Volume 15 Issue 5, 1 May 2020

Libraries of highly immature, ground-state human intestinal stem cells are established from endoscopic biopsy samples. Single cell–derived clones can be rapidly expanded for molecular genetics, 3D differentiation, disease modeling and drug discovery.

In this protocol, mice are inoculated with two separate tumors derived from the same cell line. One tumor is removed and assessed before treatment; the other is used to assess the effect of treatment.

Paraffin-embedded, fresh-frozen or chemically stained fixed human tissues are isotropically expanded by 4–5× in linear dimension to enable nanoscale-resolution imaging on conventional microscopes.

Size-selected and amplified circular DNA molecules are sequenced on the PacBio platform and processed with a custom pipeline, resulting in full-length annotated genomes of circular DNA viruses and sequences of extrachromosomal circular DNA at single-molecule resolution.

Native mass spectrometry is a powerful technique for studying intact proteins and protein complexes. Using this protocol, meaningful structural information on protein complexes ejected from sonicated native membrane vesicles can be obtained.

This protocol describes in vitro procedures for generation of synthetic single-domain antibodies called ‘sybodies’. Sybodies can be engineered to target specific protein conformations, labile membrane proteins or protein complexes.

[¹⁸F]6-fluoro-l-DOPA ([¹⁸F]FDOPA) is used for diagnostic PET imaging. Using this protocol, radiofluorination of the electron-rich catechol ring can be achieved in the presence of the amino acid group via Cu-mediated fluorination of a pinacol boronate precursor.

Electrocatalysis is now being used for many oxidation reactions in organic synthesis. This protocol describes how to set up an electrolytic cell for use in cobalt-catalyzed C–H/N–H alkyne annulations and C–H oxygenations.

The authors describe DISCOVER-seq, a method to detect off-targets of CRISPR–Cas genome editing based on ChIP-seq analysis of MRE11 recruitment to DSBs, and subsequent bioinformatics analysis of sequencing data using the BLENDER pipeline.

Here, the authors describe an international consensus procedure for determining freely dissolved concentrations (C_free) of hydrophobic organic chemicals in sediment and soil samples by passive sampling.

The HDOCK server is developed for template-based and template-free protein–protein docking, using amino acid sequences or PDB structures as inputs. HDOCK can incorporate SAXS data and can be applied to protein–RNA/DNA docking.

neuECG is the simultaneous noninvasive recording of ECG and skin sympathetic nerve activity and thus can directly record sympathetic nerve activity over a long period of time without the need for invasive procedures.