Volume 9 Issue 9, September 2014

A quick route towards new radiofluorinated tracers is important for the development of PET imaging. An efficient, reliable method for optimizing radiofluorination conditions using a microfluidic chemistry approach is described in this protocol.

When a nanoparticle enters the bloodstream, proteins bind to it to form a corona that may affect its function. This protein corona can be investigated using gel electrophoresis and LC-MS.

This protocol describes an optimized cell fractionation protocol for obtaining nuclei (or soluble and insoluble nuclear fractions) uncontaminated by cytoplasm or organelles— critical for studying nuclear RNAi or other nucleus-specific processes.

In this protocol the authors describe a biochemical approach to identify ligand-receptor interactions in discovery mode with extracellular domain IgG fusion baits, tissue-extracted preys, and shotgun proteomic analysis.

In this Protocol, the authors describe a DNA assembly method that enables users to achieve the ordered, recombination-based assembly of repetitive sequences for the development and optimization of metabolic pathways and functional genetic circuits.

Kustatscher et al. describe ChEP, an improvement on the classic chromatin pellet method that enables users to take a 'snapshot' of chromatin, making possible the isolation and identification of the full range of chromatin-binding proteins.

Interaction between a drug and its protein target results in a shift in thermal stability of that protein. The cellular thermal shift assay–CETSA–exploits this to characterize intracellular drug-protein engagement.

This protocol describes procedures for the preparation and characterization of microcrystals for serial femtosecond crystallography in lipidic cubic phase (LCP-SFX) for protein structure determination at X-ray free-electron lasers (XFELs).

Lewy bodies and Lewy neurites are found in the brains of patients with Parkinson's disease and other synucleinopathies. This protocol describes how to model this by inducing α-synuclein aggregates in a primary neuronal culture system.

The authors of this protocol describe a similarity-based, large-scale approach to predicting novel drug-drug interactions (DDIs) integrating a reference standard database of known DDIs with drug similarity information from a variety of sources.

This protocol describes how to engineer and transplant either a natural decellularized donor trachea or an artificial electrospun nanofiber scaffold into a rat, providing a model for tracheal transplantation that has been successfully used in humans.

ChIP analysis of woody plant tissue has been largely unsuccessful. Here, the Chiang lab provides their validated ChIP protocol that has been highly optimized for the analysis of wood-forming tissues.

Protoplasts can be used for transient gene expression analysis. This protocol for protoplast isolation from wood-forming tissue will be useful for genetic analysis of woody plants, particularly those that lack methods for stable transformation.

The natural state of DNA is to be supercoiled, and therefore it is relevant use this form in studying its interactions. This protocol describes how to probe the dynamics of individual naturally supercoiled circular DNA plasmids tethered between a polystyrene bead and a glass slide.

Conformational changes in protein complexes induced by ligand-drug binding, oligomerization or post-translational modifications can be determined using LC-MS/MS after cross-linking with bis(sulfosuccinimidyl)suberate.

The authors of this protocol describe an approach that enables distinguishing de novo–synthesized from pre-existing proteins in the model invertebrate Caenorhabditis elegans, as a way to determine the effect of internal and external stimuli.

Aqueous phase protein-lipid interactions have a role in cell physiology. This protocol describes the analysis of in vivo–assembled protein-lipid complexes in S. cerevisiae using TAP labels, size-exclusion chromatography, SDS-PAGE and HPTLC.

In this protocol, the authors describe deep mutational scanning, an approach that involves selecting for protein function followed by high-throughput DNA sequencing and enables quantification of the activity of protein variants on a massive scale.