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A protocol is described for predicting the structures and functions of multi-domain proteins using the freely available deep-learning-based web platform I-TASSER-MTD.
Bacteria spheroid coculture allows long-term growth of bacteria in the hypoxic, necrotic core of tumor spheroids. This enables the study of bacteria–tumor interactions and rapid development of engineered microbial therapies.
Receptor-mediated signaling occurs at nanoscale. Understanding this requires nanopatterning and imaging techniques compatible at this scale. Rapid functionalization of Ti nanopatterns allows nanoscale visualization of early steps in cell signaling.
Metal–organic frameworks have a well-defined pore architecture and tunable functional characteristics based on their structure. This protocol explains how to determine the structure of nano- (submicron-)sized crystals by three-dimensional electron diffraction.
This protocol details the construction of two types of nanocarrier based on bacterial membrane materials and their use in vaccine delivery to create cancer nanovaccines.
This extension of the TCP-seq protocol describes procedures for selective profiling of 40S and 80S ribosome subpopulations bound by a factor of interest, permitting detailed studies of the different stages of translation in mammalian and yeast cells.
This protocol describes labeling, clearing, imaging and cellular-level three-dimensional image reconstruction of intact human organs achieved with the help of a novel tissue clearing and labeling technology and a commercially available microscope.
The authors describe a protocol for growing a tumor of mouse or human origin beneath the skin of a mouse, which is widely known as the subcutaneous mouse tumor model.
Poly(A) inclusive full-length RNA isoform sequencing is a method for measuring poly(A) tail length and composition at single-mammalian-oocyte (subnanogram)-level sensitivity.
This protocol describes how to use the free, vendor-neutral software Skyline to process and annotate multidimensional lipidomic data by using expanded features such as predicted retention times, spectral libraries and ion mobility filtering.
The functions of circular RNAs are challenging to investigate because of high sequence similarity to their cognate linear mRNAs. This protocol outlines a strategy for specific targeting of circular RNAs in genome-wide pooled CRISPR–Cas13 screens.
This protocol describes the working principle and implementation of axially swept light-sheet microscopy, which can image subcellular features at organ scales in 3D. It discusses how to optimize its design and provides a detailed guide for its construction and alignment.
The development of nucleoside analogs for use as antiviral agents and antisense oligonucleotides requires efficient synthetic methods. This three-step approach starts with proline-catalyzed fluorination of simple heteroaryl-substituted aldehydes.
We present a protocol for building a scanning light-field microscope with digital adaptive optics as an add-on to a standard wide-field microscope to achieve long-term, high-speed intravital fluorescence imaging.
This protocol allows users to quantify metal-bearing engineered nanomaterials in biological tissues and cells and to analyze their dynamic behavior at trace-level concentrations, using single-cell inductively coupled plasma mass spectrometry, single-particle inductively coupled plasma mass spectrometry and synchrotron X-ray absorption fine structure.
Treatments developed in small-animal models of stroke are often not translatable to the clinic. In this protocol, a blood clot in a microcatheter is introduced into the middle cerebral artery of rhesus monkeys; controlled thrombolysis is possible.
It is crucial to know the localization of a protein to fully understand its function. SubCellBarCode is a wet lab–, mass spectrometry- and bioinformatics-based pipeline that generates proteome-wide protein subcellular localization for human cancer cell lines.
LC–HRMS is used for metabolomics studies in the biomedical and environmental sciences. MetaboAnalyst (metaboanalyst.ca) can be used to address challenges in data processing, statistical analysis, functional interpretation and multi-omics integration.
This protocol enables users to establish long-term multigenerational ctenophore cultures in the laboratory and details CRISPR–Cas9 genome editing in Mnemiopsis leidyi.
Fluorescently labeled nuclei of the enteric nervous system are isolated from adult mouse or zebrafish gut and characterized by nuclear RNA sequencing and visualization and quantification of transcripts using a custom analytical pipeline.