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The 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.
Optimization 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.
Phylogenetic 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.
This 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.
This 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.
This 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.
A 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.
We 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.
The 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.
The 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.
FiLa 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.
This 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.
The 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.
RNA-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.
This 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.
A detailed workflow covering 3D pathology, including tissue preparation, imaging with light-sheet fluorescence microscopy, tools for initial data processing in Python (e.g., stitching, intensity leveling and false coloring) and data quality control.
A web-based tool to guide the lead optimization process by improving calculation of substructure modifications of candidate compounds with improved absorption, distribution, metabolism, excretion, and toxicity profiles.
The formation and functional relevance of N6-methyladenosine sites are key unanswered questions in the field of RNA biology. The protocol describes an unbiased sequencing-based method for the characterization of the global distribution and stoichiometry of N6-methyladenosine sites.
Light-activated assembly of split-protein fragment pairs using the covalent SpyTag/SpyCatcher peptide–protein reaction can be used to modulate biological protein activity in solution, biomaterials and cells.