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Repairing the eye
Cormac SheridanÂÂ
doi : 10.1038/s41587-022-01506-9
Volume 40 Issue 10, October 2022
Baltic bacteria sink CO2 into smoothies
Vijay Shankar BalakrishnanÂÂ
Public biotech in 2021 � the numbers
Laura DeFrancesco & Riku LähteenmäkiÂ
What the COVID-19 pandemic revealed about intellectual property
E. Richard GoldÂ
Visualizing protein nanostructures in intact brain
Natalie G. BarnesÂÂ
Precision cancer targeting with antibody pairs
Robert T. Lawrence & Peter D. SenterÂ
Team architecture in 3D genomic interactions revealed through nanopore sequencing
Lipophilic siRNA conjugates yield durable silencing in extrahepatic tissues
Assessing the efficiency of Verily’s automated process for production and release of male Wolbachia-infected mosquitoes
Jérémy Bouyer, Hamidou Maiga & Marc J. B. VreysenÂ
Reply to: Assessing the efficiency of Verily’s automated process for production and release of male Wolbachia-infected mosquitoes
Jacob E. Crawford, Kaycie C. Hopkins, Anna Buchman, Tiantian Zha, Paul Howell, Evdoxia Kakani, Johanna R. Ohm, Nigel Snoad, Linus Upson, Jodi Holeman, Peter Massaro, Stephen L. Dobson, F. Stephen Mulligan & Bradley J. WhiteÂ
Fast and highly sensitive full-length single-cell RNA sequencing using FLASH-seq
Vincent Hahaut, Dinko Pavlinic, Walter Carbone, Sven Schuierer, Pierre Balmer, Mathieu Quinodoz, Magdalena Renner, Guglielmo Roma, Cameron S. Cowan & Simone PicelliÂ
doi : 10.1038/s41587-022-01312-3
We present FLASH-seq (FS), a full-length single-cell RNA sequencing (scRNA-seq) method with increased sensitivity and reduced hands-on time compared to Smart-seq3. The entire FS protocol can be performed in ~4.5 hours, is simple to automate and can be easily miniaturized to decrease resource consumption.
Scalable single-cell RNA sequencing from full transcripts with Smart-seq3xpress
Michael Hagemann-Jensen, Christoph Ziegenhain & Rickard SandbergÂ
doi : 10.1038/s41587-022-01311-4
Current single-cell RNA sequencing (scRNA-seq) methods with high cellular throughputs sacrifice full-transcript coverage and often sensitivity. Here we describe Smart-seq3xpress, which miniaturizes and streamlines the Smart-seq3 protocol to substantially reduce reagent use and increase cellular throughput.
Multi-omics single-cell data integration and regulatory inference with graph-linked embedding
Zhi-Jie Cao & Ge GaoÂ
doi : 10.1038/s41587-022-01284-4
Despite the emergence of experimental methods for simultaneous measurement of multiple omics modalities in single cells, most single-cell datasets include only one modality. A major obstacle in integrating omics data from multiple modalities is that different omics layers typically have distinct feature spaces.
DIALOGUE maps multicellular programs in tissue from single-cell or spatial transcriptomics data
Livnat Jerby-Arnon & Aviv RegevÂ
doi : 10.1038/s41587-022-01288-0
Deciphering the functional interactions of cells in tissues remains a major challenge. Here we describe DIALOGUE, a method to systematically uncover multicellular programs (MCPs)�combinations of coordinated cellular programs in different cell types that form higher-order functional units at the tissue level�from either spatial data or single-cell data obtained without spatial information.
Comparison and imputation-aided integration of five commercial platforms for targeted DNA methylome analysis
Miljana Tanić, Ismail Moghul, Simon Rodney, Pawan Dhami, Heli Vaikkinen, John Ambrose, James Barrett, Andrew Feber & Stephan BeckÂ
doi : 10.1038/s41587-022-01336-9
Targeted bisulfite sequencing (TBS) has become the method of choice for the cost-effective, targeted analysis of the human methylome at base-pair resolution. In this study, we benchmarked five commercially available TBS platforms�three hybridization capture-based (Agilent, Roche and Illumina) and two reduced-representation-based (Diagenode and NuGen)�across 11 samples.
Identifying synergistic high-order 3D chromatin conformations from genome-scale nanopore concatemer sequencing
Aditya S. Deshpande, Netha Ulahannan, Matthew Pendleton, Xiaoguang Dai, Lynn Ly, Julie M. Behr, Stefan Schwenk, Will Liao, Michael A. Augello, Carly Tyer, Priyesh Rughani, Sarah Kudman, Huasong Tian, Hannah G. Otis, Emily Adney, David Wilkes, Juan Miguel Mosquera, Christopher E. Barbieri, Ari Melnick, David Stoddart, Daniel J. Turner, Sissel Juul, Eoghan Harrington & Marcin ImieliÅ„skiÂ
doi : 10.1038/s41587-022-01289-z
High-order three-dimensional (3D) interactions between more than two genomic loci are common in human chromatin, but their role in gene regulation is unclear. Previous high-order 3D chromatin assays either measure distant interactions across the genome or proximal interactions at selected targets.
Expanding RNAi therapeutics to extrahepatic tissues with lipophilic conjugates
Kirk M. Brown, Jayaprakash K. Nair, Maja M. Janas, Yesseinia I. Anglero-Rodriguez, Lan T. H. Dang, Haiyan Peng, Christopher S. Theile, Elena Castellanos-Rizaldos, Christopher Brown, Donald Foster, Jeffrey Kurz, Jeffrey Allen, Rajanikanth Maganti, Jing Li, Shigeo Matsuda, Matthew Stricos, Tyler Chickering, Michelle Jung, Kelly Wassarman, Jeff Rollins, Lauren Woods, Alex Kelin, Dale C. Guenther, Melissa W. Mobley, John Petrulis, Robin McDougall, Timothy Racie, Jessica Bombardier, Diana Cha, Saket Agarwal, Lei Johnson, Yongfeng Jiang, Scott Lentini, Jason Gilbert, Tuyen Nguyen, Samantha Chigas, Sarah LeBlanc, Urjana Poreci, Anne Kasper, Arlin B. Rogers, Saeho Chong, Wendell Davis, Jessica E. Sutherland, Adam Castoreno, Stuart Milstein, Mark K. Schlegel, Ivan Zlatev, Klaus Charisse, Mark Keating, Muthiah Manoharan, Kevin Fitzgerald, Jing-Tao Wu, Martin A. Maier & Vasant JadhavÂ
doi : 10.1038/s41587-022-01334-x
Therapeutics based on short interfering RNAs (siRNAs) delivered to hepatocytes have been approved, but new delivery solutions are needed to target additional organs. Here we show that conjugation of 2′-O-hexadecyl (C16) to siRNAs enables safe, potent and durable silencing in the central nervous system (CNS), eye and lung in rodents and non-human primates with broad cell type specificity.
Logic-gated antibody pairs that selectively act on cells co-expressing two antigens
Simone C. Oostindie, Derek A. Rinaldi, Gijs G. Zom, Michael J. Wester, Desiree Paulet, Kusai Al-Tamimi, Els van der Meijden, Jennifer R. Scheick, Tessa Wilpshaar, Bart de Jong, Marloes Hoff-van den Broek, Rachel M. Grattan, Janita J. Oosterhoff, Julie Vignau, Sandra Verploegen, Peter Boross, Frank J. Beurskens, Diane S. Lidke, Janine Schuurman & Rob N. de JongÂ
doi : 10.1038/s41587-022-01384-1
The use of therapeutic monoclonal antibodies is constrained because single antigen targets often do not provide sufficient selectivity to distinguish diseased from healthy tissues. We present HexElect®, an approach to enhance the functional selectivity of therapeutic antibodies by making their activity dependent on clustering after binding to two different antigens expressed on the same target cell.
Prediction of protein–ligand binding affinity from sequencing data with interpretable machine learning
H. Tomas Rube, Chaitanya Rastogi, Siqian Feng, Judith F. Kribelbauer, Allyson Li, Basheer Becerra, Lucas A. N. Melo, Bach Viet Do, Xiaoting Li, Hammaad H. Adam, Neel H. Shah, Richard S. Mann & Harmen J. BussemakerÂ
doi : 10.1038/s41587-022-01307-0
Protein–ligand interactions are increasingly profiled at high throughput using affinity selection and massively parallel sequencing. However, these assays do not provide the biophysical parameters that most rigorously quantify molecular interactions.
Integrating medicine, engineering and business to educate early-stage researchers in cardiovascular device development
Gabriel Vizgan, Zachary Hill-Whilton, Colleen Gillespie, Daniel Cobos, LeAnn Johnson, Nabil Dib & Gabrielle Gold-von SimsonÂ
