Ligand functionalization of titanium nanopattern enables the analysis of cell–ligand interactions by super-resolution microscopy
Nature Protocols, Published online: 27 July 2022; doi:10.1038/s41596-022-00717-3Receptor-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. (Source: Nature Protocols)
Source: Nature Protocols - July 27, 2022 Category: Biomedical Science Authors: Kashish Jain Pakorn Kanchanawong Michael P. Sheetz Xianjing Zhou Haogang Cai Rishita Changede Source Type: research
Nanocarriers based on bacterial membrane materials for cancer vaccine delivery
Nature Protocols, Published online: 25 July 2022; doi:10.1038/s41596-022-00713-7This protocol details the construction of two types of nanocarrier based on bacterial membrane materials and their use in vaccine delivery to create cancer nanovaccines. (Source: Nature Protocols)
Source: Nature Protocols - July 25, 2022 Category: Biomedical Science Authors: Xiao Zhao Ruifang Zhao Guangjun Nie Source Type: research
Selective footprinting of 40S and 80S ribosome subpopulations (Sel-TCP-seq) to study translation and its control
Nature Protocols, Published online: 22 July 2022; doi:10.1038/s41596-022-00708-4This 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. (Source: Nature Protocols)
Source: Nature Protocols - July 22, 2022 Category: Biomedical Science Authors: Susan Wagner Jonathan Bohlen Anna Herrmannova Jan Jel ínek Thomas Preiss Leo š Shivaya Valášek Aurelio A. Teleman Source Type: research
The cell-line-derived subcutaneous tumor model in preclinical cancer research
Nature Protocols, Published online: 20 July 2022; doi:10.1038/s41596-022-00709-3The 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. (Source: Nature Protocols)
Source: Nature Protocols - July 20, 2022 Category: Biomedical Science Authors: Stephen M. Stribbling Anderson J. Ryan Source Type: research
Scalable tissue labeling and clearing of intact human organs
Nature Protocols, Published online: 20 July 2022; doi:10.1038/s41596-022-00712-8This 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. (Source: Nature Protocols)
Source: Nature Protocols - July 20, 2022 Category: Biomedical Science Authors: Hongcheng Mai Zhouyi Rong Shan Zhao Ruiyao Cai Hanno Steinke Ingo Bechmann Ali Ert ürk Source Type: research
Tutorial: design and execution of CRISPR in vivo screens
Nature Protocols, Published online: 15 July 2022; doi:10.1038/s41596-022-00700-yThis new tutorial from Braun and colleagues details how to design and execute in vivo CRISPR screens in mice to investigate a variety of phenotypes. (Source: Nature Protocols)
Source: Nature Protocols - July 15, 2022 Category: Biomedical Science Authors: Christian J. Braun Andr és Carbonell Adames Dieter Saur Roland Rad Source Type: research
Isotropic imaging across spatial scales with axially swept light-sheet microscopy
Nature Protocols, Published online: 13 July 2022; doi:10.1038/s41596-022-00706-6This 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. (Source: Nature Protocols)
Source: Nature Protocols - July 13, 2022 Category: Biomedical Science Authors: Kevin M. Dean Tonmoy Chakraborty Stephan Daetwyler Jinlong Lin Gerard Garrelts Ons M ’Saad Hannahmariam T. Mekbib Fabian F. Voigt Martina Schaettin Esther T. Stoeckli Fritjof Helmchen Joerg Bewersdorf Reto Fiolka Source Type: research
Screening circular RNAs with functional potential using the RfxCas13d/BSJ-gRNA system
Nature Protocols, Published online: 13 July 2022; doi:10.1038/s41596-022-00715-5The 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. (Source: Nature Protocols)
Source: Nature Protocols - July 13, 2022 Category: Biomedical Science Authors: Siqi Li Hao Wu Ling-Ling Chen Source Type: research
Utilizing Skyline to analyze lipidomics data containing liquid chromatography, ion mobility spectrometry and mass spectrometry dimensions
Nature Protocols, Published online: 13 July 2022; doi:10.1038/s41596-022-00714-6This 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. (Source: Nature Protocols)
Source: Nature Protocols - July 13, 2022 Category: Biomedical Science Authors: Kaylie I. Kirkwood Brian S. Pratt Nicholas Shulman Kaipo Tamura Michael J. MacCoss Brendan X. MacLean Erin S. Baker Source Type: research
Transcriptome-wide measurement of poly(A) tail length and composition at subnanogram total RNA sensitivity by PAIso-seq
Nature Protocols, Published online: 13 July 2022; doi:10.1038/s41596-022-00704-8Poly(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. (Source: Nature Protocols)
Source: Nature Protocols - July 13, 2022 Category: Biomedical Science Authors: Yusheng Liu Yiwei Zhang Jiaqiang Wang Falong Lu Source Type: research
Practical and concise synthesis of nucleoside analogs
Nature Protocols, Published online: 04 July 2022; doi:10.1038/s41596-022-00705-7The 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. (Source: Nature Protocols)
Source: Nature Protocols - July 4, 2022 Category: Biomedical Science Authors: Emma K. Davison David A. Petrone Michael Meanwell Matthew B. Nodwell Steven M. Silverman Louis-Charles Campeau Robert Britton Source Type: research
An analytical workflow for dynamic characterization and quantification of metal-bearing nanomaterials in biological matrices
Nature Protocols, Published online: 29 June 2022; doi:10.1038/s41596-022-00701-xThis 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. (Source: Nature Protocols)
Source: Nature Protocols - June 29, 2022 Category: Biomedical Science Authors: Fazel Abdolahpur Monikh Zhiling Guo Peng Zhang Martina G. Vijver Iseult Lynch Eugenia Valsami-Jones Willie J. G. M. Peijnenburg Source Type: research
A practical guide to scanning light-field microscopy with digital adaptive optics
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. (Source: Nature Protocols)
Source: Nature Protocols - June 29, 2022 Category: Biomedical Science Authors: Zhi Lu Yeyi Cai Yixin Nie Yuxin Yang Jiamin Wu Qionghai Dai Source Type: research
A clinically relevant model of focal embolic cerebral ischemia by thrombus and thrombolysis in rhesus monkeys
Nature Protocols, Published online: 27 June 2022; doi:10.1038/s41596-022-00707-5Treatments 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. (Source: Nature Protocols)
Source: Nature Protocols - June 27, 2022 Category: Biomedical Science Authors: Di Wu Jian Chen Longfei Wu Hangil Lee Jingfei Shi Mo Zhang Yanhui Ma Xiaoduo He Zixin Zhu Feng Yan Chuanjie Wu Yunxia Duan Yongjuan Fu Sijie Li Xinglong Zhi Xuxiang Zhang Shengli Li Yuchuan Ding Xunming Ji Source Type: research
SubCellBarCode: integrated workflow for robust spatial proteomics by mass spectrometry
Nature Protocols, Published online: 22 June 2022; doi:10.1038/s41596-022-00699-2It 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. (Source: Nature Protocols)
Source: Nature Protocols - June 22, 2022 Category: Biomedical Science Authors: Taner Arslan Yanbo Pan Georgios Mermelekas Mattias Vesterlund Lukas M. Orre Janne Lehti ö Source Type: research
