The use of methanol as a C1 building block
Nature Protocols, Published online: 25 April 2024; doi:10.1038/s41596-024-00978-0This protocol details methods for using methanol in methylation reactions, including the synthesis of suitable transition metal-containing catalysts, and in the synthesis of heterocycles. The methods described produce only H2 and H2O as by-products. (Source: Nature Protocols)
Source: Nature Protocols - April 25, 2024 Category: Biomedical Science Authors: Bhaskar Paul Sabuj Kundu Source Type: research
Surface photovoltage microscopy for mapping charge separation on photocatalyst particles
Nature Protocols, Published online: 23 April 2024; doi:10.1038/s41596-024-00992-2Surface photovoltage microscopy as described in this protocol allows high spatial and energy resolution mapping of surface-charge distributions on photocatalyst particles, enabling rational design of improved materials. (Source: Nature Protocols)
Source: Nature Protocols - April 23, 2024 Category: Biomedical Science Authors: Ruotian Chen Chenwei Ni Jian Zhu Fengtao Fan Can Li Source Type: research
A guide to precise measurements of isotope abundance by ESI-Orbitrap MS
Nature Protocols, Published online: 23 April 2024; doi:10.1038/s41596-024-00981-5Isotope ratio mass spectrometry as described in this protocol can be used to determine natural variation in the abundance of stable isotopes in individual compounds to provide information relevant to metabolism, ecology or climate change. (Source: Nature Protocols)
Source: Nature Protocols - April 23, 2024 Category: Biomedical Science Authors: Krist ýna Kantnerová Nils Kuhlbusch Dieter Juchelka Andreas Hilkert Sebastian Kopf Cajetan Neubauer Source Type: research
Preparation of AIEgen-based near-infrared afterglow luminescence nanoprobes for tumor imaging and image-guided tumor resection
Nature Protocols, Published online: 18 April 2024; doi:10.1038/s41596-024-00990-4This protocol describes the preparation of long-lasting aggregation-induced emission-based, near-infrared afterglow luminescence nanoprobes. Their enhanced afterglow intensity results in improved imaging sensitivity and depth in vivo. (Source: Nature Protocols)
Source: Nature Protocols - April 18, 2024 Category: Biomedical Science Authors: Chao Chen Xiaoyan Zhang Zhiyuan Gao Guangxue Feng Dan Ding Source Type: research
Luciferase- and HaloTag-based reporter assays to measure small-molecule-induced degradation pathway in living cells
Nature Protocols, Published online: 18 April 2024; doi:10.1038/s41596-024-00979-zNanoLuciferase- and HaloTag-based screening technologies are versatile tools suitable for the live-cell analysis of the entire small-molecule-induced degradation cascade to uncover the mode of action of proximity-inducing compounds such as PROTACs. (Source: Nature Protocols)
Source: Nature Protocols - April 18, 2024 Category: Biomedical Science Authors: Martin P. Schwalm Krishna Saxena Susanne M üller Stefan Knapp Source Type: research
Reprogramming fibroblast into human iBlastoids
Nature Protocols, Published online: 17 April 2024; doi:10.1038/s41596-024-00984-2A protocol for the generation of induced blastoids, an in vitro integrated model of the human blastocyst derived via somatic reprogramming. This model overcomes restrictions associated with the use of human blastocysts in embryology research. (Source: Nature Protocols)
Source: Nature Protocols - April 17, 2024 Category: Biomedical Science Authors: Jia Ping Tan Xiaodong Liu Jose M. Polo Source Type: research
Noninvasive in vivo microscopy of single neutrophils in the mouse brain via NIR-II fluorescent nanomaterials
Nature Protocols, Published online: 11 April 2024; doi:10.1038/s41596-024-00983-3Activated neutrophils labeled with NIR-II lanthanide downshifting nanoparticles can be sequentially imaged through the intact skull of a mouse model of ischemic stroke during adhesion, crawling and extravasation processes (Source: Nature Protocols)
Source: Nature Protocols - April 11, 2024 Category: Biomedical Science Authors: Ying Chen Yiwei Yang Fan Zhang Source Type: research
Control of DNA replication in vitro using a reversible replication barrier
Nature Protocols, Published online: 09 April 2024; doi:10.1038/s41596-024-00977-1This protocol describes the establishment of a reversible replication barrier using plasmid templates containing a lacO array bound by LacR repressor. The method allows fine control of replication fork movement and replication fork encounter with DNA lesions. (Source: Nature Protocols)
Source: Nature Protocols - April 9, 2024 Category: Biomedical Science Authors: Emma J. Vontalge Tamar Kavlashvili Steven N. Dahmen Matthew T. Cranford James M. Dewar Source Type: research
Anaerobic cryoEM protocols for air-sensitive nitrogenase proteins
Nature Protocols, Published online: 04 April 2024; doi:10.1038/s41596-024-00973-5It can be challenging to obtain meaningful and accurate structural information for air-sensitive proteins. This protocol describes the application of customized vacuum manifold and anaerobic chamber setups for the purification and cryo-electron microscopy analysis of air-sensitive nitrogenase enzymes. (Source: Nature Protocols)
Source: Nature Protocols - April 4, 2024 Category: Biomedical Science Authors: Rebeccah A. Warmack Belinda B. Wenke Thomas Spatzal Douglas C. Rees Source Type: research
Packaging and containerization of computational methods
Nature Protocols, Published online: 02 April 2024; doi:10.1038/s41596-024-00986-0Attempts to reproduce the computational steps described in published omics research often fail. This review provides guidelines for the packaging and containerization of software so that readers can use the exact programs used in published work. (Source: Nature Protocols)
Source: Nature Protocols - April 2, 2024 Category: Biomedical Science Authors: Mohammed Alser Brendan Lawlor Richard J. Abdill Sharon Waymost Ram Ayyala Neha Rajkumar Nathan LaPierre Jaqueline Brito Andr é M. Ribeiro-dos-Santos Nour Almadhoun Varuni Sarwal Can Firtina Tomasz Osinski Eleazar Eskin Qiyang Hu Derek Strong Byoung-Do (B Source Type: research
Standardized production of hPSC-derived cardiomyocyte aggregates in stirred spinner flasks
We present a protocol for achieving efficient generation of hPSC-CM aggregates in suspension culture, emphasizing process simplicity, robustness and GMP compliance. The strategy promotes clinical translation and other applications that require large numbers of CMs. (Source: Nature Protocols)
Source: Nature Protocols - March 28, 2024 Category: Biomedical Science Authors: Nils Kriedemann Wiebke Triebert Jana Teske Mira Mertens Annika Franke Kevin Ullmann Felix Manstein Lika Drakhlis Alexandra Haase Caroline Halloin Ulrich Martin Robert Zweigerdt Source Type: research
A practical guide for the preparation of C1-labeled α-amino acids using aldehyde catalysis with isotopically labeled CO2
Nature Protocols, Published online: 28 March 2024; doi:10.1038/s41596-024-00974-4Isotopically labeled amino acids are useful in pharmacology and for medical imaging. In this protocol, C1-labeled α-amino acids are prepared via late-stage carboxylate exchange of unprotected α-amino acids with [*C]CO2 where *C is 13C, 11C or 14C. (Source: Nature Protocols)
Source: Nature Protocols - March 28, 2024 Category: Biomedical Science Authors: Michael G. J. Doyle Braeden A. Mair Anna Sib Odey Bsharat Maxime Munch Volker Derdau Benjamin H. Rotstein Rylan J. Lundgren Source Type: research
Generating human bone marrow organoids for disease modeling and drug discovery
Nature Protocols, Published online: 26 March 2024; doi:10.1038/s41596-024-00971-7This protocol can be used to generate three-dimensional vascularized bone marrow organoids from human induced pluripotent stem cells. The organoids contain key stromal and hematopoietic cell types and can be engrafted with normal and malignant cells from adult donors to model niche interactions. (Source: Nature Protocols)
Source: Nature Protocols - March 26, 2024 Category: Biomedical Science Authors: Aude-Anais Olijnik Antonio Rodriguez-Romera Zo ë C. Wong Yuqi Shen Jasmeet S. Reyat Natalie J. Jooss Julie Rayes Bethan Psaila Abdullah O. Khan Source Type: research
Pan-evolutionary and regulatory genome architecture delineated by an integrated macro- and microsynteny approach
Nature Protocols, Published online: 21 March 2024; doi:10.1038/s41596-024-00966-4This protocol is for using PanSyn, the first software package for the identification of micro- and macrosynteny and their functional integration for comprehensive characterization of genome architecture and regulatory evolution. (Source: Nature Protocols)
Source: Nature Protocols - March 21, 2024 Category: Biomedical Science Authors: Hongwei Yu Yuli Li Wentao Han Lisui Bao Fuyun Liu Yuanting Ma Zhongqi Pu Qifan Zeng Lingling Zhang Zhenmin Bao Shi Wang Source Type: research
BridGE: a pathway-based analysis tool for detecting genetic interactions from GWAS
Nature Protocols, Published online: 21 March 2024; doi:10.1038/s41596-024-00954-8Genetic interactions have been found to influence phenotypes in a variety of systems, yet their specific contribution to complex diseases remains unclear. This protocol describes Bridging Gene sets with Epistasis (BridGE), a computational approach for discovering interactions between biological pathways from genome-wide association studies data. (Source: Nature Protocols)
Source: Nature Protocols - March 21, 2024 Category: Biomedical Science Authors: Mehrad Hajiaghabozorgi Mathew Fischbach Michael Albrecht Wen Wang Chad L. Myers Source Type: research
