Volume 15 Issue 9, 1 September 2020

This tutorial describes the main causes of sample-induced spherical aberration artifacts in 3D microscopy. In addition, the authors provide a practical ImageJ/Fiji-based solution to correct these aberrations during or after image acquisition.

Flow cytometry is used to track dynamics in microbial communities and link these changes with ecological parameters. This protocol describes how to prepare a fixed microbial cytometric mock community to standardize results over large-scale studies.

NAD⁺ is one of the noncanonical nucleotides recently found to cap the 5′ end of RNAs. This Protocol Extension describes procedures for genome-wide analysis of NAD⁺-capped RNAs by direct RNA sequencing on an Oxford Nanopore platform.

Here the authors describe a GUI-based protocol called FMAP for using funnel metadynamics to calculate the absolute binding free energy of a ligand to its molecular target and predict the ligand binding mode and mechanism.

This protocol provides standardized laboratory manufacturing practices to select, cultivate and purify bacteriophages for human clinical applications. The procedure covers all stages from phage isolation and characterization to quality control.

Proteomic cysteines can undergo redox reactions and electrophile-derived modifications. In QTRP, a thiol-reactive probe is used to covalently label, enrich and quantify the reactive cysteinome in cultured cells and tissue samples.

This protocol describes a microfluidic platform for dynamic high-throughput analysis of the phenotypes of single cells. Cell-surface markers and secreted proteins are quantified and characterized by fluorescence detection using tailored immunoassays.

Formalin fixation and paraffin embedding (FFPE) of human tissue is a central strategy for preserving pathological specimens. This protocol describes how to process these specimens for spatially resolved LC-MS by laser-capture microdissection.

Mesoporous metal films are used in many electrochemical applications. This protocol describes how to make mesoporous Au, Pt and Pd films using micelle templates and provides examples of how to use them (glucose detection and catalysis for alcohol oxidation).

GOTI (genome-wide off-target analysis by two-cell embryo injection) detects off-target mutations of CRISPR–Cas9-based genome editing and base editing. One blastomere of a two-cell mouse embryo is edited so that edited and unedited cells from the same genetic background can be compared.

This protocol describes the design and synthesis of CRISPR-responsive smart hydrogels and their actuation for both the controlled release of cargos (small molecules, enzymes, nanoparticles and living cells) and diagnostic applications.

This protocol describes how to engineer DNA nanostructures with different sizes, shapes and mechanical properties; load them with a siRNA cargo; and evaluate their ability to silence genes in mature tobacco plants.

This protocol describes a procedure for live-cell imaging of endocytic events in cultured cells using a pH-sensitive fluorophore and fast extracellular pH changes. A MATLAB-based analysis pipeline is provided to facilitate automated data processing.

This protocol describes how to engraft human cancer cells in immunocompromised adult zebrafish. The fish are first adapted to 37 °C, followed by intraperitoneal or periocular muscle transplantation of xenograft cells and fluorescence imaging.