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Extracellular respiration is a latent energy metabolism in Escherichia coli

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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FROM IDEA TO IMPLEMENTATION - COGNITIVE SOFTWARE FOR STUDENTS WITH LEARNING-DISABILITIES

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JOURNAL OF LEARNING DISABILITIES 1985年第10期18卷 613-618页

作者： MINEO, BA CAVALIER, AR Beth A. Mineo PhD is the Assistant Director and Al R. Cavalier PhD is the Director of the Bioengineering Program of the Department of Research and Program Services at the Association for Retarded Citizens National Headquarters. Address: ARC National Headquarters 2501 Avenue J Arlington TX 76011

Assesses the impact of cognitive software implementation on learning disabled students. Factors that contribute to the failure of paradigm translation into computer software; Features of microcomputer application; Nat... 详细信息

关键词： Computer Assisted Instruction Computer Software Learning Disabilities Memory Metacognition program Development

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Enabling Human-Robot Collaboration via Holistic Human Perception and Partner-Aware Control

arXiv

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arXiv 2020年

作者： Yeshasvi Tirupachuri, Venkata Sai University of Genova PhD Program in Bioengineering and Robotics

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BPS2025 - Flexible and robust labeling and tracking of non-repetitive genomic loci

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Biophysical Journal 2025年第3期124卷 353a-353a页

作者： Alex Raterink Rajarshi P. Ghosh Quanming Shi Linfeng Yang Minh Khue Nguyen Anna-Karin Gustavsson Systems Synthetic and Physical Biology PhD Program Rice University Houston TX USA Howard Hughes Medical Institute University of California Berkeley CA USA Department of Bioengineering Stanford University Stanford CA USA Department of Chemistry Rice University Houston TX USA Department of Biosciences Rice University Houston TX USA

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

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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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Prosthetic hand signals

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Significance 2018年第4期15卷 30-35页

作者： Mike Wininger Reva Johnson PhD has faculty appointments at the University of Hartford (Prosthetics Program) and Yale University (Department of Biostatistics) and is a statistician of clinical trials with the Department of Veterans Affairs. PhD is a professor in the Department of Mechanical Engineering and Bioengineering at Valparaiso University.

How Bayesian inference can decode movement intentions and control the next generation of powered prostheses. By Mike Wininger and Reva Johnson

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Dish-Trend: Intervention Modeling Simulator That Accounts for Trend Influences

Dish-Trend: Intervention Modeling Simulator That Accounts fo...

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2021 Winter Simulation Conference, WSC 2021

作者： Andjelkovic, Stefan Miskov-Zivanov, Natasa Computational and Systems Biology Joint Carnegie Mellon University University of Pittsburgh Computational Biology PhD Program University of Pittsburgh PittsburghPA15213 United States Electrical and Computer Engineering Bioengineering Computational and Systems Biology University of Pittsburgh PittsburghPA15213 United States

ISBN: (纸本)9781665433112

Simulation on directed graphs is an important method for understanding the dynamics in the systems where connectivity graphs contain cycles. Discrete Stochastic Heterogeneous Simulator (DiSH) is one of the simulation tools with wide application, which uses regulator values to calculate state updates of regulated elements. Here we present a new simulation approach DiSH-trend which also takes into account the trends in regulating elements. We demonstrate the features of trend-based regulation, as well as hybrid regulation, which is a combination of the trend-and level-based approaches. The modeling capabilities are demonstrated on a small toy model, showcasing different functionalities. Real-world capabilities are demonstrated on a larger network model of food insecurity in the Ethiopian region Oromia. Adding trend-based regulation to models results in increased modeling flexibility, and hybrid regulation improves qualitative dynamic behavior prediction. With appropriate data, DiSH-trend becomes a powerful tool for exploring intervention strategies. © 2021 IEEE.

关键词： Directed graphs

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Direct detection of adenovirus in environmental waste waters by portable optical fiber sensor platform

Direct detection of adenovirus in environmental waste waters...

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12th IEEE SENSORS 2013 Conference

作者： Yildirim, Nimet Li, Dan Long, Feng Gu, April Z. Bioengineering PhD Program Northeastern University Boston United States Department of Civil and Environmental Engineering Northeastern University Boston United States State Key Joint Laboratory of Environment Simulation and Pollution Control Environmental Science and Engineering Tsinghua University Beijing China Department of Environment Science and Engineering Tsinghua University Beijing China 360 Huntington Ave. Boston MA 02115 United States

ISBN: (纸本)9781467346405

Reusable and portable evanescent wave biosensor for rapid, sensitive and highly selective direct detection of adenoviruses was developed. Here, specific antibody for the hexon protein of the virus was used as a recognition element. Linear detection range was determined from 100PFU/ml to 2000PFU/ml. This direct detection system can be regenerated successfully with over 5 times without significant deterioration of the sensor performance. The developed biosensor system has high specificity towards adenovirus, and it was applied to environmental waste water samples for the detection of adenovirus with 95 to 117% recovery and 1.1 to 8.1% cv values (n=2). © 2013 IEEE.

关键词： Optical fibers

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Dish-Trend: Intervention Modeling Simulator That Accounts for Trend Influences

Dish-Trend: Intervention Modeling Simulator That Accounts fo...

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Simulation Winter Conference

作者： Stefan Andjelkovic Natasa Miskov-Zivanov Computational and Systems Biology Joint Carnegie Mellon University and University of Pittsburgh Computational Biology PhD Program University of Pittsburgh Pittsburgh PA USA Electrical and Computer Engineering Bioengineering Computational and Systems Biology University of Pittsburgh Pittsburgh PA USA

ISBN: (纸本)9781665433129

Simulation on directed graphs is an important method for understanding the dynamics in the systems where connectivity graphs contain cycles. Discrete Stochastic Heterogeneous Simulator (DiSH) is one of the simulation tools with wide application, which uses regulator values to calculate state updates of regulated elements. Here we present a new simulation approach DiSH-trend which also takes into account the trends in regulating elements. We demonstrate the features of trend-based regulation, as well as hybrid regulation, which is a combination of the trend- and level-based approaches. The modeling capabilities are demonstrated on a small toy model, showcasing different functionalities. Real-world capabilities are demonstrated on a larger network model of food insecurity in the Ethiopian region Oromia. Adding trend-based regulation to models results in increased modeling flexibility, and hybrid regulation improves qualitative dynamic behavior prediction. With appropriate data, DiSH-trend becomes a powerful tool for exploring intervention strategies.

关键词： Regulators Toy manufacturing industry Stochastic processes Predictive models Market research Regulation Data models

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Therapeutic Effect of Ershen Pill (二神丸) Extract on Pi (Spleen)-Shen (Kidney) Yang Deficiency-Induced Diarrhea in Rat Model

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Chinese Journal of Integrative Medicine 2019年第7期25卷 536-542页

作者： PAN Xin XU Kang XIONG Rui CHEN Zhi-min HU Chang-jiang FENG Jian LI Wen-bin College of Pharmacy Chengdu University of Traditional Chinese Medicine Chengdu (610075) China College of Pharmacy South Central University for Nationalities Wuhan (430074) China National Innovation and Attracting Talents "111" Base Bioengineering College Chongqing University Chongqing (400030) China University of California Berkeley-Chongqing University Joint PhD. Student Program in Bioengineering Stanley Hall Berkeley CA (94720) United States Key Research Institute of Quality and Efficacy Evaluation of Traditional Chinese Medicine Formula State Administration of Traditional Chinese Medicine Chengdu (610075) China

Objective: To investigate whether Ershen Pill(ESP,二神丸) could alleviate the symptom of Pi(Spleen)-Shen(Kidney) yang deficiency(PSYD)-induced diarrhea in rat model and explore its anti-diarrhea mechanism. Methods: Seventy-five Sprague-Dawley rats were divided into 5 groups by a random number table, including control, positive, model, low-dose(LD) and high-dose(HD) ESP groups, 15 rats in each group. All the rats, except those in the control group, were developed PSYD induced-diarrhea based on its pathology and etiology. The rats in positive, LD and HD ESP groups were treated with Shenling Baizhu Pill(参苓白术丸), LD(1.05 g/kg) or HD(3.50 g/kg) ESP petroleum ether extract once a day for 2 weeks, respectively. Body weight change and diarrhea index were measured. The histology scores of the kidney were evaluated via hematoxylin and eosin(HE) staining. Aquaporin-3(AQP3) expression in the colon was analyzed by immunofluorescence, quantitative reverse transcription-polymerase chain reaction(qRT-PCR) and Western blot, respectively. Results: Compared with the model group, oral administration of LD and HD ESP prevented body weight loss and inhibited diarrhea after 2-week treatment(P<0.05). Kidney deterioration was impeded, and the histology score in LD and HD ESP groups were 8.2 and 10.5, respectively, which were both higher than those in the model group(P<0.05). In addition, ESP treatment alleviated rat colitis, and HD ESP significantly improved the AQP3 positive staining intensity in the colon tissue compared with the model group. The result from Western blot revealed that AQP3 protein synthesis in colon tissue of LD and HD ESP groups increased by 2.1-and 5.9-fold compared with the model group(P<0.05). qR T-PCR result showed that AQP3 gene expression in the HD ESP group was also up-regulated by 2.5-fold normalized to the model group(P<0.05). Conclusion: ESP extract effectively alleviates the symptoms of PSYD and relieves PSYD-induced diarrhea by improving AQP3 synthesis in the col

关键词： Ershen Pill Chinese medicine petroleum ether extract anti-diarrhea AQP3 colon

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