Volume 15 Issue 9, September 2018

Swimming to a new way of decoding messages at the cell membrane.

Independent efforts shine light on the 3D genome structure by looking at multiple contacts along an allele or equalizing the distance between restriction sites for higher-resolution Hi-C maps.

A genetically encoded sensor based on G-protein-coupled receptors can detect the neurotransmitter acetylcholine in vitro and in vivo.

The combination of single-particle electron microscopy and mass spectrometry shows potential for surveys of both the structure and the identity of protein complexes in the cell.

A high-throughput platform allows biophysical measurements to probe RNA tertiary folding.

FRET improves the photostability of fluorophores for longer single-molecule tracking.

Methods choice is broad and labs are pushing protocols to address expansive biological questions.

Chemically modified DNA aptamers enable quantitative super-resolution imaging.

A review of how single-cell sequencing methods can be used to improve human stem cell and tissue engineering.

A multi-laboratory study finds that single-molecule FRET is a reproducible and reliable approach for determining accurate distances in dye-labeled DNA duplexes.

CDeep3M provides a user-friendly tool for deep-learning-based image segmentation via a cloud-based deep convolutional neural network. Demonstrations include challenging light, X-ray, and electron microscopy segmentation tasks.

A resource of multiple reaction monitoring–mass spectrometry transitions for quantitative analysis of biological small molecules is provided in METLIN-MRM, along with automated tools for analyzing such data in XCMS-MRM.

Slow off-rate modified aptamer (SOMAmer) reagents are small and versatile probes for DNA-PAINT super-resolution microscopy that enable multiplexed, quantitative, and high-resolution imaging in fixed and live cells.

Preprocessing of localization microscopy datasets using Haar wavelet kernel (HAWK) analysis enables artifact-free analysis of high-density data for improved fixed and live-cell super-resolution microscopy.

A simple transcription-factor-based protocol generates functional astrocytes rapidly and efficiently from human pluripotent stem cells.

Single DNA molecules can be detected in aqueous solutions at ambient temperatures by electron spin resonance spectroscopy with diamond sensors.

A method for generating cortical spheroids from human pluripotent stem cells produces maturing oligodendrocytes that can myelinate axons and model myelin disease and drug effects.

REVOLVER uses transfer learning on multi-region tumor sequencing data to jointly infer tumor evolution models in multiple individuals and to detect repeated evolutionary trajectories. Repeated evolution can be used to stratify the cohort.

A proximity-based labeling system, PUP-IT, identifies membrane protein interactions.

Spinal cord neural stem cells are generated from human pluripotent stem cells via a chemically defined, xeno-free method, and exhibit efficient and functional engraftment in rat spinal cord lesions.

This paper describes modifications to standard culture conditions that permit the growth of naive human pluripotent stem cells with reduced genomic instability.

Insertion of a bivalent linker between two regions of interest allows chromatin contacts to be probed without proximity ligation.