Nature Protocols最新文献

{"title":"Large-scale genome structure interrogation via recombinase-mediated rearrangements of multiplexed prime edits in repetitive elements.","authors":"Lisa M Riedmayr, Jonas Koeppel, George M Church, Leopold Parts, Raphael Ferreira","doi":"10.1038/s41596-026-01409-y","DOIUrl":"https://doi.org/10.1038/s41596-026-01409-y","url":null,"abstract":"<p><p>Large-scale interrogation of genome structure is crucial for understanding how genomic organization influences cellular function, yet existing methods are limited by the low density of achievable modifications or the toxicity of methods. Here we address this gap by presenting a versatile approach that combines gene editing and recombinase technologies. The protocol serves two critical purposes: (1) facilitating the introduction of hundreds to thousands of precise genomic edits per cell and (2) enabling the creation of a controlled platform to systematically investigate the effects of induced genomic rearrangements. Specifically, the method leverages prime editing to insert recombinase recognition sites (for example, loxP) into repetitive genomic regions, such as LINE-1 elements, thereby enabling extensive genetic modifications in human cells. This scale of genome editing has not previously been attainable and supports a wide range of studies, including genome-wide functional analyses and essentiality mapping. Inducing controlled rearrangements with recombinase and tracking cell survival under selective conditions allows direct mapping of genome architecture to cellular fitness, opening new opportunities for genome-wide functional screens and rational synthetic genome design. Unlike methods that rely on double-strand breaks or random transposon insertion, this Protocol supports a programmable installation of thousands of recombination sites at repeat elements, offering denser and more predictable substrates for controlled genome rearrangement. The full protocol takes ~12-18 weeks to complete and requires intermediate to advanced expertise in genome editing, mammalian cell culture and sequencing analysis.</p>","PeriodicalId":18901,"journal":{"name":"Nature Protocols","volume":" ","pages":""},"PeriodicalIF":18.4,"publicationDate":"2026-07-21","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"148549746","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":1,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Tutorial: biomembranes in hybrid living bioelectronics","authors":"Alice Hattar,&nbsp;Jawaher Alhammadi,&nbsp;Jeremy Treiber,&nbsp;Darius Hoven,&nbsp;Zhongmou Chao,&nbsp;Andreas Offenhaeusser,&nbsp;Susan Daniel,&nbsp;Roisin Owens,&nbsp;Alberto Salleo,&nbsp;Francesca Santoro,&nbsp;Anna-Maria Pappa","doi":"10.1038/s41596-026-01382-6","DOIUrl":"10.1038/s41596-026-01382-6","url":null,"abstract":"The integration of biological and artificial systems promises the effective coupling of living cells with electronic devices. However, to create biomimetic platforms capable of bridging biological with artificial systems, it is necessary to first enhance cell adhesion and cell interactions with engineered surfaces via the integration of techniques from materials science, nanotechnology and synthetic biology, such as structural functionalization techniques, and chemical or biological surface modifications. In this Tutorial Review we cover the use of polymer-based semiconductors and micro- and nanofabrication methods for the integration of biologically relevant cell membrane models with chip-based devices. This integration enhances cell–device coupling and provides an approach for studying membrane-level interactions. Although cell membranes are essential for understanding biological mechanisms, including drug responses, existing technologies rely on simplified synthetic models which lack biological complexity. Advances in electrical impedance measurements enable the study of membrane protein activity, providing insight into drug interactions and biomolecular processes. In addition, exploiting these hybrid systems can result in improved adhesion and electrostatic interactions, facilitating functional coatings for microdevices and neuromorphic applications. We discuss the recent advances in biomembrane–electronic interfaces, device design, surface modification, electronic materials, biomembrane formation and measurement techniques in the context of applications in drug discovery, diagnostics and neuromorphic computing, along with future directions for the field. This is a Tutorial Review on advances in bioelectronic interfaces covering research in material science for biomimetic interfaces and in synthetic biology for the reconstitution of complex biological functions.","PeriodicalId":18901,"journal":{"name":"Nature Protocols","volume":"21 10","pages":"4379-4394"},"PeriodicalIF":18.4,"publicationDate":"2026-07-15","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"148456040","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":1,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Preparation of solid-state emissive carbon quantum dots and their integration into electroluminescent light-emitting diodes.","authors":"Chenhao Li, Qian Teng, Jinyang Li, Fanglong Yuan","doi":"10.1038/s41596-026-01400-7","DOIUrl":"https://doi.org/10.1038/s41596-026-01400-7","url":null,"abstract":"<p><p>Carbon quantum dots (CQDs) have emerged as promising materials for electroluminescent light-emitting diodes (LEDs) because of their photostability, low toxicity and tunable luminescence. However, their implementation in solid-state devices is often hindered by aggregation-induced quenching (AIQ), which leads to a substantial loss of photoluminescence quantum yield (PLQY) and poor device reproducibility. Here, we present a robust, reproducible and scalable protocol for the preparation of solid-state emissive CQDs (SSE-CQDs) and their integration into electroluminescent LEDs. The protocol uses a solvothermal reaction between aromatic aldehydes and aromatic nitriles, involving Knoevenagel-type condensation, dehydration and carbonization. This synthetic strategy enables the formation of non-planar conjugated architectures with incorporated long-chain electron-donating alkoxy groups, which effectively suppress intermolecular π-π interactions and mitigate AIQ in the solid state. Compared with existing approaches that rely on host matrices or multistep post-synthetic modification, this protocol produces intrinsic SSE-CQDs, simplifying processing and improving reproducibility. Using this approach, SSE-CQDs with PLQYs exceeding 40% under ambient conditions can be reproducibly obtained and processed using standard solution-based techniques. This protocol describes in detail the synthesis, purification and basic optical characterization of SSE-CQDs, followed by their incorporation into electroluminescent device architectures. The complete workflow, from CQD synthesis to LED fabrication, can be completed within ~41.5 h. The procedures are compatible with conventional laboratory equipment and are suitable for researchers with experience in nanomaterial synthesis and optoelectronic device fabrication. This protocol provides a general and transferable platform for developing CQD-based solid-state emitters and LEDs.</p>","PeriodicalId":18901,"journal":{"name":"Nature Protocols","volume":" ","pages":""},"PeriodicalIF":18.4,"publicationDate":"2026-07-15","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"148448125","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":1,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Synthesis of single-crystal monolayer graphene on Cu/Ni(111) alloy foil.","authors":"Suming Li, Lijuan Yang, Xiaoli Zhao, Fan Dong, Rodney S Ruoff, Ming Huang","doi":"10.1038/s41596-026-01403-4","DOIUrl":"https://doi.org/10.1038/s41596-026-01403-4","url":null,"abstract":"<p><p>Graphene has attracted broad interest due to its electrical, thermal, mechanical and chemical properties, showing great promise for applications such as lightweight aerospace structures, high-performance microelectronics and efficient thermal management systems. Chemical vapor deposition on metal substrates is currently the most viable route for scalable production of large-area and high-quality graphene films. However, the synthesis typically relies on costly single-crystal metal substrates, while further refinement is needed in both efficient growth and transfer techniques to achieve reproducible high-performance materials. To address these challenges, home-made single-crystal Cu/Ni alloy foils with tunable Ni concentrations can enhance catalytic activity, thereby providing an ideal platform for controllable graphene epitaxy. Here we detail a comprehensive protocol covering the fabrication of large-area single-crystal Cu foils, preparation of single-crystal Cu/Ni alloy foils, chemical vapor deposition growth of monolayer graphene and electrochemical transfer of graphene. The entire procedure requires ~32-38 h. This protocol is intended for researchers in materials science, surface chemistry, condensed matter physics and nanotechnology, and engineers seeking to obtain high-quality single-crystal metal foils and single-crystal monolayer graphene films. It provides a reproducible, scalable approach for their preparation and characterization, targeting fundamental research and potential applications in electronics and photonics.</p>","PeriodicalId":18901,"journal":{"name":"Nature Protocols","volume":" ","pages":""},"PeriodicalIF":18.4,"publicationDate":"2026-07-14","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"148448085","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":1,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Mapping 3D genome organization at nucleosome-scale with Micro-C and Region Capture Micro-C (RCMC).","authors":"Miles K Huseyin, Clarice K Y Hong, Masahiro Nagano, Jamie A Drayton, James M Jusuf, Jin H Yang, Varshini Ramanathan, Viraat Y Goel, Sumin Kim, Anders S Hansen","doi":"10.1038/s41596-026-01393-3","DOIUrl":"https://doi.org/10.1038/s41596-026-01393-3","url":null,"abstract":"<p><p>Micro-C and Region Capture Micro-C (RCMC) are developments of chromosome conformation capture (3C) genomics methods used to identify regions of the genome in close 3D proximity at nucleosome resolution. Micro-C uses in situ MNase digestion of crosslinked chromatin, biotin labeling, proximity ligation and biotin pulldown to recover ligated nucleosomal DNA fragments, with RCMC including a subsequent capture step to enrich for specific regions of the genome. This presents an advantage over previous approaches, such as Hi-C, which rely on restriction enzymes: by digesting the genome without requiring sequence motifs and performing size selection for ligated mononucleosomes, Micro-C can achieve nucleosome-scale resolution of 3D genome organization. The addition of tiled capture of a region allows for deeper sequencing of a location of interest or for experiments with many conditions to be performed while avoiding costly sequencing of the entire genome. Micro-C enables the identification of all known 3D genome features, including interactions between enhancers and promoters that have been missed by previous methods. RCMC can achieve even greater depth and the identification of even more finely resolved interactions. The Micro-C protocol can be completed in 4 d, with an extra 2 d to complete capture, and can be performed by a competent wet laboratory scientist with experience in molecular biology.</p>","PeriodicalId":18901,"journal":{"name":"Nature Protocols","volume":" ","pages":""},"PeriodicalIF":18.4,"publicationDate":"2026-07-13","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"148437463","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":1,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Tutorial: a beginner's guide to fast neutron detection with an EJ-309 detector.","authors":"Sergey Issinski, Aref E Vakili, Ryan Oldford, Kuo-Yi Chen, Shota Higashino, Madeline Peterson, Benjamin R Luginbuhl, Alvin W Hendricks, Monika Stolar, Amanda K Brown, Curtis P Berlinguette","doi":"10.1038/s41596-026-01372-8","DOIUrl":"https://doi.org/10.1038/s41596-026-01372-8","url":null,"abstract":"<p><p>Neutron diagnostics is a key aspect of nuclear fusion research. However, the complexity of available tools and methodologies has often limited their use to specialized research communities. In this Tutorial, we provide a comprehensive description of how to detect and quantify fast neutrons using a single EJ-309 liquid organic scintillation detector. We generate fast neutrons using a bespoke benchtop reactor that mediates deuterium-deuterium nuclear fusion. This Tutorial lays out for the reader how to address technical challenges associated with detector configuration, calibration, characterization and data processing in mixed neutron/gamma-ray fields. This work aims to make neutron diagnostics accessible to broader scientific communities.</p>","PeriodicalId":18901,"journal":{"name":"Nature Protocols","volume":" ","pages":""},"PeriodicalIF":18.4,"publicationDate":"2026-07-13","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"148437406","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":1,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Tutorial: strategies for targeting organelles using nanoparticles.","authors":"Na Feng, Jialu Gao, Leyi Wang, Yiliang Qin, Lei Zheng, Ben Zhong Tang, Jing Zhang","doi":"10.1038/s41596-026-01401-6","DOIUrl":"https://doi.org/10.1038/s41596-026-01401-6","url":null,"abstract":"<p><p>Dysfunctions in specific subcellular organelles are fundamentally implicated in the pathogenesis of a wide range of critical diseases. Targeting these organelles has thus emerged as a promising strategy for achieving precise diagnostics and effective therapies. Nanotechnology serves as a powerful platform in this endeavor, enabling the rational design of nanoparticles with tailored physicochemical properties to control their intracellular trafficking and localization. This Tutorial systematically examines design strategies for nanoparticles that target key organelles, including mitochondria, lysosomes, the nucleus, the endoplasmic reticulum and the Golgi apparatus. Here we summarize organelle-specific targeting design strategies, elucidate the underlying fundamental principles and describe experimental methodologies for validating subcellular localization. Furthermore, we discuss emerging frontiers in the field. We aim to provide a systematic and actionable guide for researchers in materials science, chemistry, biology and medicine, supporting the development of next-generation organelle-targeted nanomedicines for both fundamental research and translational applications.</p>","PeriodicalId":18901,"journal":{"name":"Nature Protocols","volume":" ","pages":""},"PeriodicalIF":18.4,"publicationDate":"2026-07-08","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"148412514","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":1,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"CODAvision: best practices and a user-friendly interface for rapid, customizable segmentation of medical images.","authors":"Valentina Matos-Romero, Jaime Gómez-Becerril, André Forjaz, Lucie Dequiedt, Tyler Newton, Saurabh Joshi, Yu Shen, Eban Hanna, Praful Nair, Arrun Sivasubramanian, Jenny S H Wang, Emily L Lasse-Opsahl, Alexander T F Bell, Diogo Fróis-Vieira, Julianna Czum, Charles Steenbergen, Dao-Fu Dai, Laura D Wood, Luciane T Kagohara, Elana J Fertig, Marina Pasca di Magliano, Joseph J Shatzel, Owen J T McCarty, Jamie O Lo, Avi Rosenberg, Ralph H Hruban, Arrate Muñoz-Barrutia, Denis Wirtz, Ashley L Kiemen","doi":"10.1038/s41596-026-01404-3","DOIUrl":"10.1038/s41596-026-01404-3","url":null,"abstract":"<p><p>Image-based machine learning tools are powerful resources for analyzing medical images, with deep learning-based semantic segmentation commonly utilized to enable the spatial quantification of structures visible in images. However, dataset generation and training of segmentation algorithms requires advanced programming skills and intricate workflows, limiting their accessibility to scientists without prior coding expertise. Here we present the step-by-step instructions to carry out automatic segmentation of medical images guided by a graphical user interface using the CODAvision algorithm. This workflow simplifies the process of semantic segmentation of microanatomical structures by enabling users to train highly customizable deep learning models without extensive coding expertise. The protocol outlines best practices for creating robust training datasets, configuring model parameters and optimizing performance across diverse biomedical image modalities. CODAvision enhances the usability of the CODA algorithm by streamlining parameter configuration, model training and performance evaluation, automatically generating quantitative results and comprehensive reports. We show the use of CODA to serial histology by demonstrating robust performance across numerous medical image modalities and diverse biological questions. We provide sample results in data types, including histology, magnetic resonance imaging and computed tomography. We demonstrate the diverse use of this tool in applications, including quantification of metastatic burden in in vivo models and deconvolution of spot-based spatial transcriptomics datasets. This protocol is designed for researchers with interest in rapid design of highly customizable semantic segmentation algorithms and a basic understanding of programming and anatomy.</p>","PeriodicalId":18901,"journal":{"name":"Nature Protocols","volume":" ","pages":""},"PeriodicalIF":18.4,"publicationDate":"2026-07-07","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC13616135/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"148405368","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":1,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"A scalable high-throughput serolomics platform for profiling serum antibody responses in large-scale population-based cohorts.","authors":"Lea Kröller, Rima Jeske, Birgitta Michels, Julia Butt, Iona Millwood, Christiana Kartsonaki, Zhengming Chen, Jun Lv, Liming Li, Rasmus Gustafsson, Andrew Gordon, Frederik Romer, Hannah Fry, Sarah Clark, Michael Hill, Ling Yang, Alexander Mentzer, Tim Waterboer","doi":"10.1038/s41596-026-01391-5","DOIUrl":"10.1038/s41596-026-01391-5","url":null,"abstract":"<p><p>Seroepidemiological assays play a crucial role in tracking immunity and infectious disease exposure across populations. Here we describe an automated assay platform that robustly quantifies antibodies against up to 100 antigens in a single reaction, using Luminex suspension array technology, alongside generating ample quality control measures. This automated multiplex serology workflow is an advancement of our previously developed manual and hybrid multiplex serology platforms. It combines multiple liquid handling systems (Biomeki7, BioTek 405 LS) and bead separation technology (KingFisher Flex) to improve scalability and reproducibility and facilitate its application in large-scale population-based cohorts. Study samples undergo automated processing, and antibody levels are quantified using the Luminex Flexmap3D instrument. A custom R-based application monitors process parameters and visualizes readouts in real time. Daily quality control samples allow subsequent normalization over extended periods of time and across reagent batches. Compared with previous assay versions, the higher degree of automation requires fewer laboratory operators and results in improved robustness and a more continuous throughput. Assay robustness is excellent, with median coefficients of variations between 2.8% and 11.7%, with no relevant batch effects over a 6-month period. Reproducibility across 47 antigens and 91 duplicate samples is remarkably high (R² = 1.00). Using the automated platform, 1,820 study samples can be processed in a typical assay week. We have successfully completed the analysis for ~38,000 cohort samples, including comprehensive quality control data, in 88 assay days. Automated multiplex serology sets the foundation to generate high-quality serolomics data for large-scale cohorts in a reproducible, scalable and cost-effective fashion.</p>","PeriodicalId":18901,"journal":{"name":"Nature Protocols","volume":" ","pages":""},"PeriodicalIF":18.4,"publicationDate":"2026-07-06","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"148397464","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":1,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"iMUT-seq mapping of DSB-induced mutations with high sensitivity at single-nucleotide resolution.","authors":"Aldo S Bader, Martin Bushell","doi":"10.1038/s41596-026-01394-2","DOIUrl":"https://doi.org/10.1038/s41596-026-01394-2","url":null,"abstract":"<p><p>DNA double-strand break (DSB)-induced mutagenesis is a critical contributor to a variety of human diseases; however, the ability to quantify these mutations is limited by the low sensitivity of current methodologies. Here we describe iMUT-seq, a technique that profiles DSB-induced mutations at high sensitivity and single-nucleotide resolution around endogenous DSBs, by coupling high-depth sequencing to restriction enzyme-inducible DSBs in human cell lines. iMUT-seq uses targeted sequencing to generate high-depth DNA libraries, enabling detection of mutations at incidence rates as low as 1 in 500,000. iMUT-seq can be used to identify novel mutagenic outcomes of DSBs and characterize previously unknown mechanisms of mutagenesis. The technique involves the extraction of genomic DNA from treated cells, followed by a multiplexed polymerase chain reaction and a series of library preparation reactions to generate a DNA library ready for sequencing on Illumina next-generation sequencing platforms. Finally, this novel approach to mutation profiling requires a specific analytical pipeline with careful considerations for the uncommon per-nucleotide nature of the data. Users will need experience in raw next-generation sequencing data analysis, and experience in DNA library preparation is beneficial. Overall, iMUT-seq has the potential to provide advanced insights into DSB mutagenesis, is a powerful tool in the study of novel DNA repair components and can be adapted to other organisms and types of DNA damage.</p>","PeriodicalId":18901,"journal":{"name":"Nature Protocols","volume":" ","pages":""},"PeriodicalIF":18.4,"publicationDate":"2026-07-03","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"148382467","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":1,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}