Volume 12 Issue 2, February 2017

In this Perspective, Elaine Mardis reviews a decade of DNA sequencing technology, from the introduction of Next-Generation Sequencing to single-molecule sequencing, including future applications that promise to further biological and biomedical research.

This protocol extension describes the fabrication of optofluidic neural probes and implantation for advanced in vivo pharmacology and optogenetics in freely moving rodents.

Moreno-Romero et al. describe how to apply the INTACT method to purify endosperm nuclei from Arabidopsis. Purified nuclei can be used for ChIP-seq analysis or bisulfite sequencing.

ClusPro is a web server that performs rigid-body docking of two proteins by sampling billions of conformations. Low-energy docked structures are clustered, and centers of the largest clusters are used as likely models of the complex.

This protocol from Wang et al. describes a pulse–chase method to investigate autophagic protein degradation through click labeling of long-lived proteins. This is a safer alternative to similar classic methods that use radioactive labeling.

Friedrich et al. describe their toolkit for transposon-based insertional mutagenesis in mice for discovering cancer genes. Genome-wide transposon insertion sites are identified, mapped and quantified using QiSeq.

The metabolome or lipidome of different phenotypes can be compared using this protocol. A complete workflow for direct-infusion mass spectrometry using nanoelectrospray ionization and spectral stitching with the Galaxy platform is described.

CORRECT is a method comprising two variants, re-Guide and re-Cas, that enables efficient and scarless CRISPR/Cas9-based genome editing in hPSCs by introducing blocking mutations that hamper the re-editing of modified loci by Cas9.

This protocol provides details for dispersion and colloidal characterization of suspended engineered nanomaterials, and computational fate and transport modeling to accurately calculate dose metrics for in vitro cellular nanotoxicology experiments.

Detailed guides for the husbandry of Xenopus laevis and protocols for making reproducible spinal cord injury models and subsequent study of neural stem/progenitor cells during regeneration are described.

This protocol describes how to form and use membrane tubes supported on a passivated glass coverslip via hydration of a dry lipid mix in physiological buffer and subsequent flow-induced extrusion of the lipid reservoir into long membrane tubes.

Weitzner et al. describe a computational protocol that uses RosettaAntibody to predict antibody structures from sequence data. SnugDock is then used for docking of these structures to protein antigens.

This protocol describes the environmentally benign N-formylation and N-methylation of primary and secondary amines using carbon dioxide as the carbon source, hydrosilanes as reductants and N-heterocyclic carbenes as catalysts.

SLIP is a high-throughput, automated microscopy workflow for large strain collections. Bacterial cultures are transferred to large agar pads using replicator pins, and thousands of images are automatically acquired for single-cell quantification.

This protocol demonstrates how to establish primary epithelial cell cultures in vitro from healthy human tissue and human cancer samples using ROCK inhibitor and irradiated feeder cells.