Volume 16 Issue 11, November 2019

Growing up curious in the countryside leads to tools for manipulating endogenous proteins.

The growth of advanced, custom microscopy has outpaced commercialization, with biologists unable to benefit from these developments. We propose a complementary model for access based on shareable, traveling and configurable microscopes, with potential benefits for biologists, developers and the community.

Independent studies introduced two distinct tools, both called ‘Pepper’, for live imaging of RNA.

The hybrid voltage-indicator Voltron combines the voltage sensitivity of microbial rhodopsins with the brightness and photostability of chemical dyes.

Two teams develop methods for genealogy inference using large genomic datasets.

Researchers develop a genome-informed approach to isolate and grow targeted cells into pure cultures from microbial communities.

In silico modeling and mapping of cross-species protein–protein interactions.

Mechanical measurements would be easy if cells were homogeneous objects — they’re not.

One third of verified gene knock outs with CRISPR still show residual protein expression owing to translation reinitiation or exon skipping. Several proteins are still functional. The authors call for a systematic analysis of protein levels after genome editing.

Optobodies combine split intracellular antibodies (intrabodies) with light-controlled dimerization tools for spatiotemporal control of intrabody activity. The developed tools demonstrate the versatility and power of this approach for probing protein function.

DNA-PAINT is sped up by an order of magnitude by optimizing sequences and buffer conditions, enabling faster imaging with no compromise to image quality or resolution, improved single-molecule counting and enhanced cellular imaging.

The mesoSPIM is an open hardware axially scanned light-sheet microscope for the rapid imaging of large cleared samples with isotropic resolution.

Cleared-tissue axially swept light-sheet microscopy (ctASLM) enables high-speed, refraction index-independent imaging of live, cleared and expanded samples with isotropic, submicron resolution.

Repetitive optical selective exposure (ROSE) is an interferometric single-molecule localization microscopy method offering twofold improvement in lateral resolution with the same photon budget compared with conventional approaches.

A multi-beam two-photon microscope enables imaging of calcium activity or neurovascular dynamics in the brain with millisecond-scale temporal resolution.

Cellular lipids, labeled with a charged reporter, yield characteristic MS1 and MS2 patterns during mass spectrometry. These reporters allow sample multiplexing and sensitive detection of lipid metabolism at single cell resolution.

The Alu editing index (AEI) quantifies genome-wide editing in Alu repeats and allows comparison across samples.

SAUCIE, a deep learning platform to analyze single-cell data across samples and platforms, allows information to be obtained from the internal layers of the network, which provides additional mechanistic understanding that can be used to further tune data analysis.

The user-friendly software tool Warp enables automated, on-the-fly preprocessing of cryo-EM data, including motion correction, defocus estimation, particle picking and image denoising.

The challenge of accurate particle picking in cryo-EM analysis is addressed with Topaz, a neural-network-based algorithm that shows advantages over other tools, especially in picking unusually shaped particles.

An integrated pipeline for processing cryo-ET data implemented in EMAN2 streamlines data processing to minimize human bias, and improves the quality and resolution of resulting macromolecular structures, both in vitro and in cells.

Expression of ETV2 in human cortical organoids induces the formation of vascular-like networks, which reduces cell death within organoids and increases their functional maturation.

An engineering approach guided by machine learning results in high-performance channelrhodopsin variants that are suitable for systemic viral delivery and illumination through a thinned skull.

Fiber photometry with tapered fibers allows monitoring of neural activity in larger volumes than with flat-cleaved fibers. In addition, signals from different depths can be resolved with the same tapered fiber.