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Then A, Ewald J, Söllner N, Cooper RE, Küsel K, Ibrahim B, Schuster S. Agent-based modelling of iron cycling bacteria provides a framework for testing alternative environmental conditions and modes of action. ROYAL SOCIETY OPEN SCIENCE 2022; 9:211553. [PMID: 35620008 PMCID: PMC9115035 DOI: 10.1098/rsos.211553] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 09/28/2021] [Accepted: 04/27/2022] [Indexed: 05/03/2023]
Abstract
Iron-reducing and iron-oxidizing bacteria are of interest in a variety of environmental and industrial applications. Such bacteria often co-occur at oxic-anoxic gradients in aquatic and terrestrial habitats. In this paper, we present the first computational agent-based model of microbial iron cycling, between the anaerobic ferric iron (Fe3+)-reducing bacteria Shewanella spp. and the microaerophilic ferrous iron (Fe2+)-oxidizing bacteria Sideroxydans spp. By including the key processes of reduction/oxidation, movement, adhesion, Fe2+-equilibration and nanoparticle formation, we derive a core model which enables hypothesis testing and prediction for different environmental conditions including temporal cycles of oxic and anoxic conditions. We compared (i) combinations of different Fe3+-reducing/Fe2+-oxidizing modes of action of the bacteria and (ii) system behaviour for different pH values. We predicted that the beneficial effect of a high number of iron-nanoparticles on the total Fe3+ reduction rate of the system is not only due to the faster reduction of these iron-nanoparticles, but also to the nanoparticles' additional capacity to bind Fe2+ on their surfaces. Efficient iron-nanoparticle reduction is confined to pH around 6, being twice as high than at pH 7, whereas at pH 5 negligible reduction takes place. Furthermore, in accordance with experimental evidence our model showed that shorter oxic/anoxic periods exhibit a faster increase of total Fe3+ reduction rate than longer periods.
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Affiliation(s)
- Andre Then
- Department of Bioinformatics, Matthias-Schleiden-Institute, University of Jena, Ernst-Abbe-Platz 2, 07743 Jena, Germany
| | - Jan Ewald
- Department of Bioinformatics, Matthias-Schleiden-Institute, University of Jena, Ernst-Abbe-Platz 2, 07743 Jena, Germany
| | - Natalie Söllner
- Department of Bioinformatics, Matthias-Schleiden-Institute, University of Jena, Ernst-Abbe-Platz 2, 07743 Jena, Germany
| | - Rebecca E. Cooper
- Institute of Biodiversity, Friedrich Schiller University Jena, Jena, Germany
| | - Kirsten Küsel
- Institute of Biodiversity, Friedrich Schiller University Jena, Jena, Germany
- German Center for Integrative Biodiversity Research (iDiv) Halle-Jena-Leipzig, Leipzig, Germany
| | - Bashar Ibrahim
- Centre for Applied Mathematics and Bioinformatics, and Department of Mathematics and Natural Sciences, Gulf University for Science and Technology, Hawally 32093, Kuwait
- European Virus Bioinformatics Center, Leutragraben 1 07743 Jena, Germany
| | - Stefan Schuster
- Department of Bioinformatics, Matthias-Schleiden-Institute, University of Jena, Ernst-Abbe-Platz 2, 07743 Jena, Germany
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Madamba T, Moreira RG, Castell‐Perez E, Banerjee A, Silva D. Agent‐based simulation of cross‐contamination of
Escherichia coli
O157
:
H7
On lettuce during processing with temperature fluctuations during storage in a produce facility. Part 1: Model development. J FOOD PROCESS ENG 2022. [DOI: 10.1111/jfpe.14002] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/27/2022]
Affiliation(s)
- Tonderai Madamba
- Biological & Agricultural Engineering Department Texas A&M University College Station Texas USA
| | - Rosana G. Moreira
- Biological & Agricultural Engineering Department Texas A&M University College Station Texas USA
| | - Elena Castell‐Perez
- Biological & Agricultural Engineering Department Texas A&M University College Station Texas USA
| | - Amarnath Banerjee
- Industrial and Systems Engineering Department Texas A&M University College Station Texas USA
| | - Dilma Silva
- Computer Science and Engineering Department Texas A&M University College Station Texas USA
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Siokis A, Robert PA, Meyer-Hermann M. Agent-Based Modeling of T Cell Receptor Cooperativity. Int J Mol Sci 2020; 21:ijms21186473. [PMID: 32899840 PMCID: PMC7555007 DOI: 10.3390/ijms21186473] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/18/2020] [Revised: 09/01/2020] [Accepted: 09/02/2020] [Indexed: 11/25/2022] Open
Abstract
Immunological synapse (IS) formation is a key event during antigen recognition by T cells. Recent experimental evidence suggests that the affinity between T cell receptors (TCRs) and antigen is actively modulated during the early steps of TCR signaling. In this work, we used an agent-based model to study possible mechanisms for affinity modulation during IS formation. We show that, without any specific active mechanism, the observed affinity between receptors and ligands evolves over time and depends on the density of ligands of the antigen peptide presented by major histocompatibility complexes (pMHC) and TCR molecules. A comparison between the presence or absence of TCR–pMHC centrally directed flow due to F-actin coupling suggests that centripetal transport is a potential mechanism for affinity modulation. The model further suggests that the time point of affinity measurement during immune synapse formation is critical. Finally, a mathematical model of F-actin foci formation incorporated in the agent-based model shows that TCR affinity can potentially be actively modulated by positive/negative feedback of the F-actin foci on the TCR-pMHC association rate kon.
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Affiliation(s)
- Anastasios Siokis
- Department of Systems Immunology and Braunschweig Integrated Centre of Systems Biology, Helmholtz Centre for Infection Research, 38106 Braunschweig, Germany; (A.S.); (P.A.R.)
| | - Philippe A. Robert
- Department of Systems Immunology and Braunschweig Integrated Centre of Systems Biology, Helmholtz Centre for Infection Research, 38106 Braunschweig, Germany; (A.S.); (P.A.R.)
| | - Michael Meyer-Hermann
- Department of Systems Immunology and Braunschweig Integrated Centre of Systems Biology, Helmholtz Centre for Infection Research, 38106 Braunschweig, Germany; (A.S.); (P.A.R.)
- Institute of Biochemistry, Biotechnology and Bioinformatics, Technische Universität Braunschweig, 38106 Braunschweig, Germany
- Correspondence: ; Tel.: +49-531-391-55210
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Tan PY, Marcos, Liu Y. Modelling bacterial chemotaxis for indirectly binding attractants. J Theor Biol 2020; 487:110120. [PMID: 31857084 DOI: 10.1016/j.jtbi.2019.110120] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/17/2019] [Revised: 11/09/2019] [Accepted: 12/16/2019] [Indexed: 11/26/2022]
Abstract
In bacterial chemotaxis, chemoattractant molecules may bind either directly or indirectly with receptors within the cell periplasmic space. The indirect binding mechanism, which involves an intermediate periplasmic binding protein, has been reported to increase sensitivity to dilute attractant concentrations as well as range of response. Current mathematical models for bacterial chemotaxis at the population scale do not appear to take the periplasmic binding protein (BP) concentration or the indirect binding mechanics into account. We formulate an indirect binding extension to the existing Rivero equation for chemotactic velocity based on fundamental reversible enzyme kinetics. The formulated indirect binding expression accounts for the periplasmic BP concentration and the dissociation constants for binding between attractant and periplasmic BP, as well as between BP and chemoreceptor. We validate the indirect-binding model using capillary assay simulations of the chemotactic responses of E. coli to the indirectly-binding attractants maltose and AI-2. The predicted response agrees well with experimental data from a number of maltose capillary assay studies conducted in previous literature. The model is also able to achieve good agreement with AI-2 capillary assay data of one study out of two tested. The chemotactic response of E. coli towards AI-2 appears to be of higher complexity due to reports of variable periplasmic BP concentration as well as the low concentration of periplasmic BP relative to the total receptor concentration. Our current model is thus suitable for indirect binding chemotactic response systems with constant periplasmic BP concentration that is significantly larger than the total receptor concentration, such as the response of E. coli towards maltose. Further considerations may be taken into account to model the chemotactic response towards AI-2 with greater accuracy.
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Affiliation(s)
- Pei Yen Tan
- Advanced Environmental Biotechnology Centre, Nanyang Environment & Water Research Institute, Nanyang Technological University, 1 Cleantech Loop, 637141, Singapore
| | - Marcos
- School of Mechanical and Aerospace Engineering, Nanyang Technological University, 50 Nanyang Avenue, 639798, Singapore.
| | - Yu Liu
- Advanced Environmental Biotechnology Centre, Nanyang Environment & Water Research Institute, Nanyang Technological University, 1 Cleantech Loop, 637141, Singapore; School of Civil and Environmental Engineering, Nanyang Technological University, 50 Nanyang Avenue, 639798, Singapore
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Maia P, Pérez-Rodríguez G, Pérez-Pérez M, Fdez-Riverola F, Lourenço A, Azevedo NF. Application of agent-based modelling to assess single-molecule transport across the cell envelope of E. coli. Comput Biol Med 2019; 107:218-226. [DOI: 10.1016/j.compbiomed.2019.02.020] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/20/2018] [Revised: 02/20/2019] [Accepted: 02/21/2019] [Indexed: 01/16/2023]
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Kingsmore KM, Logsdon DK, Floyd DH, Peirce SM, Purow BW, Munson JM. Interstitial flow differentially increases patient-derived glioblastoma stem cell invasionviaCXCR4, CXCL12, and CD44-mediated mechanisms. Integr Biol (Camb) 2016; 8:1246-1260. [DOI: 10.1039/c6ib00167j] [Citation(s) in RCA: 57] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Affiliation(s)
- Kathryn M. Kingsmore
- Department of Biomedical Engineering, University of Virginia School of Medicine, Charlottesville, VA 22908, USA
| | - Daniel K. Logsdon
- Department of Biomedical Engineering, University of Virginia School of Medicine, Charlottesville, VA 22908, USA
| | - Desiree H. Floyd
- Department of Neurology, University of Virginia School of Medicine, Charlottesville, VA, 22908 USA
| | - Shayn M. Peirce
- Department of Biomedical Engineering, University of Virginia School of Medicine, Charlottesville, VA 22908, USA
| | - Benjamin W. Purow
- Department of Neurology, University of Virginia School of Medicine, Charlottesville, VA, 22908 USA
| | - Jennifer M. Munson
- Department of Biomedical Engineering, University of Virginia School of Medicine, Charlottesville, VA 22908, USA
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Piasta KN, Falke JJ. Increasing and decreasing the ultrastability of bacterial chemotaxis core signaling complexes by modifying protein-protein contacts. Biochemistry 2014; 53:5592-600. [PMID: 25119814 PMCID: PMC4159201 DOI: 10.1021/bi500849p] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
![]()
The chemosensory signaling array
of bacterial chemotaxis is composed
of functional core units containing two receptor trimers of dimers,
a homodimeric CheA kinase, and two CheW adaptor proteins. In vitro reconstitutions generate individual, functional
core units and larger functional assemblies, including dimers, hexagons,
and hexagonal arrays. Such reconstituted complexes have been shown
to have both quasi-stable and ultrastable populations that decay with
lifetimes of 1–2 days and ∼3 weeks at 22 °C, respectively,
where decay results primarily from proteolysis of the bound kinase
[Erbse, A. H., and Falke, J. J. (2009) Biochemistry 48, 6975–6987; Slivka, P. F., and Falke, J. J. (2012) Biochemistry 51, 10218–10228]. In this work, we show
that the ultrastable population can be destabilized to the quasi-stable
level via the introduction of a bulky tryptophan residue at either
one of two essential protein–protein interfaces within the
core unit: the receptor–kinase contact or kinase–adaptor
interface 1. Moreover, we demonstrate that the quasi-stable population
can be made ultrastable via the introduction of a disulfide bond that
covalently stabilizes the latter interface. The resulting disulfide
at least doubles the functional lifetime of the ultrastable population,
to ≥5.9 weeks at 22 °C, by protecting the kinase from
endogenous and exogenous proteases. Together, these results indicate
that the ultrastability of reconstituted core complexes requires well-formed
contacts among the receptor, kinase, and adaptor proteins, whereas
quasi-stability arises from less perfect contacts that allow slow
proteolysis of the bound kinase. Furthermore, the results reveal that
ultrastability, and perhaps the size or order of chemosensory complexes
and arrays, can be increased by an engineered disulfide bond that
covalently cross-links a key interface. Overall, it appears that native
ultrastability has evolved to provide an optimal rather than maximal
level of kinetic durability, suggesting that altered selective pressure
could either increase or decrease the functional lifetime of core
complexes.
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Affiliation(s)
- Kene N Piasta
- Department of Chemistry and Biochemistry and Molecular Biophysics Program, University of Colorado , Boulder, Colorado 80309-0596, United States
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Stiegelmeyer SM, Giddings MC. Agent-based modeling of competence phenotype switching in Bacillus subtilis. Theor Biol Med Model 2013; 10:23. [PMID: 23551850 PMCID: PMC3648451 DOI: 10.1186/1742-4682-10-23] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/09/2012] [Accepted: 03/21/2013] [Indexed: 11/17/2022] Open
Abstract
Background It is a fascinating phenomenon that in genetically identical bacteria populations of Bacillus subtilis, a distinct DNA uptake phenotype called the competence phenotype may emerge in 10–20% of the population. Many aspects of the phenomenon are believed to be due to the variable expression of critical genes: a stochastic occurrence termed “noise” which has made the phenomenon difficult to examine directly by lab experimentation. Methods To capture and model noise in this system and further understand the emergence of competence both at the intracellular and culture levels in B. subtilis, we developed a novel multi-scale, agent-based model. At the intracellular level, our model recreates the regulatory network involved in the competence phenotype. At the culture level, we simulated growth conditions, with our multi-scale model providing feedback between the two levels. Results Our model predicted three potential sources of genetic “noise”. First, the random spatial arrangement of molecules may influence the manifestation of the competence phenotype. In addition, the evidence suggests that there may be a type of epigenetic heritability to the emergence of competence, influenced by the molecular concentrations of key competence molecules inherited through cell division. Finally, the emergence of competence during the stationary phase may in part be due to the dilution effect of cell division upon protein concentrations. Conclusions The competence phenotype was easily translated into an agent-based model – one with the ability to illuminate complex cell behavior. Models such as the one described in this paper can simulate cell behavior that is otherwise unobservable in vivo, highlighting their potential usefulness as research tools.
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Affiliation(s)
- Suzy M Stiegelmeyer
- Syngenta Biotechnology, Inc., 3054 Cornwallis Rd., Research Triangle Park, NC 27709, USA.
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Azimi M, Jamali Y, Mofrad MRK. Accounting for diffusion in agent based models of reaction-diffusion systems with application to cytoskeletal diffusion. PLoS One 2011; 6:e25306. [PMID: 21966493 PMCID: PMC3179499 DOI: 10.1371/journal.pone.0025306] [Citation(s) in RCA: 23] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/04/2011] [Accepted: 08/31/2011] [Indexed: 12/18/2022] Open
Abstract
Diffusion plays a key role in many biochemical reaction systems seen in nature. Scenarios where diffusion behavior is critical can be seen in the cell and subcellular compartments where molecular crowding limits the interaction between particles. We investigate the application of a computational method for modeling the diffusion of molecules and macromolecules in three-dimensional solutions using agent based modeling. This method allows for realistic modeling of a system of particles with different properties such as size, diffusion coefficients, and affinity as well as the environment properties such as viscosity and geometry. Simulations using these movement probabilities yield behavior that mimics natural diffusion. Using this modeling framework, we simulate the effects of molecular crowding on effective diffusion and have validated the results of our model using Langevin dynamics simulations and note that they are in good agreement with previous experimental data. Furthermore, we investigate an extension of this framework where single discrete cells can contain multiple particles of varying size in an effort to highlight errors that can arise from discretization that lead to the unnatural behavior of particles undergoing diffusion. Subsequently, we explore various algorithms that differ in how they handle the movement of multiple particles per cell and suggest an algorithm that properly accommodates multiple particles of various sizes per cell that can replicate the natural behavior of these particles diffusing. Finally, we use the present modeling framework to investigate the effect of structural geometry on the directionality of diffusion in the cell cytoskeleton with the observation that parallel orientation in the structural geometry of actin filaments of filopodia and the branched structure of lamellipodia can give directionality to diffusion at the filopodia-lamellipodia interface.
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Affiliation(s)
- Mohammad Azimi
- Molecular Cell Biomechanics Laboratory, Department of Bioengineering, University of California, Berkeley, California, United States of America
| | - Yousef Jamali
- Molecular Cell Biomechanics Laboratory, Department of Bioengineering, University of California, Berkeley, California, United States of America
| | - Mohammad R. K. Mofrad
- Molecular Cell Biomechanics Laboratory, Department of Bioengineering, University of California, Berkeley, California, United States of America
- * E-mail:
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