1
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Tummler K, Klipp E. Data integration strategies for whole-cell modeling. FEMS Yeast Res 2024; 24:foae011. [PMID: 38544322 PMCID: PMC11042497 DOI: 10.1093/femsyr/foae011] [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: 12/02/2023] [Revised: 03/15/2024] [Accepted: 03/26/2024] [Indexed: 04/25/2024] Open
Abstract
Data makes the world go round-and high quality data is a prerequisite for precise models, especially for whole-cell models (WCM). Data for WCM must be reusable, contain information about the exact experimental background, and should-in its entirety-cover all relevant processes in the cell. Here, we review basic requirements to data for WCM and strategies how to combine them. As a species-specific resource, we introduce the Yeast Cell Model Data Base (YCMDB) to illustrate requirements and solutions. We discuss recent standards for data as well as for computational models including the modeling process as data to be reported. We outline strategies for constructions of WCM despite their inherent complexity.
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Affiliation(s)
- Katja Tummler
- Humboldt-Universität zu Berlin, Faculty of Life Sciences, Institute of Biology, Theoretical Biophysics,, Invalidenstr. 42, 10115 Berlin, Germany
| | - Edda Klipp
- Humboldt-Universität zu Berlin, Faculty of Life Sciences, Institute of Biology, Theoretical Biophysics,, Invalidenstr. 42, 10115 Berlin, Germany
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2
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Kaizu K, Takahashi K. Technologies for whole-cell modeling: Genome-wide reconstruction of a cell in silico. Dev Growth Differ 2023; 65:554-564. [PMID: 37856476 DOI: 10.1111/dgd.12897] [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: 11/20/2022] [Revised: 09/06/2023] [Accepted: 10/14/2023] [Indexed: 10/21/2023]
Abstract
With advances in high-throughput, large-scale in vivo measurement and genome modification techniques at the single-nucleotide level, there is an increasing demand for the development of new technologies for the flexible design and control of cellular systems. Computer-aided design is a powerful tool to design new cells. Whole-cell modeling aims to integrate various cellular subsystems, determine their interactions and cooperative mechanisms, and predict comprehensive cellular behaviors by computational simulations on a genome-wide scale. It has been applied to prokaryotes, yeasts, and higher eukaryotic cells, and utilized in a wide range of applications, including production of valuable substances, drug discovery, and controlled differentiation. Whole-cell modeling, consisting of several thousand elements with diverse scales and properties, requires innovative model construction, simulation, and analysis techniques. Furthermore, whole-cell modeling has been extended to multiple scales, including high-resolution modeling at the single-nucleotide and single-amino acid levels and multicellular modeling of tissues and organs. This review presents an overview of the current state of whole-cell modeling, discusses the novel computational and experimental technologies driving it, and introduces further developments toward multihierarchical modeling on a whole-genome scale.
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Affiliation(s)
- Kazunari Kaizu
- RIKEN Center for Biosystems Dynamics Research, Osaka, Japan
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3
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Plante M. Epistemology of synthetic biology: a new theoretical framework based on its potential objects and objectives. Front Bioeng Biotechnol 2023; 11:1266298. [PMID: 38053845 PMCID: PMC10694798 DOI: 10.3389/fbioe.2023.1266298] [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: 07/24/2023] [Accepted: 11/07/2023] [Indexed: 12/07/2023] Open
Abstract
Synthetic biology is a new research field which attempts to understand, modify, and create new biological entities by adopting a modular and systemic conception of the living organisms. The development of synthetic biology has generated a pluralism of different approaches, bringing together a set of heterogeneous practices and conceptualizations from various disciplines, which can lead to confusion within the synthetic biology community as well as with other biological disciplines. I present in this manuscript an epistemological analysis of synthetic biology in order to better define this new discipline in terms of objects of study and specific objectives. First, I present and analyze the principal research projects developed at the foundation of synthetic biology, in order to establish an overview of the practices in this new emerging discipline. Then, I analyze an important scientometric study on synthetic biology to complete this overview. Afterwards, considering this analysis, I suggest a three-level classification of the object of study for synthetic biology (which are different kinds of living entities that can be built in the laboratory), based on three successive criteria: structural hierarchy, structural origin, functional origin. Finally, I propose three successively linked objectives in which synthetic biology can contribute (where the achievement of one objective led to the development of the other): interdisciplinarity collaboration (between natural, artificial, and theoretical sciences), knowledge of natural living entities (past, present, future, and alternative), pragmatic definition of the concept of "living" (that can be used by biologists in different contexts). Considering this new theoretical framework, based on its potential objects and objectives, I take the position that synthetic biology has not only the potential to develop its own new approach (which includes methods, objects, and objectives), distinct from other subdisciplines in biology, but also the ability to develop new knowledge on living entities.
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Affiliation(s)
- Mirco Plante
- Collège Montmorency, Laval, QC, Canada
- Centre Armand-Frappier Santé Biotechnologie, Institut National de la Recherche Scientifique, Université du Québec, Laval, QC, Canada
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4
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Loconte V, Chen J, Vanslembrouck B, Ekman AA, McDermott G, Le Gros MA, Larabell CA. Soft X-ray tomograms provide a structural basis for whole-cell modeling. FASEB J 2023; 37:e22681. [PMID: 36519968 PMCID: PMC10107707 DOI: 10.1096/fj.202200253r] [Citation(s) in RCA: 6] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/16/2022] [Revised: 11/13/2022] [Accepted: 11/21/2022] [Indexed: 12/23/2022]
Abstract
Developing in silico models that accurately reflect a whole, functional cell is an ongoing challenge in biology. Current efforts bring together mathematical models, probabilistic models, visual representations, and data to create a multi-scale description of cellular processes. A realistic whole-cell model requires imaging data since it provides spatial constraints and other critical cellular characteristics that are still impossible to obtain by calculation alone. This review introduces Soft X-ray Tomography (SXT) as a powerful imaging technique to visualize and quantify the mesoscopic (~25 nm spatial scale) organelle landscape in whole cells. SXT generates three-dimensional reconstructions of cellular ultrastructure and provides a measured structural framework for whole-cell modeling. Combining SXT with data from disparate technologies at varying spatial resolutions provides further biochemical details and constraints for modeling cellular mechanisms. We conclude, based on the results discussed here, that SXT provides a foundational dataset for a broad spectrum of whole-cell modeling experiments.
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Affiliation(s)
- Valentina Loconte
- Department of AnatomyUniversity of California San FranciscoSan FranciscoCaliforniaUSA
- Molecular Biophysics and Integrated Bioimaging DivisionLawrence Berkeley National LaboratoryBerkeleyCaliforniaUSA
- National Center for X‐ray TomographyAdvanced Light SourceBerkeleyCaliforniaUSA
| | - Jian‐Hua Chen
- Department of AnatomyUniversity of California San FranciscoSan FranciscoCaliforniaUSA
- Molecular Biophysics and Integrated Bioimaging DivisionLawrence Berkeley National LaboratoryBerkeleyCaliforniaUSA
- National Center for X‐ray TomographyAdvanced Light SourceBerkeleyCaliforniaUSA
| | - Bieke Vanslembrouck
- Department of AnatomyUniversity of California San FranciscoSan FranciscoCaliforniaUSA
- Molecular Biophysics and Integrated Bioimaging DivisionLawrence Berkeley National LaboratoryBerkeleyCaliforniaUSA
- National Center for X‐ray TomographyAdvanced Light SourceBerkeleyCaliforniaUSA
| | - Axel A. Ekman
- National Center for X‐ray TomographyAdvanced Light SourceBerkeleyCaliforniaUSA
| | - Gerry McDermott
- Department of AnatomyUniversity of California San FranciscoSan FranciscoCaliforniaUSA
- Molecular Biophysics and Integrated Bioimaging DivisionLawrence Berkeley National LaboratoryBerkeleyCaliforniaUSA
- National Center for X‐ray TomographyAdvanced Light SourceBerkeleyCaliforniaUSA
| | - Mark A. Le Gros
- Department of AnatomyUniversity of California San FranciscoSan FranciscoCaliforniaUSA
- Molecular Biophysics and Integrated Bioimaging DivisionLawrence Berkeley National LaboratoryBerkeleyCaliforniaUSA
- National Center for X‐ray TomographyAdvanced Light SourceBerkeleyCaliforniaUSA
| | - Carolyn A. Larabell
- Department of AnatomyUniversity of California San FranciscoSan FranciscoCaliforniaUSA
- Molecular Biophysics and Integrated Bioimaging DivisionLawrence Berkeley National LaboratoryBerkeleyCaliforniaUSA
- National Center for X‐ray TomographyAdvanced Light SourceBerkeleyCaliforniaUSA
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5
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Integrative modeling of the cell. Acta Biochim Biophys Sin (Shanghai) 2022; 54:1213-1221. [PMID: 36017893 PMCID: PMC9909318 DOI: 10.3724/abbs.2022115] [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] [Indexed: 12/29/2022] Open
Abstract
A whole-cell model represents certain aspects of the cell structure and/or function. Due to the high complexity of the cell, an integrative modeling approach is often taken to utilize all available information including experimental data, prior knowledge and prior models. In this review, we summarize an emerging workflow of whole-cell modeling into five steps: (i) gather information; (ii) represent the modeled system into modules; (iii) translate input information into scoring function; (iv) sample the whole-cell model; (v) validate and interpret the model. In particular, we propose the integrative modeling of the cell by combining available (whole-cell) models to maximize the accuracy, precision, and completeness. In addition, we list quantitative predictions of various aspects of cell biology from existing whole-cell models. Moreover, we discuss the remaining challenges and future directions, and highlight the opportunity to establish an integrative spatiotemporal multi-scale whole-cell model based on a community approach.
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6
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Ahn-Horst TA, Mille LS, Sun G, Morrison JH, Covert MW. An expanded whole-cell model of E. coli links cellular physiology with mechanisms of growth rate control. NPJ Syst Biol Appl 2022; 8:30. [PMID: 35986058 PMCID: PMC9391491 DOI: 10.1038/s41540-022-00242-9] [Citation(s) in RCA: 12] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/28/2022] [Accepted: 07/28/2022] [Indexed: 11/09/2022] Open
Abstract
Growth and environmental responses are essential for living organisms to survive and adapt to constantly changing environments. In order to simulate new conditions and capture dynamic responses to environmental shifts in a developing whole-cell model of E. coli, we incorporated additional regulation, including dynamics of the global regulator guanosine tetraphosphate (ppGpp), along with dynamics of amino acid biosynthesis and translation. With the model, we show that under perturbed ppGpp conditions, small molecule feedback inhibition pathways, in addition to regulation of expression, play a role in ppGpp regulation of growth. We also found that simulations with dysregulated amino acid synthesis pathways provide average amino acid concentration predictions that are comparable to experimental results but on the single-cell level, concentrations unexpectedly show regular fluctuations. Additionally, during both an upshift and downshift in nutrient availability, the simulated cell responds similarly with a transient increase in the mRNA:rRNA ratio. This additional simulation functionality should support a variety of new applications and expansions of the E. coli Whole-Cell Modeling Project.
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Affiliation(s)
- Travis A Ahn-Horst
- Department of Bioengineering, Stanford University, Stanford, CA, 94305, USA
| | | | - Gwanggyu Sun
- Department of Bioengineering, Stanford University, Stanford, CA, 94305, USA
| | - Jerry H Morrison
- Department of Bioengineering, Stanford University, Stanford, CA, 94305, USA
| | - Markus W Covert
- Department of Bioengineering, Stanford University, Stanford, CA, 94305, USA.
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7
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Kundu S. TemporalGSSA: a numerically robust R-wrapper to facilitate computation of a metabolite-specific and simulation time-dependent trajectory from stochastic simulation algorithm (SSA)-generated datasets. J Bioinform Comput Biol 2022; 20:2250018. [DOI: 10.1142/s0219720022500184] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022]
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8
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Adler SO, Spiesser TW, Uschner F, Münzner U, Hahn J, Krantz M, Klipp E. A yeast cell cycle model integrating stress, signaling, and physiology. FEMS Yeast Res 2022; 22:6592118. [PMID: 35617157 PMCID: PMC9246278 DOI: 10.1093/femsyr/foac026] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/14/2022] [Revised: 04/22/2022] [Accepted: 05/23/2022] [Indexed: 11/25/2022] Open
Abstract
The cell division cycle in eukaryotic cells is a series of highly coordinated molecular interactions that ensure that cell growth, duplication of genetic material, and actual cell division are precisely orchestrated to give rise to two viable progeny cells. Moreover, the cell cycle machinery is responsible for incorporating information about external cues or internal processes that the cell must keep track of to ensure a coordinated, timely progression of all related processes. This is most pronounced in multicellular organisms, but also a cardinal feature in model organisms such as baker's yeast. The complex and integrative behavior is difficult to grasp and requires mathematical modeling to fully understand the quantitative interplay of the single components within the entire system. Here, we present a self-oscillating mathematical model of the yeast cell cycle that comprises all major cyclins and their main regulators. Furthermore, it accounts for the regulation of the cell cycle machinery by a series of external stimuli such as mating pheromones and changes in osmotic pressure or nutrient quality. We demonstrate how the external perturbations modify the dynamics of cell cycle components and how the cell cycle resumes after adaptation to or relief from stress.
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Affiliation(s)
- Stephan O Adler
- Theoretical Biophysics, Humboldt-Universität zu Berlin, Invalidenstr. 42, 10115 Berlin, Germany
| | - Thomas W Spiesser
- Theoretical Biophysics, Humboldt-Universität zu Berlin, Invalidenstr. 42, 10115 Berlin, Germany
| | - Friedemann Uschner
- Theoretical Biophysics, Humboldt-Universität zu Berlin, Invalidenstr. 42, 10115 Berlin, Germany.,Institute for Medical Informatics and Biometry, Technische Universität Dresden, Fetscherstr. 74, 01307 Dresden, Sachsen, Germany
| | - Ulrike Münzner
- Theoretical Biophysics, Humboldt-Universität zu Berlin, Invalidenstr. 42, 10115 Berlin, Germany.,Laboratory of Cell Systems, Institute for Protein Research, Osaka University, 3-2 Yamadaoka, 565-0871, Suita, Osaka, Japan
| | - Jens Hahn
- Theoretical Biophysics, Humboldt-Universität zu Berlin, Invalidenstr. 42, 10115 Berlin, Germany
| | - Marcus Krantz
- Theoretical Biophysics, Humboldt-Universität zu Berlin, Invalidenstr. 42, 10115 Berlin, Germany
| | - Edda Klipp
- Theoretical Biophysics, Humboldt-Universität zu Berlin, Invalidenstr. 42, 10115 Berlin, Germany
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9
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Sun G, Ahn-Horst TA, Covert MW. The E. coli Whole-Cell Modeling Project. EcoSal Plus 2021; 9:eESP00012020. [PMID: 34242084 PMCID: PMC11163835 DOI: 10.1128/ecosalplus.esp-0001-2020] [Citation(s) in RCA: 13] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/16/2020] [Accepted: 05/26/2021] [Indexed: 12/22/2022]
Abstract
The Escherichia coli whole-cell modeling project seeks to create the most detailed computational model of an E. coli cell in order to better understand and predict the behavior of this model organism. Details about the approach, framework, and current version of the model are discussed. Currently, the model includes the functions of 43% of characterized genes, with ongoing efforts to include additional data and mechanisms. As additional information is incorporated in the model, its utility and predictive power will continue to increase, which means that discovery efforts can be accelerated by community involvement in the generation and inclusion of data. This project will be an invaluable resource to the E. coli community that could be used to verify expected physiological behavior, to predict new outcomes and testable hypotheses for more efficient experimental design iterations, and to evaluate heterogeneous data sets in the context of each other through deep curation.
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Affiliation(s)
- Gwanggyu Sun
- Department of Bioengineering, Stanford University, Stanford, California, USA
| | - Travis A. Ahn-Horst
- Department of Bioengineering, Stanford University, Stanford, California, USA
| | - Markus W. Covert
- Department of Bioengineering, Stanford University, Stanford, California, USA
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10
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Tryptophan Production Maximization in a Fed-Batch Bioreactor with Modified E. coli Cells, by Optimizing Its Operating Policy Based on an Extended Structured Cell Kinetic Model. Bioengineering (Basel) 2021; 8:bioengineering8120210. [PMID: 34940363 PMCID: PMC8698263 DOI: 10.3390/bioengineering8120210] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/18/2021] [Revised: 12/04/2021] [Accepted: 12/06/2021] [Indexed: 11/17/2022] Open
Abstract
Hybrid kinetic models, linking structured cell metabolic processes to the dynamics of macroscopic variables of the bioreactor, are more and more used in engineering evaluations to derive more precise predictions of the process dynamics under variable operating conditions. Depending on the cell model complexity, such a math tool can be used to evaluate the metabolic fluxes in relation to the bioreactor operating conditions, thus suggesting ways to genetically modify the microorganism for certain purposes. Even if development of such an extended dynamic model requires more experimental and computational efforts, its use is advantageous. The approached probative example refers to a model simulating the dynamics of nanoscale variables from several pathways of the central carbon metabolism (CCM) of Escherichia coli cells, linked to the macroscopic state variables of a fed-batch bioreactor (FBR) used for the tryptophan (TRP) production. The used E. coli strain was modified to replace the PTS system for glucose (GLC) uptake with a more efficient one. The study presents multiple elements of novelty: (i) the experimentally validated modular model itself, and (ii) its efficiency in computationally deriving an optimal operation policy of the FBR.
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11
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Gondal MN, Chaudhary SU. Navigating Multi-Scale Cancer Systems Biology Towards Model-Driven Clinical Oncology and Its Applications in Personalized Therapeutics. Front Oncol 2021; 11:712505. [PMID: 34900668 PMCID: PMC8652070 DOI: 10.3389/fonc.2021.712505] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/20/2021] [Accepted: 10/26/2021] [Indexed: 12/19/2022] Open
Abstract
Rapid advancements in high-throughput omics technologies and experimental protocols have led to the generation of vast amounts of scale-specific biomolecular data on cancer that now populates several online databases and resources. Cancer systems biology models built using this data have the potential to provide specific insights into complex multifactorial aberrations underpinning tumor initiation, development, and metastasis. Furthermore, the annotation of these single- and multi-scale models with patient data can additionally assist in designing personalized therapeutic interventions as well as aid in clinical decision-making. Here, we have systematically reviewed the emergence and evolution of (i) repositories with scale-specific and multi-scale biomolecular cancer data, (ii) systems biology models developed using this data, (iii) associated simulation software for the development of personalized cancer therapeutics, and (iv) translational attempts to pipeline multi-scale panomics data for data-driven in silico clinical oncology. The review concludes that the absence of a generic, zero-code, panomics-based multi-scale modeling pipeline and associated software framework, impedes the development and seamless deployment of personalized in silico multi-scale models in clinical settings.
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Affiliation(s)
- Mahnoor Naseer Gondal
- Biomedical Informatics Research Laboratory, Department of Biology, Syed Babar Ali School of Science and Engineering, Lahore University of Management Sciences, Lahore, Pakistan
- Department of Computational Medicine and Bioinformatics, University of Michigan, Ann Arbor, MI, United States
| | - Safee Ullah Chaudhary
- Biomedical Informatics Research Laboratory, Department of Biology, Syed Babar Ali School of Science and Engineering, Lahore University of Management Sciences, Lahore, Pakistan
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12
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MARIA G. A CCM-based modular and hybrid kinetic model to simulate the tryptophan synthesis in a fed-batch bioreactor using modified E. coli cells. Comput Chem Eng 2021. [DOI: 10.1016/j.compchemeng.2021.107450] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
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13
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Raveh B, Sun L, White KL, Sanyal T, Tempkin J, Zheng D, Bharath K, Singla J, Wang C, Zhao J, Li A, Graham NA, Kesselman C, Stevens RC, Sali A. Bayesian metamodeling of complex biological systems across varying representations. Proc Natl Acad Sci U S A 2021; 118:e2104559118. [PMID: 34453000 PMCID: PMC8536362 DOI: 10.1073/pnas.2104559118] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/26/2022] Open
Abstract
Comprehensive modeling of a whole cell requires an integration of vast amounts of information on various aspects of the cell and its parts. To divide and conquer this task, we introduce Bayesian metamodeling, a general approach to modeling complex systems by integrating a collection of heterogeneous input models. Each input model can in principle be based on any type of data and can describe a different aspect of the modeled system using any mathematical representation, scale, and level of granularity. These input models are 1) converted to a standardized statistical representation relying on probabilistic graphical models, 2) coupled by modeling their mutual relations with the physical world, and 3) finally harmonized with respect to each other. To illustrate Bayesian metamodeling, we provide a proof-of-principle metamodel of glucose-stimulated insulin secretion by human pancreatic β-cells. The input models include a coarse-grained spatiotemporal simulation of insulin vesicle trafficking, docking, and exocytosis; a molecular network model of glucose-stimulated insulin secretion signaling; a network model of insulin metabolism; a structural model of glucagon-like peptide-1 receptor activation; a linear model of a pancreatic cell population; and ordinary differential equations for systemic postprandial insulin response. Metamodeling benefits from decentralized computing, while often producing a more accurate, precise, and complete model that contextualizes input models as well as resolves conflicting information. We anticipate Bayesian metamodeling will facilitate collaborative science by providing a framework for sharing expertise, resources, data, and models, as exemplified by the Pancreatic β-Cell Consortium.
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Affiliation(s)
- Barak Raveh
- Department of Bioengineering and Therapeutic Sciences, University of California, San Francisco, CA 94158
- Quantitative Biosciences Institute, University of California, San Francisco, CA 94158
- School of Computer Science and Engineering, The Hebrew University of Jerusalem, Jerusalem 9190416, Israel
| | - Liping Sun
- iHuman Institute, ShanghaiTech University, Shanghai 201210, China
| | - Kate L White
- Department of Biological Sciences, Bridge Institute, University of Southern California, Los Angeles, CA 90089
| | - Tanmoy Sanyal
- Department of Bioengineering and Therapeutic Sciences, University of California, San Francisco, CA 94158
- Quantitative Biosciences Institute, University of California, San Francisco, CA 94158
| | - Jeremy Tempkin
- Department of Bioengineering and Therapeutic Sciences, University of California, San Francisco, CA 94158
- Quantitative Biosciences Institute, University of California, San Francisco, CA 94158
| | - Dongqing Zheng
- Mork Family Department of Chemical Engineering and Materials Science, Viterbi School of Engineering, University of Southern California, Los Angeles, CA 90089
| | - Kala Bharath
- Department of Bioengineering and Therapeutic Sciences, University of California, San Francisco, CA 94158
- Quantitative Biosciences Institute, University of California, San Francisco, CA 94158
| | - Jitin Singla
- Department of Biological Sciences, Bridge Institute, University of Southern California, Los Angeles, CA 90089
- Epstein Department of Industrial and Systems Engineering, The Viterbi School of Engineering, University of Southern California, Los Angeles, CA 90089
- Information Science Institute, The Viterbi School of Engineering, University of Southern California, Los Angeles, CA 90089
| | - Chenxi Wang
- iHuman Institute, ShanghaiTech University, Shanghai 201210, China
- School of Life Science and Technology, ShanghaiTech University, Shanghai 201210, China
| | - Jihui Zhao
- iHuman Institute, ShanghaiTech University, Shanghai 201210, China
| | - Angdi Li
- iHuman Institute, ShanghaiTech University, Shanghai 201210, China
- School of Life Science and Technology, ShanghaiTech University, Shanghai 201210, China
| | - Nicholas A Graham
- Mork Family Department of Chemical Engineering and Materials Science, Viterbi School of Engineering, University of Southern California, Los Angeles, CA 90089
| | - Carl Kesselman
- Epstein Department of Industrial and Systems Engineering, The Viterbi School of Engineering, University of Southern California, Los Angeles, CA 90089
- Information Science Institute, The Viterbi School of Engineering, University of Southern California, Los Angeles, CA 90089
| | - Raymond C Stevens
- iHuman Institute, ShanghaiTech University, Shanghai 201210, China
- Department of Biological Sciences, Bridge Institute, University of Southern California, Los Angeles, CA 90089
- School of Life Science and Technology, ShanghaiTech University, Shanghai 201210, China
| | - Andrej Sali
- Department of Bioengineering and Therapeutic Sciences, University of California, San Francisco, CA 94158;
- Quantitative Biosciences Institute, University of California, San Francisco, CA 94158
- Department of Pharmaceutical Chemistry, University of California, San Francisco, CA 94158
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14
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Rees-Garbutt J, Rightmyer J, Chalkley O, Marucci L, Grierson C. Testing Theoretical Minimal Genomes Using Whole-Cell Models. ACS Synth Biol 2021; 10:1598-1604. [PMID: 34111356 DOI: 10.1021/acssynbio.0c00515] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/08/2023]
Abstract
The minimal gene set for life has often been theorized, with at least ten produced for Mycoplasma genitalium (M. genitalium). Due to the difficulty of using M. genitalium in the lab, combined with its long replication time of 12-15 h, none of these theoretical minimal genomes have been tested, even with modern techniques. The publication of the M. genitalium whole-cell model provided the first opportunity to test them, simulating the genome edits in silico. We simulated minimal gene sets from the literature, finding that they produced in silico cells that did not divide. Using knowledge from previous research, we reintroduced specific essential and low essential genes in silico; enabling cellular division. This reinforces the need to identify species-specific low essential genes and their interactions. Any genome designs created using the currently incomplete and fragmented gene essentiality information will very likely require in vivo reintroductions to correct issues and produce dividing cells.
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Affiliation(s)
- Joshua Rees-Garbutt
- BrisSynBio, University of Bristol, Bristol BS8 1TQ, U.K
- School of Biological Sciences, University of Bristol, Bristol Life Sciences Building, 24 Tyndall Avenue, Bristol BS8 1TQ, U.K
| | - Jake Rightmyer
- School of Biological Sciences, University of Bristol, Bristol Life Sciences Building, 24 Tyndall Avenue, Bristol BS8 1TQ, U.K
| | - Oliver Chalkley
- BrisSynBio, University of Bristol, Bristol BS8 1TQ, U.K
- Bristol Centre for Complexity Sciences, Department of Engineering Mathematics, University of Bristol, Bristol BS8 1UB, U.K
- Department of Engineering Mathematics, University of Bristol, Bristol BS8 1UB, U.K
| | - Lucia Marucci
- BrisSynBio, University of Bristol, Bristol BS8 1TQ, U.K
- Department of Engineering Mathematics, University of Bristol, Bristol BS8 1UB, U.K
- School of Cellular and Molecular Medicine, University of Bristol, Bristol BS8 1UB, U.K
| | - Claire Grierson
- BrisSynBio, University of Bristol, Bristol BS8 1TQ, U.K
- School of Biological Sciences, University of Bristol, Bristol Life Sciences Building, 24 Tyndall Avenue, Bristol BS8 1TQ, U.K
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15
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Kadir SR, Lilja A, Gunn N, Strong C, Hughes RT, Bailey BJ, Rae J, Parton RG, McGhee J. Nanoscape, a data-driven 3D real-time interactive virtual cell environment. eLife 2021; 10:64047. [PMID: 34191720 PMCID: PMC8245131 DOI: 10.7554/elife.64047] [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: 10/15/2020] [Accepted: 06/04/2021] [Indexed: 12/15/2022] Open
Abstract
Our understanding of cellular and structural biology has reached unprecedented levels of detail, and computer visualisation techniques can be used to create three-dimensional (3D) representations of cells and their environment that are useful in both teaching and research. However, extracting and integrating the relevant scientific data, and then presenting them in an effective way, can pose substantial computational and aesthetic challenges. Here we report how computer artists, experts in computer graphics and cell biologists have collaborated to produce a tool called Nanoscape that allows users to explore and interact with 3D representations of cells and their environment that are both scientifically accurate and visually appealing. We believe that using Nanoscape as an immersive learning application will lead to an improved understanding of the complexities of cellular scales, densities and interactions compared with traditional learning modalities.
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Affiliation(s)
- Shereen R Kadir
- 3D Visualisation Aesthetics Lab, School of Art and Design, and the ARC Centre of Excellence in Convergent Bio-Nano Science and Technology, University of New South Wales, Sydney, Australia
| | - Andrew Lilja
- 3D Visualisation Aesthetics Lab, School of Art and Design, and the ARC Centre of Excellence in Convergent Bio-Nano Science and Technology, University of New South Wales, Sydney, Australia
| | - Nick Gunn
- 3D Visualisation Aesthetics Lab, School of Art and Design, and the ARC Centre of Excellence in Convergent Bio-Nano Science and Technology, University of New South Wales, Sydney, Australia
| | - Campbell Strong
- 3D Visualisation Aesthetics Lab, School of Art and Design, and the ARC Centre of Excellence in Convergent Bio-Nano Science and Technology, University of New South Wales, Sydney, Australia
| | - Rowan T Hughes
- 3D Visualisation Aesthetics Lab, School of Art and Design, and the ARC Centre of Excellence in Convergent Bio-Nano Science and Technology, University of New South Wales, Sydney, Australia
| | - Benjamin J Bailey
- 3D Visualisation Aesthetics Lab, School of Art and Design, and the ARC Centre of Excellence in Convergent Bio-Nano Science and Technology, University of New South Wales, Sydney, Australia
| | - James Rae
- Institute for Molecular Bioscience, ARC Centre of Excellence in Convergent Bio-Nano Science and Technology, and Centre for Microscopy and Microanalysis, University of Queensland, Brisbane, Australia
| | - Robert G Parton
- Institute for Molecular Bioscience, ARC Centre of Excellence in Convergent Bio-Nano Science and Technology, and Centre for Microscopy and Microanalysis, University of Queensland, Brisbane, Australia
| | - John McGhee
- 3D Visualisation Aesthetics Lab, School of Art and Design, and the ARC Centre of Excellence in Convergent Bio-Nano Science and Technology, University of New South Wales, Sydney, Australia
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16
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Covert MW, Gillies TE, Kudo T, Agmon E. A forecast for large-scale, predictive biology: Lessons from meteorology. Cell Syst 2021; 12:488-496. [PMID: 34139161 PMCID: PMC8217727 DOI: 10.1016/j.cels.2021.05.014] [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: 12/16/2020] [Revised: 04/01/2021] [Accepted: 05/18/2021] [Indexed: 11/19/2022]
Abstract
Quantitative systems biology, in which predictive mathematical models are constructed to guide the design of experiments and predict experimental outcomes, is at an exciting transition point, where the foundational scientific principles are becoming established, but the impact is not yet global. The next steps necessary for mathematical modeling to transform biological research and applications, in the same way it has already transformed other fields, is not completely clear. The purpose of this perspective is to forecast possible answers to this question-what needs to happen next-by drawing on the experience gained in another field, specifically meteorology. We review here a number of lessons learned in weather prediction that are directly relevant to biological systems modeling, and that we believe can enable the same kinds of global impact in our field as atmospheric modeling makes today.
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Affiliation(s)
- Markus W Covert
- Department of Bioengineering, Stanford University, Stanford, CA 94305, USA.
| | - Taryn E Gillies
- Department of Bioengineering, Stanford University, Stanford, CA 94305, USA
| | - Takamasa Kudo
- Department of Chemical and Systems Biology, Stanford University, Stanford, CA 94305, USA
| | - Eran Agmon
- Department of Bioengineering, Stanford University, Stanford, CA 94305, USA
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17
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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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18
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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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19
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Thessen AE, Walls RL, Vogt L, Singer J, Warren R, Buttigieg PL, Balhoff JP, Mungall CJ, McGuinness DL, Stucky BJ, Yoder MJ, Haendel MA. Transforming the study of organisms: Phenomic data models and knowledge bases. PLoS Comput Biol 2020; 16:e1008376. [PMID: 33232313 PMCID: PMC7685442 DOI: 10.1371/journal.pcbi.1008376] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/07/2023] Open
Abstract
The rapidly decreasing cost of gene sequencing has resulted in a deluge of genomic data from across the tree of life; however, outside a few model organism databases, genomic data are limited in their scientific impact because they are not accompanied by computable phenomic data. The majority of phenomic data are contained in countless small, heterogeneous phenotypic data sets that are very difficult or impossible to integrate at scale because of variable formats, lack of digitization, and linguistic problems. One powerful solution is to represent phenotypic data using data models with precise, computable semantics, but adoption of semantic standards for representing phenotypic data has been slow, especially in biodiversity and ecology. Some phenotypic and trait data are available in a semantic language from knowledge bases, but these are often not interoperable. In this review, we will compare and contrast existing ontology and data models, focusing on nonhuman phenotypes and traits. We discuss barriers to integration of phenotypic data and make recommendations for developing an operationally useful, semantically interoperable phenotypic data ecosystem.
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Affiliation(s)
- Anne E. Thessen
- Environmental and Molecular Toxicology, Oregon State University, Corvallis, Oregon, United States of America
- Ronin Institute for Independent Scholarship, Monclair, New Jersey, United States of America
| | - Ramona L. Walls
- Bio5 Institute, University of Arizona, Tucson, Arizona, United States of America
| | - Lars Vogt
- TIB Leibniz Information Centre for Science and Technology, Hannover, Germany
| | | | | | - Pier Luigi Buttigieg
- Alfred-Wegener-Institut, Helmholtz-Zentrum für Polar- und Meeresforschung, Bremerhaven, Germany
| | - James P. Balhoff
- Renaissance Computing Institute, University of North Carolina, Chapel Hill, North Carolina, United States of America
| | - Christopher J. Mungall
- Environmental Genomics and Systems Biology, Lawrence Berkeley National Laboratory, Berkeley, California, United States of America
| | | | - Brian J. Stucky
- Florida Museum of Natural History, University of Florida, Gainesville, Florida, United States of America
| | - Matthew J. Yoder
- Illinois Natural History Survey, Champaign, Illinois, United States of America
| | - Melissa A. Haendel
- Environmental and Molecular Toxicology, Oregon State University, Corvallis, Oregon, United States of America
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20
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Agmon E, Spangler RK. A Multi-Scale Approach to Modeling E. coli Chemotaxis. ENTROPY 2020; 22:e22101101. [PMID: 33286869 PMCID: PMC7597207 DOI: 10.3390/e22101101] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 07/31/2020] [Revised: 09/25/2020] [Accepted: 09/25/2020] [Indexed: 12/25/2022]
Abstract
The degree to which we can understand the multi-scale organization of cellular life is tied to how well our models can represent this organization and the processes that drive its evolution. This paper uses Vivarium-an engine for composing heterogeneous computational biology models into integrated, multi-scale simulations. Vivarium's approach is demonstrated by combining several sub-models of biophysical processes into a model of chemotactic E. coli that exchange molecules with their environment, express the genes required for chemotaxis, swim, grow, and divide. This model is developed incrementally, highlighting cross-compartment mechanisms that link E. coli to its environment, with models for: (1) metabolism and transport, with transport moving nutrients across the membrane boundary and metabolism converting them to useful metabolites, (2) transcription, translation, complexation, and degradation, with stochastic mechanisms that read real gene sequence data and consume base pairs and ATP to make proteins and complexes, and (3) the activity of flagella and chemoreceptors, which together support navigation in the environment.
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21
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Marucci L, Barberis M, Karr J, Ray O, Race PR, de Souza Andrade M, Grierson C, Hoffmann SA, Landon S, Rech E, Rees-Garbutt J, Seabrook R, Shaw W, Woods C. Computer-Aided Whole-Cell Design: Taking a Holistic Approach by Integrating Synthetic With Systems Biology. Front Bioeng Biotechnol 2020; 8:942. [PMID: 32850764 PMCID: PMC7426639 DOI: 10.3389/fbioe.2020.00942] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/29/2020] [Accepted: 07/21/2020] [Indexed: 01/03/2023] Open
Abstract
Computer-aided design (CAD) for synthetic biology promises to accelerate the rational and robust engineering of biological systems. It requires both detailed and quantitative mathematical and experimental models of the processes to (re)design biology, and software and tools for genetic engineering and DNA assembly. Ultimately, the increased precision in the design phase will have a dramatic impact on the production of designer cells and organisms with bespoke functions and increased modularity. CAD strategies require quantitative models of cells that can capture multiscale processes and link genotypes to phenotypes. Here, we present a perspective on how whole-cell, multiscale models could transform design-build-test-learn cycles in synthetic biology. We show how these models could significantly aid in the design and learn phases while reducing experimental testing by presenting case studies spanning from genome minimization to cell-free systems. We also discuss several challenges for the realization of our vision. The possibility to describe and build whole-cells in silico offers an opportunity to develop increasingly automatized, precise and accessible CAD tools and strategies.
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Affiliation(s)
- Lucia Marucci
- Department of Engineering Mathematics, University of Bristol, Bristol, United Kingdom.,School of Cellular and Molecular Medicine, University of Bristol, Bristol, United Kingdom.,Bristol Centre for Synthetic Biology (BrisSynBio), University of Bristol, Bristol, United Kingdom
| | - Matteo Barberis
- Systems Biology, School of Biosciences and Medicine, Faculty of Health and Medical Sciences, University of Surrey, Guildford, United Kingdom.,Centre for Mathematical and Computational Biology, CMCB, University of Surrey, Guildford, United Kingdom.,Synthetic Systems Biology and Nuclear Organization, Swammerdam Institute for Life Sciences, University of Amsterdam, Amsterdam, Netherlands
| | - Jonathan Karr
- Icahn Institute for Data Science and Genomic Technology, Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, NY, United States
| | - Oliver Ray
- Department of Computer Science, University of Bristol, Bristol, United Kingdom
| | - Paul R Race
- Bristol Centre for Synthetic Biology (BrisSynBio), University of Bristol, Bristol, United Kingdom.,School of Biochemistry, University of Bristol, Bristol, United Kingdom
| | - Miguel de Souza Andrade
- Brazilian Agricultural Research Corporation/National Institute of Science and Technology - Synthetic Biology, Brasília, Brazil.,Department of Cell Biology, Institute of Biological Sciences, University of Brasília, Brasília, Brazil
| | - Claire Grierson
- Bristol Centre for Synthetic Biology (BrisSynBio), University of Bristol, Bristol, United Kingdom.,School of Biological Sciences, University of Bristol, Bristol, United Kingdom
| | - Stefan Andreas Hoffmann
- Manchester Institute of Biotechnology, The University of Manchester, Manchester, United Kingdom
| | - Sophie Landon
- Department of Engineering Mathematics, University of Bristol, Bristol, United Kingdom.,Bristol Centre for Synthetic Biology (BrisSynBio), University of Bristol, Bristol, United Kingdom
| | - Elibio Rech
- Brazilian Agricultural Research Corporation/National Institute of Science and Technology - Synthetic Biology, Brasília, Brazil
| | - Joshua Rees-Garbutt
- Bristol Centre for Synthetic Biology (BrisSynBio), University of Bristol, Bristol, United Kingdom.,School of Biological Sciences, University of Bristol, Bristol, United Kingdom
| | - Richard Seabrook
- Elizabeth Blackwell Institute for Health Research (EBI), University of Bristol, Bristol, United Kingdom
| | - William Shaw
- Department of Bioengineering, Imperial College London, London, United Kingdom
| | - Christopher Woods
- Bristol Centre for Synthetic Biology (BrisSynBio), University of Bristol, Bristol, United Kingdom.,School of Chemistry, University of Bristol, Bristol, United Kingdom
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22
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Burke PEP, Campos CBDL, Costa LDF, Quiles MG. A biochemical network modeling of a whole-cell. Sci Rep 2020; 10:13303. [PMID: 32764598 PMCID: PMC7411072 DOI: 10.1038/s41598-020-70145-4] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/20/2019] [Accepted: 07/23/2020] [Indexed: 01/18/2023] Open
Abstract
All cellular processes can be ultimately understood in terms of respective fundamental biochemical interactions between molecules, which can be modeled as networks. Very often, these molecules are shared by more than one process, therefore interconnecting them. Despite this effect, cellular processes are usually described by separate networks with heterogeneous levels of detail, such as metabolic, protein-protein interaction, and transcription regulation networks. Aiming at obtaining a unified representation of cellular processes, we describe in this work an integrative framework that draws concepts from rule-based modeling. In order to probe the capabilities of the framework, we used an organism-specific database and genomic information to model the whole-cell biochemical network of the Mycoplasma genitalium organism. This modeling accounted for 15 cellular processes and resulted in a single component network, indicating that all processes are somehow interconnected. The topological analysis of the network showed structural consistency with biological networks in the literature. In order to validate the network, we estimated gene essentiality by simulating gene deletions and compared the results with experimental data available in the literature. We could classify 212 genes as essential, being 95% of them consistent with experimental results. Although we adopted a relatively simple organism as a case study, we suggest that the presented framework has the potential for paving the way to more integrated studies of whole organisms leading to a systemic analysis of cells on a broader scale. The modeling of other organisms using this framework could provide useful large-scale models for different fields of research such as bioengineering, network biology, and synthetic biology, and also provide novel tools for medical and industrial applications.
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Affiliation(s)
- Paulo E P Burke
- University of São Paulo, Bioinformatics Graduate Program, São Carlos, SP, Brazil.
| | - Claudia B de L Campos
- Institute of Science and Technology, Federal University of São Paulo, São José dos Campos, SP, Brazil
| | - Luciano da F Costa
- São Carlos Institute of Physics, University of São Paulo, São Carlos, SP, Brazil
| | - Marcos G Quiles
- Institute of Science and Technology, Federal University of São Paulo, São José dos Campos, SP, Brazil
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23
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Macklin DN, Ahn-Horst TA, Choi H, Ruggero NA, Carrera J, Mason JC, Sun G, Agmon E, DeFelice MM, Maayan I, Lane K, Spangler RK, Gillies TE, Paull ML, Akhter S, Bray SR, Weaver DS, Keseler IM, Karp PD, Morrison JH, Covert MW. Simultaneous cross-evaluation of heterogeneous E. coli datasets via mechanistic simulation. Science 2020; 369:eaav3751. [PMID: 32703847 PMCID: PMC7990026 DOI: 10.1126/science.aav3751] [Citation(s) in RCA: 76] [Impact Index Per Article: 19.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/11/2018] [Revised: 10/28/2019] [Accepted: 05/26/2020] [Indexed: 12/24/2022]
Abstract
The extensive heterogeneity of biological data poses challenges to analysis and interpretation. Construction of a large-scale mechanistic model of Escherichia coli enabled us to integrate and cross-evaluate a massive, heterogeneous dataset based on measurements reported by various groups over decades. We identified inconsistencies with functional consequences across the data, including that the total output of the ribosomes and RNA polymerases described by data are not sufficient for a cell to reproduce measured doubling times, that measured metabolic parameters are neither fully compatible with each other nor with overall growth, and that essential proteins are absent during the cell cycle-and the cell is robust to this absence. Finally, considering these data as a whole leads to successful predictions of new experimental outcomes, in this case protein half-lives.
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Affiliation(s)
- Derek N Macklin
- Department of Bioengineering, Stanford University, Stanford, CA 94305, USA
- Allen Discovery Center at Stanford University, Stanford University, Stanford, CA 94305, USA
| | - Travis A Ahn-Horst
- Department of Bioengineering, Stanford University, Stanford, CA 94305, USA
- Allen Discovery Center at Stanford University, Stanford University, Stanford, CA 94305, USA
| | - Heejo Choi
- Department of Bioengineering, Stanford University, Stanford, CA 94305, USA
- Allen Discovery Center at Stanford University, Stanford University, Stanford, CA 94305, USA
| | - Nicholas A Ruggero
- Allen Discovery Center at Stanford University, Stanford University, Stanford, CA 94305, USA
- Department of Chemical Engineering, Stanford University, Stanford, CA 94305, USA
| | - Javier Carrera
- Department of Bioengineering, Stanford University, Stanford, CA 94305, USA
- Allen Discovery Center at Stanford University, Stanford University, Stanford, CA 94305, USA
| | - John C Mason
- Department of Bioengineering, Stanford University, Stanford, CA 94305, USA
- Allen Discovery Center at Stanford University, Stanford University, Stanford, CA 94305, USA
| | - Gwanggyu Sun
- Department of Bioengineering, Stanford University, Stanford, CA 94305, USA
- Allen Discovery Center at Stanford University, Stanford University, Stanford, CA 94305, USA
| | - Eran Agmon
- Department of Bioengineering, Stanford University, Stanford, CA 94305, USA
- Allen Discovery Center at Stanford University, Stanford University, Stanford, CA 94305, USA
| | - Mialy M DeFelice
- Department of Bioengineering, Stanford University, Stanford, CA 94305, USA
- Allen Discovery Center at Stanford University, Stanford University, Stanford, CA 94305, USA
| | - Inbal Maayan
- Department of Bioengineering, Stanford University, Stanford, CA 94305, USA
- Allen Discovery Center at Stanford University, Stanford University, Stanford, CA 94305, USA
| | - Keara Lane
- Department of Bioengineering, Stanford University, Stanford, CA 94305, USA
- Allen Discovery Center at Stanford University, Stanford University, Stanford, CA 94305, USA
| | - Ryan K Spangler
- Department of Bioengineering, Stanford University, Stanford, CA 94305, USA
- Allen Discovery Center at Stanford University, Stanford University, Stanford, CA 94305, USA
| | - Taryn E Gillies
- Department of Bioengineering, Stanford University, Stanford, CA 94305, USA
- Allen Discovery Center at Stanford University, Stanford University, Stanford, CA 94305, USA
| | - Morgan L Paull
- Department of Bioengineering, Stanford University, Stanford, CA 94305, USA
| | - Sajia Akhter
- Department of Bioengineering, Stanford University, Stanford, CA 94305, USA
| | - Samuel R Bray
- Department of Bioengineering, Stanford University, Stanford, CA 94305, USA
| | | | | | | | - Jerry H Morrison
- Allen Discovery Center at Stanford University, Stanford University, Stanford, CA 94305, USA
| | - Markus W Covert
- Department of Bioengineering, Stanford University, Stanford, CA 94305, USA.
- Allen Discovery Center at Stanford University, Stanford University, Stanford, CA 94305, USA
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24
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Retinal Drug Delivery: Rethinking Outcomes for the Efficient Replication of Retinal Behavior. APPLIED SCIENCES-BASEL 2020. [DOI: 10.3390/app10124258] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/01/2023]
Abstract
The retina is a highly organized structure that is considered to be "an approachable part of the brain." It is attracting the interest of development scientists, as it provides a model neurovascular system. Over the last few years, we have been witnessing significant development in the knowledge of the mechanisms that induce the shape of the retinal vascular system, as well as knowledge of disease processes that lead to retina degeneration. Knowledge and understanding of how our vision works are crucial to creating a hardware-adaptive computational model that can replicate retinal behavior. The neuronal system is nonlinear and very intricate. It is thus instrumental to have a clear view of the neurophysiological and neuroanatomic processes and to take into account the underlying principles that govern the process of hardware transformation to produce an appropriate model that can be mapped to a physical device. The mechanistic and integrated computational models have enormous potential toward helping to understand disease mechanisms and to explain the associations identified in large model-free data sets. The approach used is modulated and based on different models of drug administration, including the geometry of the eye. This work aimed to review the recently used mathematical models to map a directed retinal network.
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25
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Abstract
Cell-free systems are a widely used research tool in systems and synthetic biology and a promising platform for manufacturing of proteins and chemicals. In the past, cell-free biology was primarily used to better understand fundamental biochemical processes. Notably, E. coli cell-free extracts were used in the 1960s to decipher the sequencing of the genetic code. Since then, the transcription and translation capabilities of cell-free systems have been repeatedly optimized to improve energy efficiency and product yield. Today, cell-free systems, in combination with the rise of synthetic biology, have taken on a new role as a promising technology for just-in-time manufacturing of therapeutically important biologics and high-value small molecules. They have also been implemented at an industrial scale for the production of antibodies and cytokines. In this review, we discuss the evolution of cell-free technologies, in particular advancements in extract preparation, cell-free protein synthesis, and cell-free metabolic engineering applications. We then conclude with a discussion of the mathematical modeling of cell-free systems. Mathematical modeling of cell-free processes could be critical to addressing performance bottlenecks and estimating the costs of cell-free manufactured products.
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26
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Watabe M, Arjunan SNV, Chew WX, Kaizu K, Takahashi K. Cooperativity transitions driven by higher-order oligomer formations in ligand-induced receptor dimerization. Phys Rev E 2019; 100:062407. [PMID: 31962468 DOI: 10.1103/physreve.100.062407] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/27/2019] [Indexed: 06/10/2023]
Abstract
While cooperativity in ligand-induced receptor dimerization has been linked with receptor-receptor couplings via minimal representations of physical observables, effects arising from higher-order oligomer, e.g., trimer and tetramer, formations of unobserved receptors have received less attention. Here we propose a dimerization model of ligand-induced receptors in multivalent form representing physical observables under basis vectors of various aggregated receptor states. Our simulations of multivalent models not only reject Wofsy-Goldstein parameter conditions for cooperativity, but show that higher-order oligomer formations can shift cooperativity from positive to negative.
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Affiliation(s)
- Masaki Watabe
- Laboratory for Biologically Inspired Computing, RIKEN Center for Biosystems Dynamics Research, Suita, Osaka 565-0874, Japan
| | - Satya N V Arjunan
- Laboratory for Biologically Inspired Computing, RIKEN Center for Biosystems Dynamics Research, Suita, Osaka 565-0874, Japan
- Lowy Cancer Research Centre, University of New South Wales, Sydney, New South Wales 2052, Australia
| | - Wei Xiang Chew
- Laboratory for Biologically Inspired Computing, RIKEN Center for Biosystems Dynamics Research, Suita, Osaka 565-0874, Japan
- Physics Department, Faculty of Science, University of Malaya, Kuala Lumpur 50603, Malaysia
| | - Kazunari Kaizu
- Laboratory for Biologically Inspired Computing, RIKEN Center for Biosystems Dynamics Research, Suita, Osaka 565-0874, Japan
| | - Koichi Takahashi
- Laboratory for Biologically Inspired Computing, RIKEN Center for Biosystems Dynamics Research, Suita, Osaka 565-0874, Japan
- Institute for Advanced Biosciences, Keio University, Fujisawa, Kanagawa 252-8520, Japan
- Department of Biosciences and Informatics, Keio University, Yokohama, Kanagawa 223-8522, Japan
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27
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Mahajan D, Sengupta S, Sen S. Strategies to improve microbial lipid production: Optimization techniques. BIOCATALYSIS AND AGRICULTURAL BIOTECHNOLOGY 2019. [DOI: 10.1016/j.bcab.2019.101321] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
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28
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Hernández Durán A, Grünewald K, Topf M. Conserved Central Intraviral Protein Interactome of the Herpesviridae Family. mSystems 2019; 4:e00295-19. [PMID: 31575665 PMCID: PMC6774017 DOI: 10.1128/msystems.00295-19] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/10/2019] [Accepted: 09/09/2019] [Indexed: 01/08/2023] Open
Abstract
Protein interactions are major driving forces behind the functional phenotypes of biological processes. As such, evolutionary footprints are reflected in system-level collections of protein-protein interactions (PPIs), i.e., protein interactomes. We conducted a comparative analysis of intraviral protein interactomes for representative species of each of the three subfamilies of herpesviruses (herpes simplex virus 1, human cytomegalovirus, and Epstein-Barr virus), which are highly prevalent etiologic agents of important human diseases. The intraviral interactomes were reconstructed by combining experimentally supported and computationally predicted protein-protein interactions. Using cross-species network comparison, we then identified family-wise conserved interactions and protein complexes, which we defined as a herpesviral "central" intraviral protein interactome. A large number of widely accepted conserved herpesviral protein complexes are present in this central intraviral interactome, encouragingly supporting the biological coherence of our results. Importantly, these protein complexes represent most, if not all, of the essential steps required during a productive life cycle. Hence the central intraviral protein interactome could plausibly represent a minimal infectious interactome of the herpesvirus family across a variety of hosts. Our data, which have been integrated into our herpesvirus interactomics database, HVint2.0, could assist in creating comprehensive system-level computational models of this viral lineage.IMPORTANCE Herpesviruses are an important socioeconomic burden for both humans and livestock. Throughout their long evolutionary history, individual herpesvirus species have developed remarkable host specificity, while collectively the Herpesviridae family has evolved to infect a large variety of eukaryotic hosts. The development of approaches to fight herpesvirus infections has been hampered by the complexity of herpesviruses' genomes, proteomes, and structural features. The data and insights generated by our study add to the understanding of the functional organization of herpesvirus-encoded proteins, specifically of family-wise conserved features defining essential components required for a productive infectious cycle across different hosts, which can contribute toward the conceptualization of antiherpetic infection strategies with an effect on a broader range of target species. All of the generated data have been made freely available through our HVint2.0 database, a dedicated resource of curated herpesvirus interactomics purposely created to promote and assist future studies in the field.
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Affiliation(s)
- Anna Hernández Durán
- Institute of Structural and Molecular Biology, Birkbeck College, University of London, London, United Kingdom
- Division of Structural Biology, Wellcome Centre for Human Genetics, University of Oxford, Oxford, United Kingdom
| | - Kay Grünewald
- Division of Structural Biology, Wellcome Centre for Human Genetics, University of Oxford, Oxford, United Kingdom
- Department of Structural Cell Biology of Viruses, Centre for Structural Systems Biology, Heinrich Pette Institute, Leibnitz Institute of Experimental Virology, University of Hamburg, Hamburg, Germany
| | - Maya Topf
- Institute of Structural and Molecular Biology, Birkbeck College, University of London, London, United Kingdom
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Watabe M, Arjunan SNV, Chew WX, Kaizu K, Takahashi K. Simulation of live-cell imaging system reveals hidden uncertainties in cooperative binding measurements. Phys Rev E 2019; 100:010402. [PMID: 31499827 DOI: 10.1103/physreve.100.010402] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/04/2018] [Indexed: 06/10/2023]
Abstract
We propose a computational method to quantitatively evaluate the systematic uncertainties that arise from undetectable sources in biological measurements using live-cell imaging techniques. We then demonstrate this method in measuring the biological cooperativity of molecular binding networks, in particular, ligand molecules binding to cell-surface receptor proteins. Our results show how the nonstatistical uncertainties lead to invalid identifications of the measured cooperativity. Through this computational scheme, the biological interpretation can be more objectively evaluated and understood under a specific experimental configuration of interest.
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Affiliation(s)
- Masaki Watabe
- Laboratory for Biologically Inspired Computing, RIKEN Center for Biosystems Dynamics Research, Suita, Osaka 565-0874, Japan
| | - Satya N V Arjunan
- Laboratory for Biologically Inspired Computing, RIKEN Center for Biosystems Dynamics Research, Suita, Osaka 565-0874, Japan
- Lowy Cancer Research Centre, The University of New South Wales, Sydney, Australia
| | - Wei Xiang Chew
- Laboratory for Biologically Inspired Computing, RIKEN Center for Biosystems Dynamics Research, Suita, Osaka 565-0874, Japan
- Physics Department, Faculty of Science, University of Malaya, Kuala Lumpur 50603, Malaysia
| | - Kazunari Kaizu
- Laboratory for Biologically Inspired Computing, RIKEN Center for Biosystems Dynamics Research, Suita, Osaka 565-0874, Japan
| | - Koichi Takahashi
- Laboratory for Biologically Inspired Computing, RIKEN Center for Biosystems Dynamics Research, Suita, Osaka 565-0874, Japan
- Institute for Advanced Biosciences, Keio University, Fujisawa, Kanagawa 252-8520, Japan
- Department of Biosciences and Informatics, Keio University, Yokohama, Kanagawa 223-8522, Japan
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30
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Human Systems Biology and Metabolic Modelling: A Review-From Disease Metabolism to Precision Medicine. BIOMED RESEARCH INTERNATIONAL 2019; 2019:8304260. [PMID: 31281846 PMCID: PMC6590590 DOI: 10.1155/2019/8304260] [Citation(s) in RCA: 42] [Impact Index Per Article: 8.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 11/01/2018] [Revised: 02/07/2019] [Accepted: 05/20/2019] [Indexed: 01/06/2023]
Abstract
In cell and molecular biology, metabolism is the only system that can be fully simulated at genome scale. Metabolic systems biology offers powerful abstraction tools to simulate all known metabolic reactions in a cell, therefore providing a snapshot that is close to its observable phenotype. In this review, we cover the 15 years of human metabolic modelling. We show that, although the past five years have not experienced large improvements in the size of the gene and metabolite sets in human metabolic models, their accuracy is rapidly increasing. We also describe how condition-, tissue-, and patient-specific metabolic models shed light on cell-specific changes occurring in the metabolic network, therefore predicting biomarkers of disease metabolism. We finally discuss current challenges and future promising directions for this research field, including machine/deep learning and precision medicine. In the omics era, profiling patients and biological processes from a multiomic point of view is becoming more common and less expensive. Starting from multiomic data collected from patients and N-of-1 trials where individual patients constitute different case studies, methods for model-building and data integration are being used to generate patient-specific models. Coupled with state-of-the-art machine learning methods, this will allow characterizing each patient's disease phenotype and delivering precision medicine solutions, therefore leading to preventative medicine, reduced treatment, and in silico clinical trials.
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31
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Pinu FR, Beale DJ, Paten AM, Kouremenos K, Swarup S, Schirra HJ, Wishart D. Systems Biology and Multi-Omics Integration: Viewpoints from the Metabolomics Research Community. Metabolites 2019; 9:E76. [PMID: 31003499 PMCID: PMC6523452 DOI: 10.3390/metabo9040076] [Citation(s) in RCA: 312] [Impact Index Per Article: 62.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/25/2019] [Revised: 04/15/2019] [Accepted: 04/16/2019] [Indexed: 02/07/2023] Open
Abstract
The use of multiple omics techniques (i.e., genomics, transcriptomics, proteomics, and metabolomics) is becoming increasingly popular in all facets of life science. Omics techniques provide a more holistic molecular perspective of studied biological systems compared to traditional approaches. However, due to their inherent data differences, integrating multiple omics platforms remains an ongoing challenge for many researchers. As metabolites represent the downstream products of multiple interactions between genes, transcripts, and proteins, metabolomics, the tools and approaches routinely used in this field could assist with the integration of these complex multi-omics data sets. The question is, how? Here we provide some answers (in terms of methods, software tools and databases) along with a variety of recommendations and a list of continuing challenges as identified during a peer session on multi-omics integration that was held at the recent 'Australian and New Zealand Metabolomics Conference' (ANZMET 2018) in Auckland, New Zealand (Sept. 2018). We envisage that this document will serve as a guide to metabolomics researchers and other members of the community wishing to perform multi-omics studies. We also believe that these ideas may allow the full promise of integrated multi-omics research and, ultimately, of systems biology to be realized.
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Affiliation(s)
- Farhana R Pinu
- The New Zealand Institute for Plant and Food Research Limited, Private Bag 92169, Auckland 1142, New Zealand.
| | - David J Beale
- Land and Water, Commonwealth Scientific and Industrial Research Organization (CSIRO), Ecosciences Precinct, Dutton Park, Dutton Park, QLD 4102, Australia.
| | - Amy M Paten
- Land and Water, Commonwealth Scientific and Industrial Research Organization (CSIRO), Research and Innovation Park, Acton, ACT 2601, Australia.
| | - Konstantinos Kouremenos
- Trajan Scientific and Medical, Ringwood, VIC 3134, Australia.
- Bio21 Institute, The University of Melbourne, Parkville, VIC 3010, Australia.
| | - Sanjay Swarup
- Department of Biological Sciences, National University of Singapore, Singapore 117411, Singapore.
| | - Horst J Schirra
- Centre for Advanced Imaging, The University of Queensland, St Lucia, QLD 4072, Australia.
| | - David Wishart
- Department of Biological Sciences, University of Alberta, Edmonton, AB T6G 2E8, Canada.
- Department of Computing Science, University of Alberta, Edmonton, AB T6G 2E8, Canada.
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32
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Jensen PR, Matos MRA, Sonnenschein N, Meier S. Combined In-Cell NMR and Simulation Approach to Probe Redox-Dependent Pathway Control. Anal Chem 2019; 91:5395-5402. [PMID: 30896922 DOI: 10.1021/acs.analchem.9b00660] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Dynamic response of intracellular reaction cascades to changing environments is a hallmark of living systems. As metabolism is complex, mechanistic models have gained popularity for describing the dynamic response of cellular metabolism and for identifying target genes for engineering. At the same time, the detailed tracking of transient metabolism in living cells on the subminute time scale has become amenable using dynamic nuclear polarization-enhanced 13C NMR. Here, we suggest an approach combining in-cell NMR spectroscopy with perturbation experiments and modeling to obtain evidence that the bottlenecks of yeast glycolysis depend on intracellular redox state. In pre-steady-state glycolysis, pathway bottlenecks shift from downstream to upstream reactions within a few seconds, consistent with a rapid decline in the NAD+/NADH ratio. Simulations using mechanistic models reproduce the experimentally observed response and help identify unforeseen biochemical events. Remaining inaccuracies in the computational models can be identified experimentally. The combined use of rapid injection NMR spectroscopy and in silico simulations provides a promising method for characterizing cellular reactions with increasing mechanistic detail.
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Affiliation(s)
- Pernille R Jensen
- Department of Chemistry, Department of Health Technology and The Novo Nordisk Foundation Center of Biosustainability , Technical University of Denmark , 2800 Kgs Lyngby , Denmark
| | - Marta R A Matos
- Department of Chemistry, Department of Health Technology and The Novo Nordisk Foundation Center of Biosustainability , Technical University of Denmark , 2800 Kgs Lyngby , Denmark
| | - Nikolaus Sonnenschein
- Department of Chemistry, Department of Health Technology and The Novo Nordisk Foundation Center of Biosustainability , Technical University of Denmark , 2800 Kgs Lyngby , Denmark
| | - Sebastian Meier
- Department of Chemistry, Department of Health Technology and The Novo Nordisk Foundation Center of Biosustainability , Technical University of Denmark , 2800 Kgs Lyngby , Denmark
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33
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Das B, Patil AR, Mitra P. A network-based zoning for parallel whole-cell simulation. Bioinformatics 2019; 35:88-94. [PMID: 29955764 DOI: 10.1093/bioinformatics/bty530] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/21/2017] [Accepted: 06/27/2018] [Indexed: 11/12/2022] Open
Abstract
Motivation In Computational Cell Biology, whole-cell modeling and simulation is an absolute requirement to analyze and explore the cell of an organism. Despite few individual efforts on modeling, the prime obstacle hindering its development and progress is its compute-intensive nature. Towards this end, little knowledge is available on how to reduce the enormous computational overhead and which computational systems will be of use. Results In this article, we present a network-based zoning approach that could potentially be utilized in the parallelization of whole-cell simulations. Firstly, we construct the protein-protein interaction graph of the whole-cell of an organism using experimental data from various sources. Based on protein interaction information, we predict protein locality and allocate confidence score to the interactions accordingly. We then identify the modules of strictly localized interacting proteins by performing interaction graph clustering based on the confidence score of the interactions. By applying this method to Escherichia coli K12, we identified 188 spatially localized clusters. After a thorough Gene Ontology-based analysis, we proved that the clusters are also in functional proximity. We then conducted Principal Coordinates Analysis to predict the spatial distribution of the clusters in the simulation space. Our automated computational techniques can partition the entire simulation space (cell) into simulation sub-cells. Each of these sub-cells can be simulated on separate computing units of the High-Performance Computing (HPC) systems. We benchmarked our method using proteins. However, our method can be extended easily to add other cellular components like DNA, RNA and metabolites. Availability and implementation . Supplementary information Supplementary data are available at Bioinformatics online.
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Affiliation(s)
- Barnali Das
- Department of Computer Science and Engineering, Indian Institute of Technology Kharagpur, West Bengal, India
| | - Abhijeet Rajendra Patil
- Department of Computer Science and Engineering, Indian Institute of Technology Kharagpur, West Bengal, India
| | - Pralay Mitra
- Department of Computer Science and Engineering, Indian Institute of Technology Kharagpur, West Bengal, India
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34
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Fröhlich F, Loos C, Hasenauer J. Scalable Inference of Ordinary Differential Equation Models of Biochemical Processes. Methods Mol Biol 2019; 1883:385-422. [PMID: 30547409 DOI: 10.1007/978-1-4939-8882-2_16] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
Ordinary differential equation models have become a standard tool for the mechanistic description of biochemical processes. If parameters are inferred from experimental data, such mechanistic models can provide accurate predictions about the behavior of latent variables or the process under new experimental conditions. Complementarily, inference of model structure can be used to identify the most plausible model structure from a set of candidates, and, thus, gain novel biological insight. Several toolboxes can infer model parameters and structure for small- to medium-scale mechanistic models out of the box. However, models for highly multiplexed datasets can require hundreds to thousands of state variables and parameters. For the analysis of such large-scale models, most algorithms require intractably high computation times. This chapter provides an overview of the state-of-the-art methods for parameter and model inference, with an emphasis on scalability.
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Affiliation(s)
- Fabian Fröhlich
- Institute of Computational Biology, Helmholtz Zentrum München, Neuherberg, Germany
- Center for Mathematics, Technische Universität München, Garching, Germany
| | - Carolin Loos
- Institute of Computational Biology, Helmholtz Zentrum München, Neuherberg, Germany
- Center for Mathematics, Technische Universität München, Garching, Germany
| | - Jan Hasenauer
- Institute of Computational Biology, Helmholtz Zentrum München, Neuherberg, Germany.
- Center for Mathematics, Technische Universität München, Garching, Germany.
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35
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Barbhuiya MA, Uddin A, Chakraborty S. A cross-talk on compositional dynamics and codon usage patterns of mitochondrial CYB gene in Echinodermata. Mitochondrial DNA A DNA Mapp Seq Anal 2018; 30:351-366. [PMID: 30582394 DOI: 10.1080/24701394.2018.1532414] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/27/2022]
Abstract
Codon usage bias (CUB) refers to a phenomenon in which some synonymous codons are used in mature mRNA at a higher frequency than other members codifying the same amino acid. CUB is mainly determined by mutation pressure and natural selection. We used bioinformatic tools to analyze the protein coding sequences of mitochondrial CYB gene in different classes of Echinodermata to understand the patterns of codon usage. The ENC values of CYB gene in five different classes of Echinodermata were 41.64, 30.33, 43.63, 41.11, and 41.33, which suggested that the CUB of this gene was low. The relative synonymous codon usage (RSCU) values showed that the patterns of over-represented and under-represented codons were different among different classes. Correspondence analysis indicated that the plots of CYB gene were different across classes, suggesting that the pattern of codon usage was also different among five classes under study. Highly significant correlation (p < .01) between overall nucleotide composition and its 3rd codon position indicated that both mutational pressure and natural selection had an influence on the codon usage bias of CYB gene. Furthermore, PR-2 bias plot analysis showed that both mutation pressure and natural selection might have affected the pattern of codon usage in CYB gene of Echinodermata.
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Affiliation(s)
| | - Arif Uddin
- b Department of Zoology , Moinul Hoque Choudhury Memorial Science College , Hailakandi , India
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36
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Coggan JS, Calì C, Keller D, Agus M, Boges D, Abdellah M, Kare K, Lehväslaiho H, Eilemann S, Jolivet RB, Hadwiger M, Markram H, Schürmann F, Magistretti PJ. A Process for Digitizing and Simulating Biologically Realistic Oligocellular Networks Demonstrated for the Neuro-Glio-Vascular Ensemble. Front Neurosci 2018; 12:664. [PMID: 30319342 PMCID: PMC6171468 DOI: 10.3389/fnins.2018.00664] [Citation(s) in RCA: 21] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/31/2018] [Accepted: 09/04/2018] [Indexed: 01/01/2023] Open
Abstract
One will not understand the brain without an integrated exploration of structure and function, these attributes being two sides of the same coin: together they form the currency of biological computation. Accordingly, biologically realistic models require the re-creation of the architecture of the cellular components in which biochemical reactions are contained. We describe here a process of reconstructing a functional oligocellular assembly that is responsible for energy supply management in the brain and creating a computational model of the associated biochemical and biophysical processes. The reactions that underwrite thought are both constrained by and take advantage of brain morphologies pertaining to neurons, astrocytes and the blood vessels that deliver oxygen, glucose and other nutrients. Each component of this neuro-glio-vasculature ensemble (NGV) carries-out delegated tasks, as the dynamics of this system provide for each cell-type its own energy requirements while including mechanisms that allow cooperative energy transfers. Our process for recreating the ultrastructure of cellular components and modeling the reactions that describe energy flow uses an amalgam of state-of the-art techniques, including digital reconstructions of electron micrographs, advanced data analysis tools, computational simulations and in silico visualization software. While we demonstrate this process with the NGV, it is equally well adapted to any cellular system for integrating multimodal cellular data in a coherent framework.
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Affiliation(s)
- Jay S Coggan
- Blue Brain Project, École Polytechnique Fédérale de Lausanne (EPFL), Geneva, Switzerland
| | - Corrado Calì
- Biological and Environmental Sciences and Engineering Division, King Abdullah University of Science and Technology, Thuwal, Saudi Arabia
| | - Daniel Keller
- Blue Brain Project, École Polytechnique Fédérale de Lausanne (EPFL), Geneva, Switzerland
| | - Marco Agus
- Visual Computing Center, King Abdullah University of Science and Technology, Thuwal, Saudi Arabia.,CRS4, Center of Research and Advanced Studies in Sardinia, Visual Computing, Pula, Italy
| | - Daniya Boges
- Biological and Environmental Sciences and Engineering Division, King Abdullah University of Science and Technology, Thuwal, Saudi Arabia
| | - Marwan Abdellah
- Blue Brain Project, École Polytechnique Fédérale de Lausanne (EPFL), Geneva, Switzerland
| | - Kalpana Kare
- Biological and Environmental Sciences and Engineering Division, King Abdullah University of Science and Technology, Thuwal, Saudi Arabia
| | - Heikki Lehväslaiho
- Biological and Environmental Sciences and Engineering Division, King Abdullah University of Science and Technology, Thuwal, Saudi Arabia.,CSC - IT Center for Science, Espoo, Finland
| | - Stefan Eilemann
- Blue Brain Project, École Polytechnique Fédérale de Lausanne (EPFL), Geneva, Switzerland
| | - Renaud Blaise Jolivet
- Département de Physique Nucléaire et Corpusculaire, University of Geneva, Geneva, Switzerland.,The European Organization for Nuclear Research, Geneva, Switzerland
| | - Markus Hadwiger
- Visual Computing Center, King Abdullah University of Science and Technology, Thuwal, Saudi Arabia
| | - Henry Markram
- Blue Brain Project, École Polytechnique Fédérale de Lausanne (EPFL), Geneva, Switzerland
| | - Felix Schürmann
- Blue Brain Project, École Polytechnique Fédérale de Lausanne (EPFL), Geneva, Switzerland
| | - Pierre J Magistretti
- Biological and Environmental Sciences and Engineering Division, King Abdullah University of Science and Technology, Thuwal, Saudi Arabia
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Cantarelli M, Marin B, Quintana A, Earnshaw M, Court R, Gleeson P, Dura-Bernal S, Silver RA, Idili G. Geppetto: a reusable modular open platform for exploring neuroscience data and models. Philos Trans R Soc Lond B Biol Sci 2018; 373:rstb.2017.0380. [PMID: 30201843 PMCID: PMC6158222 DOI: 10.1098/rstb.2017.0380] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 06/18/2018] [Indexed: 11/25/2022] Open
Abstract
Geppetto is an open-source platform that provides generic middleware infrastructure for building both online and desktop tools for visualizing neuroscience models and data and managing simulations. Geppetto underpins a number of neuroscience applications, including Open Source Brain (OSB), Virtual Fly Brain (VFB), NEURON-UI and NetPyNE-UI. OSB is used by researchers to create and visualize computational neuroscience models described in NeuroML and simulate them through the browser. VFB is the reference hub for Drosophila melanogaster neural anatomy and imaging data including neuropil, segmented neurons, microscopy stacks and gene expression pattern data. Geppetto is also being used to build a new user interface for NEURON, a widely used neuronal simulation environment, and for NetPyNE, a Python package for network modelling using NEURON. Geppetto defines domain agnostic abstractions used by all these applications to represent their models and data and offers a set of modules and components to integrate, visualize and control simulations in a highly accessible way. The platform comprises a backend which can connect to external data sources, model repositories and simulators together with a highly customizable frontend. This article is part of a discussion meeting issue ‘Connectome to behaviour: modelling C. elegans at cellular resolution’.
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Affiliation(s)
- Matteo Cantarelli
- OpenWorm Foundation, USA .,MetaCell Limited, UK.,Department of Neuroscience, Physiology and Pharmacology, University College London, UK
| | - Boris Marin
- Department of Neuroscience, Physiology and Pharmacology, University College London, UK.,Departamento de Física, Faculdade de Filosofia, Ciências e Letras de Ribeirão Preto, Universidade de São Paulo, Brazil
| | - Adrian Quintana
- MetaCell Limited, UK.,Department of Neuroscience, Physiology and Pharmacology, University College London, UK.,EyeSeeTea Limited, UK
| | - Matt Earnshaw
- Department of Neuroscience, Physiology and Pharmacology, University College London, UK
| | - Robert Court
- Institute for Adaptive and Neural Computation, School of Informatics, University of Edinburgh, Edinburgh, UK
| | - Padraig Gleeson
- Department of Neuroscience, Physiology and Pharmacology, University College London, UK
| | | | - R Angus Silver
- Department of Neuroscience, Physiology and Pharmacology, University College London, UK
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McDonald AG, Tipton KF, Davey GP. A mechanism for bistability in glycosylation. PLoS Comput Biol 2018; 14:e1006348. [PMID: 30074989 PMCID: PMC6093706 DOI: 10.1371/journal.pcbi.1006348] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/29/2017] [Revised: 08/15/2018] [Accepted: 07/04/2018] [Indexed: 12/29/2022] Open
Abstract
Glycosyltransferases are a class of enzymes that catalyse the posttranslational modification of proteins to produce a large number of glycoconjugate acceptors from a limited number of nucleotide-sugar donors. The products of one glycosyltransferase can be the substrates of several other enzymes, causing a combinatorial explosion in the number of possible glycan products. The kinetic behaviour of systems where multiple acceptor substrates compete for a single enzyme is presented, and the case in which high concentrations of an acceptor substrate are inhibitory as a result of abortive complex formation, is shown to result in non-Michaelian kinetics that can lead to bistability in an open system. A kinetic mechanism is proposed that is consistent with the available experimental evidence and provides a possible explanation for conflicting observations on the β-1,4-galactosyltransferases. Abrupt switching between steady states in networks of glycosyltransferase-catalysed reactions may account for the observed changes in glycosyl-epitopes in cancer cells.
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Affiliation(s)
- Andrew G. McDonald
- School of Biochemistry and Immunology, Trinity College Dublin, Dublin, Ireland
- * E-mail: (AGM); (GPD)
| | - Keith F. Tipton
- School of Biochemistry and Immunology, Trinity College Dublin, Dublin, Ireland
| | - Gavin P. Davey
- School of Biochemistry and Immunology, Trinity College Dublin, Dublin, Ireland
- * E-mail: (AGM); (GPD)
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Luthert PJ, Serrano L, Kiel C. Opportunities and Challenges of Whole-Cell and -Tissue Simulations of the Outer Retina in Health and Disease. Annu Rev Biomed Data Sci 2018. [DOI: 10.1146/annurev-biodatasci-080917-013356] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Abstract
Visual processing starts in the outer retina, where photoreceptor cells sense photons that trigger electrical responses. Retinal pigment epithelial cells are located external to the photoreceptor layer and have critical functions in supporting cell and tissue homeostasis and thus sustaining a healthy retina. The high level of specialization makes the retina vulnerable to alterations that promote retinal degeneration. In this review, we discuss opportunities and challenges in proposing whole-cell and -tissue simulations of the human outer retina. An implicit position taken throughout this review is that mapping diverse data sets onto integrative computational models is likely to be a pivotal approach to understanding complex disease and developing novel interventions.
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Affiliation(s)
- Philip J. Luthert
- Institute of Ophthalmology and National Institute for Health Research (NIHR) Biomedical Research Centre, University College London, London EC1V 9EL, United Kingdom
| | - Luis Serrano
- European Molecular Biology Laboratory (EMBL)/Centre for Genomic Regulation (CRG) Systems Biology Research Unit, Barcelona Institute of Science and Technology, 08003 Barcelona, Spain
- Universitat Pompeu Fabra (UPF), 08003 Barcelona, Spain
- Institució Catalana de Recerca i Estudis Avançats (ICREA), 08010 Barcelona, Spain
| | - Christina Kiel
- European Molecular Biology Laboratory (EMBL)/Centre for Genomic Regulation (CRG) Systems Biology Research Unit, Barcelona Institute of Science and Technology, 08003 Barcelona, Spain
- Universitat Pompeu Fabra (UPF), 08003 Barcelona, Spain
- Systems Biology Ireland, Charles Institute of Dermatology, and School of Medicine, University College Dublin, Belfield, Dublin 4, Ireland
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40
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In silico optimization of a bioreactor with an E. coli culture for tryptophan production by using a structured model coupling the oscillating glycolysis and tryptophan synthesis. Chem Eng Res Des 2018. [DOI: 10.1016/j.cherd.2018.05.011] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
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41
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Hellander S, Petzold L. Reaction rates for reaction-diffusion kinetics on unstructured meshes. J Chem Phys 2018; 146:064101. [PMID: 28201913 DOI: 10.1063/1.4975167] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/03/2023] Open
Abstract
The reaction-diffusion master equation is a stochastic model often utilized in the study of biochemical reaction networks in living cells. It is applied when the spatial distribution of molecules is important to the dynamics of the system. A viable approach to resolve the complex geometry of cells accurately is to discretize space with an unstructured mesh. Diffusion is modeled as discrete jumps between nodes on the mesh, and the diffusion jump rates can be obtained through a discretization of the diffusion equation on the mesh. Reactions can occur when molecules occupy the same voxel. In this paper, we develop a method for computing accurate reaction rates between molecules occupying the same voxel in an unstructured mesh. For large voxels, these rates are known to be well approximated by the reaction rates derived by Collins and Kimball, but as the mesh is refined, no analytical expression for the rates exists. We reduce the problem of computing accurate reaction rates to a pure preprocessing step, depending only on the mesh and not on the model parameters, and we devise an efficient numerical scheme to estimate them to high accuracy. We show in several numerical examples that as we refine the mesh, the results obtained with the reaction-diffusion master equation approach those of a more fine-grained Smoluchowski particle-tracking model.
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Affiliation(s)
- Stefan Hellander
- Department of Computer Science, University of California, Santa Barbara, California 93106-5070, USA
| | - Linda Petzold
- Department of Computer Science, University of California, Santa Barbara, California 93106-5070, USA
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42
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Martínez O, Reyes-Valdés MH. On an algorithmic definition for the components of the minimal cell. PLoS One 2018; 13:e0198222. [PMID: 29856803 PMCID: PMC5983409 DOI: 10.1371/journal.pone.0198222] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/26/2018] [Accepted: 05/15/2018] [Indexed: 11/19/2022] Open
Abstract
Living cells are highly complex systems comprising a multitude of elements that are engaged in the many convoluted processes observed during the cell cycle. However, not all elements and processes are essential for cell survival and reproduction under steady-state environmental conditions. To distinguish between essential from expendable cell components and thus define the ‘minimal cell’ and the corresponding ‘minimal genome’, we postulate that the synthesis of all cell elements can be represented as a finite set of binary operators, and within this framework we show that cell elements that depend on their previous existence to be synthesized are those that are essential for cell survival. An algorithm to distinguish essential cell elements is presented and demonstrated within an interactome. Data and functions implementing the algorithm are given as supporting information. We expect that this algorithmic approach will lead to the determination of the complete interactome of the minimal cell, which could then be experimentally validated. The assumptions behind this hypothesis as well as its consequences for experimental and theoretical biology are discussed.
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Affiliation(s)
- Octavio Martínez
- Unidad de Genómica Avanzada, Laboratorio Nacional de Genómica para la Biodiversidad (LANGEBIO), Centro de Investigación y Estudios Avanzados del Instituto Politécnico Nacional, Irapuato, Guanajuato, México
- * E-mail:
| | - M. Humberto Reyes-Valdés
- Graduate Program on Plant Genetic Resources for Arid Lands, Universidad Autónoma Agraria Antonio Narro, Saltillo, Coahuila, México
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43
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Singla J, McClary KM, White KL, Alber F, Sali A, Stevens RC. Opportunities and Challenges in Building a Spatiotemporal Multi-scale Model of the Human Pancreatic β Cell. Cell 2018; 173:11-19. [PMID: 29570991 PMCID: PMC6014618 DOI: 10.1016/j.cell.2018.03.014] [Citation(s) in RCA: 45] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/15/2017] [Revised: 11/25/2017] [Accepted: 03/06/2018] [Indexed: 12/25/2022]
Abstract
The construction of a predictive model of an entire eukaryotic cell that describes its dynamic structure from atomic to cellular scales is a grand challenge at the intersection of biology, chemistry, physics, and computer science. Having such a model will open new dimensions in biological research and accelerate healthcare advancements. Developing the necessary experimental and modeling methods presents abundant opportunities for a community effort to realize this goal. Here, we present a vision for creation of a spatiotemporal multi-scale model of the pancreatic β-cell, a relevant target for understanding and modulating the pathogenesis of diabetes.
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Affiliation(s)
- Jitin Singla
- Molecular and Computational Biology, Department of Biological Sciences, University of Southern California, Los Angeles, CA 90089, USA; Department of Biological Sciences, Bridge Institute, Michelson Center for Convergent Bioscience, University of Southern California, Los Angeles, CA 90089, USA
| | - Kyle M McClary
- Department of Chemistry, Bridge Institute, Michelson Center for Convergent Bioscience, University of Southern California, Los Angeles, CA 90089, USA
| | - Kate L White
- Department of Biological Sciences, Bridge Institute, Michelson Center for Convergent Bioscience, University of Southern California, Los Angeles, CA 90089, USA; Department of Chemistry, Bridge Institute, Michelson Center for Convergent Bioscience, University of Southern California, Los Angeles, CA 90089, USA
| | - Frank Alber
- Molecular and Computational Biology, Department of Biological Sciences, University of Southern California, Los Angeles, CA 90089, USA; Department of Biological Sciences, Bridge Institute, Michelson Center for Convergent Bioscience, University of Southern California, Los Angeles, CA 90089, USA.
| | - Andrej Sali
- California Institute for Quantitative Biosciences, Department of Bioengineering and Therapeutic Sciences, Department of Pharmaceutical Chemistry, University of California, San Francisco, San Francisco, CA 94158, USA.
| | - Raymond C Stevens
- Department of Biological Sciences, Bridge Institute, Michelson Center for Convergent Bioscience, University of Southern California, Los Angeles, CA 90089, USA; Department of Chemistry, Bridge Institute, Michelson Center for Convergent Bioscience, University of Southern California, Los Angeles, CA 90089, USA.
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44
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Song Y, Yang S, Lei J. ParaCells: A GPU Architecture for Cell-Centered Models in Computational Biology. IEEE/ACM TRANSACTIONS ON COMPUTATIONAL BIOLOGY AND BIOINFORMATICS 2018; 16:994-1006. [PMID: 29994073 DOI: 10.1109/tcbb.2018.2814570] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/08/2023]
Abstract
In computational biology, the hierarchy of biological systems requires the development of flexible and powerful computational tools. Graphics processing unit (GPU) architecture has been a suitable device for parallel computing in simulating multi-cellular systems. However, in modeling complex biological systems, scientists often face two tasks, mathematical formulation and skillful programming. In particular, specific programming skills are needed for GPU programming. Therefore, the development of an easy-to-use computational architecture, which utilizes GPU for parallel computing and provides intuitive interfaces for simple implementation, is needed so that general scientists can perform GPU simulations without knowing much about the GPU architecture. Here, we introduce ParaCells, a cell-centered GPU simulation architecture for NVIDIA compute unified device architecture (CUDA). ParaCells was designed as a versatile architecture that connects the user logic (in C++) with NVIDIA CUDA runtime and is specific to the modeling of multi-cellular systems. An advantage of ParaCells is its object-oriented model declaration, which allows it to be widely applied to many biological systems through the combination of basic biological concepts. We test ParaCells with two applications. Both applications are significantly faster when compared with sequential as well as parallel OpenMP and OpenACC implementations. Moreover, the simulation programs based on ParaCells are cleaner and more readable than other versions.
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45
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Xu N, Ye C, Liu L. Genome-scale biological models for industrial microbial systems. Appl Microbiol Biotechnol 2018; 102:3439-3451. [PMID: 29497793 DOI: 10.1007/s00253-018-8803-1] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/29/2017] [Revised: 01/19/2018] [Accepted: 01/21/2018] [Indexed: 01/08/2023]
Abstract
The primary aims and challenges associated with microbial fermentation include achieving faster cell growth, higher productivity, and more robust production processes. Genome-scale biological models, predicting the formation of an interaction among genetic materials, enzymes, and metabolites, constitute a systematic and comprehensive platform to analyze and optimize the microbial growth and production of biological products. Genome-scale biological models can help optimize microbial growth-associated traits by simulating biomass formation, predicting growth rates, and identifying the requirements for cell growth. With regard to microbial product biosynthesis, genome-scale biological models can be used to design product biosynthetic pathways, accelerate production efficiency, and reduce metabolic side effects, leading to improved production performance. The present review discusses the development of microbial genome-scale biological models since their emergence and emphasizes their pertinent application in improving industrial microbial fermentation of biological products.
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Affiliation(s)
- Nan Xu
- State Key Laboratory of Food Science and Technology, Jiangnan University, 1800 Lihu Road, Wuxi, Jiangsu, 214122, China.,College of Bioscience and Biotechnology, Yangzhou University, Yangzhou, Jiangsu, 225009, China.,The Laboratory of Food Microbial-Manufacturing Engineering, Jiangnan University, Wuxi, 214122, China
| | - Chao Ye
- State Key Laboratory of Food Science and Technology, Jiangnan University, 1800 Lihu Road, Wuxi, Jiangsu, 214122, China.,Key Laboratory of Industrial Biotechnology, Ministry of Education, School of Biotechnology, Jiangnan University, 1800 Lihu Road, Wuxi, Jiangsu, 214122, China.,The Laboratory of Food Microbial-Manufacturing Engineering, Jiangnan University, Wuxi, 214122, China
| | - Liming Liu
- State Key Laboratory of Food Science and Technology, Jiangnan University, 1800 Lihu Road, Wuxi, Jiangsu, 214122, China. .,Key Laboratory of Industrial Biotechnology, Ministry of Education, School of Biotechnology, Jiangnan University, 1800 Lihu Road, Wuxi, Jiangsu, 214122, China. .,The Laboratory of Food Microbial-Manufacturing Engineering, Jiangnan University, Wuxi, 214122, China.
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46
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Smith CA, Yates CA. Spatially extended hybrid methods: a review. J R Soc Interface 2018; 15:20170931. [PMID: 29491179 PMCID: PMC5832735 DOI: 10.1098/rsif.2017.0931] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/11/2017] [Accepted: 02/08/2018] [Indexed: 12/13/2022] Open
Abstract
Many biological and physical systems exhibit behaviour at multiple spatial, temporal or population scales. Multiscale processes provide challenges when they are to be simulated using numerical techniques. While coarser methods such as partial differential equations are typically fast to simulate, they lack the individual-level detail that may be required in regions of low concentration or small spatial scale. However, to simulate at such an individual level throughout a domain and in regions where concentrations are high can be computationally expensive. Spatially coupled hybrid methods provide a bridge, allowing for multiple representations of the same species in one spatial domain by partitioning space into distinct modelling subdomains. Over the past 20 years, such hybrid methods have risen to prominence, leading to what is now a very active research area across multiple disciplines including chemistry, physics and mathematics. There are three main motivations for undertaking this review. Firstly, we have collated a large number of spatially extended hybrid methods and presented them in a single coherent document, while comparing and contrasting them, so that anyone who requires a multiscale hybrid method will be able to find the most appropriate one for their need. Secondly, we have provided canonical examples with algorithms and accompanying code, serving to demonstrate how these types of methods work in practice. Finally, we have presented papers that employ these methods on real biological and physical problems, demonstrating their utility. We also consider some open research questions in the area of hybrid method development and the future directions for the field.
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Affiliation(s)
- Cameron A Smith
- Centre for Mathematical Biology, Department of Mathematical Sciences, University of Bath, Claverton Down, Bath BA2 7AY, UK
| | - Christian A Yates
- Centre for Mathematical Biology, Department of Mathematical Sciences, University of Bath, Claverton Down, Bath BA2 7AY, UK
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47
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Maria G, Gijiu CL, Maria C, Tociu C. Interference of the oscillating glycolysis with the oscillating tryptophan synthesis in the E. coli cells. Comput Chem Eng 2018. [DOI: 10.1016/j.compchemeng.2017.10.003] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/01/2022]
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48
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Hellander S, Hellander A, Petzold L. Mesoscopic-microscopic spatial stochastic simulation with automatic system partitioning. J Chem Phys 2017; 147:234101. [PMID: 29272930 PMCID: PMC5732015 DOI: 10.1063/1.5002773] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/01/2017] [Accepted: 11/27/2017] [Indexed: 01/02/2023] Open
Abstract
The reaction-diffusion master equation (RDME) is a model that allows for efficient on-lattice simulation of spatially resolved stochastic chemical kinetics. Compared to off-lattice hard-sphere simulations with Brownian dynamics or Green's function reaction dynamics, the RDME can be orders of magnitude faster if the lattice spacing can be chosen coarse enough. However, strongly diffusion-controlled reactions mandate a very fine mesh resolution for acceptable accuracy. It is common that reactions in the same model differ in their degree of diffusion control and therefore require different degrees of mesh resolution. This renders mesoscopic simulation inefficient for systems with multiscale properties. Mesoscopic-microscopic hybrid methods address this problem by resolving the most challenging reactions with a microscale, off-lattice simulation. However, all methods to date require manual partitioning of a system, effectively limiting their usefulness as "black-box" simulation codes. In this paper, we propose a hybrid simulation algorithm with automatic system partitioning based on indirect a priori error estimates. We demonstrate the accuracy and efficiency of the method on models of diffusion-controlled networks in 3D.
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Affiliation(s)
- Stefan Hellander
- Department of Information Technology, Uppsala University, P.O.Box 337, SE-75105 Uppsala, Sweden
| | - Andreas Hellander
- Department of Information Technology, Uppsala University, P.O.Box 337, SE-75105 Uppsala, Sweden
| | - Linda Petzold
- Department of Computer Science, University of California, Santa Barbara, California 93106-5070, USA
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49
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Goldberg AP, Szigeti B, Chew YH, Sekar JA, Roth YD, Karr JR. Emerging whole-cell modeling principles and methods. Curr Opin Biotechnol 2017; 51:97-102. [PMID: 29275251 DOI: 10.1016/j.copbio.2017.12.013] [Citation(s) in RCA: 38] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/24/2017] [Revised: 12/07/2017] [Accepted: 12/11/2017] [Indexed: 11/16/2022]
Abstract
Whole-cell computational models aim to predict cellular phenotypes from genotype by representing the entire genome, the structure and concentration of each molecular species, each molecular interaction, and the extracellular environment. Whole-cell models have great potential to transform bioscience, bioengineering, and medicine. However, numerous challenges remain to achieve whole-cell models. Nevertheless, researchers are beginning to leverage recent progress in measurement technology, bioinformatics, data sharing, rule-based modeling, and multi-algorithmic simulation to build the first whole-cell models. We anticipate that ongoing efforts to develop scalable whole-cell modeling tools will enable dramatically more comprehensive and more accurate models, including models of human cells.
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Affiliation(s)
- Arthur P Goldberg
- Icahn Institute for Genomics and Multiscale Biology, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA; Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
| | - Balázs Szigeti
- Icahn Institute for Genomics and Multiscale Biology, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA; Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
| | - Yin Hoon Chew
- Icahn Institute for Genomics and Multiscale Biology, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA; Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
| | - John Ap Sekar
- Icahn Institute for Genomics and Multiscale Biology, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA; Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
| | - Yosef D Roth
- Icahn Institute for Genomics and Multiscale Biology, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA; Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
| | - Jonathan R Karr
- Icahn Institute for Genomics and Multiscale Biology, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA; Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA.
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50
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Glass JI, Merryman C, Wise KS, Hutchison CA, Smith HO. Minimal Cells-Real and Imagined. Cold Spring Harb Perspect Biol 2017; 9:cshperspect.a023861. [PMID: 28348033 DOI: 10.1101/cshperspect.a023861] [Citation(s) in RCA: 43] [Impact Index Per Article: 6.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/06/2023]
Abstract
A minimal cell is one whose genome only encodes the minimal set of genes necessary for the cell to survive. Scientific reductionism postulates the best way to learn the first principles of cellular biology would be to use a minimal cell in which the functions of all genes and components are understood. The genes in a minimal cell are, by definition, essential. In 2016, synthesis of a genome comprised of only the set of essential and quasi-essential genes encoded by the bacterium Mycoplasma mycoides created a near-minimal bacterial cell. This organism performs the cellular functions common to all organisms. It replicates DNA, transcribes RNA, translates proteins, undergoes cell division, and little else. In this review, we examine this organism and contrast it with other bacteria that have been used as surrogates for a minimal cell.
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Affiliation(s)
- John I Glass
- Synthetic Biology and Bioenergy Group, J. Craig Venter Institute, La Jolla, California 92037
| | - Chuck Merryman
- Synthetic Biology and Bioenergy Group, J. Craig Venter Institute, La Jolla, California 92037
| | - Kim S Wise
- Synthetic Biology and Bioenergy Group, J. Craig Venter Institute, La Jolla, California 92037
| | - Clyde A Hutchison
- Synthetic Biology and Bioenergy Group, J. Craig Venter Institute, La Jolla, California 92037
| | - Hamilton O Smith
- Synthetic Biology and Bioenergy Group, J. Craig Venter Institute, La Jolla, California 92037
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