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Data sharing in the age of deep learning
doi : 10.1038/s41587-023-01770-3
Volume 41 Issue 4, April 2023
Microbiome-friendly phages join the campaign for better antimicrobials
Ben JohnsonÂÂ
Integrative analysis of multimodal mass spectrometry data in MZmine 3
Robin Schmid, Steffen Heuckeroth, Ansgar Korf, Aleksandr Smirnov, Owen Myers, Thomas S. Dyrlund, Roman Bushuiev, Kevin J. Murray, Nils Hoffmann, Miaoshan Lu, Abinesh Sarvepalli, Zheng Zhang, Markus Fleischauer, Kai Dührkop, Mark Wesner, Shawn J. Hoogstra, Edward Rudt, Olena Mokshyna, Corinna Brungs, Kirill Ponomarov, Lana Mutabdžija, Tito Damiani, Chris J. Pudney, Mark Earll, Patrick O. Helmer, Timothy R. Fallon, Tobias Schulze, Albert Rivas-Ubach, Aivett Bilbao, Henning Richter, Louis-Félix Nothias, Mingxun Wang, Matej OreÅ¡iÄ�, Jing-Ke Weng, Sebastian Böcker, Astrid Jeibmann, Heiko Hayen, Uwe Karst, Pieter C. Dorrestein, Daniel Petras, Xiuxia Du & Tomáš PluskalÂ
Xenotransplantation: how close are we?
Kathryn Aschheim & Laura DeFrancescoÂ
Mapping the patent landscape of medical machine learning
Mateo Aboy, W. Nicholson Price II & Seth RakerÂ
Retrofitted E. coli genome confers phage resistance
Jared B. FudgeÂÂ
Long COVID immune phenotypes identified for blockade
Jared B. FudgeÂÂ
Base editor restores CD3δ-dependent SCID mutation
Jared B. FudgeÂÂ
Novel recombinases for large DNA insertions
George D. Lampe & Samuel H. SternbergÂ
Optical microscopy gets down to angstroms
Giorgio Tortarolo & Suliana ManleyÂ
Spatial total RNA-sequencing maps coding, noncoding and viral RNAs in tissues
Improving non-viral knock-in with modified single-stranded DNAs and small molecules
Synthetic biologics provide a path to target bHLH transcription factors
Modular, programmable RNA sensing using ADAR editing in living cells
K. Eerik Kaseniit, Noa Katz, Natalie S. Kolber, Connor C. Call, Diego L. Wengier, Will B. Cody, Elizabeth S. Sattely & Xiaojing J. GaoÂ
doi : 10.1038/s41587-022-01493-x
With the increasing availability of single-cell transcriptomes, RNA signatures offer a promising basis for targeting living cells. Molecular RNA sensors would enable the study of and therapeutic interventions for specific cell types/states in diverse contexts, particularly in human patients and non-model organisms.
Systematic discovery of recombinases for efficient integration of large DNA sequences into the human genome
Matthew G. Durrant, Alison Fanton, Josh Tycko, Michaela Hinks, Sita S. Chandrasekaran, Nicholas T. Perry, Julia Schaepe, Peter P. Du, Peter Lotfy, Michael C. Bassik, Lacramioara Bintu, Ami S. Bhatt & Patrick D. HsuÂ
doi : 10.1038/s41587-022-01494-w
Large serine recombinases (LSRs) are DNA integrases that facilitate the site-specific integration of mobile genetic elements into bacterial genomes. Only a few LSRs, such as Bxb1 and PhiC31, have been characterized to date, with limited efficiency as tools for DNA integration in human cells.
Drag-and-drop genome insertion of large sequences without double-strand DNA cleavage using CRISPR-directed integrases
Matthew T. N. Yarnall, Eleonora I. Ioannidi, Cian Schmitt-Ulms, Rohan N. Krajeski, Justin Lim, Lukas Villiger, Wenyuan Zhou, Kaiyi Jiang, Sofya K. Garushyants, Nathaniel Roberts, Liyang Zhang, Christopher A. Vakulskas, John A. Walker II, Anastasia P. Kadina, Adrianna E. Zepeda, Kevin Holden, Hong Ma, Jun Xie, Guangping Gao, Lander Foquet, Greg Bial, Sara K. Donnelly, Yoshinari Miyata, Daniel R. Radiloff, Jordana M. Henderson, Andrew Ujita, Omar O. Abudayyeh & Jonathan S. GootenbergÂ
doi : 10.1038/s41587-022-01527-4
Programmable genome integration of large, diverse DNA cargo without DNA repair of exposed DNA double-strand breaks remains an unsolved challenge in genome editing. We present programmable addition via site-specific targeting elements (PASTE), which uses a CRISPR–Cas9 nickase fused to both a reverse transcriptase and serine integrase for targeted genomic recruitment and integration of desired payloads.
Spatial mapping of the total transcriptome by in situ polyadenylation
David W. McKellar, Madhav Mantri, Meleana M. Hinchman, John S. L. Parker, Praveen Sethupathy, Benjamin D. Cosgrove & Iwijn De VlaminckÂ
doi : 10.1038/s41587-022-01517-6
Spatial transcriptomics reveals the spatial context of gene expression, but current methods are limited to assaying polyadenylated (A-tailed) RNA transcripts. Here we demonstrate that enzymatic in situ polyadenylation of RNA enables detection of the full spectrum of RNAs, expanding the scope of sequencing-based spatial transcriptomics to the total transcriptome.
High-yield genome engineering in primary cells using a hybrid ssDNA repair template and small-molecule cocktails
Brian R. Shy, Vivasvan S. Vykunta, Alvin Ha, Alexis Talbot, Theodore L. Roth, David N. Nguyen, Wolfgang G. Pfeifer, Yan Yi Chen, Franziska Blaeschke, Eric Shifrut, Shane Vedova, Murad R. Mamedov, Jing-Yi Jing Chung, Hong Li, Ruby Yu, David Wu, Jeffrey Wolf, Thomas G. Martin, Carlos E. Castro, Lumeng Ye, Jonathan H. Esensten, Justin Eyquem & Alexander MarsonÂ
doi : 10.1038/s41587-022-01418-8
Enhancing CRISPR-mediated site-specific transgene insertion efficiency by homology-directed repair (HDR) using high concentrations of double-stranded DNA (dsDNA) with Cas9 target sequences (CTSs) can be toxic to primary cells.
A split, conditionally active mimetic of IL-2 reduces the toxicity of systemic cytokine therapy
Alfredo Quijano-Rubio, Aladdin M. Bhuiyan, Huilin Yang, Isabel Leung, Elisa Bello, Lestat R. Ali, Kevin Zhangxu, Jilliane Perkins, Jung-Ho Chun, Wentao Wang, Marc J. Lajoie, Rashmi Ravichandran, Yun-Huai Kuo, Stephanie K. Dougan, Stanley R. Riddell, Jamie B. Spangler, Michael Dougan, Daniel-Adriano Silva & David BakerÂ
doi : 10.1038/s41587-022-01510-z
The therapeutic potential of recombinant cytokines has been limited by the severe side effects of systemic administration.
Targeting MYC with modular synthetic transcriptional repressors derived from bHLH DNA-binding domains
Thomas E. Speltz, Zeyu Qiao, Colin S. Swenson, Xianghang Shangguan, John S. Coukos, Christopher W. Lee, Deborah M. Thomas, Jesse Santana, Sean W. Fanning, Geoffrey L. Greene & Raymond E. MoelleringÂ
doi : 10.1038/s41587-022-01504-x
Despite unequivocal roles in disease, transcription factors (TFs) remain largely untapped as pharmacologic targets due to the challenges in targeting protein–protein and protein–DNA interactions. Here we report a chemical strategy to generate modular synthetic transcriptional repressors (STRs) derived from the bHLH domain of MAX.
Extending fluorescence anisotropy to large complexes using reversibly switchable proteins
Andrea Volpato, Dirk Ollech, Jonatan Alvelid, Martina Damenti, Barbara Müller, Andrew G York, Maria Ingaramo & Ilaria TestaÂ
doi : 10.1038/s41587-022-01489-7
The formation of macromolecular complexes can be measured by detection of changes in rotational mobility using time-resolved fluorescence anisotropy.
An engineered T7 RNA polymerase that produces mRNA free of immunostimulatory byproducts
Athanasios Dousis, Kanchana Ravichandran, Elissa M. Hobert, Melissa J. Moore & Amy E. RabideauÂ
MINSTED nanoscopy enters the Ångström localization range
Michael Weber, Henrik von der Emde, Marcel Leutenegger, Philip Gunkel, Sivakumar Sambandan, Taukeer A. Khan, Jan Keller-Findeisen, Volker C. Cordes & Stefan W. HellÂ
doi : 10.1038/s41587-022-01519-4
Super-resolution techniques have achieved localization precisions in the nanometer regime. Here we report all-optical, room temperature localization of fluorophores with precision in the Ångström range.
Author Correction: Modular, programmable RNA sensing using ADAR editing in living cells
K. Eerik Kaseniit, Noa Katz, Natalie S. Kolber, Connor C. Call, Diego L. Wengier, Will B. Cody, Elizabeth S. Sattely & Xiaojing J. GaoÂ
Author Correction: Butler enables rapid cloud-based analysis of thousands of human genomes
Sergei Yakneen, Sebastian M. Waszak, PCAWG Technical Working Group, Michael Gertz, Jan O. Korbel & PCAWG Consortium
Publisher Correction: Butler enables rapid cloud-based analysis of thousands of human genomes
Sergei Yakneen, Sebastian M. Waszak, PCAWG Technical Working Group, Michael Gertz, Jan O. Korbel & PCAWG Consortium
Integrating a healthcare innovation bootcamp into an international medical conference to democratize innovation learning
Marc D. Succi, Debby Cheng, Katherine P. Andriole, Florian J. Fintelmann, Efren J. Flores, Haipeng (Mark) Zhang, Michael S. Gee, Christopher M. Coburn & James A. BrinkÂ
