High-throughput fabrication of antimicrobial phage microgels and example applications in food decontamination
Nature Protocols, Published online: 27 February 2024; doi:10.1038/s41596-024-00964-6The authors describe how to prepare antimicrobial phage-based microgels, using polystyrene film templates, and detail their use to kill antibiotic-resistant bacteria in food contamination tests as an example application. (Source: Nature Protocols)
Source: Nature Protocols - February 27, 2024 Category: Biomedical Science Authors: Lei Tian Kyle Jackson Leon He Shadman Khan Mathura Thirugnanasampanthar Mellissa Gomez Fereshteh Bayat Tohid F. Didar Zeinab Hosseinidoust Source Type: research
Rapid reaction optimization by robust and economical quantitative benchtop 19F NMR spectroscopy
Nature Protocols, Published online: 26 February 2024; doi:10.1038/s41596-023-00951-3Optimization of chemical transformations involves screening numerous reaction parameters. This protocol outlines how screening experiments can be rapidly and economically analyzed by quantitative benchtop 19F NMR spectroscopy. (Source: Nature Protocols)
Source: Nature Protocols - February 26, 2024 Category: Biomedical Science Authors: G. Heinrich M. Kondratiuk L. J. Goo ßen M. P. Wiesenfeldt Source Type: research
Reconstructing phylogenetic trees from genome-wide somatic mutations in clonal samples
Nature Protocols, Published online: 23 February 2024; doi:10.1038/s41596-024-00962-8Phylogenetic trees from whole-genome sequencing datasets with the pipeline Sequoia are reconstructed to define the evolutionary history of clonally expanding cells and to clarify how somatic mutations shape normal cell behavior. (Source: Nature Protocols)
Source: Nature Protocols - February 23, 2024 Category: Biomedical Science Authors: Tim H. H. Coorens Michael Spencer Chapman Nicholas Williams Inigo Martincorena Michael R. Stratton Jyoti Nangalia Peter J. Campbell Source Type: research
rMATS-turbo: an efficient and flexible computational tool for alternative splicing analysis of large-scale RNA-seq data
Nature Protocols, Published online: 23 February 2024; doi:10.1038/s41596-023-00944-2This protocol provides detailed guidelines for using rMATS-turbo—the latest implementation of the popular software for the discovery and quantification of alternative splicing events from RNA sequencing data—exemplified in two representative scenarios. (Source: Nature Protocols)
Source: Nature Protocols - February 23, 2024 Category: Biomedical Science Authors: Yuanyuan Wang Zhijie Xie Eric Kutschera Jenea I. Adams Kathryn E. Kadash-Edmondson Yi Xing Source Type: research
GlYcoLISA: antigen-specific and subclass-specific IgG Fc glycosylation analysis based on an immunosorbent assay with an LC–MS readout
Nature Protocols, Published online: 21 February 2024; doi:10.1038/s41596-024-00963-7This protocol details a method for profiling the glycosylation status of antigen-specific antibodies. The protocol consists of an antibody-capture step using an immunosorbent assay similar to enzyme-linked immunosorbent assay, followed by the characterization of captured antibodies using liquid chromatography–mass spectrometry. (Source: Nature Protocols)
Source: Nature Protocols - February 21, 2024 Category: Biomedical Science Authors: David Falck Manfred Wuhrer Source Type: research
Web-based multi-omics integration using the Analyst software suite
Nature Protocols, Published online: 14 February 2024; doi:10.1038/s41596-023-00950-4This multi-omics data integration protocol, which uses the web-based Analyst tool suite, covers knowledge-driven integration using biological networks and data-driven integration through joint dimensionality reduction. (Source: Nature Protocols)
Source: Nature Protocols - February 14, 2024 Category: Biomedical Science Authors: Jessica D. Ewald Guangyan Zhou Yao Lu Jelena Kolic Cara Ellis James D. Johnson Patrick E. Macdonald Jianguo Xia Source Type: research
Isoform-specific RNA structure determination using Nano-DMS-MaP
Nature Protocols, Published online: 12 February 2024; doi:10.1038/s41596-024-00959-3A protocol for Nano-DMS-MaP, a method for in situ isoform-specific RNA structure determination. The technique employs nanopore sequencing to resolve the structures of long and highly similar RNA molecules, revealing previously hidden structural differences. (Source: Nature Protocols)
Source: Nature Protocols - February 12, 2024 Category: Biomedical Science Authors: Anne-Sophie Gribling-Burrer Patrick Bohn Redmond P. Smyth Source Type: research
Using high-resolution microscopy data to generate realistic structures for electromagnetic FDTD simulations from complex biological models
Nature Protocols, Published online: 08 February 2024; doi:10.1038/s41596-023-00947-zWe provide a detailed roadmap for scientists interested in performing FDTD computational simulations to probe the interactions of electromagnetic waves (e.g., visible light or microwave radiation) with complex structures such as organs or biological cells. (Source: Nature Protocols)
Source: Nature Protocols - February 8, 2024 Category: Biomedical Science Authors: John M. Ball Wei Li Source Type: research
Engineering megabase-sized genomic deletions with MACHETE (Molecular Alteration of Chromosomes with Engineered Tandem Elements)
Nature Protocols, Published online: 07 February 2024; doi:10.1038/s41596-024-00953-9The authors introduce MACHETE (molecular alteration of chromosomes with engineered tandem elements), a clustered regularly interspaced short palindromic repeats directed Cas9-based system for the efficient deletion of megabase-sized genomic regions. (Source: Nature Protocols)
Source: Nature Protocols - February 7, 2024 Category: Biomedical Science Authors: Francisco M. Barriga Scott W. Lowe Source Type: research
Functionalized tetrahedral DNA frameworks for the capture of circulating tumor cells
Nature Protocols, Published online: 05 February 2024; doi:10.1038/s41596-023-00943-3The controlled positioning and stoichiometry of aptamers on tetrahedral DNA frameworks enables the synthesis of targeted probes for the capture of circulating tumor cells from blood samples. (Source: Nature Protocols)
Source: Nature Protocols - February 5, 2024 Category: Biomedical Science Authors: Yirong Chen Meihua Lin Dekai Ye Shaopeng Wang Xiaolei Zuo Min Li Source Type: research
Comprehensive multiscale analysis of lactate metabolic dynamics in vitro and in vivo using highly responsive biosensors
Nature Protocols, Published online: 02 February 2024; doi:10.1038/s41596-023-00948-yFiLa biosensors allow real-time subcellular analysis of lactate metabolism. This protocol describes their preparation and characterization, and their use in in vitro and in vivo assays, under various nutritional and pharmacological conditions. (Source: Nature Protocols)
Source: Nature Protocols - February 2, 2024 Category: Biomedical Science Authors: Aoxue Wang Yejun Zou Shuning Liu Xiuze Zhang Ting Li Lijuan Zhang Ruwen Wang Yale Xia Xie Li Zhuo Zhang Tiemin Liu Zhenyu Ju Ru Wang Joseph Loscalzo Yi Yang Yuzheng Zhao Source Type: research
Human primordial germ cell-like cells specified from resetting precursors develop in human hindgut organoids
Nature Protocols, Published online: 01 February 2024; doi:10.1038/s41596-023-00945-1This protocol describes an efficient method to reconstitute the onset of gametogenesis by co-culturing resetting hPGCLCs with human hindgut organoids, providing a new framework to clarify the physiological and pathological crosstalk between hPGCs and the hindgut. (Source: Nature Protocols)
Source: Nature Protocols - February 1, 2024 Category: Biomedical Science Authors: Jo ão Pedro Alves-Lopes Frederick C. K. Wong M. Azim Surani Source Type: research
Quantitative profiling of posttranslational modifications of pathological tau via sarkosyl fractionation and mass spectrometry
Nature Protocols, Published online: 30 January 2024; doi:10.1038/s41596-023-00939-zThe identification and quantitative characterization of tau posttranslational modifications in brain tissue using mass spectrometry provide a comprehensive and untargeted approach to profiling pathological tau in neurodegenerative diseases. (Source: Nature Protocols)
Source: Nature Protocols - January 30, 2024 Category: Biomedical Science Authors: Kathrin Wenger Arthur Viode Mukesh Kumar Hanno Steen Judith A. Steen Source Type: research
Mapping protein–RNA binding in plants with individual-nucleotide-resolution UV cross-linking and immunoprecipitation (plant iCLIP2)
Nature Protocols, Published online: 26 January 2024; doi:10.1038/s41596-023-00935-3RNA-binding proteins orchestrate many aspects of plant development and environmental responses. This protocol describes an optimized plant individual-nucleotide-resolution cross-linking and immunoprecipitation method for genome-wide identification of RNA-binding protein binding sites on their cognate RNAs at single-nucleotide resolution. (Source: Nature Protocols)
Source: Nature Protocols - January 26, 2024 Category: Biomedical Science Authors: Martin Lewinski Mirko Br üggemann Tino K öster Marlene Reichel Thorsten Bergelt Katja Meyer Julian K önig Kathi Zarnack Dorothee Staiger Source Type: research
Improved sampling and DNA extraction procedures for microbiome analysis in food-processing environments
Nature Protocols, Published online: 24 January 2024; doi:10.1038/s41596-023-00949-xThis protocol describes a method for sampling the microbiome of food-processing facilities and analyzing it by using whole-metagenome sequencing. The protocol includes sampling and DNA-extraction and DNA-purification steps optimized for low-biomass samples. (Source: Nature Protocols)
Source: Nature Protocols - January 24, 2024 Category: Biomedical Science Authors: Coral Barcenilla Jos é F. Cobo-Díaz Francesca De Filippis Vincenzo Valentino Raul Cabrera Rubio Dominic O ’Neil Lisa Mahler de Sanchez Federica Armanini Niccol ò Carlino Aitor Blanco-M íguez Federica Pinto In és Calvete-Torre Carlos Sabater Susana Source Type: research
