Volume 10 Issue 2, February 2013

Engineering protein sensors to light up split-second signals in the brain

An approach to cluster and organize systems biology data yields NeXO, a data-driven ontology.

Bessel plane imaging achieves super-resolution performance and proves its value for fast three-dimensional imaging of thick fluorescent living specimens.

A combination of mutagenesis in a pathogen and RNA interference in its host cell reveals the role of non-essential bacterial genes.

The bright luminescent protein Nano-lantern is easily modified to create functional sensors.

Researchers recapitulate in the lab how an infectious parasite gains its ferociousness.

Phylogenetic profiling implicates diverse genes in small-RNA pathways.

By building engineered microenvironments, scientists probe the many talents of stem cells.

Classification of proteins by ligand binding similarity offers an alternative approach to evolutionary methods for organizing and understanding biology, allowing new insights into protein function and physiological signal transduction.

A combination of proximity ligation and in situ hybridization enables visualization of epigenetic marks in single cells.

Tagging of single transcripts with two fluorescent markers can be used to study many aspects of gene expression, including intrinsic noise in transcription or polymerase dynamics at a single gene.

A primer database covering the mouse and human genomes allows easy and flexible generation of FISH probes covering any desired locus.

A nonleaky and efficient DiCre-based conditional knockout system enables the study of essential genes in Toxoplasma gondii, revealing that the actin-myosin motor is not required for host invasion by the parasite.

Highly accurate and sensitive predictions of RNA editing sites can be obtained using RNA sequencing data from multiple individuals or species, without relying on matched genomic DNA sequence. Reanalyzing existing RNA sequencing data in this way greatly expands the catalog of human protein recoding events.

The 3′ region extraction and deep sequencing (3′READS) method accurately identifies cleavage and polyadenylation sites, avoiding common artifacts and detecting sites in A-rich contexts. It was used to greatly expand the number of characterized sites in the mouse genome, including those in long noncoding RNAs.

Classifying G protein–coupled receptors by ligand binding similarity leads to unexpected links between receptors unrelated by sequence or structure, possibly revealing insights into receptor evolution.

A reporter of caspase-1 activity based on Gaussia luciferase—iGLuc—reveals inflammasome activation in mouse cells and in vivo. iGLuc forms nonluminescent aggregates in cells that can be cleaved by specific proteases and, consequently, lead to luciferase activity. The design principle is applied to build reporters for several other proteases.

Replication-deficient lentiviral vectors are used as insertional mutagens for cancer gene discovery in the mouse. They are applied to identify oncogenes in hepatocellular carcinoma.

A single-wavelength genetically encoded sensor of extracellular glutamate is reported. The sensor—iGluSnFR—is bright and photostable under both one- and two-photon illumination and is shown to work for in vivo imaging in worms, zebrafish and mice.

A combination of in situ hybridization and a proximity ligation assay allows the visualization of histone modifications at single genomic loci with single-cell resolution in fixed tissue.