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Preview: Nature Methods - Issue - nature.com science feeds

Nature Methods - Issue - nature.com science feeds



Nature Methods is a science methodology journal publishing laboratory techniques and methods papers in the life sciences and areas of chemistry relevant to the life sciences.



 



Meta-analysis in basic biology

2016-11-29

Meta-analysis is common in clinical research, less so in basic biology, but it is also proving useful in some basic research contexts. It should help improve research reproducibility.



The Author File: Alipasha Vaziri

2016-11-29

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












Stem cells: A blood less primitive

2016-11-29

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



Biophysics: Single-molecule force analysis, unplugged

2016-11-29

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



Synthetic biology: REXER helps design bacterial genomes

2016-11-29

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



Proteomics: Proteome quantification compared

2016-11-29

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



























Proteomics: A pluripotent approach

2016-11-29

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



Imaging: Extending super-resolution's FOV

2016-11-29

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



Microscopy: OpenSPIM 2.0

2016-11-29

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



CRISPR-Cas9-AID base editor is a powerful gain-of-function screening tool

2016-11-29

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



Bright photoactivatable fluorophores for single-molecule imaging

2016-10-24

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



Simultaneous dual-color fluorescence lifetime imaging with novel red-shifted fluorescent proteins

2016-10-31

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.



Fluorescent indicators for simultaneous reporting of all four cell cycle phases

2016-10-31

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.



Genetic code expansion for multiprotein complex engineering

2016-10-17

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 scanning microscopy for 3D imaging in awake behaving animals

2016-10-17

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.



Comparison of high-throughput sequencing data compression tools

2016-10-24

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



Micro-C XL: assaying chromosome conformation from the nucleosome to the entire genome

2016-10-10

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.



ATAC-see reveals the accessible genome by transposase-mediated imaging and sequencing

2016-10-17

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.



Fast volumetric calcium imaging across multiple cortical layers using sculpted light

2016-10-31

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.



Targeted AID-mediated mutagenesis (TAM) enables efficient genomic diversification in mammalian cells

2016-10-10

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



Directed evolution using dCas9-targeted somatic hypermutation in mammalian cells

2016-10-31

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.



Complex transcriptional modulation with orthogonal and inducible dCas9 regulators

2016-10-24

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.



Phased diploid genome assembly with single-molecule real-time sequencing

2016-10-17

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 with the Nikon Ti2 for high-content analysis applications

2016-11-29

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.