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Reposted by Rosy Favicchio

Nature @nature.com · 2d

BREAKING: The Nobel Prize in Chemistry has been awarded to Susumu Kitagawa, Richard Robson and Omar M. Yaghi “for the development of metal-organic frameworks”

Stay tuned for more.
#NobelPrize

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Reposted by Rosy Favicchio

Nature Protocols @natprot.nature.com · 11d

Good to know: There is a free online training course for peer review from Nature Masterclasses

masterclasses.nature.com/focus-on-pee...

Focus on Peer Review

masterclasses.nature.com

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Rosy Favicchio @rosyf.bsky.social · 2d

This Protocol results from the Joint Undertaking for Morphological Profiling Cell Painting Consortium, and improves the Cell Painting assay by quantitatively detecting morphological phenotypes, improving the ability to group perturbations with similar behavior.

Optimizing the Cell Painting assay for image-based profiling

Nature Protocols - We provide an updated protocol for image-based profiling with Cell Painting. A detailed procedure, with standardized conditions for the assay, is presented, along with a...

rMATS-turbo: an efficient and flexible computational tool for alternative splicing analysis of large-scale RNA-seq data

Rosy Favicchio @rosyf.bsky.social · 2d

This protocol provides detailed guidelines for using rMATS-turbo, the latest implementation of the popular software for the discovery and quantification of alternative splicing events from RNA sequencing data. The software is exemplified in two representative scenarios. rdcu.be/eJYYF

Nature Protocols - This protocol provides detailed guidelines for using rMATS-turbo—the latest implementation of the popular software for the discovery and quantification of alternative...

Acoustic tweezers for high-throughput single-cell analysis

Rosy Favicchio @rosyf.bsky.social · 2d

Acoustic tweezers enable the fast, high-throughput handling of single cells and particles. This protocol covers the fabrication of a microfluidic chamber, the interdigital transducer, as well as the experimental setup for the manipulation of single cells and particles, data acquisition and analysis

Nature Protocols - A protocol for the construction of acoustic tweezers to manipulate single cells in a high-throughput, precise, selective and contact-free manner, which can be broadly adapted for...

iBEAT V2.0: a multisite-applicable, deep learning-based pipeline for infant cerebral cortical surface reconstruction

Rosy Favicchio @rosyf.bsky.social · 2d

A protocol covering a robust, multisite-applicable, infant-tailored computational pipeline that leverages deep learning and can handle T1w and T2w structural infant brain MR images from birth to 6 years of age and is effective for different imaging protocols/scanners. rdcu.be/eJYVn

Nature Protocols - The iBEAT V2.0 is a robust, multisite-applicable, infant-tailored computational pipeline that uses deep learning to process and analyze infant brain magnetic resonance images....

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

Rosy Favicchio @rosyf.bsky.social · 2d

Fibrillar aggregates of the amyloid-β protein (Aβ) are found in brain plaques of patients with Alzheimer’s disease (AD). Here, a near-infrared aggregation-induced-emission-active fluorescent probe can cross the blood–brain barrier and detect Aβ plaques in brain tissue and in vivo in mice.

Nature Protocols - We 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...

Encapsulating and stabilizing enzymes using hydrogen-bonded organic frameworks

Rosy Favicchio @rosyf.bsky.social · 2d

Enzymes are natural catalysts susceptible to non-physiological environments, limiting their industrial applications. This protocol covers a strategy for enzyme encapsulation using a hydrogen-bonded organic framework resulting in different surface chemistries to design biocatalytic HOF materials.

Nature Protocols - We present a protocol for the encapsulation and stabilization of enzymes by using hydrogen-bonded organic frameworks (HOFs)—enzyme@HOF-101—along with procedures for...

Optimizing the standardized assays for determining the catalytic activity and kinetics of peroxidase-like nanozymes

Rosy Favicchio @rosyf.bsky.social · 2d

Nanozymes are nanoparticles designed to have catalytic properties similar to those of natural enzymes. This is a protocol for measuring their catalytic behavior based on data from measured physical properties and density functional theory calculations into the Michaelis–Menten approach.

Nature Protocols - Developing optimal nanozymes requires standardized methods for measuring their catalytic activity and reaction kinetics. This protocol integrates enzyme based...

A dynamic DNA tetrahedron framework for active targeting

Rosy Favicchio @rosyf.bsky.social · 2d

Tetrahedral DNA nanostructures (TDN) can be used to deliver bioactive molecules. However, static structures and passive targeting may introduce off-target effects. Here, an active targeting strategy which uses stimuli-sensitive conformation changes allow targeted on-site cargo release.

Nature Protocols - This 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...

Web-based multi-omics integration using the Analyst software suite

Rosy Favicchio @rosyf.bsky.social · 2d

This protocol for web-based multi-omics integration covers single-omics data analysis using ExpressAnalyst and MetaboAnalyst, followed by knowledge-driven integration using OmicsNet and data-driven integration using OmicsAnalyst.

Nature Protocols - This multi-omics data integration protocol, which uses the web-based Analyst tool suite, covers knowledge-driven integration using biological networks and data-driven integration...

Preparation and quantitative analysis of multicenter luminescence materials for sensing function

Rosy Favicchio @rosyf.bsky.social · 2d

Luminescent materials are an attractive for environmental sensing. The synthesis of metal–organic frameworks bearing multiple luminescent centers such as metal cations and organic ligands, chosen for selectivity for the analytes of interest, results in a complex with sensing properties.

Nature Protocols - In many environmental or clinical settings, it is useful to detect and quantify analytes instantaneously in situ. This protocol describes how to develop metal–organic...

An end-to-end workflow for multiplexed image processing and analysis

Rosy Favicchio @rosyf.bsky.social · 2d

The protocol covers the analysis of highly multiplexed tissue imaging data, including data visualization, data preprocessing, image segmentation, single-cell feature extraction, reading data into R, spillover correction, quality control, cell phenotyping and spatially resolved single-cell analysis.

Nature Protocols - An integrated workflow for multiplexed tissue image processing and analysis, including interactive inspection of raw data, cell segmentation, feature extraction, single-cell...

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

Rosy Favicchio @rosyf.bsky.social · 2d

Misfolded alpha-synuclein (αSyn) aggregates are a hallmark in synucleinopathies. This protocol covers αSyn seed amplification assays for the detection of αSyn aggregates in cerebrospinal fluid samples from patients affected by Parkinson disease, dementia with Lewy bodies or multiple-system atrophy

Nature Protocols - The 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...

Comprehensive synthesis of Ti3C2Tx from MAX phase to MXene

Rosy Favicchio @rosyf.bsky.social · 2d

MXenes are two-dimensional materials with diverse and unique properties. This protocol provides a detailed guideline for the synthesis of a Ti3AlC2 MAX phase precursor, wet chemical etching of MAX to yield multilayer Ti3C2Tx and its delamination into single-layer flakes.

Nature Protocols - MXenes are two-dimensional materials with diverse optoelectronic, biological, mechanical and chemical properties. This protocol describes how to prepare single-layer flakes of...

Physical dynamic double-network hydrogels as dressings to facilitate tissue repair

Rosy Favicchio @rosyf.bsky.social · 2d

A protocol on the use of ureido–pyrimidinone hydrogen bonding with metal-coordination interactions between Fe3+ and catechol groups for generating double physical cross-linked hydrogels with self-healing properties, high mechanical strength and tunable responses to temperature, pH and light.

Nature Protocols - Procedures for the synthesis of physical double-network hydrogels to provide self-healing, pH-responsive, tissue-adhesive, antioxidant, photothermal and antibacterial properties....

Comprehensive isolation of extracellular vesicles and nanoparticles

Rosy Favicchio @rosyf.bsky.social · 2d

A protocol for the use of differential ultracentrifugation, filtration, concentration and high-resolution density-gradient fractionation to obtain purified fractions of distinct populations of EVs and NVEPs.

Nature Protocols - This protocol isolates large and small extracellular vesicles, as well as nonvesicular nanoparticles known as exomeres and supermeres, from cell-conditioned medium or human...

The HADDOCK2.4 web server for integrative modeling of biomolecular complexes

Rosy Favicchio @rosyf.bsky.social · 2d

HADDOCK is an integrative modeling approach which combines experimental and predicted information to guide the structure prediction of biomolecular complexes, including protein–protein, protein–ligand, protein–oligosaccharide and protein–nucleic acid complexes.

Nature Protocols - The HADDOCK2.4 web server is a modeling platform that can integrate experimental and theoretical data for guiding 3D prediction of biomolecular complexes.

CellChat for systematic analysis of cell–cell communication from single-cell transcriptomics

Rosy Favicchio @rosyf.bsky.social · 2d

CellChat is a software package for systematic inference, quantitative analysis and intuitive visualization of cell–cell communication in an easily interpretable way from single-cell transcriptomic data & enables comparative analysis of intercellular communication across different conditions.

Nature Protocols - CellChat enables systematic inference, quantitative analysis and intuitive visualization of cell–cell communication from single-cell transcriptomic data, as well as...

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

Rosy Favicchio @rosyf.bsky.social · 2d

A series of consensus protocols which describe the application of the comet assay to a wide variety of cell types, species and types of DNA damage, thereby demonstrating its versatility.

Nature Protocols - The 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...

Using clusterProfiler to characterize multiomics data

Rosy Favicchio @rosyf.bsky.social · 2d

ClusterProfiler is a software package for characterizing and interpreting omics data. Functional enrichment can be achieved using either over-representation or gene set enrichment analyses; it supports the use of a variety of databases, e.g., Gene Ontology and Kyoto Encyclopedia of Genes and Genomes

Nature Protocols - clusterProfiler is a tool for characterizing and visualizing omics data. The example procedures show integration of metabolomics and metagenomics analyses, characterization of...

Rosy Favicchio @rosyf.bsky.social · 2d

When discussing content proposals for @natprot.nature.com with potential authors I often end up covering the wide reach of our journal. Often researchers are interested in examples of articles which have seen wide uptake, accesses and use from the scientific community. Here, a🧵of readcube links:
🧪🎓

Fabrication and characterization of optoelectronic in-sensor computing devices

Rosy Favicchio @rosyf.bsky.social · 3d

Find the readcube link here:

Nature Protocols - Optoelectronic devices based on two-dimensional layered thin film semiconductors can be tuned to directly sense and process spatial and temporal information, making them suitable...