Volume 13 Issue 10, October 2016

We take the opportunity to remind our readers of the materials sharing policy at Nature Methods.

A chemist intrigued by DNA and RNA structure and two-wheeled mountainous ascents.

Constraining the magnitude of parameters of a model can control its complexity

A combination of restricting channel-rhodopsin to the soma and restricting the excitation volume with temporal focusing enables the mapping of neural circuits with high precision.

A simple tweak on the zygote's mitotic spindle generated hybrid Caenorhabditis elegans with certain tissues (such as those of the nervous system) consisting of entirely maternal genomes and others (such as the germline) consisting of entirely paternal genomes.

The Global Natural Products Social Molecular Networking knowledgebase facilitates community sharing and curation of mass spectrometry data from natural products.

Point spread function engineering streamlines multicolor super-resolution imaging and single-particle tracking.

Sequential rounds of immunoprecipitation and barcoding reveal the genome-wide occurrence of paired histone marks.

Scientists propose a more human-centric benchmark for assessing naive and primed pluripotency in human embryonic stem cells.

A combination of quantitative mass spectrometry, subcellular fractionation and stringent statistical analyses allows the description of protein translocation events at the proteome scale.

We convened an ad hoc International Working Group for Antibody Validation in order to formulate the best approaches for validating antibodies used in common research applications and to provide guidelines that ensure antibody reproducibility. We recommend five conceptual 'pillars' for antibody validation to be used in an application-specific manner.

DNA folding shapes gene expression. Emerging techniques promise to reveal the intricacies of this architectural language of chromosomes.

sc-GEM enables the dissection of cellular heterogeneity by simultaneously assaying the status of DNA mutations, gene expression and DNA methylation at multiple targeted loci in individual cells.

A straightforward method and tool, MetaMass, utilizes a list of subcellular markers to analyze and classify subcellular proteomics data from multiple experiments. An accompanying analysis reveals a wide variation in the results of subcellular fractionation protocols.

rG4-seq enables the mapping of RNA G-quadruplex structures across entire transcriptomes at nucleotide resolution.

Diffusion pseudotime (DPT) enables robust and scalable inference of cellular trajectories, branching events, metastable states and underlying gene dynamics from snapshot single-cell gene expression data.

A suite of tools and resources for Vibrio natriegens introduces the bacterium as a faster-growing alternative to E. coli for molecular biology and biotechnology applications.

Expressing guide RNAs from a tRNA scaffold enhances mutagenesis by both Cas9 and Cpf1 and allows conditional CRISPR applications in vivo.

Double-strand DNA breaks capture (DSBCapture) identifies in situ DSBs via the ligation of an Illumina adaptor into the break site and shows no bias for chromatin state or base composition. A genome-wide DSB profile shows breaks occurring more frequently in euchromatin and transcriptionally active regions.

uDISCO clearing renders whole animals transparent and capitalizes on shrinkage to image them. This method allows the analysis of intact nervous systems and whole-body screens for transplanted cells and human tissue samples after prolonged storage.

Packaging split Cas9 into AAVs increases cargo capacity and allows for efficient genome editing and gene activation in vivo. AAV–split-Cas9 activates the host immune system but does not trigger the extensive cellular damage observed with delivery of Cas9 via DNA electroporation.

Flexible mesh electronics facilitate stable long-term recordings of the same single neurons in mouse brains over months, enabling chronic recordings in behaving animals and longitudinal studies to resolve aging-dependent changes in neural activity.

The combination of cellular barcoding and treatment with a library of small molecules before injecting the treated cells into mice allows the screening for compounds that inhibit metastatic seeding.