Volume 16 Issue 6, June 2021

This Perspective from the Harvard Chan Microbiome in Public Health Center describes a generalizable and scalable approach to stool and oral microbiome and metadata collection in the Micro-N (Microbiome Among Nurses) study, to show how to carry out prospective studies of the microbiome.

This tutorial provides guidance for selecting and optimizing tissue-clearing protocols for specific samples and biological questions. In addition, instructions are provided for developing an imaging strategy and processing the resulting data.

This tutorial provides guidelines for interpreting single-cell transcriptomic maps to identify cell types, states and other biologically relevant patterns.

We present a practical workflow describing how to use deep learning to develop continuous-risk models that can predict various adverse outcomes from structured electronic health records.

The authors describe an optimized workflow for isolating single nuclei from archived postmortem tissues that does not require sorting or ultracentrifugation and can be used in snRNA and ATAC sequencing pipelines.

Mitochondrial ribosomes (mitoribosomes) translate a unique set of genes whose products are essential for cellular respiration. This protocol provides a modified ribosome profiling procedure suitable for studying translation within mitochondria.

This protocol explains how to treat cancer cells in culture directly with cold atmospheric plasma or indirectly with plasma-conditioned medium. Quantification of the reactive oxygen species present following treatment is described. Upscaling of the treatments to allow molecular biology assays is also described.

This protocol describes sample-preparation strategies for correlative 3D cryo-structured illumination microscopy and cryo-soft X-ray tomography. The authors also provide a direct comparison and recommendations regarding the selection and use of fiducials for 3D correlation.

In this protocol, the authors describe two automated versions of the Smart-seq2 method for full-length single-cell RNA sequencing: a medium-throughput variant using off-the-shelf reagents and a high-throughput version using a commercially available kit.

This protocol describes the experimental and bioinformatics analysis steps for global profiling of protein-mediated RNA-RNA interactions in mammalian cells by in situ proximity ligation and deep sequencing.

This protocol describes techniques for single-bouton stimulation and simultaneous pre- and postsynaptic recording at hippocampal mossy fiber–CA3 pyramidal neuron synapses in rat or mouse brain slices.

Chemiresistors based on monolayer-capped metal nanoparticles (MCNPs) can be used for many diagnostic applications. The protocol describes how to prepare gold MCNPs on appropriate electrodes to analyze volatile organic compounds.

In this protocol, barcodes are introduced into cells via homology-directed targeted integration, and clones are tracked in xenotransplanted hosts by high-throughput sequencing. The results can be analyzed using a freely available online program.

A new protocol describes the synthesis and application of single-walled carbon nanotube-based catecholamine nanosensors, which can be used for near-IR imaging of dopamine signaling in acute brain slices at high spatiotemporal resolution.

This protocol assembles ordered libraries of transposon insertion mutants, even for strict anaerobes. It uses cell sorting to order the library and tracks transposon insertions using barcode sequencing to locate individual mutant strains in the ordered library.

This protocol describes the surgical procedures for implantation of a wireless, battery-free optogenetic implant (NeuroLux spinal optogenetic device) for optogenetic control of spinal cord circuits in mice.

Customizable tissue perfusion chambers facilitate seeding and perfusion culture of human endothelial cells within vascularized tissue constructs.

A protocol from Public Health England for three assays (PRNT, MNA and PNA) to measure neutralizing antibodies against SARS-CoV-2 that have been used to assess the efficacy of the ChAdOx1 nCoV-19 and Ad26.COV2.S COVID-19 vaccines.

This protocol provides an RNA extraction–free nano-amplified colorimetric test that enables rapid detection of SARS-CoV-2 with the naked eye. The test uses plasmonic gold nanoparticles capped with antisense oligonucleotides as a colorimetric biosensor for point-of-care diagnosis of COVID-19.