Pub Date : 2025-11-26DOI: 10.1038/s41587-025-02905-4
Ons M’Saad, Allison Cairns, Jonathan Gulcicek, Ravi Kiran Kasula, Jacob Liao, Ilona Kondratiuk, Emma H. Bewersdorf, Phylicia Kidd, Hanieh Falahati, Juliana E. Gentile, Robert F. Niescier, Katherine Watters, Robert C. Sterner, Seong-il Lee, Xiaojia Guo, Xinran Liu, Gary Desir, Pietro De Camilli, James E. Rothman, Anthony J. Koleske, Thomas Biederer, Aaron T. Kuan, Joerg Bewersdorf
{"title":"All-optical visualization of specific molecules in the ultrastructural context of brain tissue","authors":"Ons M’Saad, Allison Cairns, Jonathan Gulcicek, Ravi Kiran Kasula, Jacob Liao, Ilona Kondratiuk, Emma H. Bewersdorf, Phylicia Kidd, Hanieh Falahati, Juliana E. Gentile, Robert F. Niescier, Katherine Watters, Robert C. Sterner, Seong-il Lee, Xiaojia Guo, Xinran Liu, Gary Desir, Pietro De Camilli, James E. Rothman, Anthony J. Koleske, Thomas Biederer, Aaron T. Kuan, Joerg Bewersdorf","doi":"10.1038/s41587-025-02905-4","DOIUrl":"https://doi.org/10.1038/s41587-025-02905-4","url":null,"abstract":"","PeriodicalId":19084,"journal":{"name":"Nature biotechnology","volume":"148 1","pages":""},"PeriodicalIF":46.9,"publicationDate":"2025-11-26","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145599675","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 : 2025-11-25DOI: 10.1038/s41587-025-02880-w
Simon Alamos, Lucas Waldburger, Amanda Dee, Lauren A. Owens, Rohan Rattan, Shirlyne Ong, Patrick M. Shih
Transcriptional regulators play key roles in plant growth, development and environmental responses; however, understanding how their regulatory activity is encoded at the protein level has been hindered by a lack of multiplexed large-scale methods to characterize protein libraries in planta. Here we present enrichment of nuclear trans -elements reporter assay in plants with sequencing (ENTRAP-seq), a high-throughput method that introduces protein-coding libraries into plant cells to drive a nuclear magnetic sorting-based reporter, enabling multiplexed measurement of regulatory activity from thousands of protein variants. Using ENTRAP-seq and machine learning, we screen 1,495 plant viruses and identify hundreds of putative transcriptional regulatory domains found in structural proteins and enzymes not associated with gene regulation. In addition, we combine ENTRAP-seq with machine-guided design to engineer the activity of a plant transcription factor in a semirational fashion. Our findings demonstrate how scalable protein function assays deployed in planta will enable the characterization of natural and synthetic coding diversity in plants.
{"title":"Multiplexed profiling of transcriptional regulators in plant cells","authors":"Simon Alamos, Lucas Waldburger, Amanda Dee, Lauren A. Owens, Rohan Rattan, Shirlyne Ong, Patrick M. Shih","doi":"10.1038/s41587-025-02880-w","DOIUrl":"https://doi.org/10.1038/s41587-025-02880-w","url":null,"abstract":"Transcriptional regulators play key roles in plant growth, development and environmental responses; however, understanding how their regulatory activity is encoded at the protein level has been hindered by a lack of multiplexed large-scale methods to characterize protein libraries in planta. Here we present enrichment of nuclear <jats:italic>trans</jats:italic> -elements reporter assay in plants with sequencing (ENTRAP-seq), a high-throughput method that introduces protein-coding libraries into plant cells to drive a nuclear magnetic sorting-based reporter, enabling multiplexed measurement of regulatory activity from thousands of protein variants. Using ENTRAP-seq and machine learning, we screen 1,495 plant viruses and identify hundreds of putative transcriptional regulatory domains found in structural proteins and enzymes not associated with gene regulation. In addition, we combine ENTRAP-seq with machine-guided design to engineer the activity of a plant transcription factor in a semirational fashion. Our findings demonstrate how scalable protein function assays deployed in planta will enable the characterization of natural and synthetic coding diversity in plants.","PeriodicalId":19084,"journal":{"name":"Nature biotechnology","volume":"20 1","pages":""},"PeriodicalIF":46.9,"publicationDate":"2025-11-25","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145593903","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 : 2025-11-24DOI: 10.1038/s41587-025-02959-4
Matthew J. Szarzanowicz, Lucas M. Waldburger, Michael Busche, Gina M. Geiselman, Liam D. Kirkpatrick, Alexander J. Kehl, Claudine Tahmin, Rita C. Kuo, Joshua McCauley, Hamreet Pannu, Ruoming Cui, Shuying Liu, Nathan J. Hillson, Jacob O. Brunkard, Jay D. Keasling, John M. Gladden, Mitchell G. Thompson, Patrick M. Shih
{"title":"Author Correction: Binary vector copy number engineering improves Agrobacterium-mediated transformation","authors":"Matthew J. Szarzanowicz, Lucas M. Waldburger, Michael Busche, Gina M. Geiselman, Liam D. Kirkpatrick, Alexander J. Kehl, Claudine Tahmin, Rita C. Kuo, Joshua McCauley, Hamreet Pannu, Ruoming Cui, Shuying Liu, Nathan J. Hillson, Jacob O. Brunkard, Jay D. Keasling, John M. Gladden, Mitchell G. Thompson, Patrick M. Shih","doi":"10.1038/s41587-025-02959-4","DOIUrl":"10.1038/s41587-025-02959-4","url":null,"abstract":"","PeriodicalId":19084,"journal":{"name":"Nature biotechnology","volume":"43 12","pages":"2068-2068"},"PeriodicalIF":41.7,"publicationDate":"2025-11-24","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.nature.comhttps://www.nature.com/articles/s41587-025-02959-4.pdf","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145583020","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 : 2025-11-19DOI: 10.1038/s41587-025-02933-0
Melanie Senior
Biopharma’s reawakened interest in cardiovascular diseases spans new targets and modalities, with more convenient formulations to boost access and adherence.
生物制药对心血管疾病重新燃起的兴趣跨越了新的目标和模式，有了更方便的配方来促进获取和依从性。
{"title":"Heart matters: new treatments, tools and access channels","authors":"Melanie Senior","doi":"10.1038/s41587-025-02933-0","DOIUrl":"10.1038/s41587-025-02933-0","url":null,"abstract":"Biopharma’s reawakened interest in cardiovascular diseases spans new targets and modalities, with more convenient formulations to boost access and adherence.","PeriodicalId":19084,"journal":{"name":"Nature biotechnology","volume":"43 12","pages":"1899-1904"},"PeriodicalIF":41.7,"publicationDate":"2025-11-19","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145545151","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 : 2025-11-19DOI: 10.1038/s41587-025-02923-2
Ken Garber
Each year, Nature Biotechnology highlights companies that received sizeable early-stage funding in the previous year. Firefly Bio seeks to improve on antibody–drug conjugates and proteolysis-targeting chimeras by combining them as degrader–antibody conjugates.
{"title":"Editor’s pick: Firefly Bio","authors":"Ken Garber","doi":"10.1038/s41587-025-02923-2","DOIUrl":"10.1038/s41587-025-02923-2","url":null,"abstract":"Each year, Nature Biotechnology highlights companies that received sizeable early-stage funding in the previous year. Firefly Bio seeks to improve on antibody–drug conjugates and proteolysis-targeting chimeras by combining them as degrader–antibody conjugates.","PeriodicalId":19084,"journal":{"name":"Nature biotechnology","volume":"43 12","pages":"1907-1908"},"PeriodicalIF":41.7,"publicationDate":"2025-11-19","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145545559","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 : 2025-11-19DOI: 10.1038/s41587-025-02929-w
Anca Tacu, Ryan Mellor, Jane Doogan, Jen Reed, Martina Micheletti, Duygu Dikicioglu
{"title":"Need for a shared language and minimum information standards for bioprocess development","authors":"Anca Tacu, Ryan Mellor, Jane Doogan, Jen Reed, Martina Micheletti, Duygu Dikicioglu","doi":"10.1038/s41587-025-02929-w","DOIUrl":"10.1038/s41587-025-02929-w","url":null,"abstract":"","PeriodicalId":19084,"journal":{"name":"Nature biotechnology","volume":"44 1","pages":"19-20"},"PeriodicalIF":41.7,"publicationDate":"2025-11-19","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.nature.comhttps://www.nature.com/articles/s41587-025-02929-w.pdf","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145545152","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 : 2025-11-17DOI: 10.1038/s41587-025-02922-3
Iris Marchal
Each year, Nature Biotechnology highlights companies that received sizeable early-stage funding in the previous year. Red Queen Therapeutics is combating infectious diseases with peptide viral fusion inhibitors.
{"title":"Editor’s pick: Red Queen Therapeutics","authors":"Iris Marchal","doi":"10.1038/s41587-025-02922-3","DOIUrl":"10.1038/s41587-025-02922-3","url":null,"abstract":"Each year, Nature Biotechnology highlights companies that received sizeable early-stage funding in the previous year. Red Queen Therapeutics is combating infectious diseases with peptide viral fusion inhibitors.","PeriodicalId":19084,"journal":{"name":"Nature biotechnology","volume":"43 12","pages":"1905-1906"},"PeriodicalIF":41.7,"publicationDate":"2025-11-17","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145531796","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 : 2025-11-17DOI: 10.1038/s41587-025-02894-4
Yiming Huang, Yiwei Sun, Carlotta Ronda, Chrystal F. Mavros, Jing Li, Justin Jacobse, Lei H. Huang, Samuel J. Resnick, Marla Giddins, Daniel E. Freedberg, Alejandro Chavez, Jeremy A. Goettel, Harris H. Wang
{"title":"Fecal exfoliome sequencing captures immune dynamics of the healthy and inflamed gut","authors":"Yiming Huang, Yiwei Sun, Carlotta Ronda, Chrystal F. Mavros, Jing Li, Justin Jacobse, Lei H. Huang, Samuel J. Resnick, Marla Giddins, Daniel E. Freedberg, Alejandro Chavez, Jeremy A. Goettel, Harris H. Wang","doi":"10.1038/s41587-025-02894-4","DOIUrl":"https://doi.org/10.1038/s41587-025-02894-4","url":null,"abstract":"","PeriodicalId":19084,"journal":{"name":"Nature biotechnology","volume":"127 1","pages":""},"PeriodicalIF":46.9,"publicationDate":"2025-11-17","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145531794","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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