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Verstovsek S, Krečak I, Heidel FH, De Stefano V, Bryan K, Zuurman MW, Zaiac M, Morelli M, Smyth A, Redondo S, Bigan E, Ruhl M, Meier C, Beffy M, Kiladjian JJ. Identifying Patients with Polycythemia Vera at Risk of Thrombosis after Hydroxyurea Initiation: The Polycythemia Vera-Advanced Integrated Models (PV-AIM) Project. Biomedicines 2023; 11:1925. [PMID: 37509564 PMCID: PMC10377437 DOI: 10.3390/biomedicines11071925] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/09/2023] [Revised: 06/13/2023] [Accepted: 06/22/2023] [Indexed: 07/30/2023] Open
Abstract
Patients with polycythemia vera (PV) are at significant risk of thromboembolic events (TE). The PV-AIM study used the Optum® de-identified Electronic Health Record dataset and machine learning to identify markers of TE in a real-world population. Data for 82,960 patients with PV were extracted: 3852 patients were treated with hydroxyurea (HU) only, while 130 patients were treated with HU and then changed to ruxolitinib (HU-ruxolitinib). For HU-alone patients, the annualized incidence rates (IR; per 100 patients) decreased from 8.7 (before HU) to 5.6 (during HU) but increased markedly to 10.5 (continuing HU). Whereas for HU-ruxolitinib patients, the IR decreased from 10.8 (before HU) to 8.4 (during HU) and was maintained at 8.3 (after switching to ruxolitinib). To better understand markers associated with TE risk, we built a machine-learning model for HU-alone patients and validated it using an independent dataset. The model identified lymphocyte percentage (LYP), neutrophil percentage (NEP), and red cell distribution width (RDW) as key markers of TE risk, and optimal thresholds for these markers were established, from which a decision tree was derived. Using these widely used laboratory markers, the decision tree could be used to identify patients at high risk for TE, facilitate treatment decisions, and optimize patient management.
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Affiliation(s)
- Srdan Verstovsek
- Department of Leukemia, The University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA
| | - Ivan Krečak
- Department of Internal Medicine, General Hospital of Sibenik-Knin County, 22000 Sibenik, Croatia
- Faculty of Medicine, University of Rijeka, 51000 Rijeka, Croatia
| | - Florian H. Heidel
- Hematology, Oncology, Stem Cell Transplantation and Palliative Care, Internal Medicine C, University Medicine Greifswald, 17475 Greifswald, Germany
| | - Valerio De Stefano
- Sezione di Ematologia, Dipartimento di Scienze Radiologiche ed Ematologiche, Università Cattolica, Fondazione Policlinico A. Gemelli IRCCS, 00168 Roma, Italy
| | - Kenneth Bryan
- Novartis Ireland Limited, Dublin 4, D04 A9N6 Dublin, Ireland
| | | | | | | | - Aoife Smyth
- Novartis Pharma AG, CH-4056 Basel, Switzerland
- Novartis Pharmaceuticals UK Limited, London W12 7FQ, UK
| | | | - Erwan Bigan
- The Boston Consulting Group, Boston, MA 02210, USA
| | - Michael Ruhl
- The Boston Consulting Group, Boston, MA 02210, USA
| | | | - Magali Beffy
- The Boston Consulting Group, Boston, MA 02210, USA
| | - Jean-Jacques Kiladjian
- Centre d’Investigations Cliniques (INSERM CIC 1427), Université de Paris, Hôpital Saint-Louis, AP-HP, 75010 Paris, France
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Bigan E, Sasidharan Nair S, Lejeune FX, Fragnaud H, Parmentier F, Mégret L, Verny M, Aaronson J, Rosinski J, Neri C. Genetic cooperativity in multi-layer networks implicates cell survival and senescence in the striatum of Huntington's disease mice synchronous to symptoms. Bioinformatics 2020; 36:186-196. [PMID: 31228193 PMCID: PMC6956776 DOI: 10.1093/bioinformatics/btz514] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/05/2018] [Revised: 06/11/2019] [Accepted: 06/18/2019] [Indexed: 02/06/2023] Open
Abstract
Motivation Huntington’s disease (HD) may evolve through gene deregulation. However, the impact of gene deregulation on the dynamics of genetic cooperativity in HD remains poorly understood. Here, we built a multi-layer network model of temporal dynamics of genetic cooperativity in the brain of HD knock-in mice (allelic series of Hdh mice). To enhance biological precision and gene prioritization, we integrated three complementary families of source networks, all inferred from the same RNA-seq time series data in Hdh mice, into weighted-edge networks where an edge recapitulates path-length variation across source-networks and age-points. Results Weighted edge networks identify two consecutive waves of tight genetic cooperativity enriched in deregulated genes (critical phases), pre-symptomatically in the cortex, implicating neurotransmission, and symptomatically in the striatum, implicating cell survival (e.g. Hipk4) intertwined with cell proliferation (e.g. Scn4b) and cellular senescence (e.g. Cdkn2a products) responses. Top striatal weighted edges are enriched in modulators of defective behavior in invertebrate models of HD pathogenesis, validating their relevance to neuronal dysfunction in vivo. Collectively, these findings reveal highly dynamic temporal features of genetic cooperativity in the brain of Hdh mice where a 2-step logic highlights the importance of cellular maintenance and senescence in the striatum of symptomatic mice, providing highly prioritized targets. Availability and implementation Weighted edge network analysis (WENA) data and source codes for performing spectral decomposition of the signal (SDS) and WENA analysis, both written using Python, are available at http://www.broca.inserm.fr/HD-WENA/. Supplementary information Supplementary data are available at Bioinformatics online.
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Affiliation(s)
- Erwan Bigan
- Sorbonnes Université, Centre National de la Recherche Scientifique, Research Unit Biology of Adaptation and Aging (B2A), Team Compensation in Neurodegenerative Diseases and Aging (Brain-C), Paris F-75252, France
| | - Satish Sasidharan Nair
- Sorbonnes Université, Centre National de la Recherche Scientifique, Research Unit Biology of Adaptation and Aging (B2A), Team Compensation in Neurodegenerative Diseases and Aging (Brain-C), Paris F-75252, France
| | - François-Xavier Lejeune
- Sorbonnes Université, Centre National de la Recherche Scientifique, Research Unit Biology of Adaptation and Aging (B2A), Team Compensation in Neurodegenerative Diseases and Aging (Brain-C), Paris F-75252, France
| | - Hélissande Fragnaud
- Sorbonnes Université, Centre National de la Recherche Scientifique, Research Unit Biology of Adaptation and Aging (B2A), Team Compensation in Neurodegenerative Diseases and Aging (Brain-C), Paris F-75252, France
| | - Frédéric Parmentier
- Sorbonnes Université, Centre National de la Recherche Scientifique, Research Unit Biology of Adaptation and Aging (B2A), Team Compensation in Neurodegenerative Diseases and Aging (Brain-C), Paris F-75252, France
| | - Lucile Mégret
- Sorbonnes Université, Centre National de la Recherche Scientifique, Research Unit Biology of Adaptation and Aging (B2A), Team Compensation in Neurodegenerative Diseases and Aging (Brain-C), Paris F-75252, France
| | - Marc Verny
- Sorbonnes Université, Centre National de la Recherche Scientifique, Research Unit Biology of Adaptation and Aging (B2A), Team Compensation in Neurodegenerative Diseases and Aging (Brain-C), Paris F-75252, France
| | | | | | - Christian Neri
- Sorbonnes Université, Centre National de la Recherche Scientifique, Research Unit Biology of Adaptation and Aging (B2A), Team Compensation in Neurodegenerative Diseases and Aging (Brain-C), Paris F-75252, France
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Levy Nogueira M, Hamraz M, Abolhassani M, Bigan E, Lafitte O, Steyaert J, Dubois B, Schwartz L. Mechanical stress increases brain amyloid β, tau, and α‐synuclein concentrations in wild‐type mice. Alzheimers Dement 2017; 14:444-453. [DOI: 10.1016/j.jalz.2017.11.003] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/04/2016] [Revised: 06/19/2017] [Accepted: 11/13/2017] [Indexed: 12/14/2022]
Affiliation(s)
- Marcel Levy Nogueira
- Institut de la Mémoire et de la Maladie d'Alzheimer (IM2A), Département de Neurologie Hôpital de la Pitié‐Salpêtrière, AP‐HP Paris France
- Institut de Recherche Translationnelle en Neurosciences (IHU‐A‐ICM) Institut du Cerveau et de la Moelle Epinière (ICM) Paris France
| | | | | | - Erwan Bigan
- Laboratoire d'informatique (LIX), UMR 7161, École Polytechnique Université Paris‐Saclay Palaiseau France
| | - Olivier Lafitte
- LAGA, UMR 7539 Université Paris 13, Sorbonne Paris Cité Villetaneuse France
| | - Jean‐Marc Steyaert
- Laboratoire d'informatique (LIX), UMR 7161, École Polytechnique Université Paris‐Saclay Palaiseau France
| | - Bruno Dubois
- Institut de la Mémoire et de la Maladie d'Alzheimer (IM2A), Département de Neurologie Hôpital de la Pitié‐Salpêtrière, AP‐HP Paris France
- Institut de Recherche Translationnelle en Neurosciences (IHU‐A‐ICM) Institut du Cerveau et de la Moelle Epinière (ICM) Paris France
- INSERM, CNRS, UMR‐S975 Institut du Cerveau et de la Moelle Epinière (ICM) Paris France
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Bigan E, Plateau P. On the Relation between Chemical Oscillations and Self-Replication. Artif Life 2017; 23:453-480. [PMID: 28985117 DOI: 10.1162/artl_a_00241] [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] [Subscribe] [Scholar Register] [Indexed: 06/07/2023]
Abstract
One proposed scenario for the emergence of biochemical oscillations is that they may have provided the basic mechanism behind cellular self-replication by growth and division. However, alternative scenarios not requiring any chemical oscillation have also been proposed. Each of the various protocell models proposed to support one or another scenario comes with its own set of specific assumptions, which makes it difficult to ascertain whether chemical oscillations are required or not for cellular self-replication. This article compares these two cases within a single whole-cell model framework. This model relies upon a membrane embedding a chemical reaction network (CRN) synthesizing all the cellular constituents, including the membrane, by feeding from an external nutrient. Assuming the osmolarity is kept constant, the system dynamics are governed by a set of nonlinear differential equations coupling the chemical concentrations and the surface-area-to-volume ratio. The resulting asymptotic trajectories are used to determine the cellular shape by minimizing the membrane bending energy (within an approximate predefined family of shapes). While the stationary case can be handled quite generally, the oscillatory one is investigated using a simple oscillating CRN example, which is used to identify features that are expected to hold for any network. It is found that cellular self-replication can be reached with or without chemical oscillations, and that a requirement common to both stationary and oscillatory cases is that a minimum spontaneous curvature of the membrane is required for the cell to divide once its area and volume are both doubled. The oscillatory case can result in a greater variety of cellular shape trajectories but raises additional constraints for cellular division and self-replication: (i) the ratio of doubling time to oscillation period should be an integer, and (ii) if the oscillation amplitude is sufficiently high, then the spontaneous curvature must be below a maximum value to avoid early division before the end of the cycle. Because of these additional stringent constraints, it is likely that early protocells did not rely upon chemical oscillations. Biochemical oscillations typical of modern evolved cells may have emerged later through evolution for other reasons (e.g., metabolic advantage) and must have required additional feedback mechanisms for such a self-replicating system to be robust against even slight environmental variations (e.g., temperature fluctuations).
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Lejeune FX, Fragnaud H, Parmentier F, Bigan E, Nair SS, Neri C. B47 Cross-integration of huntington’s disease networks. J Neurol Psychiatry 2016. [DOI: 10.1136/jnnp-2016-314597.78] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/04/2022]
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Bigan E, Paulevé L, Steyaert JM, Douady S. Necessary and sufficient conditions for protocell growth. J Math Biol 2016; 73:1627-1664. [PMID: 27091567 DOI: 10.1007/s00285-016-0998-0] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [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: 12/11/2014] [Revised: 03/10/2016] [Indexed: 11/29/2022]
Abstract
We consider a generic protocell model consisting of any conservative chemical reaction network embedded within a membrane. The membrane results from the self-assembly of a membrane precursor and is semi-permeable to some nutrients. Nutrients are metabolized into all other species including the membrane precursor, and the membrane grows in area and the protocell in volume. Faithful replication through cell growth and division requires a doubling of both cell volume and surface area every division time (thus leading to a periodic surface area-to-volume ratio) and also requires periodic concentrations of the cell constituents. Building upon these basic considerations, we prove necessary and sufficient conditions pertaining to the chemical reaction network for such a regime to be met. A simple necessary condition is that every moiety must be fed. A stronger necessary condition implies that every siphon must be either fed, or connected to species outside the siphon through a pass reaction capable of transferring net positive mass into the siphon. And in the case of nutrient uptake through passive diffusion and of constant surface area-to-volume ratio, a sufficient condition for the existence of a fixed point is that every siphon be fed. These necessary and sufficient conditions hold for any chemical reaction kinetics, membrane parameters or nutrient flux diffusion constants.
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Affiliation(s)
- Erwan Bigan
- Laboratoire d'Informatique, École Polytechnique, Palaiseau, France. .,Laboratoire Matière et Systèmes Complexes, Université Paris Diderot, Paris, France.
| | - Loïc Paulevé
- Laboratoire de Recherche en Informatique, CNRS and Université Paris Sud, Orsay, France
| | | | - Stéphane Douady
- Laboratoire Matière et Systèmes Complexes, Université Paris Diderot, Paris, France
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Simonson T, Ye-Lehmann S, Palmai Z, Amara N, Wydau-Dematteis S, Bigan E, Druart K, Moch C, Plateau P. Redesigning the stereospecificity of tyrosyl-tRNA synthetase. Proteins 2016; 84:240-53. [PMID: 26676967 DOI: 10.1002/prot.24972] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.9] [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: 07/28/2015] [Revised: 09/30/2015] [Accepted: 11/26/2015] [Indexed: 12/14/2022]
Abstract
D-Amino acids are largely excluded from protein synthesis, yet they are of great interest in biotechnology. Unnatural amino acids have been introduced into proteins using engineered aminoacyl-tRNA synthetases (aaRSs), and this strategy might be applicable to D-amino acids. Several aaRSs can aminoacylate their tRNA with a D-amino acid; of these, tyrosyl-tRNA synthetase (TyrRS) has the weakest stereospecificity. We use computational protein design to suggest active site mutations in Escherichia coli TyrRS that could increase its D-Tyr binding further, relative to L-Tyr. The mutations selected all modify one or more sidechain charges in the Tyr binding pocket. We test their effect by probing the aminoacyl-adenylation reaction through pyrophosphate exchange experiments. We also perform extensive alchemical free energy simulations to obtain L-Tyr/D-Tyr binding free energy differences. Agreement with experiment is good, validating the structural models and detailed thermodynamic predictions the simulations provide. The TyrRS stereospecificity proves hard to engineer through charge-altering mutations in the first and second coordination shells of the Tyr ammonium group. Of six mutants tested, two are active towards D-Tyr; one of these has an inverted stereospecificity, with a large preference for D-Tyr. However, its activity is low. Evidently, the TyrRS stereospecificity is robust towards charge rearrangements near the ligand. Future design may have to consider more distant and/or electrically neutral target mutations, and possibly design for binding of the transition state, whose structure however can only be modeled.
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Affiliation(s)
- Thomas Simonson
- Department of Biology, Laboratoire De Biochimie (CNRS UMR7654), Ecole Polytechnique, Palaiseau, 91128, France
| | | | - Zoltan Palmai
- Department of Biology, Laboratoire De Biochimie (CNRS UMR7654), Ecole Polytechnique, Palaiseau, 91128, France
| | - Najette Amara
- Department of Biology, Laboratoire De Biochimie (CNRS UMR7654), Ecole Polytechnique, Palaiseau, 91128, France
| | - Sandra Wydau-Dematteis
- Department of Biology, Laboratoire De Biochimie (CNRS UMR7654), Ecole Polytechnique, Palaiseau, 91128, France
| | - Erwan Bigan
- Department of Biology, Laboratoire De Biochimie (CNRS UMR7654), Ecole Polytechnique, Palaiseau, 91128, France
| | - Karen Druart
- Department of Biology, Laboratoire De Biochimie (CNRS UMR7654), Ecole Polytechnique, Palaiseau, 91128, France
| | - Clara Moch
- Department of Biology, Laboratoire De Biochimie (CNRS UMR7654), Ecole Polytechnique, Palaiseau, 91128, France
| | - Pierre Plateau
- Department of Biology, Laboratoire De Biochimie (CNRS UMR7654), Ecole Polytechnique, Palaiseau, 91128, France
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Abstract
Osmotic pressure influences cellular shape. In a growing cell, chemical reactions and dilution induce changes in osmolarity, which in turn influence the cellular shape. Using a protocell model relying upon random conservative chemical reaction networks with arbitrary stoichiometry, we find that when the membrane is so flexible that its shape adjusts itself quasi-instantaneously to balance the osmotic pressure, the protocell either grows filamentous or fails to grow. This behavior is consistent with a mathematical proof. This suggests that filamentation may be a primitive growth mode resulting from the simple physical property of balanced osmotic pressure. We also find that growth is favored if some chemical species are only present inside the protocell, but not in the outside growth medium. Such an insulation requires specific chemical schemes. Modern evolved cells such as E. coli meet these requirements through active transport mechanisms such as the phosphotransferase system.
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Affiliation(s)
- Erwan Bigan
- Laboratoire d'Informatique (LIX), École Polytechnique, F-91128 Palaiseau Cedex, France. Laboratoire Matière et Systèmes Complexes, UMR7057 CNRS, Université Paris Diderot, F-75205 Paris Cedex 13, France
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Bigan E, Steyaert JM, Douady S. Chemical Schemes for Maintaining Different Compositions Across a Semi-permeable Membrane with Application to Proto-cells. ORIGINS LIFE EVOL B 2015; 45:439-54. [PMID: 26205651 DOI: 10.1007/s11084-015-9453-2] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/26/2014] [Accepted: 01/30/2015] [Indexed: 11/25/2022]
Abstract
Osmotic pressure arising from a higher total chemical concentration inside proto-cells is thought to have played a role in the emergence and selection of self-replicating proto-cells. We present two chemical schemes through which different equilibrium compositions can coexist on each side of a semi-permeable membrane. The first scheme relies upon the concept of moieties and associated number of degrees of freedom. The second scheme relies upon the concept of siphons and of pass reaction capable of transferring matter from outside a siphon into it. Using simple example reaction networks, we show that both schemes are compatible with stationary proto-cell growth with up-concentration, but suffer from shortcomings. To alleviate these we propose a third scheme derived from the second one by having the pass reaction catalyzed by the membrane surface instead of occurring in bulk solution. This may have proven an intermediate step before having the pass reaction occurring only when the nutrient crosses the membrane. This suggests an evolutionary path for the emergence of active transport.
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Affiliation(s)
- Erwan Bigan
- Laboratoire d'Informatique, École Polytechnique, Palaiseau, France,
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da Veiga Moreira J, Peres S, Steyaert JM, Bigan E, Paulevé L, Nogueira ML, Schwartz L. Cell cycle progression is regulated by intertwined redox oscillators. Theor Biol Med Model 2015; 12:10. [PMID: 26022743 PMCID: PMC4459109 DOI: 10.1186/s12976-015-0005-2] [Citation(s) in RCA: 46] [Impact Index Per Article: 5.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/18/2015] [Accepted: 05/15/2015] [Indexed: 01/04/2023] Open
Abstract
The different phases of the eukaryotic cell cycle are exceptionally well-preserved phenomena. DNA decompaction, RNA and protein synthesis (in late G1 phase) followed by DNA replication (in S phase) and lipid synthesis (in G2 phase) occur after resting cells (in G0) are committed to proliferate. The G1 phase of the cell cycle is characterized by an increase in the glycolytic metabolism, sustained by high NAD+/NADH ratio. A transient cytosolic acidification occurs, probably due to lactic acid synthesis or ATP hydrolysis, followed by cytosolic alkalinization. A hyperpolarized transmembrane potential is also observed, as result of sodium/potassium pump (NaK-ATPase) activity. During progression of the cell cycle, the Pentose Phosphate Pathway (PPP) is activated by increased NADP+/NADPH ratio, converting glucose 6-phosphate to nucleotide precursors. Then, nucleic acid synthesis and DNA replication occur in S phase. Along with S phase, unpublished results show a cytosolic acidification, probably the result of glutaminolysis occurring during this phase. In G2 phase there is a decrease in NADPH concentration (used for membrane lipid synthesis) and a cytoplasmic alkalinization occurs. Mitochondria hyperfusion matches the cytosolic acidification at late G1/S transition and then triggers ATP synthesis by oxidative phosphorylation. We hypothesize here that the cytosolic pH may coordinate mitochondrial activity and thus the different redox cycles, which in turn control the cell metabolism.
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Affiliation(s)
| | - Sabine Peres
- LRI, Paris-Sud University, CNRS UMR8623 and INRIA Saclay, Paris, France.
| | | | - Erwan Bigan
- Ecole Polytechnique, LIX-UMR 7161, Palaiseau, France.
| | - Loïc Paulevé
- Ecole Polytechnique, LIX-UMR 7161, Palaiseau, France. .,LRI, Paris-Sud University, CNRS UMR8623 and INRIA Saclay, Paris, France.
| | - Marcel Levy Nogueira
- Ecole Polytechnique, LIX-UMR 7161, Palaiseau, France. .,Paris Institute of Translationnal Neurosciences (IHU-A-ICM), Pitié Salpêtrière Hospital, Paris, France.
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Abstract
We show that self-replication of a chemical system encapsulated within a membrane growing from within is possible without any explicit feature such as autocatalysis or metabolic closure, and without the need for their emergence through complexity. We use a protocell model relying upon random conservative chemical reaction networks with arbitrary stoichiometry, and we investigate the protocell's capability for self-replication, for various numbers of reactions in the network. We elucidate the underlying mechanisms in terms of simple minimal conditions pertaining only to the topology of the embedded chemical reaction network. A necessary condition is that each moiety must be fed, and a sufficient condition is that each siphon is fed. Although these minimal conditions are purely topological, by further endowing conservative chemical reaction networks with thermodynamically consistent kinetics, we show that the growth rate tends to increase on increasing the Gibbs energy per unit molecular weight of the nutrient and on decreasing that of the membrane precursor.
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