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Ritis D, Boulougouris GC. On the hierarchical design of biochemical-based digital computations. Comput Biol Med 2021; 135:104630. [PMID: 34311298 DOI: 10.1016/j.compbiomed.2021.104630] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/17/2021] [Revised: 07/02/2021] [Accepted: 07/02/2021] [Indexed: 11/18/2022]
Abstract
The understanding of the biochemical processes underpinning various biological systems has significantly increased in recent decades and has even prompted reverse engineering of certain of life's more complex processes. The most prominent example is modern computers designed to mimic neuron activity. This work forms part of growing endeavors to return advances in the theory of computation and electronics to biology. In this context, we present a set of requirements sufficient for the design of biochemical analogs of modern electronics in a hierarchical, modular fashion that mimics the design of modern computational devices. This theoretical approach is based on a simple enzymatic analog of the transistor and supported by numerical simulations of biochemical models of enzymatic networks equivalent to complex, and modular, interconnecting electronic circuitry (including clocks, Flip-Flops, adders, decoders, and multiplexers). Furthermore, the proposed approach has been implemented in the form of a Python library capable of creating and testing models of complex bio-analog digital computations based on the execution of an elementary universal logic gate. In tribute to Claude Shannon, our biochemical network materializes his example of a "password" recognition that moves the language of the modern theory of automata beyond combinatorial logic and towards sequential logic.
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Affiliation(s)
- Dimitrios Ritis
- Laboratory of Computational Physical Chemistry, Department of Molecular Biology and Genetics, Democritus University of Thrace, Greece
| | - Georgios C Boulougouris
- Laboratory of Computational Physical Chemistry, Department of Molecular Biology and Genetics, Democritus University of Thrace, Greece.
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Angelidou I, Chrysanthopoulou A, Mitsios A, Arelaki S, Arampatzioglou A, Kambas K, Ritis D, Tsironidou V, Moschos I, Dalla V, Stakos D, Kouklakis G, Mitroulis I, Ritis K, Skendros P. REDD1/Autophagy Pathway Is Associated with Neutrophil-Driven IL-1β Inflammatory Response in Active Ulcerative Colitis. J I 2018; 200:3950-3961. [DOI: 10.4049/jimmunol.1701643] [Citation(s) in RCA: 59] [Impact Index Per Article: 9.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/29/2017] [Accepted: 04/05/2018] [Indexed: 12/30/2022]
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Skendros P, Chrysanthopoulou A, Rousset F, Kambas K, Arampatzioglou A, Mitsios A, Bocly V, Konstantinidis T, Pellet P, Angelidou I, Apostolidou E, Ritis D, Tsironidou V, Galtsidis S, Papagoras C, Stakos D, Kouklakis G, Dalla V, Koffa M, Mitroulis I, Theodorou I, Ritis K. Regulated in development and DNA damage responses 1 (REDD1) links stress with IL-1β-mediated familial Mediterranean fever attack through autophagy-driven neutrophil extracellular traps. J Allergy Clin Immunol 2017; 140:1378-1387.e13. [PMID: 28342915 DOI: 10.1016/j.jaci.2017.02.021] [Citation(s) in RCA: 48] [Impact Index Per Article: 6.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/22/2016] [Revised: 12/15/2016] [Accepted: 02/01/2017] [Indexed: 10/19/2022]
Abstract
BACKGROUND Familial Mediterranean fever (FMF) is an IL-1β-dependent autoinflammatory disease caused by mutations of Mediterranean fever (MEFV) encoding pyrin and characterized by inflammatory attacks induced by physical or psychological stress. OBJECTIVE We investigated the underlying mechanism that links stress-induced inflammatory attacks with neutrophil activation and release of IL-1β-bearing neutrophil extracellular traps (NETs) in patients with FMF. METHODS RNA sequencing was performed in peripheral neutrophils from 3 patients with FMF isolated both during attacks and remission, 8 patients in remission, and 8 healthy subjects. NET formation and proteins were analyzed by using confocal immunofluorescence microscopy, immunoblotting, myeloperoxidase-DNA complex ELISA, and flow cytometry. Samples from patients with Still's disease and bacterial infections were used also. RESULTS The stress-related protein regulated in development and DNA damage responses 1 (REDD1) is significantly overexpressed during FMF attacks. Neutrophils from patients with FMF during remission are resistant to autophagy-mediated NET release, which can be overcome through REDD1 induction. Stress-related mediators (eg, epinephrine) decrease this threshold, leading to autophagy-driven NET release, whereas the synchronous inflammatory environment of FMF attack leads to intracellular production of IL-1β and its release through NETs. REDD1 in autolysosomes colocalizes with pyrin and nucleotide-binding domain, leucine-rich repeat/pyrin domain-containing 3. Mutated pyrin prohibits this colocalization, leading to higher IL-1β levels on NETs. CONCLUSIONS This study provides a link between stress and initiation of inflammatory attacks in patients with FMF. REDD1 emerges as a regulator of neutrophil function upstream to pyrin, is involved in NET release and regulation of IL-1β, and might constitute an important piece in the IL-1β-mediated inflammation puzzle.
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Affiliation(s)
- Panagiotis Skendros
- Laboratory of Molecular Hematology, Democritus University of Thrace, Alexandroupolis, Greece; First Department of Internal Medicine, University Hospital of Alexandroupolis, Alexandroupolis, Greece
| | - Akrivi Chrysanthopoulou
- Laboratory of Molecular Hematology, Democritus University of Thrace, Alexandroupolis, Greece
| | - François Rousset
- Université Pierre et Marie Curie, UF d'Histocompatibilité et Immunogénétique, Département d'Immunologie, Groupe Hospitalier Pitié Salpêtrière-Charles Foix, Paris, France
| | - Konstantinos Kambas
- Laboratory of Molecular Hematology, Democritus University of Thrace, Alexandroupolis, Greece
| | | | - Alexandros Mitsios
- Laboratory of Molecular Hematology, Democritus University of Thrace, Alexandroupolis, Greece
| | - Veronique Bocly
- Université Pierre et Marie Curie, UF d'Histocompatibilité et Immunogénétique, Département d'Immunologie, Groupe Hospitalier Pitié Salpêtrière-Charles Foix, Paris, France
| | | | - Philippe Pellet
- Université Pierre et Marie Curie, UF d'Histocompatibilité et Immunogénétique, Département d'Immunologie, Groupe Hospitalier Pitié Salpêtrière-Charles Foix, Paris, France
| | - Iliana Angelidou
- Laboratory of Molecular Hematology, Democritus University of Thrace, Alexandroupolis, Greece
| | - Eirini Apostolidou
- Laboratory of Molecular Hematology, Democritus University of Thrace, Alexandroupolis, Greece; First Department of Internal Medicine, University Hospital of Alexandroupolis, Alexandroupolis, Greece
| | - Dimitrios Ritis
- Laboratory of Molecular Hematology, Democritus University of Thrace, Alexandroupolis, Greece
| | - Victoria Tsironidou
- Laboratory of Molecular Hematology, Democritus University of Thrace, Alexandroupolis, Greece
| | - Sotiris Galtsidis
- Department of Molecular Biology and Genetics, Democritus University of Thrace, Alexandroupolis, Greece
| | - Charalampos Papagoras
- First Department of Internal Medicine, University Hospital of Alexandroupolis, Alexandroupolis, Greece
| | - Dimitrios Stakos
- Laboratory of Molecular Hematology, Democritus University of Thrace, Alexandroupolis, Greece
| | - Georgios Kouklakis
- First Department of Internal Medicine, University Hospital of Alexandroupolis, Alexandroupolis, Greece
| | - Vasiliki Dalla
- First Department of Internal Medicine, University Hospital of Alexandroupolis, Alexandroupolis, Greece
| | - Maria Koffa
- Department of Molecular Biology and Genetics, Democritus University of Thrace, Alexandroupolis, Greece
| | - Ioannis Mitroulis
- Department of Clinical Pathobiochemistry, Institute for Clinical Chemistry and Laboratory Medicine, Faculty of Medicine Technische Universität Dresden, Dresden, Germany
| | - Ioannis Theodorou
- Université Pierre et Marie Curie, UF d'Histocompatibilité et Immunogénétique, Département d'Immunologie, Groupe Hospitalier Pitié Salpêtrière-Charles Foix, Paris, France
| | - Konstantinos Ritis
- Laboratory of Molecular Hematology, Democritus University of Thrace, Alexandroupolis, Greece; First Department of Internal Medicine, University Hospital of Alexandroupolis, Alexandroupolis, Greece.
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