Volume 9 Issue 6, June 2014

This protocol describes a culture system, in which inner ear sensory tissue is produced in vitro from mouse embryonic stem cells under chemically defined conditions.

A detailed procedure for the synthesis of a zinc ion–selective, cyanine-based fluorescent probe and for the probe’s use for the detection of Zn²⁺ in cells and in living zebrafish.

A detailed protocol for analyzing thousands of reporters integrated in parallel (TRIP) at a genome-wide level to study the influence of local chromatin context on gene expression.

Translating ribosome affinity purification (TRAP) combines cell type–specific transgene expression with affinity purification of translating ribosomes and can be used to study the cell type–specific mRNA profiles of any genetically defined cell type.

A protocol describing how to construct a platform for two-input Boolean logic functions with concomitant DNA-based memory that enables the straightforward assembly of integrated logic-and-memory circuits that implement desired behaviors within a couple of weeks.

CDSiL-MS involves labeling cysteine and lysine side chains in proteins with N-ethylmaleimide and succinic anhydride, respectively. Information about the conformational state of the protein is inferred from the labeling kinetics as determined by mass spectrometry.

A protocol enabling the production of biofuels and renewable chemicals via the design and construction of complex biological systems in microbial organisms.

This protocol provides the means to characterize the relationship between the nanoscale organization of synaptic vesicles and their functional properties during synaptic transmission.

In this protocol from Frank Glorius and colleagues, analysis of gas chromatography data from a reaction conducted in the presence of various additives provides information on each additive's effect on the progress of the reaction and on the additive’s stability under the reaction conditions.

The authors describe an approach that can be used after in vivo imaging of dendrites and axons in adult mouse brains to prepare and image fluorescent structures of interest using focussed ion beam scanning electron microscopy.

A procedure for the preparation and use of DNA origami microscopy standards with fluorescent groups that have known fluorescent yields and are positioned at defined mutual distances.

In this protocol, the author describes an approach to specifically estimate how evolutionarily successful new alleles are in invading populations of the nematode model Caenorhabditis elegans.

This protocol describes how to analyze post-mortem artery specimens using X-ray CT and overcomes some of the difficulties relating to the different photon energy requirements for analyzing soft and hard tissues.

BATMAN is an R package developed to analyze one-dimensional NMR spectra of complex metabolite mixtures using a user-defined template library.

This protocol enables users to perform de novo motif discovery, motif enrichment analysis, motif location analysis, and motif clustering, providing a comprehensive picture of the DNA or RNA motifs that are enriched in the input sequences.

This describes how to decellularize whole organs using pressure-controlled perfusion, which enables preparation of acellular 3D scaffolds with preserved extracellular membrane protein content, organ architecture and perfusable vascular conduits.

This approach for the isolation of scaffold-specific antibacterial producers in the presence of a selective antibiotic overcomes two major bottlenecks in the new drug discovery pipeline: low hit frequency, and rediscovery of known molecules.

This Protocol provides directions on using high-pressure freezing to prepare tissue samples for electron microscopy, avoiding the need for aldehyde fixation and ethanol dehydration.

An approach to localizing breakpoints with sequence-level precision employing massively parallel sequencing performed on libraries generated from haplotype-resolved chromosomes, genomic DNA, or molecular inversion probe–captured informative regions harboring paralog-distinguishing variants.

The authors of this Protocol describe how to generate endothelial cells and pericytes and how to functionally evaluate the cells' ability to generate primary vascular plexus and incorporate it into the zebrafish vasculature.