Volume 13 Issue 12, December 2016

A physicist handy with charcoal and ink uses sculpted light to image the brain.

Cord blood provides important clues for directing human pluripotent stem cells to become pre-hematopoietic stem cells.

A nanoscopic force clamp enables high-throughput single-molecule analysis of DNA under tension without connection to a macroscopic instrument.

A CRISPR–Cas9-based approach identifies synonymous codons that can be reassigned to encode new chemical building blocks.

Careful benchmarking improves software methods for analyzing data-independent-acquisition mass spectrometry data.

A combination of protein and DNA isolation methods expands our grasp of cellular reprogramming.

An optimized illumination strategy allows for uniform single-molecule localization microscopy over large regions.

A maturing open hardware and open-source software movement seeks to expand DIY light-sheet microscopy.

Combining CRISPR-Cas9 with an enzyme that induces somatic hypermutations allows the rapid generation of diverse variants for gain-of-function screens.

Photoactivatable derivatives of the bright and photostable Janelia Fluor dyes enable improved multicolor single-particle tracking and facile localization microscopy in cells.

Two red fluorescent proteins with long Stokes shift enable simultaneous multicolor 2p imaging. CyRFP1 is well-suited for 2p structural imaging, and FRET sensors made with mCyRFP1 and mMaroon1enable multicolor 2pFLIM in brain slices. Also online, a paper by Bajar et al. reports the development of mMaroon1.

The far-red fluorescent protein mMaroon1 and a reporter based on stem-loop binding protein enables the generation of Fucci4, a 4-color cell cycle reporter system that can be used to distinguish all phases of the cell cycle. Also online, a paper by Laviv et al. uses mMaroon1 as a FRET acceptor for the newly developed CyRFP1.

A method for producing multiprotein complexes engineered with site–specifically introduced noncanonical amino acids is described, enabling applications in biochemical and biophysical analysis, as well as in biotechnology.

Random-access line scanning enables neural activity to be monitored at high speed in neurons and dendrites that are sparsely distributed in three dimensions. The approach is demonstrated in behaving mice.

A team of international scientists benchmark current compression methods for high-throughput sequencing data.

The combination of short and long crosslinkers during chromosome conformation capture allows the interrogation of structure from the nucleosome to the chromosome-wide level in yeast.

The covalent insertion of fluorophore-labeled DNA adaptors by Tn5 transposase into open chromatin allows its imaging and subsequent analysis by sequencing from exactly the same samples.

Two-photon scanning microscopy is inherently slow and thus limits volumetric calcium imaging. Prevedel et al. achieve increased volumetric imaging speed by tailoring the excitation volume via light sculpting.

Fusing a cytidine deaminase to dCas9 allows for a forward genetic screen in mammalian cells that identifies mutations conferring drug resistance.

Recruiting a hyperactive cytidine deaminase via the guide RNA to dCas9 allows for the introduction of diverse point mutations at the CRISPR target locus to create complex libraries of variants for protein engineering or dissection of protein function.

The combination of orthogonal dCas9 with two chemical-inducible dimerization systems allows precise induction of gene activation and repression as well as the creation of Boolean logic gates.

The open-source FALCON and FALCON-Unzip software utilize long-read sequencing data to generate contiguous, accurate and phased diploid assemblies, even from genomes that are highly heterozygous.

Robotic Microscopy—a combination of high-content screening methods—enables multivariate experimental approaches with large cell populations and member-level sensitivity. Here we explore how the new Nikon Ti2 line of inverted research microscopes is uniquely suited to Robotic Microscopy applications, focusing on work utilizing induced pluripotent stem cells (iPSCs) as disease models in drug screening.