A computer investigation of chemically mediated detachment in bacterial biofilms

Microbiology ◽  
2003 ◽  
Vol 149 (5) ◽  
pp. 1155-1163 ◽  
Author(s):  
Stephen M. Hunt ◽  
Martin A. Hamilton ◽  
John T. Sears ◽  
Gary Harkin ◽  
Jason Reno
Keyword(s):  
Life Cycle ◽  
Cellular Automata ◽  
Three Dimensional ◽  
Bacterial Biofilm ◽  
Diffusion Reaction ◽  
Bacterial Biofilms ◽  
Biofilm Development ◽  
Reaction Equations ◽  
Growth Movement ◽  
Cellular Automata Algorithm

A three-dimensional computer model was used to evaluate the effect of chemically mediated detachment on biofilm development in a negligible-shear environment. The model, BacLAB, combines conventional diffusion-reaction equations for chemicals with a cellular automata algorithm to simulate bacterial growth, movement and detachment. BacLAB simulates the life cycle of a bacterial biofilm from its initial colonization of a surface to the development of a mature biofilm with cell areal densities comparable to those in the laboratory. A base model founded on well established transport equations that are easily adaptable to investigate conjectures at the biological level has been created. In this study, the conjecture of a detachment mechanism involving a bacterially produced chemical detachment factor in which high local concentrations of this detachment factor cause the bacteria to detach from the biofilm was examined. The results show that the often observed ‘mushroom’-shaped structure can occur if detachment events create voids so that the remaining attached cells look like mushrooms.

scholarly journals Numerical Simulation of the Coagulation Dynamics of Blood

2008 ◽  
Vol 9 (2) ◽  
pp. 83-104 ◽  
Author(s):  
T. Bodnár ◽  
A. Sequeira
Keyword(s):  
Blood Coagulation ◽  
Computational Study ◽  
Time Integration ◽  
Three Dimensional ◽  
Circular Cross Section ◽  
Clot Formation ◽  
Diffusion Reaction ◽  
Numerical Code ◽  
Injured Region ◽  
Reaction Equations

The process of platelet activation and blood coagulation is quite complex and not yet completely understood. Recently, a phenomenological meaningful model of blood coagulation and clot formation in flowing blood that extends existing models to integrate biochemical, physiological and rheological factors, has been developed. The aim of this paper is to present results from a computational study of a simplified version of this coupled fluid-biochemistry model. A generalized Newtonian model with shear-thinning viscosity has been adopted to describe the flow of blood. To simulate the biochemical changes and transport of various enzymes, proteins and platelets involved in the coagulation process, a set of coupled advection–diffusion–reaction equations is used. Three-dimensional numerical simulations are carried out for the whole model in a straight vessel with circular cross-section, using a finite volume semi-discretization in space, on structured grids, and a multistage scheme for time integration. Clot formation and growth are investigated in the vicinity of an injured region of the vessel wall. These are preliminary results aimed at showing the validation of the model and of the numerical code.

scholarly journals Novel Antibacterial Modification of Polycarbonate for Increment Prototyping in Medicine

Materials ◽  
2021 ◽  
Vol 14 (16) ◽  
pp. 4725
Author(s):  
Tomasz Flak ◽  
Ewa Trejnowska ◽  
Szymon Skoczyński ◽  
Jadwiga Gabor ◽  
Beata Swinarew ◽  
...  
Keyword(s):  
Three Dimensional ◽  
Antibacterial Properties ◽  
Antimicrobial Properties ◽  
Modern Medicine ◽  
Bacterial Biofilm ◽  
Polymer Materials ◽  
Resistant Bacteria ◽  
Entire Volume ◽  
Increased Risk ◽  
Biofilm Development

In the era of modern medicine, the number of invasive treatments increases. Artificial devices used in medicine are associated with an increased risk of secondary infections. Bacterial biofilm development observed on the implanted surface is challenging to treat, primarily due to low antibiotics penetration. In our study, the preparation of a new polycarbonate composite, filled with nanosilver, nanosilica and rhodamine B derivative, suitable for three-dimensional printing, is described. Polymer materials with antimicrobial properties are known. However, in most cases, protection is limited to the outer layers only. The newly developed materials are protected in their entire volume. Moreover, the antibacterial properties are retained after multiple high-temperature processing were performed, allowing them to be used in 3D printing. Bacterial population reduction was observed, which gives an assumption for those materials to be clinically tested in the production of various medical devices and for the reduction of morbidity and mortality caused by multidrug-resistant bacteria.

Mathematical Modeling of Within-Host Dynamics of Toxoplasma Gondii

2011 ◽  
Author(s):  
Adam Sullivan ◽  
Xiaopeng Zhao ◽  
Chunlei Su
Keyword(s):  
Life Cycle ◽  
Toxoplasma Gondii ◽  
Cellular Automata ◽  
Three Dimensional ◽  
Host Cells ◽  
Time Step ◽  
Cellular Automata Model ◽  
Entire Life ◽  
Entire Life Cycle ◽  
The Brain

Toxoplasma gondii is a protozoan capable of replicating sexually in cats and asexually in other warm-blooded animals. By using a three dimensional mesh of both the brain and spleen, it is possible to simulate using a computational model to demonstrate the entire life-cycle within an intermediate host of the parasite as it completes the life-cycle using host cells of these organs. A cellular automata model is developed to demonstrate the dynamics of the parasite, where each cell follows the same set of rules for each discrete time-step. This cellular automata model allows for data simulations to be run of the parasite within a mouse and display graphical images and animations.

Bacterial Biofilms in Infective Endocarditis – A complex in vitro - Model to Investigate Emerging Technologies of Antimicrobial Cardiovascular Device Coatings

2020 ◽  
Author(s):  
Laura Kursawe ◽  
Alexander Lauten ◽  
Marc Martinović ◽  
Klaus Affeld ◽  
Ulrich Kertzscher ◽  
...  
Keyword(s):  
Infective Endocarditis ◽  
Heart Valves ◽  
In Vitro Model ◽  
Bacterial Biofilm ◽  
Bacterial Biofilms ◽  
Aortic Valves ◽  
Biofilm Growth ◽  
Vitro Model ◽  
Biofilm Development

<p><strong>Objective:</strong> Most biofilm flow-chambers are designed for standardized homogeneous biofilms for research purposes. These do not mimic the complexity of prosthetic heart valves, which consist of both artificial and biological material.</p> <p>Infective endocarditis (IE) is still associated with a high morbidity and mortality. IE is characterized by bacterial biofilms of the endocardium leading to destruction of the valve. Current research demonstrates that about one quarter of the patients with formal surgery indication cannot undergo surgery. This group of patients needs further options of therapy, but due to a lack of models for IE, prospects of research are low.</p> <p>Therefore, the purpose of this project was to establish an in vitro - model of infective endocarditis to allow growth of bacterial biofilms on porcine aortic valves, serving as baseline for further research.</p> <p><strong>Methods and Results: </strong>A pulsatile two-chamber circulation model was constructed that kept native porcine aortic valves under sterile, physiologic hemodynamic and temperature conditions. To exclude external contamination, sterility tests with sterile culture media were performed for 24h. During this time period, no growth of microorganisms was observed in the system and cultures after plating on standard media remained negative.</p> <p>The system was inoculated with Staphylococcus epidermidis PIA 8400 to create biofilms on porcine aortic valves. Porcine aortic roots were incubated in this system for increasing periods of time and bacterial titration to evaluate bacterial growth and biofilm development on the valves. After incubation, specimens were embedded and tissue sections were analyzed by Fluorescence in situ hybridization (FISH) for direct visualization of the biofilms and bacterial activity.</p> <p>Pilot tests for biofilm growth showed monospecies colonization consisting of cocci with time- and inocula-dependent increase. FISH visualized biofilms with ribosome-containing, and thus metabolic active cocci, tissue infiltration and similar colonization pattern as observed by FISH in human IE heart valves infected by S. epidermidis.</p> <p><strong>Conclusion:</strong> These results demonstrate the establishment of a novel complex in vitro - model for bacterial biofilm growth on porcine aortic roots. The model will allow identifying predilection sites of heart valves for bacterial adhesion and biofilm growth and it may serve as baseline for further research on IE therapy and prevention, e.g. the development of antimicrobial transcatheter approaches to IE.</p>

Random walk on rectangles and parallelepipeds algorithm for solving transient anisotropic drift-diffusion-reaction problems

2019 ◽  
Vol 25 (2) ◽  
pp. 131-146 ◽  
Author(s):  
Karl K. Sabelfeld
Keyword(s):  
Random Walk ◽  
First Passage Time ◽  
Three Dimensional ◽  
Passage Time ◽  
Diffusion Reaction ◽  
Exit Point ◽  
Drift Diffusion ◽  
Continuity Equations ◽  
Reaction Equations ◽  
Reaction Problem

Abstract In this paper a random walk on arbitrary rectangles (2D) and parallelepipeds (3D) algorithm is developed for solving transient anisotropic drift-diffusion-reaction equations. The method is meshless, both in space and time. The approach is based on a rigorous representation of the first passage time and exit point distributions for arbitrary rectangles and parallelepipeds. The probabilistic representation is then transformed to a form convenient for stochastic simulation. The method can be used to calculate fluxes to any desired part of the boundary, from arbitrary sources. A global version of the method we call here as a stochastic expansion from cell to cell (SECC) algorithm for calculating the whole solution field is suggested. Application of this method to solve a system of transport equations for electrons and holes in a semicoductor is discussed. This system consists of the continuity equations for particle densities and a Poisson equation for electrostatic potential. To validate the method we have derived a series of exact solutions of the drift-diffusion-reaction problem in a three-dimensional layer presented in the last section in details.

scholarly journals Nonuniform growth and surface friction determine bacterial biofilm morphology on soft substrates

2020 ◽  
Vol 117 (14) ◽  
pp. 7622-7632 ◽  
Author(s):  
Chenyi Fei ◽  
Sheng Mao ◽  
Jing Yan ◽  
Ricard Alert ◽  
Howard A. Stone ◽  
...  
Keyword(s):  
Three Dimensional ◽  
Surface Friction ◽  
Quantitative Agreement ◽  
Peripheral Region ◽  
Bacterial Biofilm ◽  
Bacterial Biofilms ◽  
Mechanical Instability ◽  
Hedging Strategy ◽  
3D Shapes

During development, organisms acquire three-dimensional (3D) shapes with important physiological consequences. While basic mechanisms underlying morphogenesis are known in eukaryotes, it is often difficult to manipulate them in vivo. To circumvent this issue, here we present a study of developingVibrio choleraebiofilms grown on agar substrates in which the spatiotemporal morphological patterns were altered by varying the agar concentration. Expanding biofilms are initially flat but later undergo a mechanical instability and become wrinkled. To gain mechanistic insights into this dynamic pattern-formation process, we developed a model that considers diffusion of nutrients and their uptake by bacteria, bacterial growth/biofilm matrix production, mechanical deformation of both the biofilm and the substrate, and the friction between them. Our model shows quantitative agreement with experimental measurements of biofilm expansion dynamics, and it accurately predicts two distinct spatiotemporal patterns observed in the experiments—the wrinkles initially appear either in the peripheral region and propagate inward (soft substrate/low friction) or in the central region and propagate outward (stiff substrate/high friction). Our results, which establish that nonuniform growth and friction are fundamental determinants of stress anisotropy and hence biofilm morphology, are broadly applicable to bacterial biofilms with similar morphologies and also provide insight into how other bacterial biofilms form distinct wrinkle patterns. We discuss the implications of forming undulated biofilm morphologies, which may enhance the availability of nutrients and signaling molecules and serve as a “bet hedging” strategy.

scholarly journals Escherichia coli Biofilms Have an Organized and Complex Extracellular Matrix Structure

mBio ◽  
2013 ◽  
Vol 4 (5) ◽  
Author(s):  
Chia Hung ◽  
Yizhou Zhou ◽  
Jerome S. Pinkner ◽  
Karen W. Dodson ◽  
Jan R. Crowley ◽  
...  
Keyword(s):  
Escherichia Coli ◽  
Extracellular Matrix ◽  
Biofilm Formation ◽  
Developmental Stages ◽  
Three Dimensional ◽  
Bacterial Biofilms ◽  
Content Type ◽  
Abiotic Surfaces ◽  
Biochemical Analyses ◽  
Biofilm Development

ABSTRACTBacterial biofilms are ubiquitous in nature, and their resilience is derived in part from a complex extracellular matrix that can be tailored to meet environmental demands. Although common developmental stages leading to biofilm formation have been described, how the extracellular components are organized to allow three-dimensional biofilm development is not well understood. Here we show that uropathogenicEscherichia coli(UPEC) strains produce a biofilm with a highly ordered and complex extracellular matrix (ECM). We used electron microscopy (EM) techniques to image floating biofilms (pellicles) formed by UPEC. EM revealed intricately constructed substructures within the ECM that encase individual, spatially segregated bacteria with a distinctive morphology. Mutational and biochemical analyses of these biofilms confirmed curli as a major matrix component and revealed important roles for cellulose, flagella, and type 1 pili in pellicle integrity and ECM infrastructure. Collectively, the findings of this study elucidated that UPEC pellicles have a highly organized ultrastructure that varies spatially across the multicellular community.IMPORTANCEBacteria can form biofilms in diverse niches, including abiotic surfaces, living cells, and at the air-liquid interface of liquid media. Encasing these cellular communities is a self-produced extracellular matrix (ECM) that can be composed of proteins, polysaccharides, and nucleic acids. The ECM protects biofilm bacteria from environmental insults and also makes the dissolution of biofilms very challenging. As a result, formation of biofilms within humans (during infection) or on industrial material (such as water pipes) has detrimental and costly effects. In order to combat bacterial biofilms, a better understanding of components required for biofilm formation and the ECM is required. This study defined the ECM composition and architecture of floating pellicle biofilms formed byEscherichia coli.

scholarly journals Cell position fates and collective fountain flow in bacterial biofilms revealed by light-sheet microscopy

Science ◽  
2020 ◽  
Vol 369 (6499) ◽  
pp. 71-77 ◽  
Author(s):  
Boyang Qin ◽  
Chenyi Fei ◽  
Andrew A. Bridges ◽  
Ameya A. Mashruwala ◽  
Howard A. Stone ◽  
...  
Keyword(s):  
Matrix Protein ◽  
Three Dimensional ◽  
Cell Movement ◽  
Light Sheet ◽  
Bacterial Biofilms ◽  
Biofilm Growth ◽  
Light Sheet Microscopy ◽  
The Matrix ◽  
Biofilm Development ◽  
Spatial Trajectories

Bacterial biofilms represent a basic form of multicellular organization that confers survival advantages to constituent cells. The sequential stages of cell ordering during biofilm development have been studied in the pathogen and model biofilm-former Vibrio cholerae. It is unknown how spatial trajectories of individual cells and the collective motions of many cells drive biofilm expansion. We developed dual-view light-sheet microscopy to investigate the dynamics of biofilm development from a founder cell to a mature three-dimensional community. Tracking of individual cells revealed two distinct fates: one set of biofilm cells expanded ballistically outward, while the other became trapped at the substrate. A collective fountain-like flow transported cells to the biofilm front, bypassing members trapped at the substrate and facilitating lateral biofilm expansion. This collective flow pattern was quantitatively captured by a continuum model of biofilm growth against substrate friction. Coordinated cell movement required the matrix protein RbmA, without which cells expanded erratically. Thus, tracking cell lineages and trajectories in space and time revealed how multicellular structures form from a single founder cell.

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