejandro Lopez-Tobon, Matteo Bonfanti, Dario Ricca, Katharina T. Schmid, Matthias Heinig, Fabian J. Theis, Carlo Emanuele Villa, Giuseppe Testa
{"title":"Multiplexing cortical brain organoids for the longitudinal dissection of developmental traits at single-cell resolution","authors":"Nicolò Caporale, Davide Castaldi, Marco Tullio Rigoli, Cristina Cheroni, Alessia Valenti, Sarah Stucchi, Manuel Lessi, Davide Bulgheresi, Sebastiano Trattaro, Martina Pezzali, Alessandro Vitriolo, Alejandro Lopez-Tobon, Matteo Bonfanti, Dario Ricca, Katharina T. Schmid, Matthias Heinig, Fabian J. Theis, Carlo Emanuele Villa, Giuseppe Testa","doi":"10.1038/s41592-024-02555-5","DOIUrl":"10.1038/s41592-024-02555-5","url":null,"abstract":"Dissecting human neurobiology at high resolution and with mechanistic precision requires a major leap in scalability, given the need for experimental designs that include multiple individuals and, prospectively, population cohorts. To lay the foundation for this, we have developed and benchmarked complementary strategies to multiplex brain organoids by pooling cells from different pluripotent stem cell (PSC) lines either during organoid generation (mosaic models) or before single-cell RNA sequencing (scRNA-seq) library preparation (downstream multiplexing). We have also developed a new computational method, SCanSNP, and a consensus call to deconvolve cell identities, overcoming current criticalities in doublets and low-quality cell identification. We validated both multiplexing methods for charting neurodevelopmental trajectories at high resolution, thus linking specific individuals’ trajectories to genetic variation. Finally, we modeled their scalability across different multiplexing combinations and showed that mosaic organoids represent an enabling method for high-throughput settings. Together, this multiplexing suite of experimental and computational methods provides a highly scalable resource for brain disease and neurodiversity modeling. This paper develops two approaches for multiplexing cortical organoids and SCanSNP, a method for deconvolving cell identities, to trace neurodevelopmental trajectories at scale.","PeriodicalId":18981,"journal":{"name":"Nature Methods","volume":"22 2","pages":"358-370"},"PeriodicalIF":36.1,"publicationDate":"2024-12-09","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.nature.com/articles/s41592-024-02555-5.pdf","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142801714","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 : 2024-12-06DOI: 10.1038/s41592-024-02551-9
Arunima Singh
{"title":"Molecular motion in situ","authors":"Arunima Singh","doi":"10.1038/s41592-024-02551-9","DOIUrl":"10.1038/s41592-024-02551-9","url":null,"abstract":"Algorithms help to capture macromolecular motion and structural heterogeneity in native cellular environments.","PeriodicalId":18981,"journal":{"name":"Nature Methods","volume":"21 12","pages":"2229-2230"},"PeriodicalIF":36.1,"publicationDate":"2024-12-06","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142789367","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 : 2024-12-06DOI: 10.1038/s41592-024-02550-w
Lei Tang
{"title":"More dimensions of the 3D genome","authors":"Lei Tang","doi":"10.1038/s41592-024-02550-w","DOIUrl":"10.1038/s41592-024-02550-w","url":null,"abstract":"Advances aim to capture comprehensive, dynamic genome structures in living cells.","PeriodicalId":18981,"journal":{"name":"Nature Methods","volume":"21 12","pages":"2229-2229"},"PeriodicalIF":36.1,"publicationDate":"2024-12-06","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142789400","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}