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engineering FRET biosensor for H3K9 acetylation imaging in single living cells

Med-X 2024年第1期2卷 446-461页

作者： Shitian Li Chang Sun Reed E.S.Harrison Leonardo Cheng Li Gao Longwei Liu Yingxiao Wang Qin Peng Department of Bioengineering Institute of Engineering in MedicineUniversity of CaliforniaSan DiegoLa JollaCA 92093USA Biological Sciences Graduate Program University of CaliforniaSan DiegoLa JollaCA 92093USA Institute of Systems and Physical Biology Shenzhen Bay LaboratoryShenzhen 518132China Alfred E.Mann Department of Biomedical Engineering University of Southern CaliforniaLos AngelesCA 90089USA School of Chemical Engineering and Technology North University of ChinaTaiyuanShanxi 030051China

Histone acetylation is an important epigenetic modification that governs gene expression,chromatin changes in stress response,and cell fate *** biosensors have been developed for various epigenetic events to enable spatiotemporal tracking of sub-cellular signaling *** reported histone H3 acetylation biosensor recognizing two acetyl residues lacked *** this study,using a single bromodomain of the BRD4,we have developed a genetically encoded H3K9ac *** systematically investigated different combinations of the BET family protein as binding domains and performed site-saturated mutagenesis to optimize the biosensor,achieving a dynamic FRET change up to 30%under TSA *** the application of the optimized H3K9ac biosensor,we revealed different basal active chromatin architectures in invasive tumor cells compared to benign tumor ***,we found that H3K9ac level increased dramatically when cancer cells passed through microchannels,which models the physical constraints and mechanical microenvironmental conditions that cancer cells encounter when passing through narrow spaces within the *** result highlights the chromatin plasticity in response to external mechanical *** summary,our H3K9ac biosensor provides a versatile tool for mechanistic investigation of cell fate transition in cancer and mechanotransduction.

关键词： FRET biosensor H3K9 acetylation Nuclear deformation Cancer cell migration

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Technology Roadmap for Flexible Sensors

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ACS NANO 2023年第6期17卷 5211-5295页

作者： Luo, Yifei Abidian, Mohammad Reza Ahn, Jong-Hyun Akinwande, Deji Andrews, Anne M. Antonietti, Markus Bao, Zhenan Berggren, Magnus Berkey, Christopher A. Bettinger, Christopher John Chen, Jun Chen, Peng Cheng, Wenlong Cheng, Xu Choi, Seon-Jin Chortos, Alex Dagdeviren, Canan Dauskardt, Reinhold H. Di, Chong-an Dickey, Michael D. Duan, Xiangfeng Facchetti, Antonio Fan, Zhiyong Fang, Yin Feng, Jianyou Feng, Xue Gao, Huajian Gao, Wei Gong, Xiwen Guo, Chuan Fei Guo, Xiaojun Hartel, Martin C. He, Zihan Ho, John S. Hu, Youfan Huang, Qiyao Huang, Yu Huo, Fengwei Hussain, Muhammad M. Javey, Ali Jeong, Unyong Jiang, Chen Jiang, Xingyu Kang, Jiheong Karnaushenko, Daniil Khademhosseini, Ali Kim, Dae-Hyeong Kim, Il-Doo Kireev, Dmitry Kong, Lingxuan Lee, Chengkuo Lee, Nae-Eung Lee, Pooi See Lee, Tae-Woo Li, Fengyu Li, Jinxing Liang, Cuiyuan Lim, Chwee Teck Lin, Yuanjing Lipomi, Darren J. Liu, Jia Liu, Kai Liu, Nan Liu, Ren Liu, Yuxin Liu, Yuxuan Liu, Zhiyuan Liu, Zhuangjian Loh, Xian Jun Lu, Nanshu Lv, Zhisheng Magdassi, Shlomo Malliaras, George G. Matsuhisa, Naoji Nathan, Arokia Niu, Simiao Pan, Jieming Pang, Changhyun Pei, Qibing Peng, Huisheng Qi, Dianpeng Ren, Huaying Rogers, John A. Rowe, Aaron Schmidt, Oliver G. Sekitani, Tsuyoshi Seo, Dae-Gyo Shen, Guozhen Sheng, Xing Shi, Qiongfeng Someya, Takao Song, Yanlin Stavrinidou, Eleni Su, Meng Sun, Xuemei Takei, Kuniharu Tao, Xiao-Ming Tee, Benjamin C. K. Thean, Aaron Voon-Yew Trung, Tran Quang Wan, Changjin Wang, Huiliang Wang, Joseph Wang, Ming Wang, Sihong Wang, Ting Wang, Zhong Lin Weiss, Paul S. Wen, Hanqi Xu, Sheng Xu, Tailin Yan, Hongping Yan, Xuzhou Yang, Hui Yang, Le Yang, Shuaijian Yin, Lan Yu, Cunjiang Yu, Guihua Yu, Jing Yu, Shu-Hong Yu, Xinge Zamburg, Evgeny Zhang, Haixia Zhang, Xiangyu Zhang, Xiaosheng Zhang, Xueji Zhang, Yihui Zhang, Yu Zhao, Siyuan Zhao, Xuanhe Zheng, Yuanjin Zheng, Yu-Qing Zheng, Zijian Zhou, Tao Zhu, Bowen Zhu, Ming Zhu, Rong Zhu, Yangzhi Zhu, Yong Zou, Guijin Chen, Xiaodong 08-03 Innovis Singapore 138634 Republic of Singapore Innovative Centre for Flexible Devices (iFLEX) School of Materials Science and Engineering Nanyang Technological University Singapore 639798 Singapore Department of Biomedical Engineering University of Houston Houston Texas 77024 United States School of Electrical and Electronic Engineering Yonsei University Seoul 03722 Republic of Korea Department of Electrical and Computer Engineering The University of Texas at Austin Austin Texas 78712 United States Microelectronics Research Center The University of Texas at Austin Austin Texas 78758 United States Department of Chemistry and Biochemistry California NanoSystems Institute and Department of Psychiatry and Biobehavioral Sciences Semel Institute for Neuroscience and Human Behavior and Hatos Center for Neuropharmacology University of California Los Angeles Los Angeles California 90095 United States Colloid Chemistry Department Max Planck Institute of Colloids and Interfaces 14476 Potsdam Germany Department of Chemical Engineering Stanford University Stanford California 94305 United States Laboratory of Organic Electronics Department of Science and Technology Campus Norrköping Linköping University 83 Linköping Sweden Wallenberg Initiative Materials Science for Sustainability (WISE) and Wallenberg Wood Science Center (WWSC) SE-100 44 Stockholm Sweden Department of Materials Science and Engineering Stanford University Stanford California 94301 United States Department of Biomedical Engineering and Department of Materials Science and Engineering Carnegie Mellon University Pittsburgh Pennsylvania 15213 United States Department of Bioengineering University of California Los Angeles Los Angeles California 90095 United States School of Chemistry Chemical Engineering and Biotechnology Nanyang Technological University Singapore 637457 Singapore Nanobionics Group Department of Chemical and Biological Engineering Monash University Clayton Australia 3800 Monash

Humans rely increasingly on sensors to address grand challenges and to improve quality of life in the era of digitalization and big data. For ubiquitous sensing, flexible sensors are developed to overcome the limitations of conventional rigid counterparts. Despite rapid advancement in bench-side research over the last decade, the market adoption of flexible sensors remains limited. To ease and to expedite their deployment, here, we identify bottlenecks hindering the maturation of flexible sensors and propose promising solutions. We first analyze continued...challenges in achieving satisfactory sensing performance for real-world applications and then summarize issues in compatible sensor-biology interfaces, followed by brief discussions on powering and connecting sensor networks. Issues en route to commercialization and for sustainable growth of the sector are also analyzed, highlighting environmental concerns and emphasizing nontechnical issues such as business, regulatory, and ethical considerations. Additionally, we look at future intelligent flexible sensors. In proposing a comprehensive roadmap, we hope to steer research efforts towards common goals and to guide coordinated development strategies from disparate communities. Through such collaborative

关键词： soft materials mechanics engineering flexible electronics conformable sensors bioelectronics human-machine interfaces body area sensor networks technology translation sustainable electronics

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Effect of TiO 2 concentration in PVDF-TiO 2 -PVP mixed matrix membrane performance using ultrafiltration process

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Materials Today: Proceedings 2024年 96卷 1-5页

作者： Rianyza Gayatri Erna Yuliwati Ahmad Noor Syimir Fizal Muhamad Zulhilmi Zailani Juhana Jaafar Muzafar Zulkifli Wirach Taweepreda Ahmad Naim Ahmad Yahaya Universiti Kuala Lumpur Malaysian Institute of Chemical and Bioengineering Technology Alor Gajah Melaka 78000 Malaysia Department of Material Science and Technology Faculty of Science Prince of Songkla University (PSU) Hat Yai Songkla 90110 Thailand Program Study of Chemical Engineering Faculty of Engineering Universitas Muhammadiyah Palembang Jalan A.Yani 13 Ulu Kota Palembang 30263 Indonesia Centre for Sustainability of Ecosystem & Earth Resources (Pusat ALAM) Universiti Malaysia Pahang Lebuh Persiaran Tun Khalil Yaakob 26300 Gambang Pahang Malaysia Advanced Membrane Technology Research Centre (AMTEC) Faculty of Chemical and Energy Engineering Universiti Teknologi

This study investigated how the addition of hydrophilic TiO 2 to a porous asymmetric polyvinylidene fluoride (PVDF) Ultrafiltration (UF) membrane altered its properties and performance. The hydrophilicity and flux of PVDF and polyvinylpyrrolidone (PVP) combinations will be lower, and TiO 2 will significantly impact raising those values. By mixing titanium dioxide (TiO 2 ) nanoparticles with a pore-forming agent in a dope solution, PVDF-TiO 2 -PVP membranes were prepared via non-solvent-induced phase inversion method. Experiments using PVDF membranes with varying concentrations of TiO 2 (0, 0.25, 0.5, 1, 1.5, and 2% wt) were applied to evaluate pure water flux and Bovine Serum Albumin (BSA) flux. The functional group composition of membranes was investigated by Fourier transform infrared spectroscopy. The wettability of porous membranes was determined by measuring contact angles. Results demonstrated that membranes constructed from PVDF/PVP/TiO 2 with a lower loading of TiO 2 nanoparticles had a smaller mean pore size, more apertures inside the membrane, and better membrane hydrophilicity. The highest flux of pure water (121 L/m 2 h) was achieved by the PVDF-TiO 2 -PVP mixed-matrix membrane at a TiO 2 concentration of 2 wt%.

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Scaling Ipsc Production in Different 3d Platforms in Suspension Culture for Their Use in Allogeneic Regenerative Therapies

SSRN

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SSRN 2024年

作者： Freire-Flores, Danton Kawles, Nyna Caviedes, Pablo Andrews, Barbara A. Asenjo, Juan A. Centre for Biotechnology and Bioengineering Faculty of Physical and Mathematical Sciences Universidad de Chile Beaucheff 851 Santiago8370448 Chile Department of Chemical Engineering Biotechnology and Materials Universidad de Chile Beaucheff 851 Santiago8370448 Chile Program of Molecular and Clinical Pharmacology ICBM Faculty of Medicine University of Chile Independencia 1027 Santiago8379482 Chile

Human induced pluripotent stem cells (iPSCs) exhibit significant potential for advancing regenerative medical treatments due to their pluripotency and proliferation capacity. However, the large-scale production required for allogeneic therapies necessitates efficient and scalable culture systems. Conventional 2D culture techniques are inadequate for this, driving interest for innovative bioreactor-based expansion techniques such as microcarrier-based or suspension aggregate cultures. In this study, we compare iPSC expansion and quality in microcarrier and aggregate cultures in spinner flasks, aiming to ascertain which 3D growth configuration yields superior cell mass while maintaining cellular product quality. We demonstrated comparable expansion of iPSCs on Cytodex 1 and Cultisphere G microcarriers, as well as in aggregates by day 6 in culture, achieving a final cell density of 2.6*10^6 cells/ml and 5.67*10^6 cells/ml on microcarriers respectively, and 9.76*10^6 cells/ml in aggregates, yielding 4- and 9-fold expansion on microcarriers and 15-fold in aggregates. The efficiency in the recovery of iPSCs in single-cell form was over 91.5% for all cultures. iPSCs cultured on microcarriers and as aggregates exhibit OCT3/4, SSEA4, TRA-1-60, and SOX2 pluripotency marker expression, as well as retention of differentiation potential into three germinal layers. This work supports the utilization of microcarriers and aggregates as an efficient 3D expansion platform for suspension cultures of iPSCs, in the quest to further scale production in larger stirred-tank bioreactor systems. © 2024, The Authors. All rights reserved.

关键词： Tanks (containers)

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Amplification of enzymatic and microbial fuel cells using organic electrochemical transistors

Device

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Device 2025年

作者： Saxena, Ravindra Zhang, Xu Cai, Rong Suggs, Olivia Bruggeman, Chase Hickey, David P. Ajo-Franklin, Caroline M. Verduzco, Rafael Applied Physics Graduate Program Smalley-Curl Institute Rice University Houston 77005 TX United States Department of Biosciences Rice University Houston 77005 TX United States Department of Chemical Engineering and Materials Science Michigan State University East Lansing 48824 MI United States Department of Bioengineering Rice University Houston 77005 TX United States Department of Chemical and Biomolecular Engineering Rice University Houston 77005 TX United States Rice Advanced Materials Institute Rice University Houston 77005 TX United States

Organic electrochemical transistors (OECTs) are thin-film devices operated in aqueous and biological environments for sensing chemicals and biomolecules. However, most sensor configurations involve introducing the target biomolecule directly in the OECT device. This has drawbacks because it may not be possible to have an electrolyte compatible with the target biomolecule or an environment optimal for the OECT. Here, we demonstrate a general and modular approach to building electrochemical sensors by coupling OECTs electronically with either an enzymatic fuel cell (EFC) or microbial fuel cell (MFC). We demonstrate that this modular approach can amplify currents by three orders of magnitude and enhance the signal-to-noise ratio. We also show that the power generated by the fuel cell can help tune the sensor's response for different applications. This work demonstrates a simple and versatile approach for amplifying currents from MFCs and EFCs useful for the development of bioelectronic sensors. © 2025 The Authors

关键词： amplification biosensors DTI-3: Develop electro-active bacteria enzymatic fuel cells microbial fuel cells organic electrochemical transistors power

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Deep Learning of Proteins with Local and Global Regions of Disorder

arXiv

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arXiv 2025年

作者： Zhang, Oufan Liu, Zi Hao Forman-Kay, Julie D. Head-Gordon, Teresa Kenneth S. Pitzer Theory Center Department of Chemistry University of California BerkeleyCA United States Molecular Medicine Program Hospital for Sick Children TorontoONM5S 1A8 Canada Department of Biochemistry University of Toronto TorontoONM5G 1X8 Canada Departments of Bioengineering and Chemical and Biomolecular Engineering University of California BerkeleyCA United States

Although machine learning has transformed protein structure prediction of folded protein ground states with remarkable accuracy, intrinsically disordered proteins and regions (IDPs/IDRs) are defined by diverse and dynamical structural ensembles that are predicted with low confidence by algorithms such as AlphaFold and RoseTTAFold. We present a new machine learning method, IDPForge (Intrinsically Disordered Protein, FOlded and disordered Region GEnerator), that exploits a transformer protein language diffusion model to create all-atom IDP ensembles and IDR disordered ensembles that maintains the folded domains. IDPForge does not require sequence-specific training, back transformations from coarse-grained representations, nor ensemble reweighting, as in general the created IDP/IDR conformational ensembles show good agreement with solution experimental data, and options for biasing with experimental restraints are provided if desired. We envision that IDPForge with these diverse capabilities will facilitate integrative and structural studies for proteins that contain intrinsic disorder, and is available as an open source resource for general use. © 2025, CC BY.

关键词： Deep learning

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Extracellular respiration is a latent energy metabolism in Escherichia coli

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Cell 2025年第11期188卷 2907-2924.e23页

作者： Kundu, Biki Bapi Krishnan, Jayanth Szubin, Richard Patel, Arjun Palsson, Bernhard O. Zielinski, Daniel C. Ajo-Franklin, Caroline M. PhD Program in Systems Synthetic and Physical Biology Rice University Houston 77005 TX United States Department of Bioengineering University of California San Diego La Jolla 92093 CA United States Novo Nordisk Foundation Center for Biosustainability Technical University of Denmark Kemitorvet Building 220 Kgs. Lyngby 2800 Denmark Departments of Biosciences Bioengineering Chemical and Biomolecular Engineering and The Rice Synthetic Biology Institute Rice University Houston 77005 TX United States

Diverse microbes utilize redox shuttles to exchange electrons with their environment through mediated extracellular electron transfer (EET), supporting anaerobic survival. Although mediated EET has been leveraged for bioelectrocatalysis for decades, fundamental questions remain about how these redox shuttles are reduced within cells and their role in cellular bioenergetics. Here, we integrate genome editing, electrochemistry, and systems biology to investigate the mechanism and bioenergetics of mediated EET in Escherichia coli, elusive for over two decades. In the absence of alternative electron sinks, the redox cycling of 2-hydroxy-1,4-naphthoquinone (HNQ) via the cytoplasmic nitroreductases NfsB and NfsA enables E. coli respiration on an extracellular electrode. E. coli also exhibits rapid genetic adaptation in the outer membrane porin OmpC, enhancing HNQ-mediated EET levels coupled to growth. This work demonstrates that E. coli can grow independently of classic electron transport chains and fermentation, unveiling a potentially widespread new type of anaerobic energy metabolism. © 2025 Elsevier Inc.

关键词： adaptive laboratory evolution anaerobic metabolism electron shuttles extracellular electron transfer flux balance analysis iModulon analysis nitroreductases redox homeostasis

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Dual Chemifunctional Tin(Iv) Oxide/Nanoperforated Graphene Interlayer as a Polysulfide Adsorbent for Use in High-Performance Lithium-Sulfur Batteries

SSRN

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SSRN 2023年

作者： Lee, Junho Jung, Nae Yeon Ahn, Wook Lim, Hyung-Kyu Kim, Hyun-Kyung Department of Battery Convergence Engineering Kangwon National University 1 Kangwondaehak-gil Chuncheon24341 Korea Republic of Interdisciplinary Program in Advanced Functional Materials and Devices Development Kangwon National University Chuncheon24341 Korea Republic of Division of Chemical Engineering and Bioengineering Kangwon National University 1 Kangwondaehak-gil Chuncheon24341 Korea Republic of Department of Energy Engineering Soonchunhyang University 22 Soonchunhyang-ro Shinchang-myeon Chungcheongnam-do Asan-Si31538 Korea Republic of

The development of Li-S batteries is limited by their levels of rapid capacity decay owing to polysulfide dissolution and diffusion in organic electrolytes. We addressed this critical issue by fabricating a dual chemifunctional interlayer comprising SnO2 nanoparticles and nanoperforated graphene (NPG) that could function as a polysulfide adsorbent. The synergistic effects of SnO2 and the high-density functional groups of NPG on polysulfide capture were conceptually confirmed. NPG not only supported the adsorption of Li polysulfides but also provided pathways for simple Li-ion motion within the SnO2/NPG interlayer. A cell assembled with the SnO2/NPG interlayer displayed a high rate capability and initial discharge capacity and good reversible capacity. The excellent high-rate cycling performance of the cathode could mainly be attributed to the strong chemical bonds formed between SnO2/NPG and the polysulfides, rapid electron transfer, and optimized ion diffusion pathways derived from the well-organized structure of the composite. Synthesizing dual chemifunctional interlayers using a composite of metal oxides and NPG may lead to the development of advanced Li-S batteries with numerous practical applications in the near future. © 2023, The Authors. All rights reserved.

关键词： Lithium sulfur batteries

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The Pull of Tissue engineering: A STEM Outreach program with a Modular Cyclic Stretch Device to Engage High School Students

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Biomedical engineering Education 2021年第1期2卷 31-39页

作者： Ozdemir, Tugba Senocak, Erdal Gerber, Gene Tayhan, Secil Erden Brown, Justin L. Biomedical Engineering Program Chemical and Biological Engineering Department South Dakota School of Mines and Technology Rapid City USA Department of Science Education Tokat Gaziosmanpasa University Tokat Turkey Department of Biomedical Engineering The Pennsylvania State University State College USA Department of Genetics and Bioengineering Tokat Gaziosmanpasa University Tokat Turkey

In this paper we designed a STEM outreach program with a modular tissue engineering education tool (we refer to as “modular cyclic-stretch device”) to engage high school students in STEM hands-on activities. Using simple machines such as gears and rotating cams, students were able to build a custom device to apply cyclic stretch to biomaterials. With the help of this hands-on activity, our outreach program helped students grasp tendon tissue biomechanics and understand the importance of applying biomechanical force to regenerate tendon tissue in a laboratory setting. The two-day outreach program comprised: 1. pre- and post-tests; 2. lectures; 3. laboratory sessions, including the microscopic examination of stained tissue sections and a hands-on group activity employing the modular cyclic-stretch device; and 4. homework. Assessment results suggest that our program supports improved student awareness and interest in tissue engineering as a future profession. The program elevated students’ confidence in their ability to apply engineering principles to tasks such as building a modular cyclic-stretch device and measuring the mechanical properties of biological tissues. Building an educational bioreactor improved students’ understanding of the dynamic nature of the human body and the importance of tissue engineering as an emerging discipline towards replacing or regenerating damaged organs. We propose that our modular device has great outreach potential to introduce tissue engineering concepts to high school and potentially college freshmen engineering students.

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Computational Methods to Investigate Intrinsically Disordered Proteins and their Complexes

arXiv

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arXiv 2024年

作者： Liu, Zi Hao Tsanai, Maria Zhang, Oufan Forman-Kay, Julie Head-Gordon, Teresa Molecular Medicine Program Hospital for Sick Children TorontoONM5G 0A4 Canada Kenneth S. Pitzer Center for Theoretical Chemistry Department of Chemistry University of California Berkeley BerkeleyCA94720 United States Department of Biochemistry University of Toronto TorontoONM5S 1A8 Canada Departments of Bioengineering and Chemical and Biomolecular Engineering University of California Berkeley BerkeleyCA94720 United States

In 1999 Wright and Dyson highlighted the fact that large sections of the proteome of all organisms are comprised of protein sequences that lack globular folded structures under physiological conditions. Since then the biophysics community has made significant strides in unraveling the intricate structural and dynamic characteristics of intrinsically disordered proteins (IDPs) and intrinsically disordered regions (IDRs). Unlike crystallographic beamlines and their role in streamlining acquisition of structures for folded proteins, an integrated experimental and computational approach aimed at IDPs/IDRs has emerged. In this Perspective we aim to provide a robust overview of current computational tools for IDPs and IDRs, and most recently their complexes and phase separated states, including statistical models, physics-based approaches, and machine learning methods that permit structural ensemble generation and validation against many solution experimental data types. © 2024, CC BY.

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