1
|
Cesaria M, Calcagnile M, Arima V, Bianco M, Alifano P, Cataldo R. Cyclic olefin copolymer (COC) as a promising biomaterial for affecting bacterial colonization: investigation on Vibrio campbellii. Int J Biol Macromol 2024; 271:132550. [PMID: 38782326 DOI: 10.1016/j.ijbiomac.2024.132550] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/20/2024] [Revised: 03/22/2024] [Accepted: 05/20/2024] [Indexed: 05/25/2024]
Abstract
Cyclic olefin copolymer (COC) has emerged as an interesting biocompatible material for Organ-on-a-Chip (OoC) devices monitoring growth, viability, and metabolism of cells. Despite ISO 10993 approval, systematic investigation of bacteria grown onto COC is a still not documented issue. This study discusses biofilm formations of the canonical wild type BB120 Vibrio campbellii strain on a native COC substrate and addresses the impact of the physico-chemical properties of COC compared to conventional hydroxyapatite (HA) and poly(dimethylsiloxane) (PDMS) surfaces. An interdisciplinary approach combining bacterial colony counting, light microscopy imaging and advanced digital image processing remarks interesting results. First, COC can reduce biomass adhesion with respect to common biopolymers, that is suitable for tuning biofilm formations in the biological and medical areas. Second, remarkably different biofilm morphology (dendritic complex patterns only in the case of COC) was observed among the examined substrates. Third, the observed biofilm morphogenesis was related to the interaction of COC with the conditioning layer of the planktonic biological medium. Fourth, Level Co-occurrence Matrix (CGLM)-based analysis enabled quantitative assessment of the biomass textural fractal development under different coverage conditions. All of this is of key practical relevance in searching innovative biocompatible materials for pharmaceutical, implantable and medical products.
Collapse
Affiliation(s)
- Maura Cesaria
- Department of Mathematics and Physics "Ennio De Giorgi", University of Salento, Campus Ecotekne, Via per Arnesano, 73100 Lecce, Italy.
| | - Matteo Calcagnile
- Department of Biological and Environmental Sciences and Technologies (Di.S.Te.BA.), University of Salento, c/o Campus Ecotekne-S.P. 6, 73100 Lecce, Italy
| | - Valentina Arima
- CNR NANOTEC - Institute of Nanotechnology, c/o Campus Ecotekne, Lecce, Italy
| | - Monica Bianco
- CNR NANOTEC - Institute of Nanotechnology, c/o Campus Ecotekne, Lecce, Italy
| | - Pietro Alifano
- Department of Biological and Environmental Sciences and Technologies (Di.S.Te.BA.), University of Salento, c/o Campus Ecotekne-S.P. 6, 73100 Lecce, Italy
| | - Rosella Cataldo
- Department of Mathematics and Physics "Ennio De Giorgi", University of Salento, Campus Ecotekne, Via per Arnesano, 73100 Lecce, Italy
| |
Collapse
|
2
|
Abstract
The morphogenesis of two-dimensional bacterial colonies has been well studied. However, little is known about the colony morphologies of bacteria growing in three dimensions, despite the prevalence of three-dimensional environments (e.g., soil, inside hosts) as natural bacterial habitats. Using experiments on bacteria in granular hydrogel matrices, we find that dense multicellular colonies growing in three dimensions undergo a common morphological instability and roughen, adopting a characteristic broccoli-like morphology when they exceed a critical size. Analysis of a continuum “active fluid” model of the expanding colony reveals that this behavior originates from an interplay of competition for nutrients with growth-driven colony expansion, both of which vary spatially. These results shed light on the fundamental biophysical principles underlying growth in three dimensions. How do growing bacterial colonies get their shapes? While colony morphogenesis is well studied in two dimensions, many bacteria grow as large colonies in three-dimensional (3D) environments, such as gels and tissues in the body or subsurface soils and sediments. Here, we describe the morphodynamics of large colonies of bacteria growing in three dimensions. Using experiments in transparent 3D granular hydrogel matrices, we show that dense colonies of four different species of bacteria generically become morphologically unstable and roughen as they consume nutrients and grow beyond a critical size—eventually adopting a characteristic branched, broccoli-like morphology independent of variations in the cell type and environmental conditions. This behavior reflects a key difference between two-dimensional (2D) and 3D colonies; while a 2D colony may access the nutrients needed for growth from the third dimension, a 3D colony inevitably becomes nutrient limited in its interior, driving a transition to unstable growth at its surface. We elucidate the onset of the instability using linear stability analysis and numerical simulations of a continuum model that treats the colony as an “active fluid” whose dynamics are driven by nutrient-dependent cellular growth. We find that when all dimensions of the colony substantially exceed the nutrient penetration length, nutrient-limited growth drives a 3D morphological instability that recapitulates essential features of the experimental observations. Our work thus provides a framework to predict and control the organization of growing colonies—as well as other forms of growing active matter, such as tumors and engineered living materials—in 3D environments.
Collapse
|
3
|
Chathoth K, Fostier L, Martin B, Baysse C, Mahé F. A Multi-Skilled Mathematical Model of Bacterial Attachment in Initiation of Biofilms. Microorganisms 2022; 10:microorganisms10040686. [PMID: 35456739 PMCID: PMC9029265 DOI: 10.3390/microorganisms10040686] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/21/2022] [Revised: 03/15/2022] [Accepted: 03/17/2022] [Indexed: 01/25/2023] Open
Abstract
The initial step of biofilm formation is bacteria attachment to biotic or abiotic surfaces and other bacteria through intra or interspecies interactions. Adhesion can be influenced by physicochemical conditions of the environment, such as iron. There is no available mathematical model of bacterial attachment giving realistic initiation rather than random adhesion. We describe a simple stochastic attachment model, from the simplest case in two dimensions with one bacterial species attaching on a homogeneous flat surface to more complex situations, with either several bacterial species, inhomogeneous or non-flat surfaces, or in three dimensions. The model depends on attachment probabilities (on the surface, laterally, or vertically on bacteria). Effects of each of these parameters were analyzed. This mathematical model is then applied to experimental oral microcolonies of Porphyromonas gingivalis, Streptococcus gordonii, and Treponema denticola, either as mono-, two, or three species, under different iron concentrations. The model allows to characterize the adhesion of three bacterial species and explore the effect of iron on attachment. This model appears as a powerful tool for initial attachment analysis of bacterial species. It will enable further modeling of biofilm formation in later steps with biofilm initialization more relevant to real-life subgingival biofilms.
Collapse
Affiliation(s)
- Kanchana Chathoth
- CIMIAD, NUMECAN INSERM U1241, Université de Rennes 1, F-35043 Rennes, France; (K.C.); (B.M.); (C.B.)
| | - Louis Fostier
- IRMAR, CNRS UMR 6625, Université de Rennes, F-35000 Rennes, France;
| | - Bénédicte Martin
- CIMIAD, NUMECAN INSERM U1241, Université de Rennes 1, F-35043 Rennes, France; (K.C.); (B.M.); (C.B.)
| | - Christine Baysse
- CIMIAD, NUMECAN INSERM U1241, Université de Rennes 1, F-35043 Rennes, France; (K.C.); (B.M.); (C.B.)
| | - Fabrice Mahé
- IRMAR, CNRS UMR 6625, Université de Rennes, F-35000 Rennes, France;
- Correspondence:
| |
Collapse
|
4
|
Müller M, Glombek M, Powitz J, Brüning D, Rustenbeck I. A Cellular Automaton Model as a First Model-Based Assessment of Interacting Mechanisms for Insulin Granule Transport in Beta Cells. Cells 2020; 9:E1487. [PMID: 32570905 PMCID: PMC7348896 DOI: 10.3390/cells9061487] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/24/2020] [Revised: 06/16/2020] [Accepted: 06/17/2020] [Indexed: 12/31/2022] Open
Abstract
In this paper a first model is derived and applied which describes the transport of insulin granules through the cell interior and at the membrane of a beta cell. A special role is assigned to the actin network, which significantly influences the transport. For this purpose, microscopically measured actin networks are characterized and then further ones are artificially generated. In a Cellular Automaton model, phenomenological laws for granule movement are formulated and implemented. Simulation results are compared with experiments, primarily using TIRF images and secretion rates. In this respect, good similarities are already apparent. The model is a first useful approach to describe complex granule transport processes in beta cells, and offers great potential for future extensions. Furthermore, the model can be used as a tool to validate hypotheses and associated mechanisms regarding their effect on exocytosis or other processes. For this purpose, the source code for the model is provided online.
Collapse
Affiliation(s)
- Michael Müller
- Institute of Dynamics and Vibrations, Technische Universität Braunschweig, D38106 Braunschweig, Germany; (M.G.); (J.P.)
| | - Mathias Glombek
- Institute of Dynamics and Vibrations, Technische Universität Braunschweig, D38106 Braunschweig, Germany; (M.G.); (J.P.)
| | - Jeldrick Powitz
- Institute of Dynamics and Vibrations, Technische Universität Braunschweig, D38106 Braunschweig, Germany; (M.G.); (J.P.)
| | - Dennis Brüning
- Institute of Pharmacology, Toxicology and Clinical Pharmacy, Technische Universität Braunschweig, D38106 Braunschweig, Germany;
| | - Ingo Rustenbeck
- Institute of Pharmacology, Toxicology and Clinical Pharmacy, Technische Universität Braunschweig, D38106 Braunschweig, Germany;
| |
Collapse
|
5
|
Fanesi A, Paule A, Bernard O, Briandet R, Lopes F. The Architecture of Monospecific Microalgae Biofilms. Microorganisms 2019; 7:microorganisms7090352. [PMID: 31540235 PMCID: PMC6780892 DOI: 10.3390/microorganisms7090352] [Citation(s) in RCA: 20] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/06/2019] [Revised: 09/03/2019] [Accepted: 09/06/2019] [Indexed: 11/16/2022] Open
Abstract
Microalgae biofilms have been proposed as an alternative to suspended cultures in commercial and biotechnological fields. However, little is known about their architecture that may strongly impact biofilm behavior, bioprocess stability, and productivity. In order to unravel the architecture of microalgae biofilms, four species of commercial interest were cultivated in microplates and characterized using a combination of confocal laser scanning microscopy and FTIR spectroscopy. In all the species, the biofilm biovolume and thickness increased over time and reached a plateau after seven days; however, the final biomass reached was very different. The roughness decreased during maturation, reflecting cell division and voids filling. The extracellular polymeric substances content of the matrix remained constant in some species, and increased over time in some others. Vertical profiles showed that young biofilms presented a maximum cell density at 20 μm above the substratum co-localized with matrix components. In mature biofilms, the maximum density of cells moved at a greater distance from the substratum (30–40 μm), whereas the maximum coverage of matrix components remained in a deeper layer. Carbohydrates and lipids were the main macromolecules changing during biofilm maturation. Our results revealed that the architecture of microalgae biofilms is species-specific. However, time similarly affects the structural and biochemical parameters.
Collapse
Affiliation(s)
- Andrea Fanesi
- Laboratoire Génie des Procédés et Matériaux (LGPM), CentraleSupélec, Université Paris-Saclay, 91190 Gif-sur-Yvette, France.
| | - Armelle Paule
- Laboratoire Génie des Procédés et Matériaux (LGPM), CentraleSupélec, Université Paris-Saclay, 91190 Gif-sur-Yvette, France.
| | - Olivier Bernard
- Université Côte d'Azur, Inria, BIOCORE, BP 93, 06902 Sophia Antipolis Cedex, France.
| | - Romain Briandet
- Micalis Institute, INRA, AgroParisTech, Université Paris-Saclay, 78350 Jouy-en-Josas, France.
| | - Filipa Lopes
- Laboratoire Génie des Procédés et Matériaux (LGPM), CentraleSupélec, Université Paris-Saclay, 91190 Gif-sur-Yvette, France.
| |
Collapse
|
6
|
Dzianach PA, Dykes GA, Strachan NJC, Forbes KJ, Pérez-Reche FJ. Challenges of biofilm control and utilization: lessons from mathematical modelling. J R Soc Interface 2019; 16:20190042. [PMID: 31185817 PMCID: PMC6597778 DOI: 10.1098/rsif.2019.0042] [Citation(s) in RCA: 26] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/22/2019] [Accepted: 05/10/2019] [Indexed: 12/11/2022] Open
Abstract
This article reviews modern applications of mathematical descriptions of biofilm formation. The focus is on theoretically obtained results which have implications for areas including the medical sector, food industry and wastewater treatment. Examples are given as to how models have contributed to the overall knowledge on biofilms and how they are used to predict biofilm behaviour. We conclude that the use of mathematical models of biofilms has demonstrated over the years the ability to significantly contribute to the vast field of biofilm research. Among other things, they have been used to test various hypotheses on the nature of interspecies interactions, viability of biofilm treatment methods or forces behind observed biofilm pattern formations. Mathematical models can also play a key role in future biofilm research. Many models nowadays are analysed through computer simulations and continue to improve along with computational capabilities. We predict that models will keep on providing answers to important challenges involving biofilm formation. However, further strengthening of the ties between various disciplines is necessary to fully use the tools of collective knowledge in tackling the biofilm phenomenon.
Collapse
Affiliation(s)
- Paulina A. Dzianach
- School of Natural and Computing Sciences, Medical Sciences and Nutrition, University of Aberdeen, Aberdeen, UK
- School of Public Health, Curtin University, Perth, Australia
| | - Gary A. Dykes
- School of Public Health, Curtin University, Perth, Australia
| | - Norval J. C. Strachan
- School of Natural and Computing Sciences, Medical Sciences and Nutrition, University of Aberdeen, Aberdeen, UK
| | - Ken J. Forbes
- School of Medicine, Medical Sciences and Nutrition, University of Aberdeen, Aberdeen, UK
| | - Francisco J. Pérez-Reche
- School of Natural and Computing Sciences, Medical Sciences and Nutrition, University of Aberdeen, Aberdeen, UK
| |
Collapse
|
7
|
Champigneux P, Renault-Sentenac C, Bourrier D, Rossi C, Delia ML, Bergel A. Effect of surface nano/micro-structuring on the early formation of microbial anodes with Geobacter sulfurreducens: Experimental and theoretical approaches. Bioelectrochemistry 2018; 121:191-200. [DOI: 10.1016/j.bioelechem.2018.02.005] [Citation(s) in RCA: 22] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/12/2017] [Revised: 02/03/2018] [Accepted: 02/10/2018] [Indexed: 12/24/2022]
|
8
|
Modeling thrombosis in silico: Frontiers, challenges, unresolved problems and milestones. Phys Life Rev 2018; 26-27:57-95. [PMID: 29550179 DOI: 10.1016/j.plrev.2018.02.005] [Citation(s) in RCA: 40] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/15/2017] [Revised: 02/21/2018] [Accepted: 02/24/2018] [Indexed: 12/24/2022]
Abstract
Hemostasis is a complex physiological mechanism that functions to maintain vascular integrity under any conditions. Its primary components are blood platelets and a coagulation network that interact to form the hemostatic plug, a combination of cell aggregate and gelatinous fibrin clot that stops bleeding upon vascular injury. Disorders of hemostasis result in bleeding or thrombosis, and are the major immediate cause of mortality and morbidity in the world. Regulation of hemostasis and thrombosis is immensely complex, as it depends on blood cell adhesion and mechanics, hydrodynamics and mass transport of various species, huge signal transduction networks in platelets, as well as spatiotemporal regulation of the blood coagulation network. Mathematical and computational modeling has been increasingly used to gain insight into this complexity over the last 30 years, but the limitations of the existing models remain profound. Here we review state-of-the-art-methods for computational modeling of thrombosis with the specific focus on the analysis of unresolved challenges. They include: a) fundamental issues related to physics of platelet aggregates and fibrin gels; b) computational challenges and limitations for solution of the models that combine cell adhesion, hydrodynamics and chemistry; c) biological mysteries and unknown parameters of processes; d) biophysical complexities of the spatiotemporal networks' regulation. Both relatively classical approaches and innovative computational techniques for their solution are considered; the subjects discussed with relation to thrombosis modeling include coarse-graining, continuum versus particle-based modeling, multiscale models, hybrid models, parameter estimation and others. Fundamental understanding gained from theoretical models are highlighted and a description of future prospects in the field and the nearest possible aims are given.
Collapse
|
9
|
Biomechanical Analysis of Infectious Biofilms. ADVANCES IN EXPERIMENTAL MEDICINE AND BIOLOGY 2016; 915:99-114. [PMID: 27193540 DOI: 10.1007/978-3-319-32189-9_8] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/20/2023]
Abstract
The removal of infectious biofilms from tissues or implanted devices and their transmission through fluid transport systems depends in part of the mechanical properties of their polymeric matrix. Linking the various physical and chemical microscopic interactions to macroscopic deformation and failure modes promises to unveil design principles for novel therapeutic strategies targeting biofilm eradication, and provide a predictive capability to accelerate the development of devices, water lines, etc, that minimise microbial dispersal. Here, our current understanding of biofilm mechanics is appraised from the perspective of biophysics , with an emphasis on constitutive modelling that has been highly successful in soft matter. Fitting rheometric data to viscoelastic models has quantified linear and nonlinear stress relaxation mechanisms, how they vary between species and environments, and how candidate chemical treatments alter the mechanical response. The rich interplay between growth, mechanics and hydrodynamics is just becoming amenable to computational modelling and promises to provide unprecedented characterisation of infectious biofilms in their native state.
Collapse
|
10
|
Espeso DR, Carpio A, Einarsson B. Differential growth of wrinkled biofilms. PHYSICAL REVIEW. E, STATISTICAL, NONLINEAR, AND SOFT MATTER PHYSICS 2015; 91:022710. [PMID: 25768534 DOI: 10.1103/physreve.91.022710] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/08/2014] [Indexed: 06/04/2023]
Abstract
Biofilms are antibiotic-resistant bacterial aggregates that grow on moist surfaces and can trigger hospital-acquired infections. They provide a classical example in biology where the dynamics of cellular communities may be observed and studied. Gene expression regulates cell division and differentiation, which affect the biofilm architecture. Mechanical and chemical processes shape the resulting structure. We gain insight into the interplay between cellular and mechanical processes during biofilm development on air-agar interfaces by means of a hybrid model. Cellular behavior is governed by stochastic rules informed by a cascade of concentration fields for nutrients, waste, and autoinducers. Cellular differentiation and death alter the structure and the mechanical properties of the biofilm, which is deformed according to Föppl-Von Kármán equations informed by cellular processes and the interaction with the substratum. Stiffness gradients due to growth and swelling produce wrinkle branching. We are able to reproduce wrinkled structures often formed by biofilms on air-agar interfaces, as well as spatial distributions of differentiated cells commonly observed with B. subtilis.
Collapse
Affiliation(s)
- D R Espeso
- Centro Nacional de Biotecnología, CSIC, Madrid 28049, Spain
| | - A Carpio
- Departamento de Matematica Aplicada, Universidad Complutense, Madrid 28040, Spain
| | - B Einarsson
- Center for Complex and Nonlinear Science, UC Santa Barbara, California 93106, USA
| |
Collapse
|