Volume 11 Issue 10, October 2016

This Perspective from Jay Shendure's lab reviews the past decade's development of multiplexed assays for variant effects, and also comments on the potential of these experiments for the functional interpretation of genetic variation.

Materials that change shape on illumination can be used in soft robotics and artificial muscles. This protocol describes how to make photoresponsive polymer springs using liquid crystals, chiral dopants and a photo-switch derived from azobenzene.

Mitochondrial dysfunction is linked to a range of common disorders, including inherited metabolic diseases, diabetes and cancer. Here, Koopman et al. describe a protocol to study mitochondrial function in C. elegans using the XF96 respirometer.

Dupl'áková et al. describe a protocol to separate different developmental stages of the male gametophyte (MG) in A. thaliana. To achieve this, MG is subjected to rate-zonal centrifugation through a discontinuous Percoll density gradient.

This protocol uses dual modulation of Wnt and BMP signaling pathways to differentiate human pluripotent stem cells into striated, millimeter-long muscle fibers and satellite-like cells in vitro without the need to introduce genetic material or cell sorting.

Infection of mice with Citrobacter rodentium is the gold-standard method for studying virulence of the closely related human pathogens enteropathogenic and enterohemorrhagic Escherichia coli. This protocol details the use of this important mouse model of bacterial infection.

This is a protocol for preparing human dorsal root ganglia and establishing primary sensory neuron cultures for functional analysis by electrophysiological recording and calcium imaging.

ConsensusPathDB combines molecular interaction data from multiple sources and provides a web interface to vizualize these data. This can be used to build interaction networks and to perform enrichment/over-representation analysis.

In this protocol, the variable antibody region from antigen-specific mouse memory B cells is amplified and cloned into a constant region containing vectors by a sequence/ligation-independent method and used for the production of monoclonal antibodies.

Cyclodepsipeptides are cyclic peptides in which one or more amide groups are replaced with an ester; they have diverse biological functions. This protocol describes a ‘head-to-side-chain’ cyclodepsipeptide synthesis using pipecolidepsin A as an example.

Aryl iodides are useful precursors in the synthesis of compounds used, for example, in the pharmaceutical and electronics industries. This protocol describes a transition metal–free, photo-induced aromatic Finkelstein iodination reaction.

This protocol describes a method to reprogram mouse retinal neurons to pluripotent stem cells and provides a standardized scoring method, STEM-RET, to quantify the differentiation of these cells into mature retinal tissue using a 3D culture system.

This protocol from Nguyen et al. describes the use of the plant cyclase butelase 1 for the efficient cyclization and ligation of peptides and proteins. After extraction from Clitoria ternatea, the protocol describes reactions for cyclization, ligation and synthesis of protein thioesters.

This protocol describes the study design, surgical procedure, postoperative care and analysis techniques necessary to produce a preclinical rabbit model of large bone and tooth defects in the mandible, for use in a wide range of areas in craniofacial tissue engineering.

The African turquoise killifish is an extremely short-lived vertebrate that has emerged as an excellent model for aging research. Here, Harel et al describe how to successfully engineer its genome using CRISPR/Cas9 editing or Tol2-based transgenesis.

Incorporation of carbon nanotube porins (CNTPs) into phospholipid membranes allows for the nanofluidic replication of biological ion channels. This protocol describes the fabrication and testing of CNTPs at both bulk and single-pore levels.