Genome-wide pooled CRISPR screening in neurospheres
Nature Protocols, Published online: 07 June 2023; doi:10.1038/s41596-023-00835-6The authors present a protocol for genome-wide clustered regularly interspaced short palindromic repeat screening of three-dimensional neurospheres. (Source: Nature Protocols)
Source: Nature Protocols - June 7, 2023 Category: Biomedical Science Authors: Tanaz Abid Amy B. Goodale Zohra Kalani Meghan Wyatt Elizabeth M. Gonzalez Kevin Ning Zhou Kenin Qian Dana Novikov Alexandra-Larisa Condurat Pratiti Bandopadhayay Federica Piccioni Nicole S. Persky David E. Root Source Type: research
Detect-seq, a chemical labeling and biotin pull-down approach for the unbiased and genome-wide off-target evaluation of programmable cytosine base editors
Nature Protocols, Published online: 05 June 2023; doi:10.1038/s41596-023-00837-4Detect-seq (dU-detection enabled by C-to-T transition during sequencing) enables off-target evaluation of programmable cytosine base editors. DNA is chemically labeled, and the editing intermediate dU is enriched for sequencing by biotin pull-down. (Source: Nature Protocols)
Source: Nature Protocols - June 5, 2023 Category: Biomedical Science Authors: Zhixin Lei Haowei Meng Xichen Rao Huanan Zhao Chengqi Yi Source Type: research
Genetic recording of in vivo cell proliferation by ProTracer
Nature Protocols, Published online: 02 June 2023; doi:10.1038/s41596-023-00833-8ProTracer is a genetic lineage–tracing technology that uses two recombinases to allow lifelong, noninvasive monitoring of cell proliferation for specific cell lineages in live animals. (Source: Nature Protocols)
Source: Nature Protocols - June 2, 2023 Category: Biomedical Science Authors: Xiuxiu Liu Wendong Weng Lingjuan He Bin Zhou Source Type: research
Medulloblastoma and high-grade glioma organoids for drug screening, lineage tracing, co-culture and in vivo assay
Nature Protocols, Published online: 29 May 2023; doi:10.1038/s41596-023-00839-2A protocol for the generation of medulloblastoma and high-grade glioma organoids by electroporating, respectively, cerebellum and forebrain organoids, along with procedures for their use in drug screening, lineage tracing, co-culture and in vivo assays. (Source: Nature Protocols)
Source: Nature Protocols - May 29, 2023 Category: Biomedical Science Authors: Chiara Lago Matteo Gianesello Lucia Santomaso Gloria Leva Claudio Ballabio Marica Anderle Francesco Antonica Luca Tiberi Source Type: research
Self-assembled ultraflexible probes for long-term neural recordings and neuromodulation
Nature Protocols, Published online: 29 May 2023; doi:10.1038/s41596-023-00824-9The authors describe the fabrication, assembly and long-term implantation of ultraflexible neural probes for the simultaneous recording of neural activity and neuromodulation in rodents. (Source: Nature Protocols)
Source: Nature Protocols - May 29, 2023 Category: Biomedical Science Authors: Shouliang Guan Huihui Tian Yinan Yang Mengcheng Liu Jianfei Ding Jinfen Wang Ying Fang Source Type: research
Spatial- and Fourier-domain ptychography for high-throughput bio-imaging
Nature Protocols, Published online: 29 May 2023; doi:10.1038/s41596-023-00829-4A step-by-step guide providing biomedical researchers instructions for implementing spatial- and Fourier-domain ptychography to existing setups with minimal hardware modifications. (Source: Nature Protocols)
Source: Nature Protocols - May 29, 2023 Category: Biomedical Science Authors: Shaowei Jiang Pengming Song Tianbo Wang Liming Yang Ruihai Wang Chengfei Guo Bin Feng Andrew Maiden Guoan Zheng Source Type: research
Solution-state nuclear magnetic resonance spectroscopy of crystalline cellulosic materials using a direct dissolution ionic liquid electrolyte
Nature Protocols, Published online: 26 May 2023; doi:10.1038/s41596-023-00832-9Cellulose is a burgeoning feedstock for more sustainable alternatives to fossil fuel-based materials. This protocol uses a cellulose-dissolving ionic liquid electrolyte with nuclear magnetic resonance methods to provide high-resolution structural analysis of cellulose. (Source: Nature Protocols)
Source: Nature Protocols - May 26, 2023 Category: Biomedical Science Authors: Lukas Fliri Katja Heise Tetyana Koso Aleksandar R. Todorov Daniel Rico del Cerro Sami Hietala Juha Fiskari Ilkka Kilpel äinen Michael Hummel Alistair W. T. King Source Type: research
Molecular-electromechanical system for unamplified detection of trace analytes in biofluids
We present the design, assembly and implementation of a molecular-electromechanical system composed of a tetrahedral DNA nanostructure immobilized on a graphene field-effect transistor for unamplified detection of trace amounts of analytes in biofluids. (Source: Nature Protocols)
Source: Nature Protocols - May 19, 2023 Category: Biomedical Science Authors: Xuejun Wang Changhao Dai Yungeng Wu Yunqi Liu Dacheng Wei Source Type: research
Spiral volumetric optoacoustic tomography for imaging whole-body biodynamics in small animals
Nature Protocols, Published online: 19 May 2023; doi:10.1038/s41596-023-00834-7The authors describe spiral volumetric optoacoustic tomography for the visualization of contrast agent perfusion and biodistribution in mice, featuring excellent scalability to achieve spatial resolution down to 90 µm or whole-body scans in (Source: Nature Protocols)
Source: Nature Protocols - May 19, 2023 Category: Biomedical Science Authors: Sandeep Kumar Kalva Xos é Luís Deán-Ben Michael Reiss Daniel Razansky Source Type: research
Generation of iPSC-derived human forebrain organoids assembling bilateral eye primordia
Nature Protocols, Published online: 17 May 2023; doi:10.1038/s41596-023-00814-xThis protocol enables the generation of human forebrain organoids from induced pluripotent stem cells with the intrinsic ability to assemble functionally integrated bilateral optic vesicles. (Source: Nature Protocols)
Source: Nature Protocols - May 17, 2023 Category: Biomedical Science Authors: Elke Gabriel Walid Albanna Giovanni Pasquini Anand Ramani Natasa Josipovic Aruljothi Mariappan Maria Giovanna Riparbelli Giuliano Callaini Celeste M. Karch Olivier Goureau Argyris Papantonis Volker Busskamp Toni Schneider Jay Gopalakrishnan Source Type: research
Encapsulating and stabilizing enzymes using hydrogen-bonded organic frameworks
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 their material characterization and testing of their biocatalytic performance. (Source: Nature Protocols)
Source: Nature Protocols - May 17, 2023 Category: Biomedical Science Authors: Guosheng Chen Siming Huang Xiaomin Ma Rongwei He Gangfeng Ouyang Source Type: research
The ClusPro AbEMap web server for the prediction of antibody epitopes
Nature Protocols, Published online: 15 May 2023; doi:10.1038/s41596-023-00826-7AbEMap generates large ensembles of docked antigen–antibody structures based on the structure of an antigen and either the structure or the sequence of an antibody. For each antigen residue, a likelihood score for being part of the epitope is obtained. (Source: Nature Protocols)
Source: Nature Protocols - May 15, 2023 Category: Biomedical Science Authors: Israel T. Desta Sergei Kotelnikov George Jones Usman Ghani Mikhail Abyzov Yaroslav Kholodov Daron M. Standley Dmitri Beglov Sandor Vajda Dima Kozakov Source Type: research
A distal lung organoid model to study interstitial lung disease, viral infection and human lung development
Nature Protocols, Published online: 10 May 2023; doi:10.1038/s41596-023-00827-6A protocol for the directed differentiation of human pluripotent stem cells into distal lung organoids that can be used to model interstitial lung disease, viral infection and human lung development, along with procedures for their analysis. (Source: Nature Protocols)
Source: Nature Protocols - May 10, 2023 Category: Biomedical Science Authors: Ivana Matkovic Leko Remy T. Schneider Tania A. Thimraj Nadine Schrode Daniel Beitler Hsiao-Yun Liu Kristin Beaumont Ya-Wen Chen Hans-Willem Snoeck Source Type: research
Click chemistry: a transformative technology in nuclear medicine
Nature Protocols, Published online: 26 April 2023; doi:10.1038/s41596-023-00825-8This Perspective explains how click chemistry—specifically, the copper-catalyzed azide–alkyne cycloaddition, the strain-promoted azide–alkyne cycloaddition and the inverse electron-demand Diels–Alder reaction—has revolutionized radiopharmaceutical chemistry. (Source: Nature Protocols)
Source: Nature Protocols - April 26, 2023 Category: Biomedical Science Authors: David Bauer Samantha M. Sarrett Jason S. Lewis Brian M. Zeglis Source Type: research
Addendum: Micro-CT acquisition and image processing to track and characterize pulmonary nodules in mice
Nature Protocols, Published online: 24 April 2023; doi:10.1038/s41596-023-00838-3Addendum: Micro-CT acquisition and image processing to track and characterize pulmonary nodules in mice (Source: Nature Protocols)
Source: Nature Protocols - April 24, 2023 Category: Biomedical Science Authors: May Zaw Thin Christopher Moore Thomas Snoeks Tammy Kalber Julian Downward Axel Behrens Source Type: research
