Pub Date : 2024-10-21DOI: 10.1038/s41592-024-02461-w
We developed LABEL-seq, a platform that enables measurement of protein properties and functions at scale by leveraging the intracellular self-assembly of an RNA-binding domain (RBD) and protein-encoding RNA barcode. Enrichment of RBD–protein fusions, followed by high-throughput sequencing of the co-enriched barcodes, enables the profiling of protein abundance, activity, interactions and druggability at scale.
{"title":"Measuring multiple intracellular biochemical properties of proteins with next-generation sequencing","authors":"","doi":"10.1038/s41592-024-02461-w","DOIUrl":"10.1038/s41592-024-02461-w","url":null,"abstract":"We developed LABEL-seq, a platform that enables measurement of protein properties and functions at scale by leveraging the intracellular self-assembly of an RNA-binding domain (RBD) and protein-encoding RNA barcode. Enrichment of RBD–protein fusions, followed by high-throughput sequencing of the co-enriched barcodes, enables the profiling of protein abundance, activity, interactions and druggability at scale.","PeriodicalId":18981,"journal":{"name":"Nature Methods","volume":"21 11","pages":"1988-1989"},"PeriodicalIF":36.1,"publicationDate":"2024-10-21","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142470443","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 : 2024-10-21DOI: 10.1038/s41592-024-02479-0
Xiao Wang, Han Zhu, Genki Terashi, Manav Taluja, Daisuke Kihara
Cryogenic electron microscopy (cryo-EM) has now been widely used for determining multichain protein complexes. However, modeling a large complex structure, such as those with more than ten chains, is challenging, particularly when the map resolution decreases. Here we present DiffModeler, a fully automated method for modeling large protein complex structures. DiffModeler employs a diffusion model for backbone tracing and integrates AlphaFold2-predicted single-chain structures for structure fitting. DiffModeler showed an average template modeling score of 0.88 and 0.91 for two datasets of cryo-EM maps of 0-5 Å resolution and 0.92 for intermediate resolution maps (5-10 Å), substantially outperforming existing methodologies. Further benchmarking at low resolutions (10-20 Å) confirms its versatility, demonstrating plausible performance.
{"title":"DiffModeler: large macromolecular structure modeling for cryo-EM maps using a diffusion model.","authors":"Xiao Wang, Han Zhu, Genki Terashi, Manav Taluja, Daisuke Kihara","doi":"10.1038/s41592-024-02479-0","DOIUrl":"10.1038/s41592-024-02479-0","url":null,"abstract":"<p><p>Cryogenic electron microscopy (cryo-EM) has now been widely used for determining multichain protein complexes. However, modeling a large complex structure, such as those with more than ten chains, is challenging, particularly when the map resolution decreases. Here we present DiffModeler, a fully automated method for modeling large protein complex structures. DiffModeler employs a diffusion model for backbone tracing and integrates AlphaFold2-predicted single-chain structures for structure fitting. DiffModeler showed an average template modeling score of 0.88 and 0.91 for two datasets of cryo-EM maps of 0-5 Å resolution and 0.92 for intermediate resolution maps (5-10 Å), substantially outperforming existing methodologies. Further benchmarking at low resolutions (10-20 Å) confirms its versatility, demonstrating plausible performance.</p>","PeriodicalId":18981,"journal":{"name":"Nature Methods","volume":" ","pages":""},"PeriodicalIF":36.1,"publicationDate":"2024-10-21","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142470439","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 : 2024-10-21DOI: 10.1038/s41592-024-02402-7
Rayan Chikhi, Yoann Dufresne, Paul Medvedev
Pangenome graphs signify a new frontier in genome representation. Recent advances in constructing and personalizing them mark progress in this area.
庞基因组图谱标志着基因组表示的一个新领域。最近在构建和个性化方面取得的进展标志着这一领域的进步。
{"title":"Constructing and personalizing population pangenome graphs","authors":"Rayan Chikhi, Yoann Dufresne, Paul Medvedev","doi":"10.1038/s41592-024-02402-7","DOIUrl":"10.1038/s41592-024-02402-7","url":null,"abstract":"Pangenome graphs signify a new frontier in genome representation. Recent advances in constructing and personalizing them mark progress in this area.","PeriodicalId":18981,"journal":{"name":"Nature Methods","volume":"21 11","pages":"1980-1981"},"PeriodicalIF":36.1,"publicationDate":"2024-10-21","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142470438","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 : 2024-10-21DOI: 10.1038/s41592-024-02456-7
Jessica J. Simon, Douglas M. Fowler, Dustin J. Maly
Here we describe labeling with barcodes and enrichment for biochemical analysis by sequencing (LABEL-seq), an assay for massively parallel profiling of pooled protein variants in human cells. By leveraging the intracellular self-assembly of an RNA-binding domain (RBD) with a stable, variant-encoding RNA barcode, LABEL-seq facilitates the direct measurement of protein properties and functions using simple affinity enrichments of RBD protein fusions, followed by high-throughput sequencing of co-enriched barcodes. Measurement of ~20,000 variant effects for ~1,600 BRaf variants revealed that variation at positions frequently mutated in cancer minimally impacted intracellular abundance but could dramatically alter activity, protein–protein interactions and druggability. Integrative analysis identified networks of positions with similar biochemical roles and enabled modeling of variant effects on cell proliferation and small molecule-promoted degradation. Thus, LABEL-seq enables direct measurement of multiple biochemical properties in a native cellular context, providing insights into protein function, disease mechanisms and druggability. Labeling with barcodes and enrichment for biochemical analysis by sequencing (LABEL-seq) enables massively parallel profiling of thousands of pooled protein variants in cells, yielding insight into protein function, interactions and druggability.
{"title":"Multiplexed profiling of intracellular protein abundance, activity, interactions and druggability with LABEL-seq","authors":"Jessica J. Simon, Douglas M. Fowler, Dustin J. Maly","doi":"10.1038/s41592-024-02456-7","DOIUrl":"10.1038/s41592-024-02456-7","url":null,"abstract":"Here we describe labeling with barcodes and enrichment for biochemical analysis by sequencing (LABEL-seq), an assay for massively parallel profiling of pooled protein variants in human cells. By leveraging the intracellular self-assembly of an RNA-binding domain (RBD) with a stable, variant-encoding RNA barcode, LABEL-seq facilitates the direct measurement of protein properties and functions using simple affinity enrichments of RBD protein fusions, followed by high-throughput sequencing of co-enriched barcodes. Measurement of ~20,000 variant effects for ~1,600 BRaf variants revealed that variation at positions frequently mutated in cancer minimally impacted intracellular abundance but could dramatically alter activity, protein–protein interactions and druggability. Integrative analysis identified networks of positions with similar biochemical roles and enabled modeling of variant effects on cell proliferation and small molecule-promoted degradation. Thus, LABEL-seq enables direct measurement of multiple biochemical properties in a native cellular context, providing insights into protein function, disease mechanisms and druggability. Labeling with barcodes and enrichment for biochemical analysis by sequencing (LABEL-seq) enables massively parallel profiling of thousands of pooled protein variants in cells, yielding insight into protein function, interactions and druggability.","PeriodicalId":18981,"journal":{"name":"Nature Methods","volume":"21 11","pages":"2094-2106"},"PeriodicalIF":36.1,"publicationDate":"2024-10-21","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142470444","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 : 2024-10-21DOI: 10.1038/s41592-024-02430-3
Erik Garrison, Andrea Guarracino, Simon Heumos, Flavia Villani, Zhigui Bao, Lorenzo Tattini, Jörg Hagmann, Sebastian Vorbrugg, Santiago Marco-Sola, Christian Kubica, David G. Ashbrook, Kaisa Thorell, Rachel L. Rusholme-Pilcher, Gianni Liti, Emilio Rudbeck, Agnieszka A. Golicz, Sven Nahnsen, Zuyu Yang, Moses Njagi Mwaniki, Franklin L. Nobrega, Yi Wu, Hao Chen, Joep de Ligt, Peter H. Sudmant, Sanwen Huang, Detlef Weigel, Nicole Soranzo, Vincenza Colonna, Robert W. Williams, Pjotr Prins
Pangenome graphs can represent all variation between multiple reference genomes, but current approaches to build them exclude complex sequences or are based upon a single reference. In response, we developed the PanGenome Graph Builder, a pipeline for constructing pangenome graphs without bias or exclusion. The PanGenome Graph Builder uses all-to-all alignments to build a variation graph in which we can identify variation, measure conservation, detect recombination events and infer phylogenetic relationships. PGGB is a modular framework for efficiently building unbiased pangenome graphs, supporting diverse downstream analyses.
{"title":"Building pangenome graphs","authors":"Erik Garrison, Andrea Guarracino, Simon Heumos, Flavia Villani, Zhigui Bao, Lorenzo Tattini, Jörg Hagmann, Sebastian Vorbrugg, Santiago Marco-Sola, Christian Kubica, David G. Ashbrook, Kaisa Thorell, Rachel L. Rusholme-Pilcher, Gianni Liti, Emilio Rudbeck, Agnieszka A. Golicz, Sven Nahnsen, Zuyu Yang, Moses Njagi Mwaniki, Franklin L. Nobrega, Yi Wu, Hao Chen, Joep de Ligt, Peter H. Sudmant, Sanwen Huang, Detlef Weigel, Nicole Soranzo, Vincenza Colonna, Robert W. Williams, Pjotr Prins","doi":"10.1038/s41592-024-02430-3","DOIUrl":"10.1038/s41592-024-02430-3","url":null,"abstract":"Pangenome graphs can represent all variation between multiple reference genomes, but current approaches to build them exclude complex sequences or are based upon a single reference. In response, we developed the PanGenome Graph Builder, a pipeline for constructing pangenome graphs without bias or exclusion. The PanGenome Graph Builder uses all-to-all alignments to build a variation graph in which we can identify variation, measure conservation, detect recombination events and infer phylogenetic relationships. PGGB is a modular framework for efficiently building unbiased pangenome graphs, supporting diverse downstream analyses.","PeriodicalId":18981,"journal":{"name":"Nature Methods","volume":"21 11","pages":"2008-2012"},"PeriodicalIF":36.1,"publicationDate":"2024-10-21","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142470437","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 : 2024-10-17DOI: 10.1038/s41592-024-02473-6
Very high-resolution images of the human brain obtained in vivo in a few minutes with MRI at an ultra-high magnetic field of 11.7 T reveal exquisite details. Biological and behavioral tests confirm the safety of the method, opening the door for human brain exploration at mesoscale resolution.
在 11.7 T 的超高磁场下，通过核磁共振成像技术在几分钟内获得的人体大脑超高分辨率图像揭示了精致的细节。生物和行为测试证实了这种方法的安全性，为以中尺度分辨率探索人脑打开了大门。
{"title":"Ultra-high-field MRI for fast imaging of the human brain at mesoscale resolution","authors":"","doi":"10.1038/s41592-024-02473-6","DOIUrl":"10.1038/s41592-024-02473-6","url":null,"abstract":"Very high-resolution images of the human brain obtained in vivo in a few minutes with MRI at an ultra-high magnetic field of 11.7 T reveal exquisite details. Biological and behavioral tests confirm the safety of the method, opening the door for human brain exploration at mesoscale resolution.","PeriodicalId":18981,"journal":{"name":"Nature Methods","volume":"21 11","pages":"1982-1983"},"PeriodicalIF":36.1,"publicationDate":"2024-10-17","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142470447","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 : 2024-10-17DOI: 10.1038/s41592-024-02472-7
Nicolas Boulant, Franck Mauconduit, Vincent Gras, Alexis Amadon, Caroline Le Ster, Michel Luong, Aurélien Massire, Christophe Pallier, Laure Sabatier, Michel Bottlaender, Alexandre Vignaud, Denis Le Bihan
The understanding of the human brain is one of the main scientific challenges of the twenty-first century. In the early 2000s, the French Atomic Energy Commission launched a program to conceive and build a human magnetic resonance imaging scanner operating at 11.7 T. We have now acquired human brain images in vivo at such a magnetic field. We deployed parallel transmission tools to mitigate the radiofrequency field inhomogeneity problem and tame the specific absorption rate. The safety of human imaging at such high field strength was demonstrated using physiological, vestibular, behavioral and genotoxicity measurements on the imaged volunteers. Our technology yields T2 and T2*-weighted images reaching mesoscale resolutions within short acquisition times and with a high signal and contrast-to-noise ratio. In a technological tour de force, a whole-body 11.7-T MRI scanner has been developed. Here images of the human brain are presented while safety for the imaged human volunteers has been ascertained.
了解人类大脑是二十一世纪的主要科学挑战之一。本世纪初，法国原子能委员会启动了一项计划，构想并建造一台在 11.7 T 下工作的人体磁共振成像扫描仪。现在，我们已经在这样的磁场下获取了活体人脑图像。我们采用并行传输工具来缓解射频场不均匀性问题，并控制比吸收率。通过对成像志愿者进行生理、前庭、行为和遗传毒性测量，证明了在如此高的磁场强度下进行人体成像的安全性。我们的技术能在较短的采集时间内获得达到中尺度分辨率的 T2 和 T2* 加权图像，并具有较高的信号和对比度-噪声比。
{"title":"In vivo imaging of the human brain with the Iseult 11.7-T MRI scanner","authors":"Nicolas Boulant, Franck Mauconduit, Vincent Gras, Alexis Amadon, Caroline Le Ster, Michel Luong, Aurélien Massire, Christophe Pallier, Laure Sabatier, Michel Bottlaender, Alexandre Vignaud, Denis Le Bihan","doi":"10.1038/s41592-024-02472-7","DOIUrl":"10.1038/s41592-024-02472-7","url":null,"abstract":"The understanding of the human brain is one of the main scientific challenges of the twenty-first century. In the early 2000s, the French Atomic Energy Commission launched a program to conceive and build a human magnetic resonance imaging scanner operating at 11.7 T. We have now acquired human brain images in vivo at such a magnetic field. We deployed parallel transmission tools to mitigate the radiofrequency field inhomogeneity problem and tame the specific absorption rate. The safety of human imaging at such high field strength was demonstrated using physiological, vestibular, behavioral and genotoxicity measurements on the imaged volunteers. Our technology yields T2 and T2*-weighted images reaching mesoscale resolutions within short acquisition times and with a high signal and contrast-to-noise ratio. In a technological tour de force, a whole-body 11.7-T MRI scanner has been developed. Here images of the human brain are presented while safety for the imaged human volunteers has been ascertained.","PeriodicalId":18981,"journal":{"name":"Nature Methods","volume":"21 11","pages":"2013-2016"},"PeriodicalIF":36.1,"publicationDate":"2024-10-17","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.nature.com/articles/s41592-024-02472-7.pdf","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142470441","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 : 2024-10-17DOI: 10.1038/s41592-024-02475-4
Xiongtao Ruan, Matthew Mueller, Gaoxiang Liu, Frederik Görlitz, Tian-Ming Fu, Daniel E Milkie, Joshua L Lillvis, Alexander Kuhn, Johnny Gan Chong, Jason Li Hong, Chu Yi Aaron Herr, Wilmene Hercule, Marc Nienhaus, Alison N Killilea, Eric Betzig, Srigokul Upadhyayula
Light sheet microscopy is a powerful technique for high-speed three-dimensional imaging of subcellular dynamics and large biological specimens. However, it often generates datasets ranging from hundreds of gigabytes to petabytes in size for a single experiment. Conventional computational tools process such images far slower than the time to acquire them and often fail outright due to memory limitations. To address these challenges, we present PetaKit5D, a scalable software solution for efficient petabyte-scale light sheet image processing. This software incorporates a suite of commonly used processing tools that are optimized for memory and performance. Notable advancements include rapid image readers and writers, fast and memory-efficient geometric transformations, high-performance Richardson-Lucy deconvolution and scalable Zarr-based stitching. These features outperform state-of-the-art methods by over one order of magnitude, enabling the processing of petabyte-scale image data at the full teravoxel rates of modern imaging cameras. The software opens new avenues for biological discoveries through large-scale imaging experiments.
{"title":"Image processing tools for petabyte-scale light sheet microscopy data.","authors":"Xiongtao Ruan, Matthew Mueller, Gaoxiang Liu, Frederik Görlitz, Tian-Ming Fu, Daniel E Milkie, Joshua L Lillvis, Alexander Kuhn, Johnny Gan Chong, Jason Li Hong, Chu Yi Aaron Herr, Wilmene Hercule, Marc Nienhaus, Alison N Killilea, Eric Betzig, Srigokul Upadhyayula","doi":"10.1038/s41592-024-02475-4","DOIUrl":"https://doi.org/10.1038/s41592-024-02475-4","url":null,"abstract":"<p><p>Light sheet microscopy is a powerful technique for high-speed three-dimensional imaging of subcellular dynamics and large biological specimens. However, it often generates datasets ranging from hundreds of gigabytes to petabytes in size for a single experiment. Conventional computational tools process such images far slower than the time to acquire them and often fail outright due to memory limitations. To address these challenges, we present PetaKit5D, a scalable software solution for efficient petabyte-scale light sheet image processing. This software incorporates a suite of commonly used processing tools that are optimized for memory and performance. Notable advancements include rapid image readers and writers, fast and memory-efficient geometric transformations, high-performance Richardson-Lucy deconvolution and scalable Zarr-based stitching. These features outperform state-of-the-art methods by over one order of magnitude, enabling the processing of petabyte-scale image data at the full teravoxel rates of modern imaging cameras. The software opens new avenues for biological discoveries through large-scale imaging experiments.</p>","PeriodicalId":18981,"journal":{"name":"Nature Methods","volume":" ","pages":""},"PeriodicalIF":36.1,"publicationDate":"2024-10-17","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142470440","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 : 2024-10-15DOI: 10.1038/s41592-024-02490-5
Vivien Marx
When spouses are both scientists, they mix the typical research career decisions with some marriage-related ones.
当配偶双方都是科学家时，他们在做出典型的研究职业决定的同时，也会做出一些与婚姻有关的决定。
{"title":"Scientists who marry scientists","authors":"Vivien Marx","doi":"10.1038/s41592-024-02490-5","DOIUrl":"10.1038/s41592-024-02490-5","url":null,"abstract":"When spouses are both scientists, they mix the typical research career decisions with some marriage-related ones.","PeriodicalId":18981,"journal":{"name":"Nature Methods","volume":"21 11","pages":"1962-1963"},"PeriodicalIF":36.1,"publicationDate":"2024-10-15","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142470446","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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