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Esteban-Medina M, de la Oliva Roque VM, Herráiz-Gil S, Peña-Chilet M, Dopazo J, Loucera C. drexml: A command line tool and Python package for drug repurposing. Comput Struct Biotechnol J 2024; 23:1129-1143. [PMID: 38510973 PMCID: PMC10950807 DOI: 10.1016/j.csbj.2024.02.027] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/30/2023] [Revised: 02/27/2024] [Accepted: 02/27/2024] [Indexed: 03/22/2024] Open
Abstract
We introduce drexml, a command line tool and Python package for rational data-driven drug repurposing. The package employs machine learning and mechanistic signal transduction modeling to identify drug targets capable of regulating a particular disease. In addition, it employs explainability tools to contextualize potential drug targets within the functional landscape of the disease. The methodology is validated in Fanconi Anemia and Familial Melanoma, two distinct rare diseases where there is a pressing need for solutions. In the Fanconi Anemia case, the model successfully predicts previously validated repurposed drugs, while in the Familial Melanoma case, it identifies a promising set of drugs for further investigation.
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Affiliation(s)
- Marina Esteban-Medina
- Platform for Computational Medicine, Andalusian Public Foundation Progress and Health-FPS, Seville, Spain
- Computational Systems Medicine, Institute of Biomedicine of Seville (IBIS), Hospital Virgen del Rocío, Seville, Spain
| | - Víctor Manuel de la Oliva Roque
- Platform for Computational Medicine, Andalusian Public Foundation Progress and Health-FPS, Seville, Spain
- Computational Systems Medicine, Institute of Biomedicine of Seville (IBIS), Hospital Virgen del Rocío, Seville, Spain
| | - Sara Herráiz-Gil
- Centro de Investigación Biomédica en Red de Enfermedades Raras (CIBERER-ISCIII), U714, Madrid, Spain
- Departamento de Bioingeniería, Universidad Carlos III de Madrid (UC3M), Madrid, Spain
- Regenerative Medicine and Tissue Engineering Group, Instituto de Investigación Sanitaria-Fundación Jiménez Díaz University Hospital (IIS-FJD), Madrid, Spain
- Epithelial Biomedicine Division, Centro de Investigaciones Energéticas, Medioambientales y Tecnológicas (CIEMAT), Madrid, Spain
| | - María Peña-Chilet
- Platform for Computational Medicine, Andalusian Public Foundation Progress and Health-FPS, Seville, Spain
- Platform of Big Data, AI and Biostatistics, Health Research Institute La Fe (IISLAFE), Valencia, Spain
| | - Joaquín Dopazo
- Platform for Computational Medicine, Andalusian Public Foundation Progress and Health-FPS, Seville, Spain
- Computational Systems Medicine, Institute of Biomedicine of Seville (IBIS), Hospital Virgen del Rocío, Seville, Spain
- Centro de Investigación Biomédica en Red de Enfermedades Raras (CIBERER-ISCIII), U715, Seville, Spain
- FPS/ELIXIR-es, Hospital Virgen del Rocío, Seville, Spain
| | - Carlos Loucera
- Platform for Computational Medicine, Andalusian Public Foundation Progress and Health-FPS, Seville, Spain
- Computational Systems Medicine, Institute of Biomedicine of Seville (IBIS), Hospital Virgen del Rocío, Seville, Spain
- Centro de Investigación Biomédica en Red de Enfermedades Raras (CIBERER-ISCIII), U715, Seville, Spain
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Missong H, Joshi R, Khullar N, Thareja S, Navik U, Bhatti GK, Bhatti JS. Nutrient-epigenome interactions: Implications for personalized nutrition against aging-associated diseases. J Nutr Biochem 2024; 127:109592. [PMID: 38325612 DOI: 10.1016/j.jnutbio.2024.109592] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/15/2023] [Revised: 01/28/2024] [Accepted: 01/30/2024] [Indexed: 02/09/2024]
Abstract
Aging is a multifaceted process involving genetic and environmental interactions often resulting in epigenetic changes, potentially leading to aging-related diseases. Various strategies, like dietary interventions and calorie restrictions, have been employed to modify these epigenetic landscapes. A burgeoning field of interest focuses on the role of microbiota in human health, emphasizing system biology and computational approaches. These methods help decipher the intricate interplay between diet and gut microbiota, facilitating the creation of personalized nutrition strategies. In this review, we analysed the mechanisms related to nutritional interventions while highlighting the influence of dietary strategies, like calorie restriction and intermittent fasting, on microbial composition and function. We explore how gut microbiota affects the efficacy of interventions using tools like multi-omics data integration, network analysis, and machine learning. These tools enable us to pinpoint critical regulatory elements and generate individualized models for dietary responses. Lastly, we emphasize the need for a deeper comprehension of nutrient-epigenome interactions and the potential of personalized nutrition informed by individual genetic and epigenetic profiles. As knowledge and technology advance, dietary epigenetics stands on the cusp of reshaping our strategy against aging and related diseases.
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Affiliation(s)
- Hemi Missong
- Laboratory of Translational Medicine and Nanotherapeutics, Department of Human Genetics and Molecular Medicine, School of Health Sciences, Central University of Punjab, Bathinda, Punjab, India
| | - Riya Joshi
- Laboratory of Translational Medicine and Nanotherapeutics, Department of Human Genetics and Molecular Medicine, School of Health Sciences, Central University of Punjab, Bathinda, Punjab, India
| | - Naina Khullar
- Department of Zoology, Mata Gujri College, Fatehgarh Sahib, Punjab, India
| | - Suresh Thareja
- Department of Pharmaceutical Sciences and Natural Products, Central University of Punjab, Bathinda, Punjab, India
| | - Umashanker Navik
- Department of Pharmacology, Central University of Punjab, Bathinda, Punjab, India
| | - Gurjit Kaur Bhatti
- Department of Medical Lab Technology, University Institute of Applied Health Sciences, Chandigarh University, Mohali, Punjab, India.
| | - Jasvinder Singh Bhatti
- Laboratory of Translational Medicine and Nanotherapeutics, Department of Human Genetics and Molecular Medicine, School of Health Sciences, Central University of Punjab, Bathinda, Punjab, India.
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Giannantoni L, Bardini R, Savino A, Di Carlo S. Biology System Description Language (BiSDL): a modeling language for the design of multicellular synthetic biological systems. BMC Bioinformatics 2024; 25:166. [PMID: 38664639 PMCID: PMC11046772 DOI: 10.1186/s12859-024-05782-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/11/2024] [Accepted: 04/12/2024] [Indexed: 04/28/2024] Open
Abstract
BACKGROUND The Biology System Description Language (BiSDL) is an accessible, easy-to-use computational language for multicellular synthetic biology. It allows synthetic biologists to represent spatiality and multi-level cellular dynamics inherent to multicellular designs, filling a gap in the state of the art. Developed for designing and simulating spatial, multicellular synthetic biological systems, BiSDL integrates high-level conceptual design with detailed low-level modeling, fostering collaboration in the Design-Build-Test-Learn cycle. BiSDL descriptions directly compile into Nets-Within-Nets (NWNs) models, offering a unique approach to spatial and hierarchical modeling in biological systems. RESULTS BiSDL's effectiveness is showcased through three case studies on complex multicellular systems: a bacterial consortium, a synthetic morphogen system and a conjugative plasmid transfer process. These studies highlight the BiSDL proficiency in representing spatial interactions and multi-level cellular dynamics. The language facilitates the compilation of conceptual designs into detailed, simulatable models, leveraging the NWNs formalism. This enables intuitive modeling of complex biological systems, making advanced computational tools more accessible to a broader range of researchers. CONCLUSIONS BiSDL represents a significant step forward in computational languages for synthetic biology, providing a sophisticated yet user-friendly tool for designing and simulating complex biological systems with an emphasis on spatiality and cellular dynamics. Its introduction has the potential to transform research and development in synthetic biology, allowing for deeper insights and novel applications in understanding and manipulating multicellular systems.
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Affiliation(s)
- Leonardo Giannantoni
- Department of Control and Computer Engineering, Polytechnic University of Turin, Corso Duca degli Abruzzi, 24, 100129, Turin, TO, Italy
| | - Roberta Bardini
- Department of Control and Computer Engineering, Polytechnic University of Turin, Corso Duca degli Abruzzi, 24, 100129, Turin, TO, Italy.
| | - Alessandro Savino
- Department of Control and Computer Engineering, Polytechnic University of Turin, Corso Duca degli Abruzzi, 24, 100129, Turin, TO, Italy
| | - Stefano Di Carlo
- Department of Control and Computer Engineering, Polytechnic University of Turin, Corso Duca degli Abruzzi, 24, 100129, Turin, TO, Italy
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Zhang Y, Ma Y, Zhao D, Tang Z, Zhang T, Zhang K, Dong J, Zhang H. Genetic regulation of lateral root development. PLANT SIGNALING & BEHAVIOR 2023; 18:2081397. [PMID: 35642513 PMCID: PMC10761116 DOI: 10.1080/15592324.2022.2081397] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/06/2022] [Revised: 05/17/2022] [Accepted: 05/18/2022] [Indexed: 06/15/2023]
Abstract
Lateral roots (LRs) are an important part of plant root systems. In dicots, for example, after plants adapted from aquatic to terrestrial environments, filamentous pseudorhizae evolved to allow nutrient absorption. A typical plant root system comprises a primary root, LRs, root hairs, and a root cap. Classical plant roots exhibit geotropism (the tendency to grow downward into the ground) and can synthesize plant hormones and other essential substances. Root vascular bundles and complex spatial structures enable plants to absorb water and nutrients to meet their nutrient quotas and grow. The primary root carries out most functions during early growth stages but is later overtaken by LRs, underscoring the importance of LR development water and mineral uptake and the soil fixation capacity of the root. LR development is modulated by endogenous plant hormones and external environmental factors, and its underlying mechanisms have been dissected in great detail in Arabidopsis, thanks to its simple root anatomy and the ease of obtaining mutants. This review comprehensively and systematically summarizes past research (largely in Arabidopsis) on LR basic structure, development stages, and molecular mechanisms regulated by different factors, as well as future prospects in LR research, to provide broad background knowledge for root researchers.
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Affiliation(s)
- Ying Zhang
- State Key Laboratory of North China Crop Improvement and Regulation, Key Laboratory of Hebei Province for Plant Physiology and Molecular Pathology, College of Life Sciences, Hebei Agricultural University, Baoding, Hebei, China
- Pear Engineering and Technology Research Center of Hebei, College of Horticulture, Hebei Agricultural University, Baoding, Hebei, China
| | - Yuru Ma
- Ministry of Education, Key Laboratory of Molecular and Cellular Biology, Hebei Collaboration Innovation Center for Cell Signaling, Hebei Key Laboratory of Molecular and Cellular Biology, College of Life Sciences, Hebei Normal University, Shijiazhuang, Hebei, China
| | - Dan Zhao
- Ministry of Education, Key Laboratory of Molecular and Cellular Biology, Hebei Collaboration Innovation Center for Cell Signaling, Hebei Key Laboratory of Molecular and Cellular Biology, College of Life Sciences, Hebei Normal University, Shijiazhuang, Hebei, China
- College of Life Sciences, Hengshui University, Hengshui, Hebei, China
| | - Ziyan Tang
- State Key Laboratory of North China Crop Improvement and Regulation, Key Laboratory of Hebei Province for Plant Physiology and Molecular Pathology, College of Life Sciences, Hebei Agricultural University, Baoding, Hebei, China
- College of Plant Protection, Hebei Agricultural University, Baoding, Hebei, China
| | - Tengteng Zhang
- Ministry of Education, Key Laboratory of Molecular and Cellular Biology, Hebei Collaboration Innovation Center for Cell Signaling, Hebei Key Laboratory of Molecular and Cellular Biology, College of Life Sciences, Hebei Normal University, Shijiazhuang, Hebei, China
| | - Ke Zhang
- State Key Laboratory of North China Crop Improvement and Regulation, Key Laboratory of Hebei Province for Plant Physiology and Molecular Pathology, College of Life Sciences, Hebei Agricultural University, Baoding, Hebei, China
- College of Agronomy, Hebei Agricultural University, Baoding, Hebei, China
| | - Jingao Dong
- State Key Laboratory of North China Crop Improvement and Regulation, Key Laboratory of Hebei Province for Plant Physiology and Molecular Pathology, College of Life Sciences, Hebei Agricultural University, Baoding, Hebei, China
- College of Plant Protection, Hebei Agricultural University, Baoding, Hebei, China
| | - Hao Zhang
- State Key Laboratory of North China Crop Improvement and Regulation, Key Laboratory of Hebei Province for Plant Physiology and Molecular Pathology, College of Life Sciences, Hebei Agricultural University, Baoding, Hebei, China
- Ministry of Education, Key Laboratory of Molecular and Cellular Biology, Hebei Collaboration Innovation Center for Cell Signaling, Hebei Key Laboratory of Molecular and Cellular Biology, College of Life Sciences, Hebei Normal University, Shijiazhuang, Hebei, China
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5
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Klein J, Phung H, Hajnal M, Šafránek D, Petrov T. Combining formal methods and Bayesian approach for inferring discrete-state stochastic models from steady-state data. PLoS One 2023; 18:e0291151. [PMID: 37956126 PMCID: PMC10642793 DOI: 10.1371/journal.pone.0291151] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/12/2023] [Accepted: 08/23/2023] [Indexed: 11/15/2023] Open
Abstract
Stochastic population models are widely used to model phenomena in different areas such as cyber-physical systems, chemical kinetics, collective animal behaviour, and beyond. Quantitative analysis of stochastic population models easily becomes challenging due to the combinatorial number of possible states of the population. Moreover, while the modeller easily hypothesises the mechanistic aspects of the model, the quantitative parameters associated to these mechanistic transitions are difficult or impossible to measure directly. In this paper, we investigate how formal verification methods can aid parameter inference for population discrete-time Markov chains in a scenario where only a limited sample of population-level data measurements-sample distributions among terminal states-are available. We first discuss the parameter identifiability and uncertainty quantification in this setup, as well as how the existing techniques of formal parameter synthesis and Bayesian inference apply. Then, we propose and implement four different methods, three of which incorporate formal parameter synthesis as a pre-computation step. We empirically evaluate the performance of the proposed methods over four representative case studies. We find that our proposed methods incorporating formal parameter synthesis as a pre-computation step allow us to significantly enhance the accuracy, precision, and scalability of inference. Specifically, in the case of unidentifiable parameters, we accurately capture the subspace of parameters which is data-compliant at a desired confidence level.
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Affiliation(s)
- Julia Klein
- Department of Computer and Information Sciences, University of Konstanz, Konstanz, Germany
- Centre for the Advanced Study of Collective Behaviour, University of Konstanz, Konstanz, Germany
| | - Huy Phung
- Department of Computer and Information Sciences, University of Konstanz, Konstanz, Germany
| | - Matej Hajnal
- Department of Computer and Information Sciences, University of Konstanz, Konstanz, Germany
- Centre for the Advanced Study of Collective Behaviour, University of Konstanz, Konstanz, Germany
- Systems Biology Laboratory, Faculty of Informatics, Masaryk University, Brno, Czech Republic
| | - David Šafránek
- Systems Biology Laboratory, Faculty of Informatics, Masaryk University, Brno, Czech Republic
| | - Tatjana Petrov
- Department of Computer and Information Sciences, University of Konstanz, Konstanz, Germany
- Centre for the Advanced Study of Collective Behaviour, University of Konstanz, Konstanz, Germany
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Melo S, Guerrero P, Moreira Soares M, Bordin JR, Carneiro F, Carneiro P, Dias MB, Carvalho J, Figueiredo J, Seruca R, Travasso RDM. The ECM and tissue architecture are major determinants of early invasion mediated by E-cadherin dysfunction. Commun Biol 2023; 6:1132. [PMID: 37938268 PMCID: PMC10632478 DOI: 10.1038/s42003-023-05482-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/20/2023] [Accepted: 10/18/2023] [Indexed: 11/09/2023] Open
Abstract
Germline mutations of E-cadherin cause Hereditary Diffuse Gastric Cancer (HDGC), a highly invasive cancer syndrome characterised by the occurrence of diffuse-type gastric carcinoma and lobular breast cancer. In this disease, E-cadherin-defective cells are detected invading the adjacent stroma since very early stages. Although E-cadherin loss is well established as a triggering event, other determinants of the invasive process persist largely unknown. Herein, we develop an experimental strategy that comprises in vitro extrusion assays using E-cadherin mutants associated to HDGC, as well as mathematical models epitomising epithelial dynamics and its interaction with the extracellular matrix (ECM). In vitro, we verify that E-cadherin dysfunctional cells detach from the epithelial monolayer and extrude basally into the ECM. Through phase-field modelling we demonstrate that, aside from loss of cell-cell adhesion, increased ECM attachment further raises basal extrusion efficiency. Importantly, by combining phase-field and vertex model simulations, we show that the cylindrical structure of gastric glands strongly promotes the cell's invasive ability. Moreover, we validate our findings using a dissipative particle dynamics simulation of epithelial extrusion. Overall, we provide the first evidence that cancer cell invasion is the outcome of defective cell-cell linkages, abnormal interplay with the ECM, and a favourable 3D tissue structure.
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Affiliation(s)
- Soraia Melo
- i3S - Instituto de Investigação e Inovação em Saúde, Universidade do Porto, Porto, Portugal
- Ipatimup - Institute of Molecular Pathology and Immunology of the University of Porto, University of Porto, Porto, Portugal
| | - Pilar Guerrero
- Departamento de Matemáticas and Grupo Interdisciplinar de Sistemas Complejos (GISC), Universidad Carlos III de Madrid, Leganés, Spain
| | - Maurício Moreira Soares
- Oslo Center for Biostatistics and Epidemiology, Faculty of Medicine, University of Oslo, Oslo, Norway
| | - José Rafael Bordin
- Department of Physics, Institute of Physics and Mathematics, Federal University of Pelotas, Capão do Leão, Rio Grande do Sul, Brazil
| | - Fátima Carneiro
- i3S - Instituto de Investigação e Inovação em Saúde, Universidade do Porto, Porto, Portugal
- Ipatimup - Institute of Molecular Pathology and Immunology of the University of Porto, University of Porto, Porto, Portugal
- Department of Pathology, Faculty of Medicine, University of Porto, Porto, Portugal
| | - Patrícia Carneiro
- i3S - Instituto de Investigação e Inovação em Saúde, Universidade do Porto, Porto, Portugal
- Ipatimup - Institute of Molecular Pathology and Immunology of the University of Porto, University of Porto, Porto, Portugal
| | - Maria Beatriz Dias
- CISUC, Department of Informatics Engineering, University of Coimbra, Coimbra, Portugal
| | - João Carvalho
- CFisUC, Department of Physics, University of Coimbra, Coimbra, Portugal
| | - Joana Figueiredo
- i3S - Instituto de Investigação e Inovação em Saúde, Universidade do Porto, Porto, Portugal.
- Ipatimup - Institute of Molecular Pathology and Immunology of the University of Porto, University of Porto, Porto, Portugal.
- Department of Pathology, Faculty of Medicine, University of Porto, Porto, Portugal.
| | - Raquel Seruca
- i3S - Instituto de Investigação e Inovação em Saúde, Universidade do Porto, Porto, Portugal
- Ipatimup - Institute of Molecular Pathology and Immunology of the University of Porto, University of Porto, Porto, Portugal
- Department of Pathology, Faculty of Medicine, University of Porto, Porto, Portugal
| | - Rui D M Travasso
- CFisUC, Department of Physics, University of Coimbra, Coimbra, Portugal.
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Cosme M, Thomas C, Gaucherel C. On the History of Ecosystem Dynamical Modeling: The Rise and Promises of Qualitative Models. ENTROPY (BASEL, SWITZERLAND) 2023; 25:1526. [PMID: 37998218 PMCID: PMC10670156 DOI: 10.3390/e25111526] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/21/2023] [Revised: 10/25/2023] [Accepted: 10/25/2023] [Indexed: 11/25/2023]
Abstract
Ecosystem modeling is a complex and multidisciplinary modeling problem which emerged in the 1950s. It takes advantage of the computational turn in sciences to better understand anthropogenic impacts and improve ecosystem management. For that purpose, ecosystem simulation models based on difference or differential equations were built. These models were relevant for studying dynamical phenomena and still are. However, they face important limitations in data-poor situations. As a response, several formal and non-formal qualitative dynamical modeling approaches were independently developed to overcome some limitations of the existing methods. Qualitative approaches allow studying qualitative dynamics as relevant abstractions of those provided by quantitative models (e.g., response to press perturbations). Each modeling framework can be viewed as a different assemblage of properties (e.g., determinism, stochasticity or synchronous update of variable values) designed to satisfy some scientific objectives. Based on four stated objectives commonly found in complex environmental sciences ((1) grasping qualitative dynamics, (2) making as few assumptions as possible about parameter values, (3) being explanatory and (4) being predictive), our objectives were guided by the wish to model complex and multidisciplinary issues commonly found in ecosystem modeling. We then discussed the relevance of existing modeling approaches and proposed the ecological discrete-event networks (EDEN) modeling framework for this purpose. The EDEN models propose a qualitative, discrete-event, partially synchronous and possibilistic view of ecosystem dynamics. We discussed each of these properties through ecological examples and existing analysis techniques for such models and showed how relevant they are for environmental science studies.
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Affiliation(s)
- Maximilien Cosme
- UMR AMAP, INRAE, University of Montpellier (Faculté des Sciences), IRD, CIRAD, CNRS, 34398 Montpellier, France
- UMR DECOD, Institut Agro Rennes-Angers (Campus Rennes), 65 rue de Saint-Brieuc, 35042 Rennes, France
| | - Colin Thomas
- IBISC, University of Evry, 91025 Evry, France (C.G.)
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Migliaccio G, Ferraro R, Wang Z, Cristini V, Dogra P, Caserta S. Exploring Cell Migration Mechanisms in Cancer: From Wound Healing Assays to Cellular Automata Models. Cancers (Basel) 2023; 15:5284. [PMID: 37958456 PMCID: PMC10647277 DOI: 10.3390/cancers15215284] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/12/2023] [Revised: 10/24/2023] [Accepted: 11/01/2023] [Indexed: 11/15/2023] Open
Abstract
PURPOSE Cell migration is a critical driver of metastatic tumor spread, contributing significantly to cancer-related mortality. Yet, our understanding of the underlying mechanisms remains incomplete. METHODS In this study, a wound healing assay was employed to investigate cancer cell migratory behavior, with the aim of utilizing migration as a biomarker for invasiveness. To gain a comprehensive understanding of this complex system, we developed a computational model based on cellular automata (CA) and rigorously calibrated and validated it using in vitro data, including both tumoral and non-tumoral cell lines. Harnessing this CA-based framework, extensive numerical experiments were conducted and supported by local and global sensitivity analyses in order to identify the key biological parameters governing this process. RESULTS Our analyses led to the formulation of a power law equation derived from just a few input parameters that accurately describes the governing mechanism of wound healing. This groundbreaking research provides a powerful tool for the pharmaceutical industry. In fact, this approach proves invaluable for the discovery of novel compounds aimed at disrupting cell migration, assessing the efficacy of prospective drugs designed to impede cancer invasion, and evaluating the immune system's responses.
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Affiliation(s)
- Giorgia Migliaccio
- Dipartimento di Ingegneria Chimica, dei Materiali e Della Produzione Industriale, Università Degli Studi di Napoli Federico II, 80125 Naples, Italy; (G.M.); (R.F.)
| | - Rosalia Ferraro
- Dipartimento di Ingegneria Chimica, dei Materiali e Della Produzione Industriale, Università Degli Studi di Napoli Federico II, 80125 Naples, Italy; (G.M.); (R.F.)
- CEINGE Biotecnologie Avanzate, Via Gaetano Salvatore, 80145 Naples, Italy
| | - Zhihui Wang
- Mathematics in Medicine Program, Department of Medicine, Houston Methodist Research Institute, Houston, TX 77030, USA; (Z.W.); (V.C.); (P.D.)
- Neal Cancer Center, Houston Methodist Research Institute, Houston, TX 77030, USA
- Department of Imaging Physics, University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA
- Department of Physiology and Biophysics, Weill Cornell Medical College, New York, NY 10065, USA
| | - Vittorio Cristini
- Mathematics in Medicine Program, Department of Medicine, Houston Methodist Research Institute, Houston, TX 77030, USA; (Z.W.); (V.C.); (P.D.)
- Neal Cancer Center, Houston Methodist Research Institute, Houston, TX 77030, USA
- Department of Imaging Physics, University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA
- Physiology, Biophysics, and Systems Biology Program, Graduate School of Medical Sciences, Weill Cornell Medicine, New York, NY 10065, USA
| | - Prashant Dogra
- Mathematics in Medicine Program, Department of Medicine, Houston Methodist Research Institute, Houston, TX 77030, USA; (Z.W.); (V.C.); (P.D.)
- Department of Physiology and Biophysics, Weill Cornell Medical College, New York, NY 10065, USA
| | - Sergio Caserta
- Dipartimento di Ingegneria Chimica, dei Materiali e Della Produzione Industriale, Università Degli Studi di Napoli Federico II, 80125 Naples, Italy; (G.M.); (R.F.)
- CEINGE Biotecnologie Avanzate, Via Gaetano Salvatore, 80145 Naples, Italy
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9
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Kravtsova N, Chamberlin HM, Dawes AT. Efficient parameter generation for constrained models using MCMC. Sci Rep 2023; 13:16285. [PMID: 37770498 PMCID: PMC10539337 DOI: 10.1038/s41598-023-43433-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/12/2023] [Accepted: 09/23/2023] [Indexed: 09/30/2023] Open
Abstract
Mathematical models of complex systems rely on parameter values to produce a desired behavior. As mathematical and computational models increase in complexity, it becomes correspondingly difficult to find parameter values that satisfy system constraints. We propose a Markov Chain Monte Carlo (MCMC) approach for the problem of constrained model parameter generation by designing a Markov chain that efficiently explores a model's parameter space. We demonstrate the use of our proposed methodology to analyze responses of a newly constructed bistability-constrained model of protein phosphorylation to perturbations in the underlying protein network. Our results suggest that parameter generation for constrained models using MCMC provides powerful tools for modeling-aided analysis of complex natural processes.
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Affiliation(s)
- Natalia Kravtsova
- Department of Mathematics, The Ohio State University, Columbus, OH, USA
| | - Helen M Chamberlin
- Department of Molecular Genetics, The Ohio State University, Columbus, OH, USA
| | - Adriana T Dawes
- Department of Mathematics, The Ohio State University, Columbus, OH, USA.
- Department of Molecular Genetics, The Ohio State University, Columbus, OH, USA.
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10
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Yordanov B, Dunn SJ, Gravill C, Arora H, Kugler H, Wintersteiger CM. The Reasoning Engine: A Satisfiability Modulo Theories-Based Framework for Reasoning About Discrete Biological Models. J Comput Biol 2023; 30:1046-1058. [PMID: 37733940 DOI: 10.1089/cmb.2023.0117] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 09/23/2023] Open
Abstract
We present a framework called the Reasoning Engine, which implements Satisfiability Modulo Theories (SMT)-based methods within a unified computational environment to address diverse biological analysis problems. The Reasoning Engine was used to reproduce results from key scientific studies, as well as supporting new research in stem cell biology. The framework utilizes an intermediate language for encoding partially specified discrete dynamical systems, which bridges the gap between high-level domain-specific languages and low-level SMT solvers. We provide this framework as open source together with various biological case studies, illustrating the synthesis, enumeration, optimization, and reasoning over models consistent with experimental observations to reveal novel biological insights.
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Affiliation(s)
| | | | | | - Himanshu Arora
- Bar-Ilan University, Faculty of Engineering, Ramat Gan, Israel
| | - Hillel Kugler
- Bar-Ilan University, Faculty of Engineering, Ramat Gan, Israel
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11
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Thompson JC, Zavala VM, Venturelli OS. Integrating a tailored recurrent neural network with Bayesian experimental design to optimize microbial community functions. PLoS Comput Biol 2023; 19:e1011436. [PMID: 37773951 PMCID: PMC10540976 DOI: 10.1371/journal.pcbi.1011436] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/23/2022] [Accepted: 08/16/2023] [Indexed: 10/01/2023] Open
Abstract
Microbiomes interact dynamically with their environment to perform exploitable functions such as production of valuable metabolites and degradation of toxic metabolites for a wide range of applications in human health, agriculture, and environmental cleanup. Developing computational models to predict the key bacterial species and environmental factors to build and optimize such functions are crucial to accelerate microbial community engineering. However, there is an unknown web of interactions that determine the highly complex and dynamic behavior of these systems, which precludes the development of models based on known mechanisms. By contrast, entirely data-driven machine learning models can produce physically unrealistic predictions and often require significant amounts of experimental data to learn system behavior. We develop a physically-constrained recurrent neural network that preserves model flexibility but is constrained to produce physically consistent predictions and show that it can outperform existing machine learning methods in the prediction of certain experimentally measured species abundance and metabolite concentrations. Further, we present a closed-loop, Bayesian experimental design algorithm to guide data collection by selecting experimental conditions that simultaneously maximize information gain and target microbial community functions. Using a bioreactor case study, we demonstrate how the proposed framework can be used to efficiently navigate a large design space to identify optimal operating conditions. The proposed methodology offers a flexible machine learning approach specifically tailored to optimize microbiome target functions through the sequential design of informative experiments that seek to explore and exploit community functions.
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Affiliation(s)
- Jaron C. Thompson
- Department of Chemical and Biological Engineering, University of Wisconsin-Madison, Madison, Wisconsin, United States of America
- Department of Biochemistry, University of Wisconsin-Madison, Madison, Wisconsin, United States of America
| | - Victor M. Zavala
- Department of Chemical and Biological Engineering, University of Wisconsin-Madison, Madison, Wisconsin, United States of America
| | - Ophelia S. Venturelli
- Department of Chemical and Biological Engineering, University of Wisconsin-Madison, Madison, Wisconsin, United States of America
- Department of Biochemistry, University of Wisconsin-Madison, Madison, Wisconsin, United States of America
- Department of Bacteriology, University of Wisconsin-Madison, Madison, Wisconsin, United States of America
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12
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Haus ES, Drengstig T, Thorsen K. Structural identifiability of biomolecular controller motifs with and without flow measurements as model output. PLoS Comput Biol 2023; 19:e1011398. [PMID: 37639454 PMCID: PMC10491402 DOI: 10.1371/journal.pcbi.1011398] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/08/2022] [Revised: 09/08/2023] [Accepted: 07/28/2023] [Indexed: 08/31/2023] Open
Abstract
Controller motifs are simple biomolecular reaction networks with negative feedback. They can explain how regulatory function is achieved and are often used as building blocks in mathematical models of biological systems. In this paper we perform an extensive investigation into structural identifiability of controller motifs, specifically the so-called basic and antithetic controller motifs. Structural identifiability analysis is a useful tool in the creation and evaluation of mathematical models: it can be used to ensure that model parameters can be determined uniquely and to examine which measurements are necessary for this purpose. This is especially useful for biological models where parameter estimation can be difficult due to limited availability of measureable outputs. Our aim with this work is to investigate how structural identifiability is affected by controller motif complexity and choice of measurements. To increase the number of potential outputs we propose two methods for including flow measurements and show how this affects structural identifiability in combination with, or in the absence of, concentration measurements. In our investigation, we analyze 128 different controller motif structures using a combination of flow and/or concentration measurements, giving a total of 3648 instances. Among all instances, 34% of the measurement combinations provided structural identifiability. Our main findings for the controller motifs include: i) a single measurement is insufficient for structural identifiability, ii) measurements related to different chemical species are necessary for structural identifiability. Applying these findings result in a reduced subset of 1568 instances, where 80% are structurally identifiable, and more complex/interconnected motifs appear easier to structurally identify. The model structures we have investigated are commonly used in models of biological systems, and our results demonstrate how different model structures and measurement combinations affect structural identifiability of controller motifs.
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Affiliation(s)
- Eivind S. Haus
- Department of Electrical Engineering and Computer Science, University of Stavanger, Stavanger, Norway
| | - Tormod Drengstig
- Department of Electrical Engineering and Computer Science, University of Stavanger, Stavanger, Norway
| | - Kristian Thorsen
- Department of Electrical Engineering and Computer Science, University of Stavanger, Stavanger, Norway
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13
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Tatka LT, Smith LP, Hellerstein JL, Sauro HM. Adapting modeling and simulation credibility standards to computational systems biology. J Transl Med 2023; 21:501. [PMID: 37496031 PMCID: PMC10369698 DOI: 10.1186/s12967-023-04290-5] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/18/2023] [Accepted: 06/19/2023] [Indexed: 07/28/2023] Open
Abstract
Computational models are increasingly used in high-impact decision making in science, engineering, and medicine. The National Aeronautics and Space Administration (NASA) uses computational models to perform complex experiments that are otherwise prohibitively expensive or require a microgravity environment. Similarly, the Food and Drug Administration (FDA) and European Medicines Agency (EMA) have began accepting models and simulations as forms of evidence for pharmaceutical and medical device approval. It is crucial that computational models meet a standard of credibility when using them in high-stakes decision making. For this reason, institutes including NASA, the FDA, and the EMA have developed standards to promote and assess the credibility of computational models and simulations. However, due to the breadth of models these institutes assess, these credibility standards are mostly qualitative and avoid making specific recommendations. On the other hand, modeling and simulation in systems biology is a narrower domain and several standards are already in place. As systems biology models increase in complexity and influence, the development of a credibility assessment system is crucial. Here we review existing standards in systems biology, credibility standards in other science, engineering, and medical fields, and propose the development of a credibility standard for systems biology models.
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Affiliation(s)
- Lillian T Tatka
- Department of Bioengineering, University of Washington, Seattle, WA, USA.
| | - Lucian P Smith
- Department of Bioengineering, University of Washington, Seattle, WA, USA
| | | | - Herbert M Sauro
- Department of Bioengineering, University of Washington, Seattle, WA, USA
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14
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Konur S, Gheorghe M, Krasnogor N. Verifiable biology. J R Soc Interface 2023; 20:20230019. [PMID: 37160165 PMCID: PMC10169095 DOI: 10.1098/rsif.2023.0019] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/11/2023] Open
Abstract
The formalization of biological systems using computational modelling approaches as an alternative to mathematical-based methods has recently received much interest because computational models provide a deeper mechanistic understanding of biological systems. In particular, formal verification, complementary approach to standard computational techniques such as simulation, is used to validate the system correctness and obtain critical information about system behaviour. In this study, we survey the most frequently used computational modelling approaches and formal verification techniques for computational biology. We compare a number of verification tools and software suites used to analyse biological systems and biochemical networks, and to verify a wide range of biological properties. For users who have no expertise in formal verification, we present a novel methodology that allows them to easily apply formal verification techniques to analyse their biological or biochemical system of interest.
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Affiliation(s)
- Savas Konur
- Department of Computer Science, University of Bradford, Richmond Building, Bradford BD7 1DP, UK
| | - Marian Gheorghe
- Department of Computer Science, University of Bradford, Richmond Building, Bradford BD7 1DP, UK
| | - Natalio Krasnogor
- School of Computing Science, Newcastle University, Science Square, Newcastle upon Tyne NE4 5TG, UK
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15
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Wysocka EM, Page M, Snowden J, Simpson TI. Comparison of rule- and ordinary differential equation-based dynamic model of DARPP-32 signalling network. PeerJ 2022; 10:e14516. [PMID: 36540795 PMCID: PMC9760030 DOI: 10.7717/peerj.14516] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/26/2022] [Accepted: 11/14/2022] [Indexed: 12/23/2022] Open
Abstract
Dynamic modelling has considerably improved our understanding of complex molecular mechanisms. Ordinary differential equations (ODEs) are the most detailed and popular approach to modelling the dynamics of molecular systems. However, their application in signalling networks, characterised by multi-state molecular complexes, can be prohibitive. Contemporary modelling methods, such as rule- based (RB) modelling, have addressed these issues. The advantages of RB modelling over ODEs have been presented and discussed in numerous reviews. In this study, we conduct a direct comparison of the time courses of a molecular system founded on the same reaction network but encoded in the two frameworks. To make such a comparison, a set of reactions that underlie an ODE model was manually encoded in the Kappa language, one of the RB implementations. A comparison of the models was performed at the level of model specification and dynamics, acquired through model simulations. In line with previous reports, we confirm that the Kappa model recapitulates the general dynamics of its ODE counterpart with minor differences. These occur when molecules have multiple sites binding the same interactor. Furthermore, activation of these molecules in the RB model is slower than in the ODE one. As reported for other molecular systems, we find that, also for the DARPP-32 reaction network, the RB representation offers a more expressive and flexible syntax that facilitates access to fine details of the model, easing model reuse. In parallel with these analyses, we report a refactored model of the DARPP-32 interaction network that can serve as a canvas for the development of more complex dynamic models to study this important molecular system.
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Affiliation(s)
- Emilia M. Wysocka
- School of Informatics, University of Edinburgh, Edinburgh, United Kingdom
| | | | | | - T. Ian Simpson
- School of Informatics, University of Edinburgh, Edinburgh, United Kingdom
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16
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Gagnon LG, Czaikowski ME, Peacock-López E. Dynamic properties of a self-replicating peptide network with inhibition. J Chem Phys 2022; 157:225101. [PMID: 36546800 DOI: 10.1063/5.0119945] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022] Open
Abstract
In this paper, we report an open system consisting of three self-replicating peptides, in which peptide 1 inhibits the duplex template of peptide 2, peptide 2 inhibits duplex 3, and peptide 3 inhibits duplex 1 to complete the negative feedback loop. This interacting chemical network yields oscillations in the concentrations of all species over time and establishes a possible mechanism for pre-biotic chemical systems organization. The first focus of our analysis is the effect of altering rates of duplex formation and inhibition on oscillations. We then examine the autocatalytic rate constant in the symmetric and asymmetric cases.
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Affiliation(s)
- Lucille G Gagnon
- Department of Chemistry, Williams College, Williamstown, Massachusetts 01267, USA
| | - Maia E Czaikowski
- Department of Chemistry, Williams College, Williamstown, Massachusetts 01267, USA
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17
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Thomas C, Cosme M, Gaucherel C, Pommereau F. Model-checking ecological state-transition graphs. PLoS Comput Biol 2022; 18:e1009657. [PMID: 35666771 PMCID: PMC9203009 DOI: 10.1371/journal.pcbi.1009657] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/18/2021] [Revised: 06/16/2022] [Accepted: 05/08/2022] [Indexed: 11/18/2022] Open
Abstract
Model-checking is a methodology developed in computer science to automatically assess the dynamics of discrete systems, by checking if a system modelled as a state-transition graph satisfies a dynamical property written as a temporal logic formula. The dynamics of ecosystems have been drawn as state-transition graphs for more than a century, ranging from state-and-transition models to assembly graphs. Model-checking can provide insights into both empirical data and theoretical models, as long as they sum up into state-transition graphs. While model-checking proved to be a valuable tool in systems biology, it remains largely underused in ecology apart from precursory applications. This article proposes to address this situation, through an inventory of existing ecological STGs and an accessible presentation of the model-checking methodology. This overview is illustrated by the application of model-checking to assess the dynamics of a vegetation pathways model. We select management scenarios by model-checking Computation Tree Logic formulas representing management goals and built from a proposed catalogue of patterns. In discussion, we sketch bridges between existing studies in ecology and available model-checking frameworks. In addition to the automated analysis of ecological state-transition graphs, we believe that defining ecological concepts with temporal logics could help clarify and compare them.
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Affiliation(s)
- Colin Thomas
- IBISC, Univ. Évry, Univ. Paris-Saclay, 91020 Évry-Courcouronne, France
- AMAP, Univ. Montpellier, INRAE, CIRAD, CNRS, IRD, Montpellier, France
| | - Maximilien Cosme
- AMAP, Univ. Montpellier, INRAE, CIRAD, CNRS, IRD, Montpellier, France
| | - Cédric Gaucherel
- AMAP, Univ. Montpellier, INRAE, CIRAD, CNRS, IRD, Montpellier, France
| | - Franck Pommereau
- IBISC, Univ. Évry, Univ. Paris-Saclay, 91020 Évry-Courcouronne, France
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18
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Abstract
The gastrointestinal ecosystem is formed from interactions between the host, indigenous gut microbiota, and external world. When colonizing the gut, bacteria must overcome barriers imposed by the intestinal environment, such as host immune responses and microbiota-mediated nutrient limitation. Thus, understanding bacterial colonization requires determining how the gut landscape interacts with microbes attempting to establish within the ecosystem. However, the complicated network of interactions between elements of the intestinal environment makes it challenging to uncover emergent properties of the system using only reductionist methods. A systems biology approach, which aims to investigate complex systems by examining the behavior and relationships of all elements of the system, may afford a more holistic perspective of the colonization process. Here, we examine the confluence between the gut landscape and bacterial colonization through the lens of systems biology. We offer an overview of the conceptual and methodological underpinnings of systems biology, followed by a discussion of key elements of the gut ecosystem as they pertain to bacterial establishment and growth. We conclude by reintegrating these elements to guide future comprehensive investigations of the ecosystem in the context of bacterial intestinal colonization.
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Affiliation(s)
- Madeline R. Barron
- Department of Microbiology & Immunology, University of Michigan Medical School, Ann Arbor, Michigan, USA
| | - Vincent B. Young
- Department of Microbiology & Immunology, University of Michigan Medical School, Ann Arbor, Michigan, USA
- Department of Internal Medicine, Division of Infectious Diseases, University of Michigan Medical School, Ann Arbor, Michigan, USA
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19
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Amar A, Hubbard EJA, Kugler H. Modeling the C. elegans germline stem cell genetic network using automated reasoning. Biosystems 2022; 217:104672. [PMID: 35469833 PMCID: PMC9142837 DOI: 10.1016/j.biosystems.2022.104672] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/08/2021] [Revised: 03/31/2022] [Accepted: 04/04/2022] [Indexed: 11/18/2022]
Abstract
Computational methods and tools are a powerful complementary approach to experimental work for studying regulatory interactions in living cells and systems. We demonstrate the use of formal reasoning methods as applied to the Caenorhabditis elegans germ line, which is an accessible system for stem cell research. The dynamics of the underlying genetic networks and their potential regulatory interactions are key for understanding mechanisms that control cellular decision-making between stem cells and differentiation. We model the “stem cell fate” versus entry into the “meiotic development” pathway decision circuit in the young adult germ line based on an extensive study of published experimental data and known/hypothesized genetic interactions. We apply a formal reasoning framework to derive predictive networks for control of differentiation. Using this approach we simultaneously specify many possible scenarios and experiments together with potential genetic interactions, and synthesize genetic networks consistent with all encoded experimental observations. In silico analysis of knock-down and overexpression experiments within our model recapitulate published phenotypes of mutant animals and can be applied to make predictions on cellular decision-making. A methodological contribution of this work is demonstrating how to effectively model within a formal reasoning framework a complex genetic network with a wealth of known experimental data and constraints. We provide a summary of the steps we have found useful for the development and analysis of this model and can potentially be applicable to other genetic networks. This work also lays a foundation for developing realistic whole tissue models of the C. elegans germ line where each cell in the model will execute a synthesized genetic network.
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Affiliation(s)
- Ani Amar
- The Faculty of Engineering, Bar-Ilan University, Ramat Gan 5290002, Israel.
| | - E Jane Albert Hubbard
- Skirball Institute of Biomolecular Medicine, Department of Cell Biology, Department of Pathology, NYU Grossman School of Medicine, 540 First Avenue, New York, NY 10016, United States of America.
| | - Hillel Kugler
- The Faculty of Engineering, Bar-Ilan University, Ramat Gan 5290002, Israel.
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20
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Abstract
Extracting mechanistic knowledge from the spatial and temporal phenotypes of morphogenesis is a current challenge due to the complexity of biological regulation and their feedback loops. Furthermore, these regulatory interactions are also linked to the biophysical forces that shape a developing tissue, creating complex interactions responsible for emergent patterns and forms. Here we show how a computational systems biology approach can aid in the understanding of morphogenesis from a mechanistic perspective. This methodology integrates the modeling of tissues and whole-embryos with dynamical systems, the reverse engineering of parameters or even whole equations with machine learning, and the generation of precise computational predictions that can be tested at the bench. To implement and perform the computational steps in the methodology, we present user-friendly tools, computer code, and guidelines. The principles of this methodology are general and can be adapted to other model organisms to extract mechanistic knowledge of their morphogenesis.
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Affiliation(s)
- Jason M Ko
- Department of Biological Sciences, University of Maryland, Baltimore County, Baltimore, MD, USA
| | - Reza Mousavi
- Department of Biological Sciences, University of Maryland, Baltimore County, Baltimore, MD, USA
| | - Daniel Lobo
- Department of Biological Sciences, University of Maryland, Baltimore County, Baltimore, MD, USA.
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21
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Rodenburg SYA, Seidl MF, de Ridder D, Govers F. Uncovering the Role of Metabolism in Oomycete-Host Interactions Using Genome-Scale Metabolic Models. Front Microbiol 2021; 12:748178. [PMID: 34707596 PMCID: PMC8543037 DOI: 10.3389/fmicb.2021.748178] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/27/2021] [Accepted: 09/10/2021] [Indexed: 12/17/2022] Open
Abstract
Metabolism is the set of biochemical reactions of an organism that enables it to assimilate nutrients from its environment and to generate building blocks for growth and proliferation. It forms a complex network that is intertwined with the many molecular and cellular processes that take place within cells. Systems biology aims to capture the complexity of cells, organisms, or communities by reconstructing models based on information gathered by high-throughput analyses (omics data) and prior knowledge. One type of model is a genome-scale metabolic model (GEM) that allows studying the distributions of metabolic fluxes, i.e., the "mass-flow" through the network of biochemical reactions. GEMs are nowadays widely applied and have been reconstructed for various microbial pathogens, either in a free-living state or in interaction with their hosts, with the aim to gain insight into mechanisms of pathogenicity. In this review, we first introduce the principles of systems biology and GEMs. We then describe how metabolic modeling can contribute to unraveling microbial pathogenesis and host-pathogen interactions, with a specific focus on oomycete plant pathogens and in particular Phytophthora infestans. Subsequently, we review achievements obtained so far and identify and discuss potential pitfalls of current models. Finally, we propose a workflow for reconstructing high-quality GEMs and elaborate on the resources needed to advance a system biology approach aimed at untangling the intimate interactions between plants and pathogens.
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Affiliation(s)
- Sander Y. A. Rodenburg
- Laboratory of Phytopathology, Wageningen University & Research, Wageningen, Netherlands
- Bioinformatics Group, Wageningen University & Research, Wageningen, Netherlands
| | - Michael F. Seidl
- Laboratory of Phytopathology, Wageningen University & Research, Wageningen, Netherlands
- Theoretical Biology & Bioinformatics group, Department of Biology, Utrecht University, Wageningen, Netherlands
| | - Dick de Ridder
- Bioinformatics Group, Wageningen University & Research, Wageningen, Netherlands
| | - Francine Govers
- Laboratory of Phytopathology, Wageningen University & Research, Wageningen, Netherlands
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22
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Bardini R, Benso A, Politano G, Di Carlo S. Nets-within-nets for modeling emergent patterns in ontogenetic processes. Comput Struct Biotechnol J 2021; 19:5701-5721. [PMID: 34765090 PMCID: PMC8554175 DOI: 10.1016/j.csbj.2021.10.008] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/30/2021] [Revised: 10/05/2021] [Accepted: 10/05/2021] [Indexed: 11/16/2022] Open
Abstract
Ontogenesis is the development of an organism from its earliest stage to maturity, including homeostasis maintenance throughout adulthood despite environmental perturbations. Almost all cells of a multicellular organism share the same genomic information. Nevertheless, phenotypic diversity and complex supra-cellular architectures emerge at every level, starting from tissues and organs. This is possible thanks to a robust and dynamic interplay of regulative mechanisms. To study ontogenesis, it is necessary to consider different levels of regulation, both genetic and epigenetic. Each cell undergoes a specific path across a landscape of possible regulative states affecting both its structure and its functions during development. This paper proposes using the Nets-Within-Nets formalism, which combines Petri Nets' simplicity with the capability to represent and simulate the interplay between different layers of regulation connected by non-trivial and context-dependent hierarchical relations. In particular, this work introduces a modeling strategy based on Nets-Within-Nets that can model several critical processes involved in ontogenesis. Moreover, it presents a case study focusing on the first phase of Vulval Precursor Cells specification in C.Elegans. The case study shows that the proposed model can simulate the emergent morphogenetic pattern corresponding to the observed developmental outcome of that phase, in both the physiological case and different mutations. The model presented in the results section is available online at https://github.com/sysbio-polito/NWN_CElegans_VPC_model/.
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Affiliation(s)
- Roberta Bardini
- Politecnico di Torino, Control and Computer Engineering Department, Corso Duca degli Abruzzi 24, Torino 10129, Italy
| | - Alfredo Benso
- Politecnico di Torino, Control and Computer Engineering Department, Corso Duca degli Abruzzi 24, Torino 10129, Italy
| | - Gianfranco Politano
- Politecnico di Torino, Control and Computer Engineering Department, Corso Duca degli Abruzzi 24, Torino 10129, Italy
| | - Stefano Di Carlo
- Politecnico di Torino, Control and Computer Engineering Department, Corso Duca degli Abruzzi 24, Torino 10129, Italy
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23
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Barbiero P, Viñas Torné R, Lió P. Graph Representation Forecasting of Patient's Medical Conditions: Toward a Digital Twin. Front Genet 2021; 12:652907. [PMID: 34603366 PMCID: PMC8481902 DOI: 10.3389/fgene.2021.652907] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/13/2021] [Accepted: 06/24/2021] [Indexed: 01/05/2023] Open
Abstract
Objective: Modern medicine needs to shift from a wait and react, curative discipline to a preventative, interdisciplinary science aiming at providing personalized, systemic, and precise treatment plans to patients. To this purpose, we propose a "digital twin" of patients modeling the human body as a whole and providing a panoramic view over individuals' conditions. Methods: We propose a general framework that composes advanced artificial intelligence (AI) approaches and integrates mathematical modeling in order to provide a panoramic view over current and future pathophysiological conditions. Our modular architecture is based on a graph neural network (GNN) forecasting clinically relevant endpoints (such as blood pressure) and a generative adversarial network (GAN) providing a proof of concept of transcriptomic integrability. Results: We tested our digital twin model on two simulated clinical case studies combining information at organ, tissue, and cellular level. We provided a panoramic overview over current and future patient's conditions by monitoring and forecasting clinically relevant endpoints representing the evolution of patient's vital parameters using the GNN model. We showed how to use the GAN to generate multi-tissue expression data for blood and lung to find associations between cytokines conditioned on the expression of genes in the renin-angiotensin pathway. Our approach was to detect inflammatory cytokines, which are known to have effects on blood pressure and have previously been associated with SARS-CoV-2 infection (e.g., CXCR6, XCL1, and others). Significance: The graph representation of a computational patient has potential to solve important technological challenges in integrating multiscale computational modeling with AI. We believe that this work represents a step forward toward next-generation devices for precision and predictive medicine.
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24
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Wu SJ. Root locus-based stability analysis for biological systems. J Bioinform Comput Biol 2021; 19:2150023. [PMID: 34514968 DOI: 10.1142/s0219720021500232] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022]
Abstract
Background: The first objective for realizing and handling biological systems is to choose a suitable model prototype and then perform structure and parameter identification. Afterwards, a theoretical analysis is needed to understand the characteristics, abilities, and limitations of the underlying systems. Generalized Michaelis-Menten kinetics (MM) and S-systems are two well-known biochemical system theory-based models. Research on steady-state estimation of generalized MM systems is difficult because of their complex structure. Further, theoretical analysis of S-systems is still difficult because of the power-law structure, and even the estimation of steady states can be easily achieved via algebraic equations. Aim: We focus on how to flexibly use control technologies to perform deeper biological system analysis. Methods: For generalized MM systems, the root locus method (proposed by Walter R. Evans) is used to predict the direction and rate (flux) limitations of the reaction and to estimate the steady states and stability margins (relative stability). Mode analysis is additionally introduced to discuss the transient behavior and the setting time. For S-systems, the concept of root locus, mode analysis, and the converse theorem are used to predict the dynamic behavior, to estimate the setting time and to analyze the relative stability of systems. Theoretical results were examined via simulation in a Simulink/MATLAB environment. Results: Four kinds of small functional modules (a system with reversible MM kinetics, a system with a singular or nearly singular system matrix and systems with cascade or branch pathways) are used to describe the proposed strategies clearly. For the reversible MM kinetics system, we successfully predict the direction and the rate (flux) limitations of reactions and obtain the values of steady state and net flux. We observe that theoretically derived results are consistent with simulation results. Good prediction is observed ([Formula: see text]% accuracy). For the system with a (nearly) singular matrix, we demonstrate that the system is neither globally exponentially stable nor globally asymptotically stable but globally semistable. The system possesses an infinite gain margin (GM denoting how much the gain can increase before the system becomes unstable) regardless of how large or how small the values of independent variables are, but the setting time decreases and then increases or always decreases as the values of independent variables increase. For S-systems, we first demonstrate that the stability of S-systems can be determined by linearized systems via root loci, mode analysis, and block diagram-based simulation. The relevant S-systems possess infinite GM for the values of independent variables varying from zero to infinity, and the setting time increases as the values of independent variables increase. Furthermore, the branch pathway maintains oscillation until a steady state is reached, but the oscillation phenomenon does not exist in the cascade pathway because in this system, all of the root loci are located on real lines. The theoretical predictions of dynamic behavior for these two systems are consistent with the simulation results. This study provides a guideline describing how to choose suitable independent variables such that systems possess satisfactory performance for stability margins, setting time and dynamic behavior. Conclusion: The proposed root locus-based analysis can be applied to any kind of differential equation-based biological system. This research initiates a method to examine system dynamic behavior and to discuss operating principles.
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Affiliation(s)
- Shinq-Jen Wu
- Department of Electrical Engineering, Da-Yeh University, 168 University Rd., Dacun, Changhua 51591, Taiwan, R.O.C
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25
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Schölzel C, Blesius V, Ernst G, Dominik A. Characteristics of mathematical modeling languages that facilitate model reuse in systems biology: a software engineering perspective. NPJ Syst Biol Appl 2021; 7:27. [PMID: 34083542 PMCID: PMC8175692 DOI: 10.1038/s41540-021-00182-w] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/18/2019] [Accepted: 04/19/2021] [Indexed: 02/06/2023] Open
Abstract
Reuse of mathematical models becomes increasingly important in systems biology as research moves toward large, multi-scale models composed of heterogeneous subcomponents. Currently, many models are not easily reusable due to inflexible or confusing code, inappropriate languages, or insufficient documentation. Best practice suggestions rarely cover such low-level design aspects. This gap could be filled by software engineering, which addresses those same issues for software reuse. We show that languages can facilitate reusability by being modular, human-readable, hybrid (i.e., supporting multiple formalisms), open, declarative, and by supporting the graphical representation of models. Modelers should not only use such a language, but be aware of the features that make it desirable and know how to apply them effectively. For this reason, we compare existing suitable languages in detail and demonstrate their benefits for a modular model of the human cardiac conduction system written in Modelica.
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Affiliation(s)
- Christopher Schölzel
- Technische Hochschule Mittelhessen - University of Applied Sciences, Giessen, Germany.
| | - Valeria Blesius
- Technische Hochschule Mittelhessen - University of Applied Sciences, Giessen, Germany
| | - Gernot Ernst
- Vestre Viken Hospital Trust, Kongsberg, Norway
- University of Oslo, Oslo, Norway
| | - Andreas Dominik
- Technische Hochschule Mittelhessen - University of Applied Sciences, Giessen, Germany
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Qualitative Modeling, Analysis and Control of Synthetic Regulatory Circuits. Methods Mol Biol 2021; 2229:1-40. [PMID: 33405215 DOI: 10.1007/978-1-0716-1032-9_1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/04/2023]
Abstract
Qualitative modeling approaches are promising and still underexploited tools for the analysis and design of synthetic circuits. They can make predictions of circuit behavior in the absence of precise, quantitative information. Moreover, they provide direct insight into the relation between the feedback structure and the dynamical properties of a network. We review qualitative modeling approaches by focusing on two specific formalisms, Boolean networks and piecewise-linear differential equations, and illustrate their application by means of three well-known synthetic circuits. We describe various methods for the analysis of state transition graphs, discrete representations of the network dynamics that are generated in both modeling frameworks. We also briefly present the problem of controlling synthetic circuits, an emerging topic that could profit from the capacity of qualitative modeling approaches to rapidly scan a space of design alternatives.
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Zheng J, Shi B, Xia S, Yang G, Zhou XN. Spatial patterns of <em>Plasmodium vivax</em> transmission explored by multivariate auto-regressive state-space modelling - A case study in Baoshan Prefecture in southern China. GEOSPATIAL HEALTH 2021; 16. [PMID: 33733649 DOI: 10.4081/gh.2021.879] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/09/2020] [Accepted: 08/21/2020] [Indexed: 06/12/2023]
Abstract
The transition from the control phase to elimination of malaria in China through the national malaria elimination programme has focussed attention on the need for improvement of the surveillance- response systems. It is now understood that routine passive surveillance is inadequate in the parasite elimination phase that requires supplementation by active surveillance in foci where cluster cases have occurred. This study aims to explore the spatial clusters and temporal trends of malaria cases by the multivariate auto-regressive state-space model (MARSS) along the border to Myanmar in southern China. Data for indigenous cases spanning the period from 2007 to 2010 were extracted from the China's Infectious Diseases Information Reporting Management System (IDIRMS). The best MARSS model indicated that malaria transmission in the study area during 36 months could be grouped into three clusters. The estimation of malaria transmission patterns showed a downward trend across all clusters. The proposed methodology used in this study offers a simple and rapid, yet effective way to categorize patterns of foci which provide assistance for active monitoring of malaria in the elimination phase.
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Affiliation(s)
- Jinxin Zheng
- National Institute of Parasitic Diseases, Chinese Center for Disease Control and Prevention, Shanghai, China; Key Laboratory of Parasite and Vector Biology, National Health Commission, Shanghai, China; National Center for International Research on Tropical Diseases, Ministry of Science and Technology, Shanghai, China; Chinese Center for Tropical Diseases Research, Shanghai.
| | - Benyun Shi
- School of Computer Science and Technology, Nanjing Tech University, Nanjing, Jiangsu.
| | - Shang Xia
- National Institute of Parasitic Diseases, Chinese Center for Disease Control and Prevention, Shanghai, China; Key Laboratory of Parasite and Vector Biology, National Health Commission, Shanghai, China; National Center for International Research on Tropical Diseases, Ministry of Science and Technology, Shanghai, China; Chinese Center for Tropical Diseases Research, Shanghai.
| | - Guojing Yang
- Hainan Medical University, Laboratory of Tropical Environment and Health, Haikou, Hainan, China; Department of Epidemiology and Public Health, Swiss Tropical and Public Health Institute; University of Basel, Basel.
| | - Xiao-Nong Zhou
- National Institute of Parasitic Diseases, Chinese Center for Disease Control and Prevention, Shanghai, China; Key Laboratory of Parasite and Vector Biology, National Health Commission, Shanghai, China; National Center for International Research on Tropical Diseases, Ministry of Science and Technology, Shanghai, China; Chinese Center for Tropical Diseases Research, Shanghai.
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Afreen R, Tyagi S, Singh GP, Singh M. Challenges and Perspectives of Polyhydroxyalkanoate Production From Microalgae/Cyanobacteria and Bacteria as Microbial Factories: An Assessment of Hybrid Biological System. Front Bioeng Biotechnol 2021; 9:624885. [PMID: 33681160 PMCID: PMC7933458 DOI: 10.3389/fbioe.2021.624885] [Citation(s) in RCA: 21] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/01/2020] [Accepted: 01/29/2021] [Indexed: 11/13/2022] Open
Abstract
Polyhydroxyalkanoates (PHAs) are the biopolymer of choice if we look for a substitute of petroleum-based non-biodegradable plastics. Microbial production of PHAs as carbon reserves has been studied for decades and PHAs are gaining attention for a wide range of applications in various fields. Still, their uneconomical production is the major concern largely attributed to high cost of organic substrates for PHA producing heterotrophic bacteria. Therefore, microalgae/cyanobacteria, being photoautotrophic, prove to have an edge over heterotrophic bacteria. They have minimal metabolic requirements, such as inorganic nutrients (CO2, N, P, etc.) and light, and they can survive under adverse environmental conditions. PHA production under photoautotrophic conditions has been reported from cyanobacteria, the only candidate among prokaryotes, and few of the eukaryotic microalgae. However, an efficient cultivation system is still required for photoautotrophic PHA production to overcome the limitations associated with (1) stringent management of closed photobioreactors and (2) optimization of monoculture in open pond culture. Thus, a hybrid system is a necessity, involving the participation of microalgae/cyanobacteria and bacteria, i.e., both photoautotrophic and heterotrophic components having mutual interactive benefits for each other under different cultivation regime, e.g., mixotrophic, successive two modules, consortium based, etc. Along with this, further strategies like optimization of culture conditions (N, P, light exposure, CO2 dynamics, etc.), bioengineering, efficient downstream processes, and the application of mathematical/network modeling of metabolic pathways to improve PHA production are the key areas discussed here. Conclusively, this review aims to critically analyze cyanobacteria as PHA producers and proposes economically sustainable production of PHA from microbial autotrophs and heterotrophs in "hybrid biological system."
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Affiliation(s)
- Rukhsar Afreen
- Department of Zoology, Gargi College, University of Delhi, New Delhi, India
| | - Shivani Tyagi
- Department of Zoology, Gargi College, University of Delhi, New Delhi, India
| | - Gajendra Pratap Singh
- Mathematical Sciences and Interdisciplinary Research Lab (Math Sci Int R-Lab), School of Computational and Integrative Sciences, Jawaharlal Nehru University, New Delhi, India
| | - Mamtesh Singh
- Department of Zoology, Gargi College, University of Delhi, New Delhi, India
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Aghamiri SS, Singh V, Naldi A, Helikar T, Soliman S, Niarakis A. Automated inference of Boolean models from molecular interaction maps using CaSQ. Bioinformatics 2021; 36:4473-4482. [PMID: 32403123 PMCID: PMC7575051 DOI: 10.1093/bioinformatics/btaa484] [Citation(s) in RCA: 32] [Impact Index Per Article: 10.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/30/2019] [Revised: 04/17/2020] [Accepted: 05/06/2020] [Indexed: 12/16/2022] Open
Abstract
Motivation Molecular interaction maps have emerged as a meaningful way of representing biological mechanisms in a comprehensive and systematic manner. However, their static nature provides limited insights to the emerging behaviour of the described biological system under different conditions. Computational modelling provides the means to study dynamic properties through in silico simulations and perturbations. We aim to bridge the gap between static and dynamic representations of biological systems with CaSQ, a software tool that infers Boolean rules based on the topology and semantics of molecular interaction maps built with CellDesigner. Results We developed CaSQ by defining conversion rules and logical formulas for inferred Boolean models according to the topology and the annotations of the starting molecular interaction maps. We used CaSQ to produce executable files of existing molecular maps that differ in size, complexity and the use of Systems Biology Graphical Notation (SBGN) standards. We also compared, where possible, the manually built logical models corresponding to a molecular map to the ones inferred by CaSQ. The tool is able to process large and complex maps built with CellDesigner (either following SBGN standards or not) and produce Boolean models in a standard output format, Systems Biology Marked Up Language-qualitative (SBML-qual), that can be further analyzed using popular modelling tools. References, annotations and layout of the CellDesigner molecular map are retained in the obtained model, facilitating interoperability and model reusability. Availability and implementation The present tool is available online: https://lifeware.inria.fr/∼soliman/post/casq/ and distributed as a Python package under the GNU GPLv3 license. The code can be accessed here: https://gitlab.inria.fr/soliman/casq. Supplementary information Supplementary data are available at Bioinformatics online.
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Affiliation(s)
- Sara Sadat Aghamiri
- GenHotel, Département de Biologie, Univ. èvry, Université Paris-Saclay, Genopole, èvry 91025, France
| | - Vidisha Singh
- GenHotel, Département de Biologie, Univ. èvry, Université Paris-Saclay, Genopole, èvry 91025, France
| | - Aurélien Naldi
- Département de Biologie, Institut de Biologie de l'Ecole Normale Supérieure (IBENS), ècole Normale Supérieure, CNRS, INSERM, Université PSL, Paris 75005, France
| | - Tomáš Helikar
- Department of Biochemistry, University of Nebraska-Lincoln, Lincoln, NE 68588, USA
| | - Sylvain Soliman
- Lifeware Group, Inria Saclay-île de France, Palaiseau 91120, France
| | - Anna Niarakis
- GenHotel, Département de Biologie, Univ. èvry, Université Paris-Saclay, Genopole, èvry 91025, France
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31
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Johnson ME, Chen A, Faeder JR, Henning P, Moraru II, Meier-Schellersheim M, Murphy RF, Prüstel T, Theriot JA, Uhrmacher AM. Quantifying the roles of space and stochasticity in computer simulations for cell biology and cellular biochemistry. Mol Biol Cell 2021; 32:186-210. [PMID: 33237849 PMCID: PMC8120688 DOI: 10.1091/mbc.e20-08-0530] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/12/2020] [Revised: 10/13/2020] [Accepted: 11/17/2020] [Indexed: 12/29/2022] Open
Abstract
Most of the fascinating phenomena studied in cell biology emerge from interactions among highly organized multimolecular structures embedded into complex and frequently dynamic cellular morphologies. For the exploration of such systems, computer simulation has proved to be an invaluable tool, and many researchers in this field have developed sophisticated computational models for application to specific cell biological questions. However, it is often difficult to reconcile conflicting computational results that use different approaches to describe the same phenomenon. To address this issue systematically, we have defined a series of computational test cases ranging from very simple to moderately complex, varying key features of dimensionality, reaction type, reaction speed, crowding, and cell size. We then quantified how explicit spatial and/or stochastic implementations alter outcomes, even when all methods use the same reaction network, rates, and concentrations. For simple cases, we generally find minor differences in solutions of the same problem. However, we observe increasing discordance as the effects of localization, dimensionality reduction, and irreversible enzymatic reactions are combined. We discuss the strengths and limitations of commonly used computational approaches for exploring cell biological questions and provide a framework for decision making by researchers developing new models. As computational power and speed continue to increase at a remarkable rate, the dream of a fully comprehensive computational model of a living cell may be drawing closer to reality, but our analysis demonstrates that it will be crucial to evaluate the accuracy of such models critically and systematically.
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Affiliation(s)
- M. E. Johnson
- Thomas C. Jenkins Department of Biophysics, Johns Hopkins University, Baltimore, MD, 21218
| | - A. Chen
- Thomas C. Jenkins Department of Biophysics, Johns Hopkins University, Baltimore, MD, 21218
| | - J. R. Faeder
- Department of Computational and Systems Biology, University of Pittsburgh School of Medicine, Pittsburgh, PA, 15260
| | - P. Henning
- Institute for Visual and Analytic Computing, University of Rostock, 18055 Rostock, Germany
| | - I. I. Moraru
- Department of Cell Biology, Center for Cell Analysis and Modeling, University of Connecticut Health Center, Farmington, CT 06030
| | - M. Meier-Schellersheim
- Laboratory of Immune System Biology, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD 20892
| | - R. F. Murphy
- Computational Biology Department, Department of Biological Sciences, Department of Biomedical Engineering, Machine Learning Department, Carnegie Mellon University, Pittsburgh, PA 15289
| | - T. Prüstel
- Laboratory of Immune System Biology, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD 20892
| | - J. A. Theriot
- Department of Biology and Howard Hughes Medical Institute, University of Washington, Seattle, WA 98195
| | - A. M. Uhrmacher
- Institute for Visual and Analytic Computing, University of Rostock, 18055 Rostock, Germany
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32
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Modeling and Analysis of Cardiac Hybrid Cellular Automata via GPU-Accelerated Monte Carlo Simulation. MATHEMATICS 2021. [DOI: 10.3390/math9020164] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/29/2022]
Abstract
The heart consists of a complex network of billions of cells. Under physiological conditions, cardiac cells propagate electrical signals in space, generating the heartbeat in a synchronous and coordinated manner. When such a synchronization fails, life-threatening events can arise. The inherent complexity of the underlying nonlinear dynamics and the large number of biological components involved make the modeling and the analysis of electrophysiological properties in cardiac tissue still an open challenge. We consider here a Hybrid Cellular Automata (HCA) approach modeling the cardiac cell-cell membrane resistance with a free variable. We show that the modeling approach can reproduce important and complex spatiotemporal properties paving the ground for promising future applications. We show how GPU-based technology can considerably accelerate the simulation and the analysis. Furthermore, we study the cardiac behavior within a unidimensional domain considering inhomogeneous resistance and we perform a Monte Carlo analysis to evaluate our approach.
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33
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Musilova J, Sedlar K. Tools for time-course simulation in systems biology: a brief overview. Brief Bioinform 2021; 22:6076933. [PMID: 33423059 DOI: 10.1093/bib/bbaa392] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/28/2020] [Revised: 11/27/2020] [Accepted: 11/30/2020] [Indexed: 11/13/2022] Open
Abstract
Dynamic modeling of biological systems is essential for understanding all properties of a given organism as it allows us to look not only at the static picture of an organism but also at its behavior under various conditions. With the increasing amount of experimental data, the number of tools that enable dynamic analysis also grows. However, various tools are based on different approaches, use different types of data and offer different functions for analyses; so it can be difficult to choose the most suitable tool for a selected type of model. Here, we bring a brief overview containing descriptions of 50 tools for the reconstruction of biological models, their time-course simulation and dynamic analysis. We examined each tool using test data and divided them based on the qualitative and quantitative nature of the mathematical apparatus they use.
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Affiliation(s)
- Jana Musilova
- Department of Biomedical Engineering, Faculty of Electrical Engineering and Communication, Brno University of Technology, Brno, Czechia
| | - Karel Sedlar
- Department of Biomedical Engineering, Faculty of Electrical Engineering and Communication, Brno University of Technology, Brno, Czechia
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Cahan P, Cacchiarelli D, Dunn SJ, Hemberg M, de Sousa Lopes SMC, Morris SA, Rackham OJL, Del Sol A, Wells CA. Computational Stem Cell Biology: Open Questions and Guiding Principles. Cell Stem Cell 2021; 28:20-32. [PMID: 33417869 PMCID: PMC7799393 DOI: 10.1016/j.stem.2020.12.012] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
Computational biology is enabling an explosive growth in our understanding of stem cells and our ability to use them for disease modeling, regenerative medicine, and drug discovery. We discuss four topics that exemplify applications of computation to stem cell biology: cell typing, lineage tracing, trajectory inference, and regulatory networks. We use these examples to articulate principles that have guided computational biology broadly and call for renewed attention to these principles as computation becomes increasingly important in stem cell biology. We also discuss important challenges for this field with the hope that it will inspire more to join this exciting area.
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Affiliation(s)
- Patrick Cahan
- Institute for Cell Engineering, Department of Biomedical Engineering, Department of Molecular Biology and Genetics, Johns Hopkins School of Medicine, Baltimore, MD 21205, USA.
| | - Davide Cacchiarelli
- Telethon Institute of Genetics and Medicine (TIGEM), Armenise/Harvard Laboratory of Integrative Genomics, Pozzuoli, Italy d Department of Translational Medicine, University of Naples "Federico II," Naples, Italy
| | - Sara-Jane Dunn
- DeepMind, 14-18 Handyside Street, London N1C 4DN, UK; Wellcome-MRC Cambridge Stem Cell Institute, University of Cambridge, Jeffrey Cheah Biomedical Centre, Puddicombe Way, Cambridge Biomedical Campus, Cambridge CB2 0AW, UK
| | - Martin Hemberg
- Wellcome Sanger Institute, Wellcome Genome Campus, Hinxton CB10 1SA, UK
| | | | - Samantha A Morris
- Department of Developmental Biology, Department of Genetics, Center of Regenerative Medicine, Washington University School of Medicine, St. Louis, MO 63110, USA
| | - Owen J L Rackham
- Centre for Computational Biology and The Program for Cardiovascular and Metabolic Disorders, Duke-NUS Medical School, Singapore, Singapore
| | - Antonio Del Sol
- Luxembourg Centre for Systems Biomedicine (LCSB), University of Luxembourg, 6 Avenue du Swing, Belvaux 4366, Luxembourg; CIC bioGUNE, Bizkaia Technology Park, 801 Building, 48160 Derio, Spain; IKERBASQUE, Basque Foundation for Science, Bilbao 48013, Spain
| | - Christine A Wells
- Centre for Stem Cell Systems, Faculty of Medicine, Dentistry and Health Sciences, The University of Melbourne, Melbourne, VIC 3010, Australia
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Fuzzy Matching for Cellular Signaling Networks in a Choroidal Melanoma Model. ADVANCES IN INTELLIGENT SYSTEMS AND COMPUTING 2021. [DOI: 10.1007/978-3-030-54568-0_9] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
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Harline K, Martínez-Gómez J, Specht CD, Roeder AHK. A Life Cycle for Modeling Biology at Different Scales. FRONTIERS IN PLANT SCIENCE 2021; 12:710590. [PMID: 34539702 PMCID: PMC8446664 DOI: 10.3389/fpls.2021.710590] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/16/2021] [Accepted: 07/22/2021] [Indexed: 05/12/2023]
Abstract
Modeling has become a popular tool for inquiry and discovery across biological disciplines. Models allow biologists to probe complex questions and to guide experimentation. Modeling literacy among biologists, however, has not always kept pace with the rise in popularity of these techniques and the relevant advances in modeling theory. The result is a lack of understanding that inhibits communication and ultimately, progress in data gathering and analysis. In an effort to help bridge this gap, we present a blueprint that will empower biologists to interrogate and apply models in their field. We demonstrate the applicability of this blueprint in two case studies from distinct subdisciplines of biology; developmental-biomechanics and evolutionary biology. The models used in these fields vary from summarizing dynamical mechanisms to making statistical inferences, demonstrating the breadth of the utility of models to explore biological phenomena.
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Affiliation(s)
- Kate Harline
- Section of Plant Biology, School of Integrative Plant Science, Cornell University, Ithaca, NY, United States
- Weill Institute for Cell and Molecular Biology, Cornell University, Ithaca, NY, United States
- *Correspondence: Kate Harline,
| | - Jesús Martínez-Gómez
- Section of Plant Biology, School of Integrative Plant Science, Cornell University, Ithaca, NY, United States
- L.H. Bailey Hortorium, Cornell University, Ithaca, NY, United States
| | - Chelsea D. Specht
- Section of Plant Biology, School of Integrative Plant Science, Cornell University, Ithaca, NY, United States
- L.H. Bailey Hortorium, Cornell University, Ithaca, NY, United States
| | - Adrienne H. K. Roeder
- Section of Plant Biology, School of Integrative Plant Science, Cornell University, Ithaca, NY, United States
- Weill Institute for Cell and Molecular Biology, Cornell University, Ithaca, NY, United States
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Sinisi S, Alimguzhin V, Mancini T, Tronci E, Leeners B. Complete populations of virtual patients for in silico clinical trials. Bioinformatics 2020; 36:5465-5472. [PMID: 33325489 DOI: 10.1093/bioinformatics/btaa1026] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/06/2020] [Revised: 10/30/2020] [Accepted: 11/30/2020] [Indexed: 02/06/2023] Open
Abstract
MOTIVATION Model-based approaches to safety and efficacy assessment of pharmacological drugs, treatment strategies, or medical devices (In Silico Clinical Trial, ISCT) aim to decrease time and cost for the needed experimentations, reduce animal and human testing, and enable precision medicine. Unfortunately, in presence of non-identifiable models (e.g., reaction networks), parameter estimation is not enough to generate complete populations of Virtual Patient (VPs), i.e., populations guaranteed to show the entire spectrum of model behaviours (phenotypes), thus ensuring representativeness of the trial. RESULTS We present methods and software based on global search driven by statistical model checking that, starting from a (non-identifiable) quantitative model of the human physiology (plus drugs PK/PD) and suitable biological and medical knowledge elicited from experts, compute a population of VPs whose behaviours are representative of the whole spectrum of phenotypes entailed by the model (completeness) and pairwise distinguishable according to user-provided criteria. This enables full granularity control on the size of the population to employ in an ISCT, guaranteeing representativeness while avoiding over-representation of behaviours.We proved the effectiveness of our algorithm on a non-identifiable ODE-based model of the female Hypothalamic-Pituitary-Gonadal axis, by generating a population of 4 830 264 VPs stratified into 7 levels (at different granularity of behaviours), and assessed its representativeness against 86 retrospective health records from Pfizer, Hannover Medical School and University Hospital of Lausanne. The datasets are respectively covered by our VPs within Average Normalised Mean Absolute Error of 15%, 20%, and 35% (90% of the latter dataset is covered within 20% error).
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Affiliation(s)
- S Sinisi
- Computer Science Department, Sapienza University of Rome, Italy
| | - V Alimguzhin
- Computer Science Department, Sapienza University of Rome, Italy
| | - T Mancini
- Computer Science Department, Sapienza University of Rome, Italy
| | - E Tronci
- Computer Science Department, Sapienza University of Rome, Italy
| | - B Leeners
- Division of Reproductive Endocrinology, University Hospital Zurich, Switzerland
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Akgül A, Khoshnaw SHA, Abdalrahman AS. Mathematical modeling for enzyme inhibitors with slow and fast subsystems. ARAB JOURNAL OF BASIC AND APPLIED SCIENCES 2020. [DOI: 10.1080/25765299.2020.1844369] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/23/2022] Open
Affiliation(s)
- Ali Akgül
- Department of Mathematics, Art and Science Faculty, Siirt University, Siirt, Turkey
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Ballweg R, Engevik KA, Montrose MH, Aihara E, Zhang T. Extracting Insights From Temporal Data by Integrating Dynamic Modeling and Machine Learning. Front Physiol 2020; 11:1012. [PMID: 32903488 PMCID: PMC7435055 DOI: 10.3389/fphys.2020.01012] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/27/2020] [Accepted: 07/24/2020] [Indexed: 12/14/2022] Open
Abstract
Biological processes are dynamic. As a result, temporal analyses are necessary to fully understand the complex interactions that occurs within these systems. One example of a multifaceted biological process is restitution: the initial step in complex wound repair. Restitution is a dynamic process that depends on an elegant orchestration between damaged cells and their intact neighbors. Such orchestration enables the quick repair of the damaged area, which is essential to preserve epithelial integrity and prevent further injury. High quality dynamic data of the cellular and molecular events that make up the gastric restitution process has been documented. However, comprehensive dynamic models that connect all relevant molecular interactions to cellular behaviors are challenging to construct and experimentally validate. In order to efficiently provide feedback to ongoing experimental work, we have integrated dynamical modeling and machine learning to efficiently extract data-driven insights without incorporating detailed mechanisms. Dynamical models convert time course data into a set of static features, which are then subjected to machine learning analysis. The integrated analysis provides data-driven insights into how repair might be regulated in individual gastric organoids. We have provided a “proof of concept” of how such an analysis pipeline can be used to analyze any temporal dataset and provide timely data-driven insights.
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Affiliation(s)
- Richard Ballweg
- Department of Pharmacology and Systems Physiology, University of Cincinnati College of Medicine, Cincinnati, OH, United States
| | - Kristen A Engevik
- Department of Pharmacology and Systems Physiology, University of Cincinnati College of Medicine, Cincinnati, OH, United States
| | - Marshall H Montrose
- Department of Pharmacology and Systems Physiology, University of Cincinnati College of Medicine, Cincinnati, OH, United States
| | - Eitaro Aihara
- Department of Pharmacology and Systems Physiology, University of Cincinnati College of Medicine, Cincinnati, OH, United States
| | - Tongli Zhang
- Department of Pharmacology and Systems Physiology, University of Cincinnati College of Medicine, Cincinnati, OH, United States
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Bianconi F, Antonini C, Tomassoni L, Valigi P. Application of conditional robust calibration to ordinary differential equations models in computational systems biology: a comparison of two sampling strategies. IET Syst Biol 2020; 14:107-119. [PMID: 32406375 PMCID: PMC8687221 DOI: 10.1049/iet-syb.2018.5091] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/22/2018] [Revised: 07/30/2019] [Accepted: 11/15/2019] [Indexed: 01/01/2023] Open
Abstract
Mathematical modelling is a widely used technique for describing the temporal behaviour of biological systems. One of the most challenging topics in computational systems biology is the calibration of non-linear models; i.e. the estimation of their unknown parameters. The state-of-the-art methods in this field are the frequentist and Bayesian approaches. For both of them, the performance and accuracy of results greatly depend on the sampling technique employed. Here, the authors test a novel Bayesian procedure for parameter estimation, called conditional robust calibration (CRC), comparing two different sampling techniques: uniform and logarithmic Latin hypercube sampling. CRC is an iterative algorithm based on parameter space sampling and on the estimation of parameter density functions. They apply CRC with both sampling strategies to the three ordinary differential equations (ODEs) models of increasing complexity. They obtain a more precise and reliable solution through logarithmically spaced samples.
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Affiliation(s)
| | - Chiara Antonini
- Department of Engineering, University of Perugia, G. Duranti 95, 06132 Perugia, Italy
| | - Lorenzo Tomassoni
- Department of Engineering, University of Perugia, G. Duranti 95, 06132 Perugia, Italy
| | - Paolo Valigi
- Department of Engineering, University of Perugia, G. Duranti 95, 06132 Perugia, Italy
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41
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Validation of Modeling and Simulation Methods in Computational Biology. ADVANCES IN EXPERIMENTAL MEDICINE AND BIOLOGY 2020. [PMID: 32468548 DOI: 10.1007/978-3-030-32622-7_30] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register]
Abstract
In recent years, a highly sophisticated array of modeling and simulation tools in all areas of biological and biomedical research has been developed. These tools have the potential to provide new insights into biological mechanisms integrating subcellular, cellular, tissue, organ, and potentially whole organism levels. Current research is focused on how to use these methods for translational medical research, such as for disease diagnosis and understanding, as well as drug discovery. In addition, these approaches enhance the ability to use human-derived data and to contribute to the refinement of high-cost experimental-based research. Additionally, the conflicting conceptual frameworks and conceptions of modeling and simulation methods from the broad public of users could have a significant impact on the successful implementation of aforementioned applications. This in turn could result in successful collaborations across academic, clinical, and industrial sectors. To that end, this study provides an overview of the frameworks and disciplines used for validation of computational methodologies in biomedical sciences.
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Varga MJ, Fu Y, Loggia S, Yogurtcu ON, Johnson ME. NERDSS: A Nonequilibrium Simulator for Multibody Self-Assembly at the Cellular Scale. Biophys J 2020; 118:3026-3040. [PMID: 32470324 DOI: 10.1016/j.bpj.2020.05.002] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/27/2019] [Revised: 04/24/2020] [Accepted: 05/05/2020] [Indexed: 12/13/2022] Open
Abstract
Currently, a significant barrier to building predictive models of cellular self-assembly processes is that molecular models cannot capture minutes-long dynamics that couple distinct components with active processes, whereas reaction-diffusion models cannot capture structures of molecular assembly. Here, we introduce the nonequilibrium reaction-diffusion self-assembly simulator (NERDSS), which addresses this spatiotemporal resolution gap. NERDSS integrates efficient reaction-diffusion algorithms into generalized software that operates on user-defined molecules through diffusion, binding and orientation, unbinding, chemical transformations, and spatial localization. By connecting the fast processes of binding with the slow timescales of large-scale assembly, NERDSS integrates molecular resolution with reversible formation of ordered, multisubunit complexes. NERDSS encodes models using rule-based formatting languages to facilitate model portability, usability, and reproducibility. Applying NERDSS to steps in clathrin-mediated endocytosis, we design multicomponent systems that can form lattices in solution or on the membrane, and we predict how stochastic but localized dephosphorylation of membrane lipids can drive lattice disassembly. The NERDSS simulations reveal the spatial constraints on lattice growth and the role of membrane localization and cooperativity in nucleating assembly. By modeling viral lattice assembly and recapitulating oscillations in protein expression levels for a circadian clock model, we illustrate the adaptability of NERDSS. NERDSS simulates user-defined assembly models that were previously inaccessible to existing software tools, with broad applications to predicting self-assembly in vivo and designing high-yield assemblies in vitro.
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Affiliation(s)
- Matthew J Varga
- TC Jenkins Department of Biophysics, Johns Hopkins University, Baltimore, Maryland
| | - Yiben Fu
- TC Jenkins Department of Biophysics, Johns Hopkins University, Baltimore, Maryland
| | - Spencer Loggia
- TC Jenkins Department of Biophysics, Johns Hopkins University, Baltimore, Maryland
| | - Osman N Yogurtcu
- Center for Biologics Evaluation and Research, Food and Drug Administration, Silver Spring, Maryland
| | - Margaret E Johnson
- TC Jenkins Department of Biophysics, Johns Hopkins University, Baltimore, Maryland.
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Schivo S, Khurana S, Govindaraj K, Scholma J, Kerkhofs J, Zhong L, Huang X, van de Pol J, Langerak R, van Wijnen AJ, Geris L, Karperien M, Post JN. ECHO, the executable CHOndrocyte: A computational model to study articular chondrocytes in health and disease. Cell Signal 2020; 68:109471. [DOI: 10.1016/j.cellsig.2019.109471] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/19/2018] [Revised: 11/01/2019] [Accepted: 11/12/2019] [Indexed: 12/18/2022]
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Ascolani G, Skerry TM, Lacroix D, Dall'Ara E, Shuaib A. Revealing hidden information in osteoblast's mechanotransduction through analysis of time patterns of critical events. BMC Bioinformatics 2020; 21:114. [PMID: 32183690 PMCID: PMC7079370 DOI: 10.1186/s12859-020-3394-0] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/09/2019] [Accepted: 02/04/2020] [Indexed: 12/21/2022] Open
Abstract
BACKGROUND Mechanotransduction in bone cells plays a pivotal role in osteoblast differentiation and bone remodelling. Mechanotransduction provides the link between modulation of the extracellular matrix by mechanical load and intracellular activity. By controlling the balance between the intracellular and extracellular domains, mechanotransduction determines the optimum functionality of skeletal dynamics. Failure of this relationship was suggested to contribute to bone-related diseases such as osteoporosis. RESULTS A hybrid mechanical and agent-based model (Mech-ABM), simulating mechanotransduction in a single osteoblast under external mechanical perturbations, was utilised to simulate and examine modulation of the activation dynamics of molecules within mechanotransduction on the cellular response to mechanical stimulation. The number of molecules and their fluctuations have been analysed in terms of recurrences of critical events. A numerical approach has been developed to invert subordination processes and to extract the direction processes from the molecular signals in order to derive the distribution of recurring events. These predict that there are large fluctuations enclosing information hidden in the noise which is beyond the dynamic variations of molecular baselines. Moreover, studying the system under different mechanical load regimes and altered dynamics of feedback loops, illustrate that the waiting time distributions of each molecule are a signature of the system's state. CONCLUSIONS The behaviours of the molecular waiting times change with the changing of mechanical load regimes and altered dynamics of feedback loops, presenting the same variation of patterns for similar interacting molecules and identifying specific alterations for key molecules in mechanotransduction. This methodology could be used to provide a new tool to identify potent molecular candidates to modulate mechanotransduction, hence accelerate drug discovery towards therapeutic targets for bone mass upregulation.
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Affiliation(s)
- Gianluca Ascolani
- Department of Oncology and Metabolism, University of Sheffield, Sheffield, UK
- Insigneo Institute of In Silico Medicine, University of Sheffield, Sheffield, UK
| | - Timothy M Skerry
- Department of Oncology and Metabolism, University of Sheffield, Sheffield, UK
| | - Damien Lacroix
- Insigneo Institute of In Silico Medicine, University of Sheffield, Sheffield, UK
- Department of Mechanical Engineering, University of Sheffield, Sheffield, UK
| | - Enrico Dall'Ara
- Department of Oncology and Metabolism, University of Sheffield, Sheffield, UK
- Insigneo Institute of In Silico Medicine, University of Sheffield, Sheffield, UK
| | - Aban Shuaib
- Department of Oncology and Metabolism, University of Sheffield, Sheffield, UK.
- Insigneo Institute of In Silico Medicine, University of Sheffield, Sheffield, UK.
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45
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Piangerelli M, Maestri S, Merelli E. Visualising 2-simplex formation in metabolic reactions. J Mol Graph Model 2020; 97:107576. [PMID: 32179422 DOI: 10.1016/j.jmgm.2020.107576] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/05/2019] [Revised: 02/07/2020] [Accepted: 02/28/2020] [Indexed: 01/20/2023]
Abstract
Understanding in silico the dynamics of metabolic reactions made by a large number of molecules has led to the development of different tools for visualising molecular interactions. However, most of them are mainly focused on quantitative aspects. We investigate the potentiality of the topological interpretation of the interaction-as-perception at the basis of a multiagent system, to tackle the complexity of visualising the emerging behaviour of a complex system. We model and simulate the glycolysis process as a multiagent system, and we perform topological data analysis of the molecular perceptions graphs, gained during the formation of the enzymatic complexes, to visualise the set of emerging patterns. Identifying expected patterns in terms of simplicial structures allows us to characterise metabolic reactions from a qualitative point of view and conceivably reveal the simulation reactivity trend.
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Affiliation(s)
- Marco Piangerelli
- Computer Science, School of Science and Technologies, University of Camerino, Via Madonna delle Carceri 7, Camerino, 62032, Italy.
| | - Stefano Maestri
- Computer Science, School of Science and Technologies, University of Camerino, Via Madonna delle Carceri 7, Camerino, 62032, Italy; CPT - Centre de Physique Théorique, Aix-Marseille University, 163 Avenue de Luminy, 13288, Marseille Cedex 9, France.
| | - Emanuela Merelli
- Computer Science, School of Science and Technologies, University of Camerino, Via Madonna delle Carceri 7, Camerino, 62032, Italy.
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Santibáñez R, Garrido D, Martin AJM. Pleione: A tool for statistical and multi-objective calibration of Rule-based models. Sci Rep 2019; 9:15104. [PMID: 31641245 PMCID: PMC6805871 DOI: 10.1038/s41598-019-51546-6] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/07/2019] [Accepted: 09/24/2019] [Indexed: 11/17/2022] Open
Abstract
Mathematical models based on Ordinary Differential Equations (ODEs) are frequently used to describe and simulate biological systems. Nevertheless, such models are often difficult to understand. Unlike ODE models, Rule-Based Models (RBMs) utilise formal language to describe reactions as a cumulative number of statements that are easier to understand and correct. They are also gaining popularity because of their conciseness and simulation flexibility. However, RBMs generally lack tools to perform further analysis that requires simulation. This situation arises because exact and approximate simulations are computationally intensive. Translating RBMs into ODEs is commonly used to reduce simulation time, but this technique may be prohibitive due to combinatorial explosion. Here, we present the software called Pleione to calibrate RBMs. Parameter calibration is essential given the incomplete experimental determination of reaction rates and the goal of using models to reproduce experimental data. The software distributes stochastic simulations and calculations and incorporates equivalence tests to determine the fitness of RBMs compared with data. The primary features of Pleione were thoroughly tested on a model of gene regulation in Escherichia coli. Pleione yielded satisfactory results regarding calculation time and error reduction for multiple simulators, models, parameter search strategies, and computing infrastructures.
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Affiliation(s)
- Rodrigo Santibáñez
- Network Biology Lab, Centro de Genómica y Bioinformática, Facultad de Ciencias, Universidad Mayor, Santiago, 8580745, Chile
- Department of Chemical and Bioprocess Engineering, School of Engineering, Pontificia Universidad Católica de Chile, Santiago, 7820436, Chile
| | - Daniel Garrido
- Department of Chemical and Bioprocess Engineering, School of Engineering, Pontificia Universidad Católica de Chile, Santiago, 7820436, Chile
| | - Alberto J M Martin
- Network Biology Lab, Centro de Genómica y Bioinformática, Facultad de Ciencias, Universidad Mayor, Santiago, 8580745, Chile.
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Androulakis IP. The quest for digital health: From diseases to patients. Comput Chem Eng 2019. [DOI: 10.1016/j.compchemeng.2019.05.030] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/26/2022]
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Alkhudhayr H, Steggles J. A compositional framework for Boolean networks. Biosystems 2019; 186:103960. [PMID: 31022423 DOI: 10.1016/j.biosystems.2019.04.004] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/20/2018] [Revised: 02/04/2019] [Accepted: 04/08/2019] [Indexed: 11/26/2022]
Abstract
Boolean networks are a widely used qualitative approach for modelling and analysing biological systems. However, their application is restricted by the well-known state space explosion problem which means that modelling large-scale, realistic biological systems is challenging. In this paper we set out to facilitate the construction and analysis of large scale biological models by developing a formal framework for the composition of Boolean networks. The compositional approach we present is based on merging entities between Boolean networks using a binary Boolean operator and we formalise the preservation of behaviour under composition using a notion of compatibility. We investigate characterising compatibility in terms of the composed models by developing a trace alignment property. In particular, we use a formalisation of the interference that can occur in a composed model to define an extended trace alignment property that we show completely characterises compatibility.
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Affiliation(s)
- H Alkhudhayr
- School of Computing, Newcastle University, Newcastle upon Tyne, UK; Faculty of Computing and Information Technology, King Abdulaziz University, Rabigh, Saudi Arabia.
| | - J Steggles
- School of Computing, Newcastle University, Newcastle upon Tyne, UK.
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Anuradha, Patel S, Patle R, Parameswaran P, Jain A, Shard A. Design, computational studies, synthesis and biological evaluation of thiazole-based molecules as anticancer agents. Eur J Pharm Sci 2019; 134:20-30. [PMID: 30965082 DOI: 10.1016/j.ejps.2019.04.005] [Citation(s) in RCA: 37] [Impact Index Per Article: 7.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/22/2018] [Revised: 03/27/2019] [Accepted: 04/02/2019] [Indexed: 01/04/2023]
Abstract
BACKGROUND Abolition of cancer warrants effective treatment modalities directed towards specific pathways dysregulated in tumor proliferation and survival. The antiapoptotic Bcl-2 proteins are significantly altered in several tumor types which position them as striking targets for therapeutic intervention. Here we designed, computationally evaluated, synthesized, and biologically tested structurally optimized thiazole-based small molecules as anticancer agents. METHODS The virtually designed 200 molecules were subjected to rigorous docking and in silico ADME-Toxicity studies. Out of this, 23 skeletally diverse thiazole-based molecules which passed pan assay interference compounds (PAINS) filter and were synthetically feasible were synthesized in 3 steps using cheap and readily available reagents. The molecules were in vitro evaluated against Bcl-2-Jurkat, A-431 cancerous cell lines and ARPE-19 cell lines. Molecular Dynamics (MD) simulation studies were performed to analyse conformational changes induced by ligand 32 in Bcl-2. Flow cytometry analysis of compound 32 treated Bcl-2 cells was done to check apoptosis. RESULTS The molecules exhibited appreciable interactions with Bcl-2 and were having acceptable drug like properties as tested in silico. The multi step synthesis yielded 23 skeletally diverse thiazole-based molecules in up to 80% yield. The molecules simultaneously inhibited Bcl-2 Jurkat cells in vitro without causing detectable toxicity to normal cells (ARPE-19 cells). Among them molecules 32, 50, 53, 57 and 59 showed considerable activities against Bcl-2 Jurkat and A-431cell lines at concentrations ranging from 32-46 μM and 34-52 μM, respectively. The standard doxorubicin exhibited IC50 in Bcl-2 Jurkat and A-431cell lines at 45.87 μM and 42.37 μM, respectively. The molecule 32, almost equipotent in both the cell lines was subjected to molecular dynamics (MD) simulation with Bcl-2 protein (4IEH). It was shown that 32 interacted with protein majorly via hydrophobic interactions and few H-bonding interactions. Fluorescence-activated cell sorting (FACS) analysis established that molecule is dragging cancerous cells towards apoptosis. DISCUSSION AND CONCLUSION The chemical intuition was checked by computation coupled with biological results confirmed that thiazole-based hits have the potential to be developed downstream into potent and safer leads against antiapoptotic Bcl-2 cells.
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Affiliation(s)
- Anuradha
- Department of Medicinal Chemistry, National Institute of Pharmaceutical Education and Research Ahmedabad, Opposite Air Force Station, Gandhinagar, Gujarat, 382355, India
| | - Sagarkumar Patel
- Department of Medicinal Chemistry, National Institute of Pharmaceutical Education and Research Ahmedabad, Opposite Air Force Station, Gandhinagar, Gujarat, 382355, India
| | - Rajkumar Patle
- Department of Medicinal Chemistry, National Institute of Pharmaceutical Education and Research Ahmedabad, Opposite Air Force Station, Gandhinagar, Gujarat, 382355, India
| | - Preethi Parameswaran
- Department of Medicinal Chemistry, National Institute of Pharmaceutical Education and Research Ahmedabad, Opposite Air Force Station, Gandhinagar, Gujarat, 382355, India
| | - Alok Jain
- Department of Biotechnology, National Institute of Pharmaceutical Education and Research Ahmedabad, Opposite Air Force Station, Gandhinagar, Gujarat 382355, India.
| | - Amit Shard
- Department of Medicinal Chemistry, National Institute of Pharmaceutical Education and Research Ahmedabad, Opposite Air Force Station, Gandhinagar, Gujarat, 382355, India.
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Kirkpatrick C, Schuchardt A, Baltz D, Cotner S. Computer-Based and Bench-Based Undergraduate Research Experiences Produce Similar Attitudinal Outcomes. CBE LIFE SCIENCES EDUCATION 2019; 18:ar10. [PMID: 30821601 PMCID: PMC6757217 DOI: 10.1187/cbe.18-07-0112] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/14/2023]
Abstract
Course-based undergraduate research experiences (CUREs) have the potential to improve undergraduate biology education by involving large numbers of students in research. CUREs can take a variety of forms with different affordances and constraints, complicating the evaluation of design features that might contribute to successful outcomes. In this study, we compared students' responses to three different research experiences offered within the same course. One of the research experiences involved purely computational work, whereas the other two offerings were bench-based research experiences. We found that students who participated in computer-based research reported at least as much interest in their research projects, a higher sense of achievement, and a higher level of satisfaction with the course compared with students who did bench-based research projects. In open-ended comments, similar proportions of students in each research area expressed some sense of project ownership as contributing positively to their course experiences. Their comments also supported the finding that experiencing a sense of achievement was a predictor of course satisfaction. We conclude that both computer-based and bench-based CUREs can have positive impacts on students' attitudes. Development of more computer-based CUREs might allow larger numbers of students to benefit from participating in a research experience.
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Affiliation(s)
- Catherine Kirkpatrick
- Department of Biology Teaching and Learning, University of Minnesota, Minneapolis, MN 55455
| | - Anita Schuchardt
- Department of Biology Teaching and Learning, University of Minnesota, Minneapolis, MN 55455
| | - Daniel Baltz
- Department of Biology Teaching and Learning, University of Minnesota, Minneapolis, MN 55455
| | - Sehoya Cotner
- Department of Biology Teaching and Learning, University of Minnesota, Minneapolis, MN 55455
- *Address correspondence to: Sehoya Cotner ()
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