Volume 18 Issue 11, November 2023

This protocol presents a workflow for the enrichment of plant nuclei from cells targeted by pathogenic bacterial effectors during bacterial infection.

The authors describe a new base editing system—the transformer base editor—to induce efficient editing with no observable genome-wide or transcriptome-wide off-target mutations, both in mammalian cells and in mice.

This protocol can be used to generate kidney organoids with elongated proximalized nephrons displaying improved proximal tubule maturity compared with those generated using standard kidney organoid protocols.

The authors provide an expanded CRISPR–Cas9-assisted recombineering toolkit for rapid and efficient engineering of genetically intractable Pseudomonas aeruginosa isolates.

The assembly and organization of functional cargo using synthetic DNA scaffolds on biomaterials enable precise presentation of modulatory signals to immune cells.

Procedures for the synthesis of physical double-network hydrogels to provide self-healing, pH-responsive, tissue-adhesive, antioxidant, photothermal and antibacterial properties. Used as wound dressings, the hydrogels can also be removed on demand.

Invasion–adhesion-directed expression sequencing adapts the 10x Genomics 5′ single-cell RNA sequencing protocol to enable generation of bacterial and eukaryotic DNA libraries to identify adherent or invasive bacteria and the associated host transcriptome at a single-cell level.

Microbial pathogens develop resistance to clinically used drugs, and finding new therapeutics is an ongoing challenge. The photoimmuno-antimicrobial strategy described in this protocol is a general approach to target specific elimination.

This protocol provides structure-guided capsid library approaches to evolve new adeno-associated viral vectors for enhanced CNS gene delivery with altered tissue tropism, higher transduction efficiency and the ability to evade pre-existing humoral immunity.

Structure-based virtual screening via docking can find molecules strongly binding to a target. This protocol describes how to use machine learning to improve this by building a target-specific scoring function and evaluating it on that target.

The authors provide a protocol to microscopically identify and isolate single maize meiocytes and pollen grains for RNA-seq with a modified version of CEL-Seq2. Staging of developmentally synchronized anthers is performed in parallel with expression analysis.

There is increasing concern about the harmful effects of micro- and nanoplastics (MNPs). This protocol describes how to generate MNP samples and perform ecotoxicity experiments by taking into account their physicochemical properties and behavior.

An integrated workflow for multiplexed tissue image processing and analysis, including interactive inspection of raw data, cell segmentation, feature extraction, single-cell analysis and spatial analysis.

¹⁸F-labeled cysteine residues, synthesized via metal-free radiodeoxyfluorination, and ¹⁸F-labeled ruthenium-containing peptide sequences, via ruthenium-assisted radiodeoxyfluorination, can be used as tracers for positron emission tomography imaging.