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High-resolution dynamic imaging of chromatin DNA communication using Oligo-LiveFISH

Cell 2025年

作者： Zhu, Yanyu Balaji, Ashwin Han, Mengting Andronov, Leonid Roy, Anish R. Wei, Zheng Chen, Crystal Miles, Leanne Cai, Sa Gu, Zhengxi Tse, Ariana Yu, Betty Chentzu Uenaka, Takeshi Lin, Xueqiu Spakowitz, Andrew J. Moerner, W.E. Qi, Lei S. Department of Bioengineering Stanford University Stanford 94305 CA United States Department of Chemistry Stanford University Stanford 94305 CA United States Biophysics PhD Program Stanford University Stanford 94305 CA United States Computational Biology Program Public Health Sciences Division and Translational Data Science IRC Fred Hutchinson Cancer Center Seattle 98109 WA United States Department of Chemical Engineering Stanford University Stanford 94305 CA United States Department of Materials Science and Engineering Stanford University Stanford 94305 CA United States Institute for Stem Cell Biology & Regenerative Medicine and Department of Pathology Stanford University School of Medicine Stanford 94305 CA United States Sarafan ChEM-H Stanford University Stanford 94305 CA United States Chan Zuckerberg Biohub San Francisco 94080 CA United States

Three-dimensional (3D) genome dynamics are crucial for cellular functions and disease. However, real-time, live-cell DNA visualization remains challenging, as existing methods are often confined to repetitive regions, suffer from low resolution, or require complex genome engineering. Here, we present Oligo-LiveFISH, a high-resolution, reagent-based platform for dynamically tracking non-repetitive genomic loci in diverse cell types, including primary cells. Oligo-LiveFISH utilizes fluorescent guide RNA (gRNA) oligo pools generated by computational design, in vitro transcription, and chemical labeling, delivered as ribonucleoproteins. Utilizing machine learning, we characterized the impact of gRNA design and chromatin features on imaging efficiency. Multi-color Oligo-LiveFISH achieved 20-nm spatial resolution and 50-ms temporal resolution in 3D, capturing real-time enhancer and promoter dynamics. Our measurements and dynamic modeling revealed two distinct modes of chromatin communication, and active transcription slows enhancer-promoter dynamics at endogenous genes like FOS. Oligo-LiveFISH offers a versatile platform for studying 3D genome dynamics and their links to cellular processes and disease. © 2025 Elsevier Inc.

关键词： CRISPR imaging DNA communication dynamic tracking enhancer-promoter interaction high-resolution imaging live DNA imaging non-repetitive genome imaging Oligo-LiveFISH polymer modeling primary cell

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Graphene Nanoribbons/Manganese Oxide Nanocomposite Modified Electrode for Detection of Antimicrobial Drug Nitrofurantoin

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Journal of Nanomaterials 2023年第1期2023卷

作者： Nagarajan, Ramila D. Magesh, Vasanth Sundramoorthy, Ashok K. Murugan, Preethika Atchudan, Raji Ganapathy, Dhanraj Arya, Sandeep Mahmoud Karami, Abdulnasser Govindasamy, Mani Department of Chemistry V.V.Vanniaperumal College for Women Tamil Nadu Virudhunagar626001 India Centre for Nano-Biosensors Department of Prosthodontics Saveetha Dental College and Hospitals Saveetha Institute of Medical and Technical Sciences Poonamallee High Road Velappanchavadi Tamil Nadu Chennai600077 India Augsburg University Am Technologiezentrum 8 Augsburg86159 Germany School of Chemical Engineering Yeungnam University Gyeongsan38541 Korea Republic of Department of Physics University of Jammu Jammu and Kashmir Jammu180006 India Department of Chemistry College of Science King Saud University Riyadh11451 Saudi Arabia International PhD Program in Innovative Technology of Biomedical Engineering and Medical Devices Ming Chi University of Technology New Taipei City243303 Taiwan

The design and development of a new kind of cost-effective electrode material with excellent selectivity and stability are still a great challenge in the field of electrochemical sensors. Recently, researchers have paid more attention to the electrochemical reduction of nitro compounds due to their hazardous nature. Nitro compounds play a vital role in various industrial applications. However, the direct discharge of nitro compounds to the environment as industrial wastewater is harmful. In this study, a nanocomposite made of 1D graphene nanoribbons decorated with manganese dioxide (GNR-MnO2) was prepared to fabricate an electrochemical transducer for the determination of nitrofurantoin (NFT) in biofluids. First, 1D GNR was prepared by unzipping of multiwalled carbon nanotubes. Second, the GNR was decorated with MnO2 by the hydrothermal reduction method. As-prepared GNR-MnO2 nanocomposite was comprehensively characterized by field emission scanning electron microscopy with EDX, XRD, UV-visible, electrochemical impedance spectroscopy, and cyclic voltammetry. Moreover, GNR-MnO2-coated glassy carbon electrode (GCE) exhibited good electrocatalytic activity toward NFT. The electroreduction of NFT was found at -0.40 V which was 50 mV lower than bare GCE. GNR-MnO2 nanocomposite modified GCE showed a well-defined linear reduction peak current for NFT from 10 nM to 1,000 μM. The selectivity of the sensor was also analyzed in the presence of other nitro compounds which confirmed that NFT can be selectively detected at -0.4 V. The GNR-MnO2 modified electrode was also able to separate reduction peaks of other nitro compounds. In addition, the detection of NFT was carried out in human urine samples with a good recovery of 99.60%-98.60%. © 2023 Ramila D. Nagarajan et al.

关键词： Scanning electron microscopy

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Hamiltonicity via cohomology of right-angled Artin groups

arXiv

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arXiv 2021年

作者： Flores, Ramón Kahrobaei, Delaram Koberda, Thomas Department of Geometry and Topology University of Seville Spain Department of Computer Science University of York United Kingdom New York University Tandon School of Engineering PhD Program in Computer Science CUNY Graduate Center Department of Mathematics University of Virginia CharlottesvilleVA22904 United States

Let Γ be a finite graph and let A(Γ) be the corresponding right-angled Artin group. We characterize the Hamiltonicity of Γ via the structure of the cohomology algebra of A(Γ). In doing so, we define and develop a new canonical graph associated to a matrix, which as a consequence provides a novel perspective on the matrix determinant. Copyright © 2021, The Authors. All rights reserved.

关键词： Topology

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Facilitating light utilization and electron transfer of TiO2 nanotube arrays for catalyzing photoelectrochemical water reduction via acid etching and copper doping

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Materials Today Chemistry 2023年 34卷

作者： Hsu, Chuan-Chih Kubendhiran, Subbiramaniyan Lai, Jhih-Hong Saukani, Muhammad Yougbaré, Sibidou Chen, Hung-Ming Hsiao, Yu-Cheng Wu, Yung-Fu Lin, Lu-Yin Division of Cardiovascular Surgery Department of Surgery School of Medicine College of Medicine Taipei Medical University Taiwan Division of Cardiovascular Surgery Department of Surgery Taipei Medical University Hospital Taiwan Department of Chemical Engineering and Biotechnology National Taipei University of Technology Taipei Taiwan Department of Mechanical Engineering Faculty of Engineering Universitas Islam Kalimantan MAB Jl. Adhyaksa No. 2 Banjarmasin70124 Indonesia /Nanoro 03 B.P 7192 03 Ouagadougou Burkina Faso Gingen Technology Co. LTD Rm. 7 10F. No.189 Sec. 2 Keelung Rd. Xinyi Dist. Taipei11054 Taiwan Cell Physiology and Molecular Image Research Center Wan Fang Hospital Taipei Medical University Taipei11696 Taiwan International PhD Program in Biomedical Engineering College of Biomedical Engineering Taipei Medical University Taipei11031 Taiwan Stanford Byers Center for Biodesign Stanford University CA94305-5428 United States Graduate Institute of Biomedical Optomechatronics College of Biomedical Engineering Taipei Medical University Taipei11031 Taiwan Department of Chemical Engineering Ming Chi University of Technology New Taipei City24301 Taiwan

Photoelectrochemical catalytic capability mainly relies on light absorption and charge transfer efficiency. TiO2 nanotube array (TNA) having suitable band edges and one-dimensional hollow structure is regarded as one of efficient photoelectrocatalysts toward water reduction. In this study, two strategies are firstly applied to modify TNA as the photocatalyst of water reduction. Ti foils are etched by acid to produce multiple light reflections planes for improving light absorption, and Cu is doped in TNA to enhance charge transfer efficiency. The optimal Cu-doped TNA electrode on the acid-etched Ti foil presents a much smaller overpotential of 91 mV at 10 mA/cm2 compared with that of the undoped TNA (524 mV). A smaller Tafel slope of 134 mV/dec is obtained for the optimal Cu-doped TNA electrode than that of the undoped TNA (167 mV/dec). After measuring the photoelectrochemical performance for 1000 cycles, overpotential and charge-transfer resistance of modified TNA are largely reduced owing to activation. Current retention of 96.7% is achieved after continuously illuminating for 10 h. Highly improved photoelectrochemical catalytic ability of TNA modified by acid etching and Cu doping provides new pages for material modifications on substrate and active material. © 2023 Elsevier Ltd

关键词： Light absorption

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How Microbes Shape Their Communities? A Microbial Community Model Based on Functional Genes

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Genomics, Proteomics & Bioinformatics 2019年第1期17卷 91-105页

作者： Xiaoqing Jiang Xin Li Longshu Yang Chunhong Liu Qi Wang Weilai Chi Huaiqiu Zhu State Key Laboratory for Turbulence and Complex Systems Department of Biomedical Engineering College of Engineering Peking University Center for Quantitative Biology Peking University Peking University-Tsinghua University-National Institute of Biological Sciences Joint Biological (PTN) PhD Program and College of Life Sciences Peking University Center for Protein Science Peking University

Exploring the mechanisms of maintaining microbial community structure is important to understand biofilm development or microbiota dysbiosis. In this paper, we propose a functional gene-based composition prediction(FCP) model to predict the population structure composition within a microbial community. The model predicts the community composition well in both a low-complexity community as acid mine drainage(AMD) microbiota, and a complex community as human gut microbiota. Furthermore, we define community structure shaping(CSS) genes as functional genes crucial for shaping the microbial community. We have identified CSS genes in AMD and human gut microbiota samples with FCP model and find that CSS genes change with the conditions. Compared to essential genes for microbes, CSS genes are significantly enriched in the genes involved in mobile genetic elements, cell motility, and defense mechanisms, indicating that the functions of CSS genes are focused on communication and strategies in response to the environment factors. We further find that it is the minority, rather than the majority, which contributes to maintaining community structure. Compared to health control samples, we find that some functional genes associated with metabolism of amino acids, nucleotides, and lipopolysaccharide are more likely to be CSS genes in the disease group. CSS genes may help us to understand critical cellular processes and be useful in seeking addable gene circuitries to maintain artificial self-sustainable communities. Our study suggests that functional genes are important to the assembly of microbial communities.

关键词： Metagenomics Dynamics model Community structure Acid mine drainage Human gut microbiota

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Thermalization of fluorescent protein exciton-polaritons at room temperature

arXiv

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arXiv 2022年

作者： Satapathy, Sitakanta Liu, Bin Deshmukh, Prathmesh Molinaro, Paul M. Dirnberger, Florian Khatoniar, Mandeep Koder, Ronald L. Menon, Vinod M. Department of Physics Center for Discovery and Innovation The City College of New York 85 St. Nicholas Terrace New YorkNY10031 United States The PhD Program in Physics The Graduate Center of the City University of New York 365 5th Ave New YorkNY10016 United States Department of Electrical Engineering and Computer Science University of Michigan Ann ArborMI48109 United States

Fluorescent proteins (FPs) have recently emerged as a serious contender for realizing ultra-low threshold room temperature exciton-polariton condensation and lasing. Our contribution investigates the thermalization of FP microcavity exciton-polaritons upon optical pumping under ambient conditions. We realize polariton cooling using a new FP molecule, called mScarlet, coupled strongly to the optical modes in a Fabry-Pérot cavity. Interestingly, at the threshold excitation energy (fluence) of ~9 nJ/pulse (15.6 mJ/cm2), we observe an effective temperature, Teff ~350 ± 35 K close to the lattice temperature indicative of strongly thermalized exciton-polaritons at equilibrium. This efficient thermalization results from the interplay of radiative pumping facilitated by the energetics of the lower polariton branch and the cavity Qfactor. Direct evidence for dramatic switching from an equilibrium state into a metastable state is observed for the organic cavity polariton device at room temperature via deviation from the Maxwell-Boltzmann statistics at k1 = 0 above the threshold. Thermalized polariton gases in organic systems at equilibrium hold substantial promise for designing room temperature polaritonic circuits, switches, and lattices for analog simulation. © 2022, CC BY-NC-SA.

关键词： Polariton

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Determinant of importance-performance and willingness to participate in Komodo adaptive conservation programs

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Journal for Nature Conservation 2024年 81卷

作者： Sianipar, Imelda Masni Juniaty Lee, Chun-Hung Wang, Hurng-Jyuhn Kim, Doo-Chul Suryawan, I Wayan Koko PhD Student in Asia-Pacific Regional Studies College of Humanities and Social Sciences National Dong Hwa University Department of International Relations Faculty of Social Science and Political Science Universitas Kristen Indonesia Department of Natural Resources and Environmental Studies College of Environmental Studies and Oceanography National Dong Hwa University Program in Asia-Pacific Regional Studies College of Humanities and Social Sciences National Dong Hwa University Department of Rural Environment Management Graduate School of Environmental and Life Science Okayama University Ph.D Program in Asia-Pacific Regional Studies College of Humanities and Social Sciences National Dong Hwa University Department of Environmental Engineering Faculty of Infrastructure Planning Universitas Pertamina Jalan Sinabung II Terusan Simprug

This study delves into the evaluation of the Komodo dragons Adaptive Conservation program (KACP) at Komodo National Park in Indonesia through Importance-Performance Analysis (IPA). It aims to understand how the programs components align with community priorities and assess its effectiveness. Utilizing a mixed-methods approach, this research analyzes community perceptions of KACP's critical elements, spanning eco-tourism initiatives to environmental protection strategies. The community is categorized into local advocates, eco-tourism enthusiasts, and eco-community harmonizers, identifying how each group perceives and interacts with various facets of KACP. The findings reveal significant differences in perceptions of importance and performance among these groups, providing insights into areas of strength and those needing improvement. Additionally, the study includes an analysis of demographic influences on these perceptions through Logit and Probit models, aiming to understand the impacts across different community segments. The results highlight the necessity for an adaptive and responsive design in conservation efforts, considering community expectations and ecological impacts. Despite offering comprehensive insights, the study acknowledges limitations in the demographic scope and suggests future research directions, such as longitudinal studies and an expanded analysis of variables. These findings offer critical guidance for policymakers and conservation practitioners to enhance conservation programs’ effectiveness and community alignment, emphasizing the need to adapt to the challenges and changes introduced by KACP. © 2024 Elsevier GmbH

关键词： Adaptive capacity Community perception Conservation strategy evaluation Importance-performance analysis Protected areas

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A technical review of wireless security for the internet of things: Software defined radio perspective

arXiv

引用

arXiv 2020年

作者： Uribe, Jose de Jesus Rugeles Guillen, Edward Paul Cardoso, Leonardo S. Applied Sciences PhD program Universidad Militar Nueva Granada Bogot Colombia Telecommunications Engineering program Universidad Militar Nueva Granada Bogota Colombia Univ Lyon INSA Lyon Inria CITI Lyon France

The increase of cyberattacks using IoT devices has exposed the vulnerabilities in the infrastructures that make up the IoT and have shown how small devices can affect networks and services functioning. This paper presents a review of the vulnerabilities of the wireless technologies that bear the IoT and assessing the experiences in implementing wireless attacks targeting the Internet of Things using Software-Defined Radio (SDR) technologies. A systematic literature review was conducted. The types of vulnerabilities and attacks that can affect the wireless technologies that stand the IoT ecosystem and SDR radio platforms were compared. On the IoT system model layer, perception layer was identified as the most vulnerable. Most attacks at this level occur due to limitations in hardware, physical exposure of devices, and heterogeneity of technologies. Future cybersecurity systems based on SDR radios have notable advantages due to their flexibility to adapt to new communication technologies and their potential for the development of advanced tools. However, cybersecurity challenges for the Internet of Things are so complex that it is needed to merge SDR hardware with cognitive techniques and intelligent techniques such as deep learning to adapt to rapid technological changes. Copyright © 2020, The Authors. All rights reserved.

关键词： Radio

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Dual-Targeting EGCG/NO-Supplying protein assembled nanoparticles with Multi-Synergistic effects against atherosclerosis

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Chemical engineering Journal 2024年 493卷

作者： Lin, Chi Cheng, Tsai-Mu Liu, Yun-Chun Hsu, Fang-Yu Shih, Chun-Ming Tsai, Min-Lang Shih, Chun-Che Mi, Fwu-Long Graduate Institute of Medical Sciences College of Medicine Taipei Medical University Taipei11031 Taiwan The PhD Program for Translational Medicine College of Medical Science and Technology Taipei Medical University Taipei11031 Taiwan Taipei Heart Institute Taipei Medical University Taipei11031 Taiwan Department of Food Science National Taiwan Ocean University Keelung20224 Taiwan Department of Biochemistry and Molecular Cell Biology School of Medicine College of Medicine Taipei Medical University Taipei11031 Taiwan Division of Cardiology and Cardiovascular Research Center Taipei Medical University Hospital Taipei11031 Taiwan Division of Cardiovascular Surgery Department of Surgery Wan Fang Hospital Taipei Medical University Taipei11031 Taiwan Institute of Clinical Medicine School of Medicine National Yang-Ming Chiao Tung University Taipei Taiwan Department of Surgery School of Medicine College of Medicine Taipei Medical University Taipei11031 Taiwan Graduate Institute of Nanomedicine and Medical Engineering College of Biomedical Engineering Taipei Medical University Taipei11031 Taiwan International Ph.D. Program for Cell Therapy and Regeneration Medicine College of Medicine Taipei Medical University Taipei Taiwan

Limited therapeutic options are available to effectively preventing atherosclerosis. Inflammatory endothelial cells, foamy macrophages, and high protease levels contribute to atherosclerotic plaque formation. Studies have shown that catechins effectively scavenge reactive oxygen species (ROS), inhibit monocyte adhesion and reduce cholesterol levels, while nitric oxide (NO) enhances endothelial function. However, due to the poor stability and bioavailability of catechins and the toxicity from the burst release of current synthetic small molecules NO donor, effective delivery of these bioactive compounds to treat atherosclerosis is still a challenge. Herein, a catechin/protein-based NO donor co-delivery nanosystem was designed for combinatorial anti-atherosclerotic therapy. We engineered a (−)-epigallocatechin-3-gallate (EGCG)/NO-releasing protein co-assembled nanocomplex based on specific catechin-protein interactions. Furthermore, the nanocomplex was surface modified with fucoidan (Fu), a sulfated polysaccharide with anti-inflammatory activity. This nanocomplex exhibits sensitivity to ROS, pH, and enzymes. The Fu-functionalized nanoparticles specifically accumulates in atherosclerotic plaques mediated by P-selectin on inflamed endothelial cells and scavenger receptor A (SR-A) on foamy macrophages. Under environmental stimuli that simulate the condition of plaque, the nanoparticles are readily activated to release EGCG and NO in response to excess ROS and high protease levels, exerting the multi-synergistic anti-atherosclerosic effects on reducing monocyte adhesion, promoting NO production to proliferate endothelial cells, lowering ROS levels, and decreasing the foam cell formation in vitro, and reducing lipid accumulation, plaque size, and inflammatory cytokines release in high-fat diet-induced atherosclerosis model in ApoE−/− mice. The integration of plaques targeting ability and multiple therapeutic functions can provide an advanced therapeutic strategy for athero

关键词： Nitric oxide

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Symmetries and synchronization from whole-neural activity in C. elegans connectome: Integration of functional and structural networks

arXiv

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arXiv 2024年

作者： Avila, Bryant Augusto, Pedro Phillips, David Gili, Tommaso Zimmer, Manuel Makse, Hernán A. Levich Institute and Physics Department City College of New York New YorkNY10031 United States Vienna Austria Vienna Biocenter PhD Program Doctoral School the University of Vienna Medical University of Vienna Vienna Austria Mechanical Engineering Department University of New Mexico AlbuquerqueNM87131 United States Networks Unit IMT Scuola Alti Studi Lucca Piazza San Francesco 15 Lucca55100 Italy Department of Radiology Neuroradiology Service Memorial Sloan Kettering Cancer Center New YorkNY10065 United States CUNY Neuroscience Graduate Center City University of New York New YorkNY10031 United States

Understanding the dynamical behavior of complex systems from their underlying network architectures is a long-standing question in complexity theory. Therefore, many metrics have been devised to extract network features like motifs, centrality, and modularity measures. It has previously been proposed that network symmetries are of particular importance since they are expected to underly the synchronization of a system’s units, which is ubiquitously observed in nervous system activity patterns. However, perfectly symmetrical structures are difficult to assess in noisy measurements of biological systems, like neuronal connectomes. Here, we devise a principled method to infer network symmetries from combined connectome and neuronal activity data. Using nervous system-wide population activity recordings of the *** backward locomotor system, we infer structures in the connectome called fibration symmetries, which can explain which group of neurons synchronize their activity. Our analysis suggests functional building blocks in the animal’s motor periphery, providing new testable hypotheses on how descending interneuron circuits communicate with the motor periphery to control behavior. Our approach opens a new door to exploring the structure-function relations in other complex systems, like the nervous systems of larger animals. © 2024, CC BY.

关键词： Synchronization

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