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Proteomics method for identifying POT1-associated complexes at telomeres using ChIP-Mass spectrometry 使用chip -质谱技术鉴定端粒中pot1相关复合物的蛋白质组学方法。
IF 4.3 3区 生物学
Methods Pub Date : 2026-03-01 Epub Date: 2026-01-21 DOI: 10.1016/j.ymeth.2026.01.007
Nikita Harish Zade , Meghna Jain , Manoj Garg , Rahul Checker , Arkasubhra Ghosh , Ekta Khattar
{"title":"Proteomics method for identifying POT1-associated complexes at telomeres using ChIP-Mass spectrometry","authors":"Nikita Harish Zade ,&nbsp;Meghna Jain ,&nbsp;Manoj Garg ,&nbsp;Rahul Checker ,&nbsp;Arkasubhra Ghosh ,&nbsp;Ekta Khattar","doi":"10.1016/j.ymeth.2026.01.007","DOIUrl":"10.1016/j.ymeth.2026.01.007","url":null,"abstract":"<div><div>POT1 is the only single stranded telomere binding protein in the shelterin complex. Together with TPP1, POT1 plays a crucial role in regulating telomere length and protecting telomeres from DNA damage repair proteins. The activation of DNA damage repair proteins at telomeres can be detrimental to cells, so their activity must be suppressed. POT1 interacts with other telomeric proteins (TRF2, TRF1, TIN2 and RAP1) via its association with TPP1. These proteins function together to protect and maintain the telomeres. Despite extensive knowledge of POT1′s role within the shelterin complex, the full spectrum of its interactors at the single-stranded telomeric overhang remains poorly defined. To study these interactions, we generated an endogenous Flag-tag knock-in of POT1 using the CRISPR-Cas9 gene editing system. To address the risk of unintended gene disruption associated with this technique, we conducted an in-depth characterization of the endogenously Flag-tagged POT1 clone to ensure that its telomere and TPP1 binding functions remained intact. Further, we performed proteomic profiling of the Flag-tagged POT1 within the chromatin fraction using ChIP-MS to explore its proteome. Our analysis uncovered a novel set of POT1-associated proteins at the extremes of telomeres. Given that POT1 exclusively binds to the single-stranded 3′ overhang of telomeres, the proteomic data obtained indicates POT1 interactions occurring at the extreme ends of telomeres. In conclusion, our study reveals previously uncharacterized POT1 associated proteins using ChIP mass spectrometric approach, paving the way for further investigations into telomere biology and potential therapies targeting telomere regulation.</div></div>","PeriodicalId":390,"journal":{"name":"Methods","volume":"247 ","pages":"Pages 161-174"},"PeriodicalIF":4.3,"publicationDate":"2026-03-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"146040153","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":3,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
引用次数: 0
Rapid and improved surface passivation method for Single-Molecule experiments 快速改进的单分子表面钝化方法。
IF 4.3 3区 生物学
Methods Pub Date : 2026-03-01 Epub Date: 2026-01-07 DOI: 10.1016/j.ymeth.2026.01.003
Alyssa N. Gonneville , Alyssa E. Ward , Narisa Ria Naidoo , Francisco N. Barrera , Rajan Lamichhane
{"title":"Rapid and improved surface passivation method for Single-Molecule experiments","authors":"Alyssa N. Gonneville ,&nbsp;Alyssa E. Ward ,&nbsp;Narisa Ria Naidoo ,&nbsp;Francisco N. Barrera ,&nbsp;Rajan Lamichhane","doi":"10.1016/j.ymeth.2026.01.003","DOIUrl":"10.1016/j.ymeth.2026.01.003","url":null,"abstract":"<div><div>Single-molecule fluorescence experiments are a powerful tool for studying biomolecular interactions, including protein dynamics and oligomerization, protein–protein interactions, and protein-nucleic acid interactions. Biomolecules are commonly immobilized on the microscope surface to extend the observation time. However, non-specific interactions between biomolecules and the surface present a major challenge. The first critical step in these experiments is preparing the surface using polyethylene glycol (PEG) coated slides, which facilitate biomolecule immobilization while minimizing non-specific interactions. The surface treatment typically uses PEG-SVA (Succinimidyl Valerate) coated slides, and the protocol for the treatment is lengthy and time-consuming. To overcome this issue, we have developed a process that uses PEG-Silane to improve efficiency while maintaining reproducibility. <em>Here</em>, we present a one-step, rapid PEGylation methodology that can be completed in minutes rather than hours. We demonstrate its validity and feasibility through single-molecule fluorescence resonance energy transfer (smFRET) and single-molecule photobleaching experiments across various biological samples.</div></div>","PeriodicalId":390,"journal":{"name":"Methods","volume":"247 ","pages":"Pages 95-106"},"PeriodicalIF":4.3,"publicationDate":"2026-03-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145942009","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":3,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
引用次数: 0
Precision mapping of NF-κB-DNA binding: high-resolution insights via dynamic UV-laser footprinting NF-κB-DNA结合的精确定位:通过动态紫外激光足迹的高分辨率见解
IF 4.3 3区 生物学
Methods Pub Date : 2026-03-01 Epub Date: 2026-01-07 DOI: 10.1016/j.ymeth.2026.01.005
Imtiaz Nisar Lone , Gözdem Çavdar , Zahari Peshev , Seyit Kale , Dimitar Angelov
{"title":"Precision mapping of NF-κB-DNA binding: high-resolution insights via dynamic UV-laser footprinting","authors":"Imtiaz Nisar Lone ,&nbsp;Gözdem Çavdar ,&nbsp;Zahari Peshev ,&nbsp;Seyit Kale ,&nbsp;Dimitar Angelov","doi":"10.1016/j.ymeth.2026.01.005","DOIUrl":"10.1016/j.ymeth.2026.01.005","url":null,"abstract":"<div><div>Sequence-specific binding is at the core of all DNA-templated processes, including the initiation of DNA replication, gene expression and DNA repair. Yet the kinetics and precision of these interactions remain difficult to capture at high resolution. <em>Here</em>, we present Dynamic UV Laser Footprinting (DULF), a novel technique that integrates UV laser footprinting with stopped-flow mixing to probe transcription factor (TF)-DNA interactions at millisecond temporal and single base-pair spatial resolution. Using NF-κB as a model TF, we demonstrate the feasibility of DULF in visualizing the spatiotemporal details of a sequence-specific TF-DNA interaction. The high temporal resolution of our data reveals that TF-DNA binding proceeds through a rapid recognition step and a subsequent slower stabilization phase. DULF also revealed that the p50 homodimer binds specifically to DNA outside the canonical binding site, emphasizing the role of flanking sequences in these interactions. All-atom molecular dynamics simulations confirmed that DNA sequence context, including flanking base pairs, modulates NF-κB binding stability and induces local structural changes such as bending, groove widening, and base unstacking. DULF offers a unique opportunity to study DNA-protein interactions at unprecedented resolution, providing insights into the mechanism of sequence-specific binding and stabilization of chromatin interactors.</div></div>","PeriodicalId":390,"journal":{"name":"Methods","volume":"247 ","pages":"Pages 50-62"},"PeriodicalIF":4.3,"publicationDate":"2026-03-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145922632","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":3,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
引用次数: 0
ERAPID: an end‑to‑end RNA‑seq analysis pipeline for integrative candidate biomarker discovery with applications to neuropsychiatric disorders ERAPID:一个端到端RNA - seq分析管道,用于综合候选生物标志物的发现,并应用于神经精神疾病。
IF 4.3 3区 生物学
Methods Pub Date : 2026-03-01 Epub Date: 2026-01-05 DOI: 10.1016/j.ymeth.2026.01.001
Jihye Park , Seoyeon Youn , Kyuho Kang , Keunsoo Kang
{"title":"ERAPID: an end‑to‑end RNA‑seq analysis pipeline for integrative candidate biomarker discovery with applications to neuropsychiatric disorders","authors":"Jihye Park ,&nbsp;Seoyeon Youn ,&nbsp;Kyuho Kang ,&nbsp;Keunsoo Kang","doi":"10.1016/j.ymeth.2026.01.001","DOIUrl":"10.1016/j.ymeth.2026.01.001","url":null,"abstract":"<div><div>RNA sequencing datasets in the gene expression omnibus (GEO) increasingly include NCBI-generated count matrices, enabling streamlined signature gene discovery. We present ERAPID, a computational framework that automatically processes this public data for robust differential expression analysis. The pipeline integrates metadata harmonization, surrogate variable analysis (SVA) to capture latent technical variation for batch correction, dual differential expression methods (DESeq2 and dream), gene set enrichment analysis (GSEA), and evidence-based gene prioritization via automated literature mining. ERAPID delivers interactive dashboards (volcano/MA plots, heatmaps, enrichment reports, searchable DEG tables) and supports an optional meta‑analysis step. Applied to a neuropsychiatric cohort (GSE80655), ERAPID completed analysis on a standard laptop in under an hour, recapitulating the reported association of <em>EGR1</em> with schizophrenia. In an Alzheimer’s disease (AD) case study integrating four GEO datasets, ERAPID identified 17 DEGs consistently altered across all AD‑versus‑control comparisons (e.g., <em>ADCYAP1</em>, <em>PPEF1</em>, <em>VGF</em>, and <em>CRH</em>), with KEGG Alzheimer’s disease and oxidative phosphorylation pathways showing negative enrichment. Thus, ERAPID lowers the barrier to reusing public transcriptomes for signature gene discovery and biological interpretation.</div></div>","PeriodicalId":390,"journal":{"name":"Methods","volume":"247 ","pages":"Pages 34-40"},"PeriodicalIF":4.3,"publicationDate":"2026-03-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145916601","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":3,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
引用次数: 0
The clinical potential and limitations of metal-organic frameworks (MOFs) in dentistry 金属-有机框架(MOFs)在牙科中的临床潜力和局限性。
IF 4.3 3区 生物学
Methods Pub Date : 2026-03-01 Epub Date: 2026-01-10 DOI: 10.1016/j.ymeth.2026.01.006
Wael Sheet Hussein , Ali Fawzi Al-Hussainy , Soumya V. Menon , Laxmidhar Maharana , A. Sabarivani , Gunjan Mukherjee , Aashna Sinha , Khabilov Nigman , Hayder Naji Sameer , Rasim M. Salih , Mohaned Adil , Saman Kalantari
{"title":"The clinical potential and limitations of metal-organic frameworks (MOFs) in dentistry","authors":"Wael Sheet Hussein ,&nbsp;Ali Fawzi Al-Hussainy ,&nbsp;Soumya V. Menon ,&nbsp;Laxmidhar Maharana ,&nbsp;A. Sabarivani ,&nbsp;Gunjan Mukherjee ,&nbsp;Aashna Sinha ,&nbsp;Khabilov Nigman ,&nbsp;Hayder Naji Sameer ,&nbsp;Rasim M. Salih ,&nbsp;Mohaned Adil ,&nbsp;Saman Kalantari","doi":"10.1016/j.ymeth.2026.01.006","DOIUrl":"10.1016/j.ymeth.2026.01.006","url":null,"abstract":"<div><div>Nanoparticles (NPs) are intentionally incorporated into dental products to enhance material quality. Recently, metal–organic framework (MOF) NPs have attracted significant attention owing to their unique characteristics absent in their larger-scale counterparts. These properties make MOFs suitable for various functional platforms. MOF-based nanomaterials exhibit high antibacterial potential, owing to their biocompatibility, biodegradability, and safety for living organisms. They have also become a prominent component in the development of anticancer agents and in the manufacture of commercial medical products. Consequently, MOFs are becoming increasingly important in dentistry. They show promising therapeutic potential for inhibiting oral infectious diseases, such as those caused by bacterial plaque, and have a broad range of other biomedical applications, including the diagnosis and treatment of dental diseases. However, significant challenges hinder their transition from laboratory testing to widespread clinical use in hospitals. Key issues include long-term toxicity and biocompatibility concerns, unpredictable pharmacokinetics that can lead to unintended accumulation in organs like the liver and spleen, and the potential for adverse immune reactions. Other major obstacles are particle aggregation in biological fluids, the complex formation of a “protein corona” that can alter the NPs’ intended function, and the high cost of large-scale production under consistent Good Manufacturing Practices (GMP). This article discusses MOFs and their potential applications in identifying cancer biomarkers and treating tooth infections and oral cancers. It highlights their unique porous features, which help combat oral biofilms and detect microorganisms. The summary also addresses the primary clinical challenges that must be addressed to ensure the safe development of MOF-based therapies.</div></div>","PeriodicalId":390,"journal":{"name":"Methods","volume":"247 ","pages":"Pages 107-131"},"PeriodicalIF":4.3,"publicationDate":"2026-03-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145958439","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":3,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
引用次数: 0
Navigating the frontier of human microglia isolation—standardization and translational insight 导航人类小胶质细胞分离的前沿-标准化和翻译见解
IF 4.3 3区 生物学
Methods Pub Date : 2026-03-01 Epub Date: 2026-01-08 DOI: 10.1016/j.ymeth.2026.01.002
Pankaj Pal , Monika Sharma , Sukesh Kumar Gupta
{"title":"Navigating the frontier of human microglia isolation—standardization and translational insight","authors":"Pankaj Pal ,&nbsp;Monika Sharma ,&nbsp;Sukesh Kumar Gupta","doi":"10.1016/j.ymeth.2026.01.002","DOIUrl":"10.1016/j.ymeth.2026.01.002","url":null,"abstract":"<div><div>The expanding field of neuroscience has increasingly recognized the critical role of microglia, the resident immune cells of the central nervous system (CNS), in human health and disease. This review embarks on an in-depth exploration of the current landscape of human microglia extraction techniques. With a focus on the unique challenges and opportunities presented by human tissue samples, we delve into various sources of human microglia, including primary brain tissue and stem cell-derived models, addressing the ethical and logistical considerations inherent to these methodologies. Laboratory techniques for microglia extraction are scrutinized, highlighting adaptations for human samples in enzymatic digestion, mechanical dissociation, density gradient centrifugation, and cell sorting, alongside innovations in cryopreservation and viability assessment. Critical perspectives are offered on technical hurdles, technique selection for human research, and the horizon of emerging technologies. Standardization efforts and international guidelines are discussed, underscoring their significance in fostering reproducibility and comparability across studies. The review also illuminates applications of human microglia in disease modeling, drug discovery, and understanding neurodevelopmental and neurodegenerative processes. Concluding remarks emphasize future directions of human microglia research, advocating for methodological precision and integration of next-generation technologies to unlock new therapeutic avenues. This review serves as a comprehensive guide for researchers navigating the complex terrain of human microglia extraction, aiming to catalyze advancements in neuroscience research through methodological innovation and standardization.</div></div>","PeriodicalId":390,"journal":{"name":"Methods","volume":"247 ","pages":"Pages 63-84"},"PeriodicalIF":4.3,"publicationDate":"2026-03-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145922633","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":3,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
引用次数: 0
Cross-modal image generation with uncertainty quantification from echocardiogram to MRI 从超声心动图到MRI的不确定量化的交叉模态图像生成。
IF 4.3 3区 生物学
Methods Pub Date : 2026-03-01 Epub Date: 2025-12-23 DOI: 10.1016/j.ymeth.2025.12.012
Zakia Zinat Choudhury , Samiran Dey , Haoming Wang , Sean Coffey , Tapabrata Chakraborti , Brendan McCane
{"title":"Cross-modal image generation with uncertainty quantification from echocardiogram to MRI","authors":"Zakia Zinat Choudhury ,&nbsp;Samiran Dey ,&nbsp;Haoming Wang ,&nbsp;Sean Coffey ,&nbsp;Tapabrata Chakraborti ,&nbsp;Brendan McCane","doi":"10.1016/j.ymeth.2025.12.012","DOIUrl":"10.1016/j.ymeth.2025.12.012","url":null,"abstract":"<div><div>Medical imaging is fundamental to cardiovascular diagnostics, with modalities such as Transthoracic Echocardiography (TTE) and Cardiac Magnetic Resonance (CMR) offering complementary strengths. TTE provides real-time, non-invasive visualization of cardiac function but is often limited by operator dependency and incomplete views. In contrast, CMR delivers comprehensive, high-resolution structural assessments, although it comes with greater time and cost burdens. To address these limitations, this study explores cross-modal generative modeling techniques for synthesizing CMR-like images directly from TTE. We propose a novel architecture that combines a UNet backbone with a vision transformer, utilizing the UNet for feature extraction and the transformer for global attention to improve image synthesis quality. Quantitative and qualitative evaluations demonstrate the model’s ability to produce realistic and anatomically consistent CMR images, with strong potential to improve diagnostic accuracy and clinical decision-making across multiple image modalities.</div></div>","PeriodicalId":390,"journal":{"name":"Methods","volume":"247 ","pages":"Pages 1-11"},"PeriodicalIF":4.3,"publicationDate":"2026-03-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145831859","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":3,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
引用次数: 0
MetaChrome: an open-source, user-friendly tool for automated metaphase chromosome analysis MetaChrome:一个开源的,用户友好的工具,用于自动中期染色体分析。
IF 4.3 3区 生物学
Methods Pub Date : 2026-03-01 Epub Date: 2025-12-29 DOI: 10.1016/j.ymeth.2025.12.013
Md Abdul Kader Sagar , Yamini Dalal , Gianluca Pegoraro , Ganesan Arunkumar
{"title":"MetaChrome: an open-source, user-friendly tool for automated metaphase chromosome analysis","authors":"Md Abdul Kader Sagar ,&nbsp;Yamini Dalal ,&nbsp;Gianluca Pegoraro ,&nbsp;Ganesan Arunkumar","doi":"10.1016/j.ymeth.2025.12.013","DOIUrl":"10.1016/j.ymeth.2025.12.013","url":null,"abstract":"<div><div>DNA Fluorescence In Situ Hybridization (DNA FISH) is an essential technique to study chromosome biology and genetics, enabling precise visualization of specific genomic loci to study structural abnormalities, gene mapping, and chromosomal rearrangements. High-Throughput Imaging (HTI) can automate the analysis of DNA FISH chromosome images, but the accurate and automated segmentation of mitotic chromosomes and simultaneous colocalization of DNA FISH signals remains a challenge. While several commercial automated karyotyping tools partially solve these issues, open-source software that effectively combines robust chromosome segmentation with comprehensive colocalization analysis capabilities remains necessary. To address this unmet need, we developed MetaChrome, an open-source software platform built around a graphical user interface and explicitly designed for automated metaphase chromosome analysis. MetaChrome leverages fine-tuned deep learning models to automate metaphase chromosome segmentation, together with colocalization analysis of chromosome-specific FISH probes and immunofluorescent-labeled proteins. Importantly, MetaChrome achieves enhanced segmentation accuracy compared to traditional image processing methods by adopting a Cellpose segmentation model fine-tuned with manually annotated metaphase chromosome datasets. The fine-tuned model ensures the precise assignment of DNA FISH spots to individual chromosomes in an automated manner. This facilitates rapid identification of chromosomal abnormalities, reduces human error, and advances high-throughput chromosome analysis workflows, addressing a key bottleneck in chromosome biology research.</div></div>","PeriodicalId":390,"journal":{"name":"Methods","volume":"247 ","pages":"Pages 12-24"},"PeriodicalIF":4.3,"publicationDate":"2026-03-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145877422","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":3,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
引用次数: 0
Syntenins at the crossroads of host–virus interactions 在宿主-病毒相互作用的十字路口的联蛋白
IF 4.3 3区 生物学
Methods Pub Date : 2026-03-01 Epub Date: 2026-01-27 DOI: 10.1016/j.ymeth.2026.01.009
Yevheniia Kharkivska , Olha Shkel , Yun Kyung Kim
{"title":"Syntenins at the crossroads of host–virus interactions","authors":"Yevheniia Kharkivska ,&nbsp;Olha Shkel ,&nbsp;Yun Kyung Kim","doi":"10.1016/j.ymeth.2026.01.009","DOIUrl":"10.1016/j.ymeth.2026.01.009","url":null,"abstract":"<div><div>Syntenin is a multifunctional PDZ-domain adaptor protein that orchestrates membrane trafficking, cytoskeletal remodeling, and exosome biogenesis. Initially identified as a syndecan-binding molecule, syntenin has since emerged as a central hub connecting membrane receptors to intracellular signaling pathways that regulate adhesion, motility, immune signaling, and cellular plasticity. While extensively studied in cancer and neural development, recent discoveries reveal that a wide range of viruses exploit syntenin to facilitate their replication, assembly, or dissemination. This review consolidates current evidence across diverse viral infections to elucidate the molecular mechanisms underlying the interaction between syntenin and viruses. Coronaviruses utilize syntenin to link PDZ-binding motifs to p38 MAPK-driven inflammation and endosomal entry. Papillomaviruses and Epstein–Barr virus hijack the CD63-syntenin-ALIX complex to control vesicle-mediated trafficking. Hepatitis C virus employs it to secrete E2-coated, antibody-resistant exosomes. Dengue virus harnesses its mosquito homolog AeSyntenin to package sfRNA for transmission. Human T-cell leukemia virus type 1 employs its Tax-1 oncoprotein to bind the PDZ domains of syntenin, remodel extracellular vesicle cargo, and promote viral spread. In contrast, during human immunodeficiency virus infection, syntenin restricts viral fusion at the plasma membrane, though the nucleocapsid mimics its PDZ tandem to promote virion release. Collectively, these findings establish syntenin as a dynamic regulator at the host–virus interface, capable of exerting both proviral and antiviral effects. Emerging pharmacological strategies targeting syntenin PDZ domains further underscore its potential as a broad-spectrum, host-directed antiviral target.</div></div>","PeriodicalId":390,"journal":{"name":"Methods","volume":"247 ","pages":"Pages 175-183"},"PeriodicalIF":4.3,"publicationDate":"2026-03-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"146074260","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":3,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
引用次数: 0
Viral-mediated fluorescent labelling of activated hippocampal memory engrams to study epigenetic dynamics associated with gene expression 病毒介导的激活海马记忆印记荧光标记研究与基因表达相关的表观遗传动力学。
IF 4.3 3区 生物学
Methods Pub Date : 2026-03-01 Epub Date: 2026-01-08 DOI: 10.1016/j.ymeth.2026.01.004
Víctor Pola-Véliz , Sebastián B. Arredondo , Yennyfer Arancibia , Juan Ahumada , Sebastián Estay , Nicole Vidal , Paola A. Haeger , Marco Fuenzalida , Lorena Varela-Nallar , Fernando J. Bustos , Martin Montecino , Brigitte van Zundert
{"title":"Viral-mediated fluorescent labelling of activated hippocampal memory engrams to study epigenetic dynamics associated with gene expression","authors":"Víctor Pola-Véliz ,&nbsp;Sebastián B. Arredondo ,&nbsp;Yennyfer Arancibia ,&nbsp;Juan Ahumada ,&nbsp;Sebastián Estay ,&nbsp;Nicole Vidal ,&nbsp;Paola A. Haeger ,&nbsp;Marco Fuenzalida ,&nbsp;Lorena Varela-Nallar ,&nbsp;Fernando J. Bustos ,&nbsp;Martin Montecino ,&nbsp;Brigitte van Zundert","doi":"10.1016/j.ymeth.2026.01.004","DOIUrl":"10.1016/j.ymeth.2026.01.004","url":null,"abstract":"<div><div>Memory formation activates a relatively sparse population of engram cells that store long-term memories. Changes in the epigenetic landscape and 3D chromatin architecture have been proposed as key candidate regulators of transcriptional waves that control gene expression in engram cells; however, isolating chromatin efficiently from engram cells has remained challenging. Double-transgenic <em>T</em>argeted <em>R</em>ecombination in <em>A</em>ctive <em>P</em>opulations (dTRAP) mice have enabled indelible EYFP labeling of hippocampal engram cells expressing the immediate-early gene (IEG) <em>Arc</em> when ArcCreER<sup>T2</sup> mice are crossed with R26R-STOP-floxed-EYFP mice and exposed to learning paradigms. A major limitation of dTRAP mice is that labeling of activated hippocampal Arc<sup>+</sup> neurons with soluble EYFP compromises the efficiency of fluorescence-activated nuclear sorting (FANS) of engram nuclei, and hence isolation of chromatin. Here, we used viral-mediated delivery of GFP-KASH (AAV-PHP.eB-FLEX-EGFP-KASH) to ArcCreER<sup>T2</sup> mice -generating vkTRAP mice- to enable precise and robust endogenous perinuclear fluorescent tagging of activated hippocampal neurons following contextual fear conditioning (CFC). At 24 h post-CFC (24 h-CFC), vkTRAP mice exhibited a robust freezing behavior. Electrophysiological recordings in CA1 hippocampal slices showed occluded long-term potentiation (LTP). Efficient FANS-based isolation of hippocampal engram nuclei enabled chromatin immunoprecipitation (ChIP) assays (detecting H3K4me3, H3K9ac and H3K27ac) at promoters of immediate-early (<em>Egr1</em>) and plasticity-related (<em>Dlg4</em>/PSD95) genes. Expression peaks of both <em>Egr1</em> and <em>Dlg4/</em>PSD95 transcripts during memory acquisition (1 h-CFC) and consolidation (24 h-CFC) were accompanied by active epigenetic histone mark profiles. We conclude that vkTRAP provides a robust model to study epigenomic regulation in engram cells.</div></div>","PeriodicalId":390,"journal":{"name":"Methods","volume":"247 ","pages":"Pages 85-94"},"PeriodicalIF":4.3,"publicationDate":"2026-03-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145942002","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":3,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
引用次数: 0
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