Volume 12 Issue 11, November 2017

This protocol describes the synthesis and application of hydrogel matrices comprising a poly(ethylene glycol) backbone, functionalized with cell adhesion cues and laminin-111. Uses include expanding stem cells and differentiating them into organoids.

This protocol describes how to combine confocal and atomic force microscopy (AFM) to study the interactions between single viruses and their cell-surface receptors on live cells.

Chemical synthesis of proteins (e.g., histones) allows precise insertion of modified amino acids. This protocol uses palladium chemistry to remove protecting groups and a removable solubilizing tag for the synthesis of lipophilic peptide segments.

This massively parallel pipeline enables high-throughput generation and confirmation of variants by Gateway cloning, barcoding, and next-generation sequencing, and their stratification by multiplexed interaction profiling and experimental validation.

DNase I hypersensitive sites (DHSs) are regions of accessible chromatin that are indicative of regions involved in the regulation of gene expression. scDNase-seq allows genome-wide detection of DHSs from a low number of cells, including single cells.

Recent studies have uncovered substantial cross talk between the ubiquitylation and SUMOylation pathways. Using sequential affinity purification and mass spectrometry, this protocol enables the identification of proteins that are modified by both pathways.

This protocol describes the construction and use of the Activity Recording CAFE, an automated image-tracking-based system for the integrated measurement of sleep and feeding in individual Drosophila.

The levels of monoamines and their cofactors in cerebrospinal fluid are strong indicators for dopamine and serotonin biosynthesis and turnover. This protocol describes a set of HPLC-based approaches for the quantitative detection of these molecules.

Crystal-phase-controlled synthesis of noble metal nanomaterials is a promising strategy to tune their physicochemical properties. Gold nanomaterials with unusual crystal structures (e.g., hcp, hcp/fcc and 4H) can be prepared under mild conditions.

This protocol describes how to produce cell-derived matrices from fibroblasts. These matrices can be used to provide a 3D scaffold for cell culture and to investigate cell behavior in complex microenvironments.

Many intra- and extracellular signals induce structural changes in proteins. Schopper et al., describe a limited proteolysis–based mass spectrometry (LiP-MS) approach to characterizing these changes at a proteome-wide scale.

Conjugation of oligosaccharides to probes and surfaces is useful in the development of biochemical assays to assess carbohydrate–protein interactions. In this protocol, conjugation is enabled by using a bifunctional oligo(ethylene glycol) linker.

Flow chemistry is an attractive alternative to batch chemistry in cases in which improved safety and reaction efficiency can be achieved. This protocol describes the assembly of a continuous flow apparatus from readily available and affordable parts.