Volume 18 Issue 2, February 2023

Cryogenic electron microscopy is well suited to uncovering structural heterogeneity in protein complexes, but analyses of such heterogeneous datasets are challenging. CryoDRGN is a machine learning approach to reconstructing heterogeneous ensembles of cryogenic electron microscopy density maps.

An approach to reproducing episodes of hypotension-mimicking orthostatic challenges while monitoring arterial blood pressure and sympathetic nerve activity over several months in preclinical models of chronic neurological disorders, using a combination of available telemetry technologies, optogenetics and neuronal tract tracing.

This protocol describes how to perform an open thoracic surgery for epicardial implantation of wireless cardiac bioelectronic devices in adult rats and the methodology for a full biocompatibility assessment of the physiological response to the implanted device.

This protocol describes the design and implementation of an in vitro platform for highly multiplexed profiling of antibody reactivity using custom DNA-barcoded peptide libraries and deep sequencing.

Simultaneous electrophysiological recordings are obtained from multiple brain regions using Neuropixels probes. The procedure covers the implantation of a headframe, the targeted positioning of probes and their insertion through a perforated imaging window.

This protocol details quantum dot-based single-virus tracking, an imaging approach to monitoring the infection behavior of individual viruses or viral components in live cells by using semiconductor nanoparticles (quantum dots) as fluorescent labels.

Targeted liquid chromatography–tandem mass spectrometry-based metabolomics using in vitro (organoids) and in vivo (gnotobiotic mice colonized with mono- or multi-species bacterial cultures) systems examines the role of specific microbially driven pathways of the mammalian gut–brain axis.

Ubiquitination and downstream reactions are dynamic, reversible processes with functionally transient intermediates. This protocol describes the preparation of stable mimics that can be used for structural and functional studies.

This protocol describes the procedure for the fabrication of electrochemical liquid cells for in situ liquid cell transmission electron microscopy. This allows direct visualization of complex electrochemical reactions at the nano scale in real time.

This protocol describes how to design, implement and analyze the data from a forced desynchrony protocol to assess endogenous circadian rhythmicity and to separate circadian from evoked components of daily rhythms in physiology and behavior.

Many applications of metal–organic frameworks relate to their nanometer-sized pores. This protocol describes three postsynthetic methods for making metal–organic frameworks with multiple levels of pores: Soxhlet washing, linker hydrolysis and linker thermolysis.

This protocol describes N⁶-methyladenosine (m⁶A)-SAC-seq, site-specific base-resolution m⁶A sequencing in the whole transcriptome, including preparing the enzyme and synthesizing the allyl-SAM cofactor required for library preparation, and data analysis for m⁶A sites.