Volume 10 Issue 11, November 2013

Sensors show calcium movement in tiny, cellular antennae.

The P value reported by tests is a probabilistic significance, not a biological one.

The removal or knockdown of an epigenetic repressor, Mbd3, results in near-complete reprogramming of mouse and human somatic cells to pluripotency.

Single-cell modeling of chromosomal organization could help scientists untangle how genomic organization informs function and vice versa.

Transcription activator–like effectors (TALEs) fused to enzymes that change chromatin signatures interrogate the role of enhancers in gene expression.

Genes that restore pluripotency to mature mouse cells can initiate similar reprogramming in more distantly related species.

Researchers define rational design principles to make a small-molecule ligand-binding protein from scratch.

An automated training regimen coaches rats to willingly submit themselves to repeated brain imaging.

Measuring DNA methylation at specific sites in single cells sheds light on early embryo development.

Two surveys of over 1,700 publications whose authors use quantitative real-time PCR (qPCR) reveal a lack of transparent and comprehensive reporting of essential technical information. Reporting standards are significantly improved in publications that cite the Minimum Information for Publication of Quantitative Real-Time PCR Experiments (MIQE) guidelines, although such publications are still vastly outnumbered by those that do not.

Researchers scale up how to crowdsource the mapping of neural circuits. These projects entice crowds by tapping into their spirit of play.

Network-based stratification (NBS) enables the subtyping of tumors on the basis of their mutational profiles, providing new avenues for cancer research and precision oncology.

IntOGen-mutations is a discovery tool for cancer researchers to find driver mutations in genes and pathways.

By fusing genomic data, the eXtasy tool effectively prioritizes rare human exomic sequence variants as causal disease variants.

A system to control gene expression based on a destabilized form of Cre recombinase is reported. Drug-induced stabilization of Cre triggers recombination of 'floxed' alleles in the genome and is here used to genetically modify the activity of neural circuits in the mouse brain.

This paper introduces and benchmarks a statistic, the hierarchical interaction score, a statistic for measuring functional interactions between genes from large-scale data, and provides accessible methods for calculating this score.

A statistical method that uses spike-ins to model the dependence of technical noise on transcript abundance in single-cell RNA-seq experiments allows identification of genes wherein observed variability in read counts can be reliably interpreted as a signal of biological variability as opposed to the effect of technical noise.

Smart-seq2 improves yield and length in single cell-derived cDNA libraries and uses off-the-shelf reagents.

An algorithm and software tool, Borges, utilizes nonspecific tertiary-structure fragment information available in the Protein Data Bank to phase protein X-ray diffraction data.

An approach combining the sampling methodology and energy function of Rosetta with the X-ray refinement methodology of Phenix enables improved low-resolution crystallographic refinement.

By targeting calcium indicators to primary cilia, micrometer-long protrusions from the cellular plasma membrane, the authors measure Ca²⁺ signaling in these sensory organelles.

This paper reports a strategy for combining somatic mutation profiles of human tumors with gene networks to stratify tumors into biologically and clinically relevant subtypes. The method is applied to ovarian, uterine and lung cancers.

A set of Cas9 endonucleases orthogonal to the Streptococcus pyogenes enzyme is identified. This will enable simultaneous addressing of multiple RNA-guided activities to different genomic target sites with the CRISPR-Cas9 system.

An analog implementation of structured illumination using matched microlens and pinhole arrays allows up to 100-Hz 3D two-color imaging with 145-nm lateral and 350-nm axial resolution.

An automated experimental and software pipeline for large-scale FISH enables spatial transcriptomics in thousands of single human cells at single-molecule resolution.