Volume 19 Issue 9, September 2022

Your name is on the door to your new lab. Life is getting exciting and turbulent.

Parhyale hawaiensis comes from tropical intertidal shores and mangroves. In research, it is used to explore topics ranging from embryonic development and regeneration, to tidal rhythms and environmental pollution.

Light microscopy enables researchers to observe cellular mechanisms with high spatial and temporal resolution. However, the increasing complexity of current imaging technologies, coupled with financial constraints of potential users, hampers the general accessibility and potential reach of cutting-edge microscopy. Open microscopy can address this issue by making well-designed and well-documented hardware and software solutions openly available to a broad audience. In this Comment, we provide a definition of open microscopy and present recent projects in the field. We discuss current and future challenges of open microscopy and their implications for funders, policymakers, researchers and scientists. We believe that open microscopy requires a holistic approach. Sample preparation, designing and building of hardware components, writing software, data acquisition and data interpretation must go hand in hand to enable interdisciplinary and reproducible science to the benefit of society.

Here we discuss barriers to reproducibility in regard to microscopes and related hardware, along with best practices for sharing novel designs created using computer-aided design (CAD). We hope to start a fruitful community discussion on how instrument development, especially in microscopy, can become more open and reproducible, ultimately leading to better, more trustworthy science.

Researchers describe Retro-Cascorder, a tool that employs prokaryotic retrons and CRISPR integrases to write transcriptional events into the genome of Escherichia coli.

plexDIA increases throughput of proteomics analysis with low sample amounts.

A method to develop gastrulating embryoids from stem cells ex utero.

The NeuroCAAS platform simplifies data analysis in the neuroscience space for users and enhances reproducibility.

Different nucleotides and derivatives can be read out by MspA-PBA, an engineered nanopore.

As new technology enables researchers to find and characterize less-common post-translational modifications that drive gene expression and cellular metabolism, the movement to catalog the entire human proteome gains momentum

New computational method uses convolutional neural networks for cis-regulatory sequence analysis to analyze and cluster scATAC-seq data.

PROBER is a fast and sensitive episome-based method to identify sequence-specific DNA-binding proteins from living cells using proximity proteomics. This method quantifies steady-state and inducible association of transcription factors and corresponding chromatin regulators to specific DNA sequences as well as binding quantitative trait loci present as a result of single nucleotide variants.

Cell type-specific inference of differential expression (C-SIDE) is a statistical model that identifies which genes (within a determined cell type) are differentially expressed on the basis of spatial position, pathological changes or cell–cell interactions. C-SIDE facilitates differential expression analysis in spatial transcriptomics by jointly modeling cell type mixtures and spatially varying gene expression.

This Review covers advances in methods for studying metabolism at the subcellular level and how they have influenced our understanding of cancer biology.

In this Perspective, technologies and challenges in the cardiac tissue engineering field are discussed and strategies to overcome these challenges are proposed.

A systematic exploration of MINFLUX nanoscopy with DNA-PAINT labeling leads to improved nanoscopy in fixed cells and MINFLUX imaging with increased multiplexing, as exemplified by three-color imaging of mitochondria in mammalian cells.

C-SIDE facilitates accurate cell type-specific differential expression analysis for multiple spatially resolved transcriptomics technologies by cell type mixture modeling.

Using a sequence-based deep neural network, scBasset facilitates various tasks of single-cell ATAC-seq analysis in a unified framework.

MIRA facilitates accurate inference of cell state trees and regulatory mechanisms driving cell fate decisions using single-cell multimodal data profiling gene expression and chromatin accessibility.

US-align is a universal protocol for monomeric and oligomeric structural alignments of protein, RNA and DNA molecules, built on the coupling of a uniform TM-score objective function and the heuristic iterative searching algorithm.

The DAQ score assesses the consistency of amino acid assignment in protein structure models with local density from cryo-EM maps. The method complements existing quality metrics and is a versatile tool for highlighting problematic regions of model structures.

This paper explores the use of scanning transmission electron microscopy (STEM) to vitrified biological samples for biomolecular structure elucidation. Integrated differential phase contrast (iDPC)–STEM imaging of keyhole limpet hemocyanin and tobacco mosaic virus enabled cryo-EM structure determination at 6.5 and 3.5 Å resolution, respectively.

Thermostable antibodies called SPEARs enable rapid immunostaining with improved tissue penetration.