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Nature Protocols is an interactive online resource for all laboratory protocols relevant to biological and biomedical research. Nature Protocols includes a free-to-access community site, 'Protocols Network', containing protocols that are posted direc

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Scale-up approach for the preparation of magnetic ferrite nanocubes and other shapes with benchmark performance for magnetic hyperthermia applications

Nature Protocols, Published online: 27 January 2023; doi:10.1038/s41596-022-00779-3This protocol describes a solvothermal-based process to prepare gram-scale ferrite nanoparticles with well-defined shapes (nanocubes, nanostars, faceted and spherical) having heating properties appealing for clinical magnetic hyperthermia treatments.

Measuring DNA modifications with the comet assay: a compendium of protocols

Nature Protocols, Published online: 27 January 2023; doi:10.1038/s41596-022-00754-yThe comet assay is commonly used to assess DNA damage. This collection of consensus protocols includes adaptations for a wide range of species and sample types, assay formats and detection of different types of DNA lesions.

Design and construction of a microfluidics workstation for high-throughput multi-wavelength fluorescence and transmittance activated droplet analysis and sorting

Nature Protocols, Published online: 27 January 2023; doi:10.1038/s41596-022-00796-2Single-cell screening and sorting is useful for addressing many biological questions. The high-throughput droplet analyzer and sorter described in this protocol has been designed so that it can be constructed without specialist engineering training.

Whole-mouse clearing and imaging at the cellular level with vDISCO

Nature Protocols, Published online: 25 January 2023; doi:10.1038/s41596-022-00788-2A full-body nanobody-based immunolabeling and clearing method that renders mice transparent in 3 weeks, enhancing the signal of fluorescent proteins and allowing their reliable detection and quantification, at cellular resolution, within an entire body.

Preparation of near-infrared AIEgen-active fluorescent probes for mapping amyloid-β plaques in brain tissues and living mice

Nature Protocols, Published online: 25 January 2023; doi:10.1038/s41596-022-00789-1We present a protocol for the synthesis and usage of QM-FN-SO3, a near-infrared aggregation-induced-emission-active fluorescent probe capable of crossing the blood–brain barrier and ultrasensitively lighting up amyloid-β plaques in living mice.

A dynamic DNA tetrahedron framework for active targeting

Nature Protocols, Published online: 20 January 2023; doi:10.1038/s41596-022-00791-7This Protocol Extension presents an updated tetrahedral DNA nanostructure for the delivery of various bioactive molecules that enables an active targeting strategy to be used for stimuli-sensitive conformation changes and on-site cargo release.

Author Correction: Proteome-wide structural changes measured with limited proteolysis-mass spectrometry: an advanced protocol for high-throughput applications

Nature Protocols, Published online: 18 January 2023; doi:10.1038/s41596-023-00808-9Author Correction: Proteome-wide structural changes measured with limited proteolysis-mass spectrometry: an advanced protocol for high-throughput applications

Seed amplification assay for the detection of pathologic alpha-synuclein aggregates in cerebrospinal fluid

Nature Protocols, Published online: 18 January 2023; doi:10.1038/s41596-022-00787-3The amplification of misfolded alpha-synuclein aggregates in vitro can be used for the detection, via fluorescent dyes, of pathologic amyloids in cerebrospinal fluid samples from patients affected by Parkinson’s disease, dementia with Lewy bodies or multiple-system atrophy.

Mapping the common gene networks that underlie related diseases

Nature Protocols, Published online: 18 January 2023; doi:10.1038/s41596-022-00797-1This protocol describes how to use NetColoc, a freely available tool for evaluating the extent to which two related diseases, each characterized by a set of mapped genes, are colocalized in a reference gene interaction network.

Genome-wide measurement of DNA replication fork directionality and quantification of DNA replication initiation and termination with Okazaki fragment sequencing

Nature Protocols, Published online: 18 January 2023; doi:10.1038/s41596-022-00793-5A protocol for quantitative genome-wide detection of replication initiation, fork progression and termination, based on purification and strand-specific sequencing of Okazaki fragments isolated from mammalian or yeast cells.

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