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Generating ‘smarter’ biotechnology
doi : 10.1038/s41587-023-01695-x
Volume 41 Issue 2, February 2023
Industry appetite for natural killer cells intensifies
Cormac SheridanÂÂ
Small innovators advance microbes as alternatives to chemical crop sprays
Emily WaltzÂÂ
Putting CRISPR into African hands to future-proof crops
Linda NordlingÂÂ
Fresh from the biotech pipeline: fewer approvals, but biologics gain share
Melanie SeniorÂÂ
Delivering 3 billion doses of Comirnaty in 2021
Nicholas Warne, Margaret Ruesch, Pamela Siwik, Paul Mensah, John Ludwig, Michael Hripcsak, Ranga Godavarti, Andrew Prigodich & Mikael DolstenÂ
Drug licensing as evidence of evolution, diffusion and catch-up in East Asia
Jianan HuangÂ
Capturing haplotype variation in populations using pangenome references
Jared B. FudgeÂÂ
Consequences of cis-regulatory sequence variation
Jared B. FudgeÂÂ
DISCO-MS combines spatial proteomics with whole-organ imaging
Anne DoerrÂÂ
Capturing the diversity of protein modifications on presented tumor antigens
A competitive precision CRISPR method to identify the fitness effects of transcription factor binding sites
Päivi Pihlajamaa, Otto Kauko, Biswajyoti Sahu, Teemu Kivioja & Jussi TaipaleÂ
doi : 10.1038/s41587-022-01444-6
Here we describe a competitive genome editing method that measures the effect of mutations on molecular functions, based on precision CRISPR editing using template libraries with either the original or altered sequence, and a sequence tag, enabling direct comparison between original and mutated cells.
Mostly natural sequencing-by-synthesis for scRNA-seq using Ultima sequencing
Sean K. Simmons, Gila Lithwick-Yanai, Xian Adiconis, Florian Oberstrass, Nika Iremadze, Kathryn Geiger-Schuller, Pratiksha I. Thakore, Chris J. Frangieh, Omer Barad, Gilad Almogy, Orit Rozenblatt-Rosen, Aviv Regev, Doron Lipson & Joshua Z. LevinÂ
doi : 10.1038/s41587-022-01452-6
Here we introduce a mostly natural sequencing-by-synthesis (mnSBS) method for single-cell RNA sequencing (scRNA-seq), adapted to the Ultima genomics platform, and systematically benchmark it against current scRNA-seq technology.
Multiplexed, single-molecule, epigenetic analysis of plasma-isolated nucleosomes for cancer diagnostics
Vadim Fedyuk, Nir Erez, Noa Furth, Olga Beresh, Ekaterina Andreishcheva, Abhijeet Shinde, Daniel Jones, Barak Bar Zakai, Yael Mavor, Tamar Peretz, Ayala Hubert, Jonathan E. Cohen, Azzam Salah, Mark Temper, Albert Grinshpun, Myriam Maoz, Aviad Zick, Guy Ron & Efrat ShemaÂ
doi : 10.1038/s41587-022-01447-3
The analysis of cell-free DNA (cfDNA) in plasma provides information on pathological processes in the body. Blood cfDNA is in the form of nucleosomes, which maintain their tissue- and cancer-specific epigenetic state.
Scalable in situ single-cell profiling by electrophoretic capture of mRNA using EEL FISH
Lars E. Borm, Alejandro Mossi Albiach, Camiel C. A. Mannens, Jokubas Janusauskas, Ceren Özgün, David Fernández-GarcÃÂa, Rebecca Hodge, Francisca Castillo, Charlotte R. H. Hedin, Eduardo J. Villablanca, Per Uhlén, Ed S. Lein, Simone Codeluppi & Sten LinnarssonÂ
doi : 10.1038/s41587-022-01455-3
Methods to spatially profile the transcriptome are dominated by a trade-off between resolution and throughput. Here we develop a method named Enhanced ELectric Fluorescence in situ Hybridization (EEL FISH) that can rapidly process large tissue samples without compromising spatial resolution.
DeepConsensus improves the accuracy of sequences with a gap-aware sequence transformer
Gunjan Baid, Daniel E. Cook, Kishwar Shafin, Taedong Yun, Felipe Llinares-López, Quentin Berthet, Anastasiya Belyaeva, Armin Töpfer, Aaron M. Wenger, William J. Rowell, Howard Yang, Alexey Kolesnikov, Waleed Ammar, Jean-Philippe Vert, Ashish Vaswani, Cory Y. McLean, Maria Nattestad, Pi-Chuan Chang & Andrew CarrollÂ
doi : 10.1038/s41587-022-01435-7
Circular consensus sequencing with Pacific Biosciences (PacBio) technology generates long (10–25 kilobases), accurate ‘HiFi’ reads by combining serial observations of a DNA molecule into a consensus sequence.
Post-translational modifications reshape the antigenic landscape of the MHC I immunopeptidome in tumors
Assaf Kacen, Aaron Javitt, Matthias P. Kramer, David Morgenstern, Tomer Tsaban, Merav D. Shmueli, Guo Ci Teo, Felipe da Veiga Leprevost, Eilon Barnea, Fengchao Yu, Arie Admon, Lea Eisenbach, Yardena Samuels, Ora Schueler-Furman, Yishai Levin, Alexey I. Nesvizhskii & Yifat MerblÂ
doi : 10.1038/s41587-022-01464-2
Post-translational modification (PTM) of antigens provides an additional source of specificities targeted by immune responses to tumors or pathogens, but identifying antigen PTMs and assessing their role in shaping the immunopeptidome is challenging.
Human ureteric bud organoids recapitulate branching morphogenesis and differentiate into functional collecting duct cell types
Min Shi, Kyle W. McCracken, Ankit B. Patel, Weitao Zhang, Lioba Ester, M. Todd Valerius & Joseph V. BonventreÂ
doi : 10.1038/s41587-022-01429-5
Directed differentiation of human pluripotent stem cells (hPSCs) into functional ureteric and collecting duct (CD) epithelia is essential to kidney regenerative medicine. Here we describe highly efficient, serum-free differentiation of hPSCs into ureteric bud (UB) organoids and functional CD cells.
Engineering circular RNA for enhanced protein production
Robert Chen, Sean K. Wang, Julia A. Belk, Laura Amaya, Zhijian Li, Angel Cardenas, Brian T. Abe, Chun-Kan Chen, Paul A. Wender & Howard Y. ChangÂ
doi : 10.1038/s41587-022-01393-0
Circular RNAs (circRNAs) are stable and prevalent RNAs in eukaryotic cells that arise from back-splicing.
Modular cytokine receptor-targeting chimeras for targeted degradation of cell surface and extracellular proteins
Katarina Pance, Josef A. Gramespacher, James R. Byrnes, Fernando Salangsang, Juan-Antonio C. Serrano, Adam D. Cotton, Veronica Steri & James A. WellsÂ
doi : 10.1038/s41587-022-01456-2
Targeted degradation of cell surface and extracellular proteins via lysosomal delivery is an important means to modulate extracellular biology. However, these approaches have limitations due to lack of modularity, ease of development, restricted tissue targeting and applicability to both cell surface and extracellular proteins.
Real-time denoising enables high-sensitivity fluorescence time-lapse imaging beyond the shot-noise limit
Xinyang Li, Yixin Li, Yiliang Zhou, Jiamin Wu, Zhifeng Zhao, Jiaqi Fan, Fei Deng, Zhaofa Wu, Guihua Xiao, Jing He, Yuanlong Zhang, Guoxun Zhang, Xiaowan Hu, Xingye Chen, Yi Zhang, Hui Qiao, Hao Xie, Yulong Li, Haoqian Wang, Lu Fang & Qionghai DaiÂ
doi : 10.1038/s41587-022-01450-8
A fundamental challenge in fluorescence microscopy is the photon shot noise arising from the inevitable stochasticity of photon detection. Noise increases measurement uncertainty and limits imaging resolution, speed and sensitivity.
Author Correction: Engineering circular RNA for enhanced protein production
Robert Chen, Sean K. Wang, Julia A. Belk, Laura Amaya, Zhijian Li, Angel Cardenas, Brian T. Abe, Chun-Kan Chen, Paul A. Wender & Howard Y. ChangÂ
Retaining postdocs by recognizing their worth
Esra Yalcin, Rosa Martinez-Corral & Mayank ChughÂ
