Determining small-molecule permeation through lipid membranes
Nature Protocols, Published online: 24 August 2022; doi:10.1038/s41596-022-00734-2This protocol includes a suite of procedures for measuring the passive permeability of solutes through membranes using fluorescence-based assays that report either volume or pH changes of synthetic vesicles or live cells. (Source: Nature Protocols)
Source: Nature Protocols - August 24, 2022 Category: Biomedical Science Authors: Jacopo Frallicciardi Matteo Gabba Bert Poolman Source Type: research
Constructing a cost-efficient, high-throughput and high-quality single-molecule localization microscope for super-resolution imaging
Nature Protocols, Published online: 24 August 2022; doi:10.1038/s41596-022-00730-6This protocol provides a step-by-step guide to building an affordable single-molecule localization microscopy setup for high-throughput super-resolution imaging by using off-the-shelf and machined parts. (Source: Nature Protocols)
Source: Nature Protocols - August 24, 2022 Category: Biomedical Science Authors: John S. H. Danial Jeff Y. L. Lam Yunzhao Wu Matthew Woolley Eleni Dimou Matthew R. Cheetham Derya Emin David Klenerman Source Type: research
Small-animal blood exchange is an emerging approach for systemic aging research
Nature Protocols, Published online: 19 August 2022; doi:10.1038/s41596-022-00731-5Small-animal blood exchange replaces or dilutes blood components more precisely than parabiosis does. This protocol describes the exchange process, provides blueprints of the required device and derives equations for simulating dilution of biomolecules. (Source: Nature Protocols)
Source: Nature Protocols - August 19, 2022 Category: Biomedical Science Authors: Melod Mehdipour Payam Amiri Chao Liu Jonalyn DeCastro Cameron Kato Colin M. Skinner Michael J. Conboy Kiana Aran Irina M. Conboy Source Type: research
Principles of reproducible metabolite profiling of enriched lymphocytes in tumors and ascites from human ovarian cancer
Nature Protocols, Published online: 19 August 2022; doi:10.1038/s41596-022-00729-zIdentifying metabolites in cells of the tumor microenvironment is an area of intense study. This protocol describes specimen collection, enrichment of human immune cell populations and analysis by flow cytometry and LC–MS. (Source: Nature Protocols)
Source: Nature Protocols - August 19, 2022 Category: Biomedical Science Authors: Marisa K. Kilgour Sarah MacPherson Lauren G. Zacharias Jodi LeBlanc Sindy Babinszky Gabrielle Kowalchuk Scott Parks Ryan D. Sheldon Russell G. Jones Ralph J. DeBerardinis Phineas T. Hamilton Peter H. Watson Julian J. Lum Source Type: research
Directed differentiation of human pluripotent stem cells into diverse organ-specific mesenchyme of the digestive and respiratory systems
Nature Protocols, Published online: 17 August 2022; doi:10.1038/s41596-022-00733-3This protocol uses signaling networks and molecular markers recently elucidated from single-cell transcriptomic analysis of mouse foregut organogenesis to differentiate human pluripotent stem cells into digestive and respiratory organ-specific mesenchyme. (Source: Nature Protocols)
Source: Nature Protocols - August 17, 2022 Category: Biomedical Science Authors: Keishi Kishimoto Kentaro Iwasawa Alice Sorel Carlos Ferran-Heredia Lu Han Mitsuru Morimoto James M. Wells Takanori Takebe Aaron M. Zorn Source Type: research
Constructing and interpreting volcano plots and activity maps to navigate homogeneous catalyst landscapes
Nature Protocols, Published online: 17 August 2022; doi:10.1038/s41596-022-00726-2Volcano plots and activity maps are powerful tools for studying homogeneous catalysis. This protocol describes how to build these from computed DFT data and use them to predict and rationalize the performance of homogeneous catalysts. (Source: Nature Protocols)
Source: Nature Protocols - August 17, 2022 Category: Biomedical Science Authors: Rub én Laplaza Shubhajit Das Matthew D. Wodrich Cl émence Corminboeuf Source Type: research
Nacre-inspired underwater superoleophobic films with high transparency and mechanical robustness
Nature Protocols, Published online: 15 August 2022; doi:10.1038/s41596-022-00725-3Contamination of water by oil is a problem both in the environment and in engineering applications. This protocol describes how to prepare a transparent superoleophobic film that can coat lenses or make separation membranes for use underwater. (Source: Nature Protocols)
Source: Nature Protocols - August 15, 2022 Category: Biomedical Science Authors: Wei Chen Pengchao Zhang Shaokang Yu Ruhua Zang Liming Xu Shutao Wang Bailiang Wang Jingxin Meng Source Type: research
Isolation of mitochondria-derived mitovesicles and subpopulations of microvesicles and exosomes from brain tissues
Nature Protocols, Published online: 12 August 2022; doi:10.1038/s41596-022-00719-1This protocol describes the isolation from brain tissue of extracellular vesicle subpopulations, including microvesicles, exosomes and mitochondria-derived mitovesicles, using a high-resolution (iodixanol) density step gradient. Extracellular vesicle characterization and analysis are also presented. (Source: Nature Protocols)
Source: Nature Protocols - August 12, 2022 Category: Biomedical Science Authors: Pasquale D ’Acunzo Yohan Kim Jonathan M. Ungania Roc ío Pérez-González Chris N. Goulbourne Efrat Levy Source Type: research
Designing and executing prime editing experiments in mammalian cells
Nature Protocols, Published online: 08 August 2022; doi:10.1038/s41596-022-00724-4This protocol describes prime editing (PE) and twinPE experiments as well as the design and optimization of pegRNAs. The authors provide guidelines for selecting the proper PE system for a given application and how to perform PE in mammalian cells. (Source: Nature Protocols)
Source: Nature Protocols - August 8, 2022 Category: Biomedical Science Authors: Jordan L. Doman Alexander A. Sousa Peyton B. Randolph Peter J. Chen David R. Liu Source Type: research
I-TASSER-MTD: a deep-learning-based platform for multi-domain protein structure and function prediction
Nature Protocols, Published online: 05 August 2022; doi:10.1038/s41596-022-00728-0A 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. (Source: Nature Protocols)
Source: Nature Protocols - August 5, 2022 Category: Biomedical Science Authors: Xiaogen Zhou Wei Zheng Yang Li Robin Pearce Chengxin Zhang Eric W. Bell Guijun Zhang Yang Zhang Source Type: research
High-throughput proteomic sample preparation using pressure cycling technology
Nature Protocols, Published online: 05 August 2022; doi:10.1038/s41596-022-00727-1High-throughput lysis and proteolytic digestion of biopsy-level tissue specimens is a major bottleneck for clinical proteomics. This protocol describes pressure cycling technology (PCT)-assisted sample preparation of biopsy tissues. (Source: Nature Protocols)
Source: Nature Protocols - August 5, 2022 Category: Biomedical Science Authors: Xue Cai Zhangzhi Xue Chunlong Wu Rui Sun Liujia Qian Liang Yue Weigang Ge Xiao Yi Wei Liu Chen Chen Huanhuan Gao Jing Yu Luang Xu Yi Zhu Tiannan Guo Source Type: research
Single-cell RNA and protein profiling of immune cells from the mouse brain and its border tissues
Nature Protocols, Published online: 05 August 2022; doi:10.1038/s41596-022-00716-4This protocol enables single-cell multi-omic analysis of the mouse brain immune compartment to explore immune cell heterogeneity and activation in the healthy and diseased brain, using a workflow based on HD flow cytometry, scRNA-seq and CITE-seq. (Source: Nature Protocols)
Source: Nature Protocols - August 5, 2022 Category: Biomedical Science Authors: Isabelle Scheyltjens Hannah Van Hove Karen De Vlaminck Daliya Kancheva Jonathan Bastos M ónica Vara-Pérez Ana Rita Pombo Antunes Liesbet Martens Charlotte L. Scott Jo A. Van Ginderachter Yvan Saeys Martin Guilliams Niels Vandamme Kiavash Movahedi Source Type: research
Prototype mouse models for researching SEND-based mRNA delivery and gene therapy
Nature Protocols, Published online: 03 August 2022; doi:10.1038/s41596-022-00721-7In this Perspective, the authors propose genetically engineered mouse models to further the understanding and use of a recently discovered tool, selective endogenous encapsidation for cellular delivery via virus-like particles, in gene delivery and gene therapy applications. (Source: Nature Protocols)
Source: Nature Protocols - August 3, 2022 Category: Biomedical Science Authors: Channabasavaiah B. Gurumurthy Rolen M. Quadros Masato Ohtsuka Source Type: research
A rapid screening platform to coculture bacteria within tumor spheroids
Nature Protocols, Published online: 29 July 2022; doi:10.1038/s41596-022-00723-5Bacteria 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. (Source: Nature Protocols)
Source: Nature Protocols - July 29, 2022 Category: Biomedical Science Authors: Tetsuhiro Harimoto Dhruba Deb Tal Danino Source Type: research
Single-crystal structure determination of nanosized metal–organic frameworks by three-dimensional electron diffraction
Nature Protocols, Published online: 27 July 2022; doi:10.1038/s41596-022-00720-8Metal–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. (Source: Nature Protocols)
Source: Nature Protocols - July 27, 2022 Category: Biomedical Science Authors: Taimin Yang Tom Willhammar Hongyi Xu Xiaodong Zou Zhehao Huang Source Type: research
