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 (Source: Nature Protocols)
Source: Nature Protocols - January 18, 2023 Category: Biomedical Science Authors: Liliana Malinovska Valentina Cappelletti Devon Kohler Ilaria Piazza Tsung-Heng Tsai Monika Pepelnjak Patrick Stalder Christian D örig Fabian Sesterhenn Franziska Els ässer Lucie Kralickova Nigel Beaton Lukas Reiter Natalie de Souza Olga Vitek Paola Pico Source Type: research
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. (Source: Nature Protocols)
Source: Nature Protocols - January 18, 2023 Category: Biomedical Science Authors: Xia Wu Yaqun Liu Yves d ’Aubenton-Carafa Claude Thermes Olivier Hyrien Chun-Long Chen Nataliya Petryk Source Type: research
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. (Source: Nature Protocols)
Source: Nature Protocols - January 18, 2023 Category: Biomedical Science Authors: Sara Brin Rosenthal Sarah N. Wright Sophie Liu Christopher Churas Daisy Chilin-Fuentes Chi-Hua Chen Kathleen M. Fisch Dexter Pratt Jason F. Kreisberg Trey Ideker Source Type: research
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. (Source: Nature Protocols)
Source: Nature Protocols - January 18, 2023 Category: Biomedical Science Authors: Luis Concha-Marambio Sandra Pritzkow Mohammad Shahnawaz Carly M. Farris Claudio Soto Source Type: research
A ‘print–pause–print’ protocol for 3D printing microfluidics using multimaterial stereolithography
Nature Protocols, Published online: 06 January 2023; doi:10.1038/s41596-022-00792-6Making microfluidic chips using 3D printers allows rapid fabrication of ready-to-use products from digital 3D designs with minimal human intervention. This ‘print–pause–print’ protocol describes how to make transparent, multimaterial chips. (Source: Nature Protocols)
Source: Nature Protocols - January 6, 2023 Category: Biomedical Science Authors: Yong Tae Kim Alireza Ahmadianyazdi Albert Folch Source Type: research
In vitro reconstitution of COPII vesicles from Arabidopsis thaliana suspension-cultured cells
Nature Protocols, Published online: 04 January 2023; doi:10.1038/s41596-022-00781-9This protocol describes an in vitro vesicle formation system to reconstitute, purify and characterize plant-derived coat protein complex II vesicles from Arabidopsis thaliana suspension-cultured cells. (Source: Nature Protocols)
Source: Nature Protocols - January 4, 2023 Category: Biomedical Science Authors: Baiying Li Yonglun Zeng Sze Wan Lo Yusong Guo Liwen Jiang Source Type: research
A chemo-mechanical cochleostomy preserves hearing for the in vivo functional imaging of cochlear cells
Nature Protocols, Published online: 04 January 2023; doi:10.1038/s41596-022-00786-4A surgical procedure that preserves hearing while creating an imaging window in the mouse cochlea, enabling the functional imaging of cochlear cells in vivo. (Source: Nature Protocols)
Source: Nature Protocols - January 4, 2023 Category: Biomedical Science Authors: Jinkyung Kim Anthony J. Ricci Source Type: research
In situ electrochemical Raman spectroscopy and ab initio molecular dynamics study of interfacial water on a single-crystal surface
Nature Protocols, Published online: 04 January 2023; doi:10.1038/s41596-022-00782-8This protocol combines shell-isolated nanoparticle-enhanced Raman spectroscopy and ab initio molecular dynamics simulations to unravel the directional molecular features of interfacial water, enabling a better understanding of electrocatalysis. (Source: Nature Protocols)
Source: Nature Protocols - January 4, 2023 Category: Biomedical Science Authors: Yao-Hui Wang Shunning Li Ru-Yu Zhou Shisheng Zheng Yue-Jiao Zhang Jin-Chao Dong Zhi-Lin Yang Feng Pan Zhong-Qun Tian Jian-Feng Li Source Type: research
A new era begins at Nature Protocols
Nature Protocols, Published online: 23 December 2022; doi:10.1038/s41596-022-00798-0There have been some changes to the editorial team at Nature Protocols in 2022 that represent the end of one era and the start of another. (Source: Nature Protocols)
Source: Nature Protocols - December 23, 2022 Category: Biomedical Science Source Type: research
Author Correction: Fractionation of lignocellulosic biomass to produce uncondensed aldehyde-stabilized lignin
Nature Protocols, Published online: 23 December 2022; doi:10.1038/s41596-022-00760-0Author Correction: Fractionation of lignocellulosic biomass to produce uncondensed aldehyde-stabilized lignin (Source: Nature Protocols)
Source: Nature Protocols - December 23, 2022 Category: Biomedical Science Authors: Masoud Talebi Amiri Graham R. Dick Ydna M. Questell-Santiago Jeremy S. Luterbacher Source Type: research
Proteome-wide structural changes measured with limited proteolysis-mass spectrometry: an advanced protocol for high-throughput applications
Nature Protocols, Published online: 16 December 2022; doi:10.1038/s41596-022-00771-xLiP-MS is an approach based on limited proteolysis that can be used to probe structural changes in proteins. This update highlights recent changes to the method to improve throughput, proteome coverage and data analysis. (Source: Nature Protocols)
Source: Nature Protocols - December 16, 2022 Category: Biomedical Science Authors: Liliana Malinovska Valentina Cappelletti Devon Kohler Ilaria Piazza Tsung-Heng Tsai Monika Pepelnjak Patrick Stalder Christian D örig Fabian Sesterhenn Franziska Els ässer Lucie Kralickova Nigel Beaton Lukas Reiter Natalie de Souza Olga Vitek Paola Pico Source Type: research
Comprehensive multi-attribute method workflow for biotherapeutic characterization and current good manufacturing practices testing
Nature Protocols, Published online: 16 December 2022; doi:10.1038/s41596-022-00785-5The multi-attribute method directly characterizes and monitors multiple product quality attributes of a biopharmaceutical product via proteolytic digestion of the sample followed by reversed-phase chromatographic separation and high-resolution liquid chromatography-mass spectrometry analysis. (Source: Nature Protocols)
Source: Nature Protocols - December 16, 2022 Category: Biomedical Science Authors: Silvia Mill án-Martín Craig Jakes Sara Carillo Richard Rogers Da Ren Jonathan Bones Source Type: research
Monomicellar assembly to synthesize structured and functional mesoporous carbonaceous nanomaterials
We describe the template-directed assembly of monomicelles to make mesoporous materials with different structures. (Source: Nature Protocols)
Source: Nature Protocols - December 14, 2022 Category: Biomedical Science Authors: Liang Peng Huarong Peng Wei Li Dongyuan Zhao Source Type: research
Purification, full-length sequencing and genomic origin mapping of eccDNA
Nature Protocols, Published online: 14 December 2022; doi:10.1038/s41596-022-00783-7A protocol for purification, full-length sequencing and genomic origin mapping of extrachromosomal circle DNA using a three-step purification strategy combined with rolling-circle amplification and Oxford Nanopore sequencing. (Source: Nature Protocols)
Source: Nature Protocols - December 14, 2022 Category: Biomedical Science Authors: Yuangao Wang Meng Wang Yi Zhang Source Type: research
Micro-CT acquisition and image processing to track and characterize pulmonary nodules in mice
Nature Protocols, Published online: 09 December 2022; doi:10.1038/s41596-022-00769-5A micro-computed X-ray tomography-based approach for quantifying the number and volume of lung cancer nodules over time, enabling the tracking of individual nodule formation, tumor growth and response to therapy. (Source: Nature Protocols)
Source: Nature Protocols - December 9, 2022 Category: Biomedical Science Authors: May Zaw Thin Christopher Moore Thomas Snoeks Tammy Kalber Julian Downward Axel Behrens Source Type: research
