Volume 10 Issue 8, August 2013

Proteins are sociable and interact with other proteins. A new web resource helps to score experimental data about these relations.

Relate your data to the world around them using the age-old custom of telling a story.

The first fluorescent protein cloned from a vertebrate species is a promising tool for clinical diagnostics and research.

Researchers leash cells to molecular tethers as an easy way to measure single-molecular binding forces.

Antibody-like probes report the localization and amount of endogenous proteins in living cells.

Protein engineering and small-molecule probe design allows the study of individual members of large protease families.

Targeted nucleases based on the CRISPR/Cas9 system can in some cases cleave at imperfectly matched 'off-target' sites.

As new research applications for antibody-based assays emerge, the quest for quality intensifies in a crowded marketplace.

Massive parallelization of scanning-based super-resolution imaging allows fast imaging of large fields of view.

Methods for high-throughput and high-resolution dissection of enhancers in Drosophila are described by two independent groups.

We present a summary of the scientific deliberations and major conclusions that arose from a workshop on the BRAIN Initiative.

Much of what is known about mammalian cell regulation has been achieved with the aid of transiently transfected cells. However, overexpression can violate balanced gene dosage, affecting protein folding, complex assembly and downstream regulation. To avoid these problems, genome engineering technologies now enable the generation of stable cell lines expressing modified proteins at (almost) native levels.

International Cancer Genome Consortium members review and recommend computational approaches for identifying mutations that drive cancer progression from among the many sequence variants present in tumor genomes.

The Contaminant Repository for Affinity Purification (CRAPome) is a database of annotated negative control-data that can be used for filtering out nonspecific interactions in affinity purification-mass spectrometry experiments.

Two incoherently superimposed orthogonal standing waves are used to create a pattern of 116,000 'doughnuts' for fast, highly parallelized coordinate-targeted super-resolution microscopy of living cells, with a large field of view.

RNA polymerase III–driven single guide RNA and a germ line promoter–driven expression of Cas9 enzyme allow heritable, targeted genome modifications in Caenorhabditis elegans.

A multiplexing strategy for data-independent acquisition (DIA)-based mass spectrometry addresses the limitation of low precursor selectivity to make DIA more practical for peptide analysis.

A method to identify genomic elements that promote cap-independent translation is described and is used to identify such elements in the human genome.

Four spectrally distinct near-infrared fluorescent proteins based on bacterial phytochromes are described, expanding the possibilities for multicolor in vivo imaging experiments in nontransparent organisms.

Lipid Blast is an in silico–generated tandem mass spectral library covering more than 119,000 lipid compounds from 26 different classes, providing a useful tool for lipid identification in metabolomics studies.

Designed β-strand peptides stabilize integral membrane proteins for biochemical and structural studies, enabling electron microscopy analysis of the dynamic conformations of the ABC transporter MsbA.

Transcription activator–like effectors are used for in vivo activation and repression of endogenous promoters and enhancers in the fruit fly.

A cellular engineering approach coupled with mass spectrometry allows the cell-of-origin of intra- and extracellular proteins to be determined from co-cultured cells.

Identifying tissue-specific expression of a selection marker and putative enhancer-driven expression of GFP with flow cytometry enriches for active enhancers.

The combination of controlled three-dimensional assembly and electrical stimulation allows the maturation of stem cell–derived cardiomyocytes.

A method to tightly attach cell-derived extracellular matrix (ECM) to the culture surface is described. It is applied to generate bone marrow mesenchymal stem cell–derived ECM, which supports culture of human hematopoietic stem and progenitor cells.

A simple method to immortalize largely unfractionated mouse bone marrow cells to generate hematopoietic progenitor cell lines is described.