Nature biotechnology最新文献_第10页

Model-directed generation of artificial CRISPR–Cas13a guide RNA sequences improves nucleic acid detection 以模型为导向生成人工 CRISPR-Cas13a 引导 RNA 序列，提高核酸检测能力

IF 46.9 1区生物学

Nature biotechnology Pub Date : 2024-10-11 DOI: 10.1038/s41587-024-02422-w

Sreekar Mantena, Priya P. Pillai, Brittany A. Petros, Nicole L. Welch, Cameron Myhrvold, Pardis C. Sabeti, Hayden C. Metsky

引用次数: 0

An antigen discovery pipeline integrates multi-omics data and informs immunotherapy 抗原发现管道整合了多组学数据并为免疫疗法提供信息

IF 46.9 1区生物学

Nature biotechnology Pub Date : 2024-10-11 DOI: 10.1038/s41587-024-02427-5

引用次数: 0

One-step nanoscale expansion microscopy reveals individual protein shapes 一步式纳米级扩展显微镜揭示单个蛋白质的形状

IF 46.9 1区生物学

Nature biotechnology Pub Date : 2024-10-09 DOI: 10.1038/s41587-024-02431-9

Ali H. Shaib, Abed Alrahman Chouaib, Rajdeep Chowdhury, Jonas Altendorf, Daniel Mihaylov, Chi Zhang, Donatus Krah, Vanessa Imani, Russell K. W. Spencer, Svilen Veselinov Georgiev, Nikolaos Mougios, Mehar Monga, Sofiia Reshetniak, Tiago Mimoso, Han Chen, Parisa Fatehbasharzad, Dagmar Crzan, Kim-Ann Saal, Mohamad Mahdi Alawieh, Nadia Alawar, Janna Eilts, Jinyoung Kang, Alireza Soleimani, Marcus Müller, Constantin Pape, Luis Alvarez, Claudia Trenkwalder, Brit Mollenhauer, Tiago F. Outeiro, Sarah Köster, Julia Preobraschenski, Ute Becherer, Tobias Moser, Edward S. Boyden, A. Radu Aricescu, Markus Sauer, Felipe Opazo, Silvio O. Rizzoli

{"title":"One-step nanoscale expansion microscopy reveals individual protein shapes","authors":"Ali H. Shaib, Abed Alrahman Chouaib, Rajdeep Chowdhury, Jonas Altendorf, Daniel Mihaylov, Chi Zhang, Donatus Krah, Vanessa Imani, Russell K. W. Spencer, Svilen Veselinov Georgiev, Nikolaos Mougios, Mehar Monga, Sofiia Reshetniak, Tiago Mimoso, Han Chen, Parisa Fatehbasharzad, Dagmar Crzan, Kim-Ann Saal, Mohamad Mahdi Alawieh, Nadia Alawar, Janna Eilts, Jinyoung Kang, Alireza Soleimani, Marcus Müller, Constantin Pape, Luis Alvarez, Claudia Trenkwalder, Brit Mollenhauer, Tiago F. Outeiro, Sarah Köster, Julia Preobraschenski, Ute Becherer, Tobias Moser, Edward S. Boyden, A. Radu Aricescu, Markus Sauer, Felipe Opazo, Silvio O. Rizzoli","doi":"10.1038/s41587-024-02431-9","DOIUrl":"https://doi.org/10.1038/s41587-024-02431-9","url":null,"abstract":"The attainable resolution of fluorescence microscopy has reached the subnanometer range, but this technique still fails to image the morphology of single proteins or small molecular complexes. Here, we expand the specimens at least tenfold, label them with conventional fluorophores and image them with conventional light microscopes, acquiring videos in which we analyze fluorescence fluctuations. One-step nanoscale expansion (ONE) microscopy enables the visualization of the shapes of individual membrane and soluble proteins, achieving around 1-nm resolution. We show that conformational changes are readily observable, such as those undergone by the ~17-kDa protein calmodulin upon Ca2+ binding. ONE is also applied to clinical samples, analyzing the morphology of protein aggregates in cerebrospinal fluid from persons with Parkinson disease, potentially aiding disease diagnosis. This technology bridges the gap between high-resolution structural biology techniques and light microscopy, providing new avenues for discoveries in biology and medicine.","PeriodicalId":19084,"journal":{"name":"Nature biotechnology","volume":"30 1","pages":""},"PeriodicalIF":46.9,"publicationDate":"2024-10-09","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142385123","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

A circularly permuted CasRx platform for efficient, site-specific RNA editing 用于高效、特定位点 RNA 编辑的环状包被 CasRx 平台

IF 46.9 1区生物学

Nature biotechnology Pub Date : 2024-10-09 DOI: 10.1038/s41587-024-02430-w

Yuanming Wang, Kaiwen Ivy Liu, Mengying Mandy Liu, Kean Hean Ooi, Tram Anh Nguyen, Jiunn En Chee, Shun Xiang Danny Teo, Shan He, Jie Wen Douglas Tay, Seok Yee Teo, Kai Shin Liew, Xiao Yu Ge, Zhi Jian Ng, Hasmik Avagyan, Hao Liu, Zirong Yi, Keziah Chang, Eng Piew Louis Kok, Runjia Chen, Chun En Yau, Jun Wei Koh, Yue Wan, Meng How Tan

{"title":"A circularly permuted CasRx platform for efficient, site-specific RNA editing","authors":"Yuanming Wang, Kaiwen Ivy Liu, Mengying Mandy Liu, Kean Hean Ooi, Tram Anh Nguyen, Jiunn En Chee, Shun Xiang Danny Teo, Shan He, Jie Wen Douglas Tay, Seok Yee Teo, Kai Shin Liew, Xiao Yu Ge, Zhi Jian Ng, Hasmik Avagyan, Hao Liu, Zirong Yi, Keziah Chang, Eng Piew Louis Kok, Runjia Chen, Chun En Yau, Jun Wei Koh, Yue Wan, Meng How Tan","doi":"10.1038/s41587-024-02430-w","DOIUrl":"https://doi.org/10.1038/s41587-024-02430-w","url":null,"abstract":"Inactive Cas13 orthologs have been fused to a mutant human ADAR2 deaminase domain at the C terminus to enable programmable adenosine-to-inosine (A-to-I) RNA editing in selected transcripts. Although promising, existing RNA-editing tools generally suffer from a trade-off between efficacy and specificity, and off-target editing remains an unsolved problem. Here we describe the development of an optimized RNA-editing platform by rational protein engineering, CasRx-based Programmable Editing of RNA Technology (xPERT). We demonstrate that the topological rearrangement of a CasRx K940L mutant by circular permutation results in a robust scaffold for the tethering of a deaminase domain. We benchmark our tool against the REPAIR system and show that xPERT exhibits strong on-target activity like REPAIRv1 but low off-target editing like REPAIRv2. Our xPERT platform can be used to alter RNA sequence information without risking genome damage, effect temporary cellular changes and customize protein function.","PeriodicalId":19084,"journal":{"name":"Nature biotechnology","volume":"58 1","pages":""},"PeriodicalIF":46.9,"publicationDate":"2024-10-09","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142385124","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

Rapid species-level metagenome profiling and containment estimation with sylph 利用 sylph 快速绘制物种级元基因组图谱并估算遏制率

IF 46.9 1区生物学

Nature biotechnology Pub Date : 2024-10-08 DOI: 10.1038/s41587-024-02412-y

Jim Shaw, Yun William Yu

{"title":"Rapid species-level metagenome profiling and containment estimation with sylph","authors":"Jim Shaw, Yun William Yu","doi":"10.1038/s41587-024-02412-y","DOIUrl":"https://doi.org/10.1038/s41587-024-02412-y","url":null,"abstract":"Profiling metagenomes against databases allows for the detection and quantification of microorganisms, even at low abundances where assembly is not possible. We introduce sylph, a species-level metagenome profiler that estimates genome-to-metagenome containment average nucleotide identity (ANI) through zero-inflated Poisson k-mer statistics, enabling ANI-based taxa detection. On the Critical Assessment of Metagenome Interpretation II (CAMI2) Marine dataset, sylph was the most accurate profiling method of seven tested. For multisample profiling, sylph took >10-fold less central processing unit time compared to Kraken2 and used 30-fold less memory. Sylph’s ANI estimates provided an orthogonal signal to abundance, allowing for an ANI-based metagenome-wide association study for Parkinson disease (PD) against 289,232 genomes while confirming known butyrate–PD associations at the strain level. Sylph took <1 min and 16 GB of random-access memory to profile metagenomes against 85,205 prokaryotic and 2,917,516 viral genomes, detecting 30-fold more viral sequences in the human gut compared to RefSeq. Sylph offers precise, efficient profiling with accurate containment ANI estimation even for low-coverage genomes.","PeriodicalId":19084,"journal":{"name":"Nature biotechnology","volume":"10 1","pages":""},"PeriodicalIF":46.9,"publicationDate":"2024-10-08","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142384472","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

Author Correction: The cost of drug patent expiration date errors 作者更正：药品专利到期日错误的代价

IF 33.1 1区生物学

Nature biotechnology Pub Date : 2024-10-08 DOI: 10.1038/s41587-024-02459-x

S. Sean Tu, Dinis Cheian, Sarah Gabriele, Benjamin N. Rome, Aaron S. Kesselheim

引用次数: 0

A framework for expanding discovery efforts with compressed phenotypic screens 利用压缩表型筛选扩大发现工作的框架

IF 46.9 1区生物学

Nature biotechnology Pub Date : 2024-10-07 DOI: 10.1038/s41587-024-02404-y

引用次数: 0

Author Correction: Efficient genetic code expansion without host genome modifications 作者更正：无需修改宿主基因组即可高效扩展遗传密码

IF 46.9 1区生物学

Nature biotechnology Pub Date : 2024-10-07 DOI: 10.1038/s41587-024-02454-2

Alan Costello, Alexander A. Peterson, David L. Lanster, Zhiyi Li, Gavriela D. Carver, Ahmed H. Badran

引用次数: 0

Mapping multimodal phenotypes to perturbations in cells and tissue with CRISPRmap 利用 CRISPRmap 将多模式表型映射到细胞和组织的扰动上

IF 46.9 1区生物学

Nature biotechnology Pub Date : 2024-10-07 DOI: 10.1038/s41587-024-02386-x

Jiacheng Gu, Abhishek Iyer, Ben Wesley, Angelo Taglialatela, Giuseppe Leuzzi, Sho Hangai, Aubrianna Decker, Ruoyu Gu, Naomi Klickstein, Yuanlong Shuai, Kristina Jankovic, Lucy Parker-Burns, Yinuo Jin, Jia Yi Zhang, Justin Hong, Xiang Niu, Jonathon A. Costa, Mikael G. Pezet, Jacqueline Chou, Hans-Willem Snoeck, Dan A. Landau, Elham Azizi, Edmond M. Chan, Alberto Ciccia, Jellert T. Gaublomme

{"title":"Mapping multimodal phenotypes to perturbations in cells and tissue with CRISPRmap","authors":"Jiacheng Gu, Abhishek Iyer, Ben Wesley, Angelo Taglialatela, Giuseppe Leuzzi, Sho Hangai, Aubrianna Decker, Ruoyu Gu, Naomi Klickstein, Yuanlong Shuai, Kristina Jankovic, Lucy Parker-Burns, Yinuo Jin, Jia Yi Zhang, Justin Hong, Xiang Niu, Jonathon A. Costa, Mikael G. Pezet, Jacqueline Chou, Hans-Willem Snoeck, Dan A. Landau, Elham Azizi, Edmond M. Chan, Alberto Ciccia, Jellert T. Gaublomme","doi":"10.1038/s41587-024-02386-x","DOIUrl":"https://doi.org/10.1038/s41587-024-02386-x","url":null,"abstract":"Unlike sequencing-based methods, which require cell lysis, optical pooled genetic screens enable investigation of spatial phenotypes, including cell morphology, protein subcellular localization, cell–cell interactions and tissue organization, in response to targeted CRISPR perturbations. Here we report a multimodal optical pooled CRISPR screening method, which we call CRISPRmap. CRISPRmap combines in situ CRISPR guide-identifying barcode readout with multiplexed immunofluorescence and RNA detection. Barcodes are detected and read out through combinatorial hybridization of DNA oligos, enhancing barcode detection efficiency. CRISPRmap enables in situ barcode readout in cell types and contexts that were elusive to conventional optical pooled screening, including cultured primary cells, embryonic stem cells, induced pluripotent stem cells, derived neurons and in vivo cells in a tissue context. We conducted a screen in a breast cancer cell line of the effects of DNA damage repair gene variants on cellular responses to commonly used cancer therapies, and we show that optical phenotyping pinpoints likely pathogenic patient-derived mutations that were previously classified as variants of unknown clinical significance.","PeriodicalId":19084,"journal":{"name":"Nature biotechnology","volume":"18 1","pages":""},"PeriodicalIF":46.9,"publicationDate":"2024-10-07","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142383681","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

Scalable, compressed phenotypic screening using pooled perturbations 利用集合扰动进行可扩展的压缩表型筛选

IF 46.9 1区生物学

Nature biotechnology Pub Date : 2024-10-07 DOI: 10.1038/s41587-024-02403-z

Nuo Liu, Walaa E. Kattan, Benjamin E. Mead, Conner Kummerlowe, Thomas Cheng, Sarah Ingabire, Jaime H. Cheah, Christian K. Soule, Anita Vrcic, Jane K. McIninch, Sergio Triana, Manuel Guzman, Tyler T. Dao, Joshua M. Peters, Kristen E. Lowder, Lorin Crawford, Ava P. Amini, Paul C. Blainey, William C. Hahn, Brian Cleary, Bryan Bryson, Peter S. Winter, Srivatsan Raghavan, Alex K. Shalek

{"title":"Scalable, compressed phenotypic screening using pooled perturbations","authors":"Nuo Liu, Walaa E. Kattan, Benjamin E. Mead, Conner Kummerlowe, Thomas Cheng, Sarah Ingabire, Jaime H. Cheah, Christian K. Soule, Anita Vrcic, Jane K. McIninch, Sergio Triana, Manuel Guzman, Tyler T. Dao, Joshua M. Peters, Kristen E. Lowder, Lorin Crawford, Ava P. Amini, Paul C. Blainey, William C. Hahn, Brian Cleary, Bryan Bryson, Peter S. Winter, Srivatsan Raghavan, Alex K. Shalek","doi":"10.1038/s41587-024-02403-z","DOIUrl":"https://doi.org/10.1038/s41587-024-02403-z","url":null,"abstract":"High-throughput phenotypic screens using biochemical perturbations and high-content readouts are constrained by limitations of scale. To address this, we establish a method of pooling exogenous perturbations followed by computational deconvolution to reduce required sample size, labor and cost. We demonstrate the increased efficiency of compressed experimental designs compared to conventional approaches through benchmarking with a bioactive small-molecule library and a high-content imaging readout. We then apply compressed screening in two biological discovery campaigns. In the first, we use early-passage pancreatic cancer organoids to map transcriptional responses to a library of recombinant tumor microenvironment protein ligands, uncovering reproducible phenotypic shifts induced by specific ligands distinct from canonical reference signatures and correlated with clinical outcome. In the second, we identify the pleotropic modulatory effects of a chemical compound library with known mechanisms of action on primary human peripheral blood mononuclear cell immune responses. In sum, our approach empowers phenotypic screens with information-rich readouts to advance drug discovery efforts and basic biological inquiry.","PeriodicalId":19084,"journal":{"name":"Nature biotechnology","volume":"12 1","pages":""},"PeriodicalIF":46.9,"publicationDate":"2024-10-07","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142383680","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