Volume 11 Issue 5, May 2014

Lessons from the volleyball court help to compare ways to measure how much flies eat.

Nonparametric tests robustly compare skewed or ranked data.

Researchers sequence RNA directly within tissue.

Researchers design a chemical decaging strategy for studying protein function in cells.

A nuclear-transfer technique informed by cell-cycle synchronization could simplify generation of therapeutic stem cells.

Engineered bacteria sense and record conditions in the gut.

Models are presented of background fluorescence resonance energy transfer (FRET) for non-interacting membrane proteins.

A curved beam of light provides microscopists with a new tool to overcome imaging challenges.

A systematic analysis of genome-wide short interfering RNA (siRNA) screens in human cells identifies widespread off-target effects.

Some researchers run and hide from the task of authenticating cell lines. A few simple steps save time and money.

Two methods are used to identify cis-regulatory sequences by looking at their function.

Authors discuss how synthetic biology approaches could be applied to assemble synthetic quasibiological systems able to replicate and evolve, illuminating universal properties of life and the search for its origins.

This Review discusses large-scale de novo DNA synthesis via oligos or arrays, describes gene assembly and error correction and considers applications for large-scale DNA synthesis.

This Review introduces tools to build transcriptional circuits and explains how the choice of different tools can affect circuit behavior and how its operation can be affected by the cellular host.

This Perspective takes the reader through the important steps in bacterial genome assembly and activation and concludes with an outlook on how customized genomes may be achieved.

A minimal Mos transposon for integration of transgenes into the Caenorhabditis elegans genome expands the genetic toolbox in this model organism.

This Analysis compares four commonly used assays to measure food intake in flies and identifies radioisotope-labeling and the capillary feeder (CAFE) as the most reproducible and sensitive.

Single-photon Airy beam excitation in light-sheet fluorescence microscopy combined with a simple deconvolution allows high-contrast imaging over a large field of view and minimal redundancy in illumination.

A computational approach and software tool, cctbx.xfel, enables the determination of accurate macromolecular structure factors using a relatively small number of serial femtosecond crystallography diffraction snapshots.

Methods are described for preparing unbiased libraries for transcriptome profiling of cells sorted according to the abundance of a transcript of interest.

An approach for quantifying the similarity between dynamic ensembles of biomolecular structures is described and applied to RNA ensembles studied by nuclear magnetic resonance spectroscopy and molecular dynamics simulations.

Biomolecular interactions are directly detected and visualized in solution with a single-molecule method that measures time-dependent diffusion coefficient and mobility of electrokinetically trapped species.

Screening of cells transduced with a lentivirus library harboring nucleosome-free regions of mammalian genomes identifies cis elements that regulate transcription.

Putative enhancer elements of a genomic region of interest are cloned in front of a reporter gene, integrated in a single site in mouse embryonic stem cells, and screened for enhancer activity using flow cytometry and high-throughput sequencing.

Three new red-excitable monomeric fluorescent proteins obtained by structure-guided mutagenesis of mNeptune are described in this work. The authors show the use of one of them, mCardinal, to visualize the differentiation of myoblasts into myocytes in living mice.

Excitation using rotating polarized light and detection of periodic signals from rectangular nanoareas allows widef-ield super-resolution imaging of biological structures in cells and in tissue with reduced background.

A method based on the split-ubiquitin assay monitors interactions between membrane proteins within human cells.

Synthetic biology spans many disciplines and has many different goals but all rely on well-characterized basic tools. In this Focus experts discuss the current status of essential methods, going from DNA synthesis to genetic circuit design to whole genome assembly and how these tools can be deployed for applications from medical research to addressing the origin of life.