Volume 10 Issue 3, March 2013

A better way to identify miRNA target sites.

Make navigational elements distinct and unobtrusive to maintain visual priority of data.

Targeted gene modification can be guided by programmable RNA in bacteria, zebrafish and mammalian cells.

An electrochemical gene-delivery method enables rapid modification of gene expression in postmitotic neurons in vivo, changing their identity and connectivity pattern.

A semilinear amplification method allows uniform amplification across a single cell's genome.

A comprehensive mass spectrometric map of the yeast proteome is a valuable resource for both discovery-based and targeted proteome analyses.

An early biomarker of cancer reports from inside the mouse.

Two groups describe near-infrared fluorophores that can be used in applications ranging from cellular to clinical imaging.

Forcing cells through a small opening in a microfluidic channel lets foreign particles enter.

Mass spectrometrists travel top down, middle down and bottom up to study post-translational modifications on proteins and their biological functions.

Synthetic transcription factors act synergistically.

Statistical analysis of single-molecule tracking data maps the number of states occupied by a molecule in a bacterial cell.

A review of zymography techniques is presented. Zymography approaches yield valuable information about enzyme forms and localization of activity in tissues or in whole organisms.

A report on the results of the first large-scale community-based critical assessment of protein function annotation (CAFA) experiment.

In this analysis, the authors directly compared the performance of flow cytometry data processing algorithms to manual gating approaches. The results offer information of practical utility about the performance of the algorithms as applied to different data sets and challenges.

The combination of several TALE-TFs that bind the same gene promoter at different positions induces high and tunable activation, even in heterochromatic genes, and offers the promise of engineering complex synthetic gene expression systems.

TAL effector (TALE)–based transcription factors robustly induce transcription when targeted to DNase I hypersensitive sites in a gene promoter in human cells, even more so when several TALE transcription factors work in synergy at the same promoter. Tunable expression of endogenous genes will be of great interest in basic research and in synthetic biology.

iceFISH labels nascent RNA along a single chromosome, revealing chromosome territories and potential regulatory mechanisms working at the chromosome scale.

A modular optogenetic method for higher-order protein oligomerization uses a single cryptochrome 2-based fusion for rapid, reversible and tunable oligomerization in response to blue light. Inducible aggregation can be used to specifically activate different signaling pathways.

This microRNA target–prediction program, based on biophysical parameters of mRNA and microRNA, outperforms current programs when it comes to finding noncanonical sites.

A technique based on the fusion of zebrafish blastulae, which leads to conjoined organisms that share a common blood stream, or parabiosis, is described. This procedure permits the in vivo visualization of hematopoietic cell migration and homing to niches and peripheral tissues in zebrafish parabiotes of different genetic backgrounds.

A combination of clickable, photoreactive sterol probes and mass spectrometry yields a chemoproteomic strategy for profiling protein-cholesterol interaction in living cells.

This paper reports an analytical method for single-particle tracking data. It identifies diffusive states of intracellular proteins and the rates of transition between them.