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  1. Book: Computational systems biology in medicine and biotechnology

    Cortassa, Sonia / Aon, Miguel A.

    methods and protocols

    (Methods in molecular biology ; 2399 ; Springer protocols)

    2022  

    Author's details edited by Sonia Cortassa (Laboratory of Cardiovascular Science, National Institute on Aging, NIH, Baltimore, Maryland, USA), Miguel A. Aon (Translational Gerontology Branch; Laboratory of Cardiovascular Science, National Institute on Aging, NIH, Baltimore, Maryland, USA)
    Series title Methods in molecular biology ; 2399
    Springer protocols
    Collection
    Language English
    Size xiv, 493 Seiten, Illustrationen, Diagramme
    Publisher Humana Press
    Publishing place New York, NY
    Publishing country United States
    Document type Book
    HBZ-ID HT021388963
    ISBN 978-1-0716-1830-1 ; 9781071618318 ; 1-0716-1830-X ; 1071618318
    Database Catalogue ZB MED Medicine, Health

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  2. Article ; Online: Computational Systems Biology and Artificial Intelligence.

    Aon, Miguel A

    Methods in molecular biology (Clifton, N.J.)

    2022  Volume 2399, Page(s) 1–6

    Abstract: Aware of the rapid evolution of computational systems biology (CSB), which is the focus of this book, we address the emergence of artificial intelligence (AI). Consequently, one of the main purposes of this Introduction is to assess where the ... ...

    Abstract Aware of the rapid evolution of computational systems biology (CSB), which is the focus of this book, we address the emergence of artificial intelligence (AI). Consequently, one of the main purposes of this Introduction is to assess where the relationship between CSB and AI stands today, and to venture a vision for CSB.
    MeSH term(s) Algorithms ; Artificial Intelligence ; Systems Biology
    Language English
    Publishing date 2022-05-23
    Publishing country United States
    Document type Journal Article ; Research Support, N.I.H., Intramural
    ISSN 1940-6029
    ISSN (online) 1940-6029
    DOI 10.1007/978-1-0716-1831-8_1
    Database MEDical Literature Analysis and Retrieval System OnLINE

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  3. Book: Systems biology of metabolic and signaling networks

    Aon, Miguel A.

    energy, mass and information transfer

    (Springer series in biophysics ; 16)

    2014  

    Author's details Miguel A. Aon ... ed
    Series title Springer series in biophysics ; 16
    Collection
    Keywords Systembiologie ; Signaltransduktion ; Stoffwechsel
    Subject Metabolismus ; Verstoffwechselung ; Metabolische Regulation ; Signalübertragung ; Signalvermittlung
    Language English
    Size X, 375 S. : Ill., graph. Darst., 235 mm x 155 mm
    Publisher Springer
    Publishing place Berlin u.a.
    Publishing country Germany
    Document type Book
    HBZ-ID HT017708578
    ISBN 978-3-642-38504-9 ; 3-642-38504-4 ; 978-3-642-38505-6 ; 3-642-38505-2
    Database Catalogue ZB MED Nutrition, Environment, Agriculture

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  4. Book ; Online: Mitochondria: Hubs of Cellular Signaling, Energetics and Redox Balance

    Camara, Amadou K. S. / Aon, Miguel A.

    2017  

    Abstract: Poised at the convergence of most catabolic and anabolic pathways, mitochondria are the center of heterotrophic aerobic life, representing a hub in the overall metabolic network of cells. The energetic functions performed by mitochondria face the ... ...

    Abstract Poised at the convergence of most catabolic and anabolic pathways, mitochondria are the center of heterotrophic aerobic life, representing a hub in the overall metabolic network of cells. The energetic functions performed by mitochondria face the unavoidable redox hurdle of handling huge amounts of oxygen while keeping its own as well as the cellular redox environment under control. Reactive oxygen species (ROS) are produced in the respiratory chain as a result of the energy supplying function of mitochondria. Originally considered an unavoidable by-product of oxidative phosphorylation, ROS have become crucial signaling molecules when their levels are kept within physiological range. This occurs when their production and scavenging are balanced within mitochondria and cells.-

    Mitochondria-generated hydrogen peroxide can act as a signaling molecule within mitochondria or in the cytoplasm, affecting multiple networks that control, for example, cell cycle, stress response, cell migration and adhesion, energy metabolism, redox balance, cell contraction, and ion channels. However, under pathophysiological conditions, excessive ROS levels can happen due to either overproduction, overwhelming of antioxidant defenses, or both. Under oxidative stress, detrimental effects of ROS include oxidation of protein, lipids, and nucleic acids; mitochondrial depolarization and calcium overload; and cell-wide oscillations mediated by ROS-induced ROS release mechanisms. Mitochondrial dysfunction is central in the pathogenesis of numerous human maladies including cardiomyopathies and neurodegeneration. Diseases characterized by altered nutrient metabolism, such as diabetes and cancer, exhibit elevated ROS levels.-

    These may contribute to pathogenesis by increasing DNA mutation, affecting regulatory signaling and transcription, and promoting inflammation. Under metabolic stress, several ionic channels present in the inner and outer mitochondrial membranes can have pro-life and -death effects. In the present E-book, based on the Frontiers Research Topic entitled: Mitochondria: Hubs of cellular signaling, energetics and redox balance, we address one of the fundamental questions that the field of ROS biology faces today: how do mitochondria accomplish a reliable energy provision and at the same time keep ROS levels within physiological, non-harming, limits but crucial for cellular signaling function? Additionally, and within the perspective of mitochondria as signaling-energetic hubs in the extensive cellular metabolic network, we ask how can their collective dynamics scale from the subcellular to the cellular, tissue and organ levels to affect function in health and disease
    Keywords Physiology ; Science (General)
    Size 1 electronic resource (228 p.)
    Publisher Frontiers Media SA
    Document type Book ; Online
    Note English ; Open Access
    HBZ-ID HT020095943
    ISBN 9782889452392 ; 2889452395
    Database ZB MED Catalogue: Medicine, Health, Nutrition, Environment, Agriculture

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  5. Article ; Online: From the seminal discovery of proteoglycogen and glycogenin to emerging knowledge and research on glycogen biology.

    Curtino, Juan A / Aon, Miguel A

    The Biochemical journal

    2019  Volume 476, Issue 21, Page(s) 3109–3124

    Abstract: Although the discovery of glycogen in the liver, attributed to Claude Bernard, happened more than 160 years ago, the mechanism involved in the initiation of glucose polymerization remained unknown. The discovery of glycogenin at the core of glycogen's ... ...

    Abstract Although the discovery of glycogen in the liver, attributed to Claude Bernard, happened more than 160 years ago, the mechanism involved in the initiation of glucose polymerization remained unknown. The discovery of glycogenin at the core of glycogen's structure and the initiation of its glucopolymerization is among one of the most exciting and relatively recent findings in Biochemistry. This review focuses on the initial steps leading to the seminal discoveries of proteoglycogen and glycogenin at the beginning of the 1980s, which paved the way for subsequent foundational breakthroughs that propelled forward this new research field. We also explore the current, as well as potential, impact this research field is having on human health and disease from the perspective of glycogen storage diseases. Important new questions arising from recent studies, their links to basic mechanisms involved in the de novo glycogen biogenesis, and the pervading presence of glycogenin across the evolutionary scale, fueled by high throughput -omics technologies, are also addressed.
    MeSH term(s) Animals ; Glucose/metabolism ; Glucosyltransferases/chemistry ; Glucosyltransferases/genetics ; Glucosyltransferases/metabolism ; Glycogen/chemistry ; Glycogen/metabolism ; Glycogen Storage Disease/enzymology ; Glycogen Storage Disease/genetics ; Glycogen Storage Disease/metabolism ; Glycoproteins/chemistry ; Glycoproteins/genetics ; Glycoproteins/metabolism ; Glycosylation ; Humans ; Liver/enzymology ; Liver/metabolism ; Polymerization
    Chemical Substances Glycoproteins ; glycogenin ; Glycogen (9005-79-2) ; Glucosyltransferases (EC 2.4.1.-) ; Glucose (IY9XDZ35W2)
    Language English
    Publishing date 2019-10-31
    Publishing country England
    Document type Journal Article ; Research Support, N.I.H., Intramural ; Research Support, Non-U.S. Gov't ; Review
    ZDB-ID 2969-5
    ISSN 1470-8728 ; 0006-2936 ; 0306-3275 ; 0264-6021
    ISSN (online) 1470-8728
    ISSN 0006-2936 ; 0306-3275 ; 0264-6021
    DOI 10.1042/BCJ20190441
    Database MEDical Literature Analysis and Retrieval System OnLINE

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  6. Article: From chronology to the biology of aging, and its tuning by mitochondrial health: overview of the Bioenergetics, Mitochondria, and Metabolism subgroup symposium at the 2021 Virtual 65th Annual Meeting of the Biophysical Society.

    Cortassa, Sonia / Aon, Miguel A

    Biophysical reviews

    2021  Volume 13, Issue 3, Page(s) 311–314

    Abstract: A distinguished group of researchers congregated at one of the symposia during the 2021 Virtual Meeting organized by the Biophysical Society, to speak about the critically important role played by mitochondrial functionality in healthy aging. The latest ... ...

    Abstract A distinguished group of researchers congregated at one of the symposia during the 2021 Virtual Meeting organized by the Biophysical Society, to speak about the critically important role played by mitochondrial functionality in healthy aging. The latest research trends expressed by the speakers during the meeting resulted in an updated display of novel emerging molecular targets involved in keeping mitochondrial health during metabolic disorder and until late in life. Besides offering insightful views on the impact of mitochondrial healthy function on the biology of aging in different organs such as the liver and cardiac and skeletal muscle, their distinct experimental approaches showed a significant convergence in results, a reassuring hallmark of scientific excellence. The interdisciplinary crossroad of biology, biophysics, and biochemistry, evidenced during the symposium organized by the Bioenergetics, Mitochondria, and Metabolism subgroup, is another example of fruitful collaboration at one of the scientific frontiers represented by human aging.
    Language English
    Publishing date 2021-05-24
    Publishing country Germany
    Document type Journal Article
    ZDB-ID 2486483-3
    ISSN 1867-2469 ; 1867-2450
    ISSN (online) 1867-2469
    ISSN 1867-2450
    DOI 10.1007/s12551-021-00808-7
    Database MEDical Literature Analysis and Retrieval System OnLINE

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  7. Article ; Online: Unraveling Pathways of Health and Lifespan with Integrated Multiomics Approaches.

    Aon, Miguel A / Bernier, Michel / de Cabo, Rafael

    Methods in molecular biology (Clifton, N.J.)

    2022  Volume 2399, Page(s) 193–218

    Abstract: Distinct and shared pathways of health and lifespan can be untangled following a concerted approach led by experimental design and a rigorous analytical strategy where the confounding effects of diet and feeding regimens can be dissected. In this chapter, ...

    Abstract Distinct and shared pathways of health and lifespan can be untangled following a concerted approach led by experimental design and a rigorous analytical strategy where the confounding effects of diet and feeding regimens can be dissected. In this chapter, we use integrated analysis of multiomics (transcriptomics-metabolomics) data in liver from mice to gain insight into pathways associated with improved health and survival. We identify a unique metabolic hub involving glycine-serine-threonine metabolism at the core of lifespan, and a pattern of shared pathways related to improved health.
    MeSH term(s) Animals ; Diet ; Longevity ; Metabolomics ; Mice ; Serine ; Threonine
    Chemical Substances Threonine (2ZD004190S) ; Serine (452VLY9402)
    Language English
    Publishing date 2022-05-23
    Publishing country United States
    Document type Journal Article ; Research Support, N.I.H., Intramural
    ISSN 1940-6029
    ISSN (online) 1940-6029
    DOI 10.1007/978-1-0716-1831-8_9
    Database MEDical Literature Analysis and Retrieval System OnLINE

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  8. Article ; Online: Fractal dynamics of individual mitochondrial oscillators measure local inter-mitochondrial coupling.

    Kurz, Felix T / Aon, Miguel A / Schlemmer, Heinz-Peter / Jende, Johann M E / O'Rourke, Brian / Armoundas, Antonis A

    Biophysical journal

    2023  Volume 122, Issue 8, Page(s) 1459–1469

    Abstract: Mitochondrial inner membrane potentials in cardiomyocytes may oscillate in cycles of depolarization/repolarization when the mitochondrial network is exposed to metabolic or oxidative stress. The frequencies of such oscillations are dynamically changing ... ...

    Abstract Mitochondrial inner membrane potentials in cardiomyocytes may oscillate in cycles of depolarization/repolarization when the mitochondrial network is exposed to metabolic or oxidative stress. The frequencies of such oscillations are dynamically changing while clusters of weakly coupled mitochondrial oscillators adjust to a common phase and frequency. Across the cardiac myocyte, the averaged signal of the mitochondrial population follows self-similar or fractal dynamics; however, fractal properties of individual mitochondrial oscillators have not yet been examined. We show that the largest synchronously oscillating cluster exhibits a fractal dimension, D, that is indicative of self-similar behavior with D=1.27±0.11, in contrast to the remaining network mitochondria whose fractal dimension is close to that of Brownian noise, D=1.58±0.10. We further demonstrate that fractal behavior is correlated with local coupling mechanisms, whereas it is only weakly linked to measures of functional connections between mitochondria. Our findings suggest that individual mitochondrial fractal dimensions may serve as a simple measure of local mitochondrial coupling.
    MeSH term(s) Fractals ; Mitochondria ; Oxidative Stress ; Membrane Potential, Mitochondrial ; Mitochondrial Membranes
    Language English
    Publishing date 2023-03-10
    Publishing country United States
    Document type Journal Article ; Research Support, Non-U.S. Gov't ; Research Support, N.I.H., Extramural
    ZDB-ID 218078-9
    ISSN 1542-0086 ; 0006-3495
    ISSN (online) 1542-0086
    ISSN 0006-3495
    DOI 10.1016/j.bpj.2023.03.011
    Database MEDical Literature Analysis and Retrieval System OnLINE

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  9. Article ; Online: Short-term periodic restricted feeding elicits metabolome-microbiome signatures with sex dimorphic persistence in primate intervention.

    Yanai, Hagai / Park, Bongsoo / Koh, Hyunwook / Jang, Hyo Jung / Vaughan, Kelli L / Tanaka-Yano, Mayuri / Aon, Miguel / Blanton, Madison / Messaoudi, Ilhem / Diaz-Ruiz, Alberto / Mattison, Julie A / Beerman, Isabel

    Nature communications

    2024  Volume 15, Issue 1, Page(s) 1088

    Abstract: Dietary restriction has shown benefits in physiological, metabolic, and molecular signatures associated with aging but is a difficult lifestyle to maintain for most individuals. In mice, a less restrictive diet that allows for cyclical periods of reduced ...

    Abstract Dietary restriction has shown benefits in physiological, metabolic, and molecular signatures associated with aging but is a difficult lifestyle to maintain for most individuals. In mice, a less restrictive diet that allows for cyclical periods of reduced calories mitigates aging phenotypes, yet the effects of such an intervention in a genetically heterogenous, higher-order mammal has not been examined. Here, using middle-aged rhesus macaques matched for age and sex, we show that a regimen of 4 days of low-calorie intake followed by 10 days of ad libitum feeding (4:10 diet) performed in repeating cycles over 12 weeks led to significant loss of weight and fat percentage, despite the free access to food for most of the study duration. We show the 4-day restriction period is sufficient to drive alterations to the serum metabolome characterized by substantial differences in lipid classes. These phenotypes were paralleled by changes in the gut microbiome of restricted monkeys that highlight the involvement of a microbiome-metabolome axis. This regimen shows promising phenotypes, with some sex-dimorphic responses, including residual memory of the diet. As many calorie restriction interventions are difficult to sustain, we propose that this short-term diet may be easier to adhere to and have benefits directly relevant to human aging.
    MeSH term(s) Humans ; Mice ; Animals ; Middle Aged ; Macaca mulatta ; Energy Intake/physiology ; Caloric Restriction ; Gastrointestinal Microbiome ; Metabolome ; Mammals
    Language English
    Publishing date 2024-02-05
    Publishing country England
    Document type Journal Article
    ZDB-ID 2553671-0
    ISSN 2041-1723 ; 2041-1723
    ISSN (online) 2041-1723
    ISSN 2041-1723
    DOI 10.1038/s41467-024-45359-z
    Database MEDical Literature Analysis and Retrieval System OnLINE

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  10. Article ; Online: Integrated Multiomics, Bioinformatics, and Computational Modeling Approaches to Central Metabolism in Organs.

    Cortassa, Sonia / Villon, Pierre / Sollott, Steven J / Aon, Miguel A

    Methods in molecular biology (Clifton, N.J.)

    2022  Volume 2399, Page(s) 151–170

    Abstract: Data-driven research led by computational systems biology methods, encompassing bioinformatics of multiomics datasets and mathematical modeling, are critical for discovery. Herein, we describe a multiomics (metabolomics-fluxomics) approach as applied to ... ...

    Abstract Data-driven research led by computational systems biology methods, encompassing bioinformatics of multiomics datasets and mathematical modeling, are critical for discovery. Herein, we describe a multiomics (metabolomics-fluxomics) approach as applied to heart function in diabetes. The methodology presented has general applicability and enables the quantification of the fluxome or set of metabolic fluxes from cytoplasmic and mitochondrial compartments in central catabolic pathways of glucose and fatty acids. Additionally, we present, for the first time, a general method to reduce the dimension of detailed kinetic, and in general stoichiometric models of metabolic networks at the steady state, to facilitate their optimization and avoid numerical problems. Representative results illustrate the powerful mechanistic insights that can be gained from this integrative and quantitative methodology.
    MeSH term(s) Computational Biology ; Computer Simulation ; Metabolic Networks and Pathways ; Metabolome ; Metabolomics/methods ; Models, Biological
    Language English
    Publishing date 2022-05-18
    Publishing country United States
    Document type Journal Article ; Research Support, N.I.H., Intramural
    ISSN 1940-6029
    ISSN (online) 1940-6029
    DOI 10.1007/978-1-0716-1831-8_7
    Database MEDical Literature Analysis and Retrieval System OnLINE

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