Biofilm-control strategies based on enzymic disruption of the extracellular polymeric substance matrix – a modelling study

A kinetic model is proposed to assess the feasibility of strategies for the removal of biofilms by using substances that induce detachment by affecting the cohesiveness of the matrix of extracellular polymeric substances (EPSs). The model uses a two-state description of the EPS (natural EPS and compromised EPS) to provide a unified representation of diverse mechanisms of action of detachment-promoting agents (DPAs), which include enzymes that degrade the EPS and other agents described in the literature. A biofilm-cohesiveness factor describes local increases in detachment rates resultant from losses in cohesive strength. The kinetic model was implemented in an individual-based biofilm-modelling framework, including detachment rates dependent on local cohesiveness. The efficacy of treatments with DPAs was assessed by three-dimensional model simulations. Changes in treatment efficacy were evaluated quantitatively by using a Thiele modulus, which quantifies the relationship between diffusion of the DPA through the biofilm matrix and DPA decay rate, and a Damköhler number relating the rate of EPS reaction with a DPA and the rate of EPS production by the micro-organisms in the biofilm. This study demonstrates the feasibility and limits of implementing biofilm-control strategies based on attacking the EPS.

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Surface Functionalization-Dependent Physicochemical Interactions between Nanoparticles and the Biofilm EPS Matrix

10.5194/biofilms9-93 ◽

2020 ◽

Author(s):

Dishon Hiebner ◽

Caio Barros ◽

Laura Quinn ◽

Stefania Vitale ◽

Eoin Casey

Keyword(s):

Laser Scanning ◽

Three Dimensional ◽

Engineered Nanoparticles ◽

Laser Scanning Microscopy ◽

Confocal Laser ◽

Innovative Strategy ◽

Biofilm Control ◽

Physicochemical Interactions ◽

The Matrix ◽

Underlying Mechanisms

<p>The contribution of the biofilm extracellular polymeric substance (EPS) matrix to reduced antimicrobial susceptibility in biofilms is widely recognised.&#160; As such, directly targeting the EPS matrix is a promising biofilm control strategy that allows for efficient disruption of the matrix to allow an increase in susceptibility to antibiofilm agents. To this end, engineered nanoparticles (NPs) have received considerable attention. However, the fundamental understanding of the physicochemical interactions occurring between NPs and the EPS matrix has not yet been fully elucidated. An insight into the underlying mechanisms involved when a NP interacts with molecules in the EPS matrix will aid in the design of more efficient systems for biofilm control. The use of highly specific fluorescent probes in confocal laser scanning microscopy (CLSM) to illustrate the spatial distribution of EPS macromolecules within the biofilm is demonstrated. Three-dimensional (3D) colocalization analysis was used to assess the affinity of differently functionalized silica NPs (SiNPs) for specific EPS macromolecules from <em>Pseudomonas fluorescens</em> biofilms. Results show that both the charge and surface functional groups of SiNPs dramatically affect the extent to which SiNPs interact and localize with EPS macromolecules, including proteins, polysaccharides, and DNA. This research not only develops an innovative strategy for biofilm-nanoparticle interaction studies but also provides a platform on which to build more efficient NP systems for biofilm control.</p>

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A computational model of the collective fluid dynamics of motile micro-organisms

Journal of Fluid Mechanics ◽

10.1017/s0022112001007339 ◽

2002 ◽

Vol 455 ◽

pp. 149-174 ◽

Cited By ~ 45

Author(s):

MATTHEW M. HOPKINS ◽

LISA J. FAUCI

Keyword(s):

Fluid Dynamics ◽

Stokes Equations ◽

Temporal Dynamics ◽

Three Dimensional ◽

Two Dimensions ◽

Point Sources ◽

Physical Factors ◽

Modelling Framework ◽

Long Time ◽

Micro Organisms

A mathematical model and numerical method for studying the collective dynamics of geotactic, gyrotactic and chemotactic micro-organisms immersed in a viscous fluid is presented. The Navier–Stokes equations of fluid dynamics are solved in the presence of a discrete collection of micro-organisms. These microbes act as point sources of gravitational force in the fluid equations, and thus affect the fluid flow. Physical factors, e.g. vorticity and gravity, as well as sensory factors affect swimming speed and direction. In the case of chemotactic microbes, the swimming orientation is a function of a molecular field. In the model considered here, the molecules are a nutrient whose consumption results in an upward gradient of concentration that drives its downward diffusion. The resultant upward chemotactically induced accumulation of cells results in (Rayleigh–Taylor) instability and eventually in steady or chaotic convection that transports molecules and affects the translocation of organisms. Computational results that examine the long-time behaviour of the full nonlinear system are presented.The actual dynamical system consisting of fluid and suspended swimming organisms is obviously three-dimensional, as are the basic modelling equations. While the computations presented in this paper are two-dimensional, they provide results that match remarkably well the spatial patterns and long-time temporal dynamics of actual experiments; various physically applicable assumptions yield steady states, chaotic states, and bottom-standing plumes. The simplified representation of microbes as point particles allows the variation of input parameters and modelling details, while performing calculations with very large numbers of particles (≈104–105), enough so that realistic cell concentrations and macroscopic fluid effects can be modelled with one particle representing one microbe, rather than some collection of microbes. It is demonstrated that this modelling framework can be used to test hypotheses concerning the coupled effects of microbial behaviour, fluid dynamics and molecular mixing. Thus, not only are insights provided into the differing dynamics concerning purely geotactic and gyrotactic microbes, the dynamics of competing strategies for chemotaxis, but it is demonstrated that relatively economical explorations in two dimensions can deliver striking insights and distinguish among hypotheses.

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The Crystal Lattice of the Pyrenoid Matrix of Prorocentrum Micans

Journal of Cell Science ◽

10.1242/jcs.5.1.251 ◽

1969 ◽

Vol 5 (1) ◽

pp. 251-269

Author(s):

K. KOWALLIK

Keyword(s):

Average Distance ◽

Three Dimensional ◽

Close Packing ◽

Unit Membrane ◽

Three Dimensional Model ◽

Prorocentrum Micans ◽

Constant Matrix ◽

Crystal Lattices ◽

Protein Storage ◽

The Matrix

The pyrenoid matrix of the marine dinoflagellate Prorocentrum micans is shown to consist of regular close-packed units, which form a cubic face-centred lattice. Numerous lamellae usually consisting of two apposed thylakoids traverse the pyrenoid matrix. They normally run strikingly parallel to each other, with an average distance of 139 nm between each stack. The three-layered unit membrane of the thylakoids penetrating the pyrenoid is 70 Å thick, the same as the unit membrane of the chloroplast thylakoids. The total thickness of one thylakoid measures 190-220 Å. The globular units of the pyrenoid matrix have a calculated mean diameter of 232 Å, forming different line and dot patterns (hexagonal and cubic arrays) due to different section angles. Hexagonal patterns on prints result from projections of superimposed close-packed layers; they do not belong to one close-packing. Line patterns parallel to the thylakoid direction are composed without exception of 11 contrasted lines (6 and 5 alternating). This fact suggests that a definite number of units is arranged between the thylakoid stacks, thus producing the constant matrix thickness. Comparable regions in the chloroplast matrix cannot be confused with the pyrenoid matrix, as they never display an ordered structure. A three-dimensional model of the matrix is presented. Starch is stored only in the cytoplasm; there is no visible connexion with the pyrenoid. On the evidence of protein storage in similar crystal lattices both in plants and animals it is suggested that the pyrenoid may also be an organelle for protein storage in some groups of algae.

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Mathematical model for microbial fuel cells with anodic biofilms and anaerobic digestion

Water Science & Technology ◽

10.2166/wst.2008.095 ◽

2008 ◽

Vol 57 (7) ◽

pp. 965-971 ◽

Cited By ~ 94

Author(s):

C. Picioreanu ◽

K. P. Katuri ◽

I. M. Head ◽

M. C. M. van Loosdrecht ◽

K. Scott

Keyword(s):

Fuel Cells ◽

Anaerobic Digestion ◽

Microbial Fuel Cells ◽

Three Dimensional ◽

Bulk Liquid ◽

Anode Surface ◽

Three Dimensional Model ◽

Heterogeneous Distribution ◽

Model Simulations ◽

Modelling Framework

This study describes the integration of IWA's anaerobic digestion model (ADM1) within a computational model of microbial fuel cells (MFCs). Several populations of methanogenic and electroactive microorganisms coexist suspended in the anolyte and in the biofilm attached to the anode. A number of biological, chemical and electrochemical reactions occur in the bulk liquid, in the biofilm and at the electrode surface, involving glucose, organic acids, H2 and redox mediators. Model output includes the evolution in time of important measurable MFC parameters (current production, consumption of substrates, suspended and attached biomass growth). Two- and three-dimensional model simulations reveal the importance of current and biomass heterogeneous distribution over the planar anode surface. Voltage- and power–current characteristics can be calculated at different moments in time to evaluate the limiting regime in which the MFC operates. Finally, model simulations are compared with experimental results showing that, in a batch MFC, smaller electrical resistance of the circuit leads to selection of electroactive bacteria. Higher coulombic yields are so obtained because electrons from substrate are transferred to anode rather than following the methanogenesis pathway. In addition to higher currents, faster COD consumption rates are so achieved. The potential of this general modelling framework is in the understanding and design of more complex cases of wastewater-fed microbial fuel cells.

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Three-Dimensional Structure of Ratings of Exploratory Responses Shown by a Semantic Differential

Psychological Reports ◽

10.2466/pr0.1964.14.1.187 ◽

1964 ◽

Vol 14 (1) ◽

pp. 187-196 ◽

Cited By ~ 1

Author(s):

Edmund S. Howe

Keyword(s):

Three Dimensional ◽

Semantic Differential ◽

Activity Level ◽

Total Variance ◽

Dimensional Structure ◽

Primary Concern ◽

Three Dimensional Model ◽

The Matrix ◽

Major Variable ◽

Professional Evaluation

Ten exploratory responses systematically varying in rated Activity Level were judged by 38 psychotherapists against a 21-scale Semantic Differential. Factorization of the matrix of rs among scales by the Multiple Grouping Method yielded three factors. Factor 1, properly labeled as Precision/Potency, accounts for 44% of the total variance. Factors 2 and 3, respectively interpreted as Professional Evaluation and Objectivity, together explain 44% of the total variance. All three factors are similar in structure to those observed in an earlier study using a heterogeneous group of therapist's responses; but the evaluative factor, as anticipated, is no longer the major source of variance. The implications of the findings for quantification of the therapist's verbal behavior are discussed. It is suggested that at bottom Ptecision/Potency defines a major variable studied under various guises by others; that an independent Objectivity factor will inevitably occur for exploratory statements but not for interpretive statements; and that Professional Evaluation is not necessarily the primary concern of the rater when confronted by therapist's statements in a rating situation. A three-dimensional model of the 10 responses is presented.

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Designing TIMP (tissue inhibitor of metalloproteinases) variants that are selective metalloproteinase inhibitors

Biochemical Society Symposium ◽

10.1042/bss0700201 ◽

2003 ◽

Vol 70 ◽

pp. 201-212 ◽

Cited By ~ 51

Author(s):

Hideaki Nagase ◽

Keith Brew

Keyword(s):

Three Dimensional ◽

Therapeutic Interventions ◽

Tissue Inhibitors Of Metalloproteinases ◽

Structural Basis ◽

Structural Elements ◽

Ridge Structure ◽

Extracellular Matrix Components ◽

Metalloproteinase Inhibitors ◽

The Matrix ◽

A Disintegrin And Metalloproteinase

The tissue inhibitors of metalloproteinases (TIMPs) are endogenous inhibitors of the matrix metalloproteinases (MMPs), enzymes that play central roles in the degradation of extracellular matrix components. The balance between MMPs and TIMPs is important in the maintenance of tissues, and its disruption affects tissue homoeostasis. Four related TIMPs (TIMP-1 to TIMP-4) can each form a complex with MMPs in a 1:1 stoichiometry with high affinity, but their inhibitory activities towards different MMPs are not particularly selective. The three-dimensional structures of TIMP-MMP complexes reveal that TIMPs have an extended ridge structure that slots into the active site of MMPs. Mutation of three separate residues in the ridge, at positions 2, 4 and 68 in the amino acid sequence of the N-terminal inhibitory domain of TIMP-1 (N-TIMP-1), separately and in combination has produced N-TIMP-1 variants with higher binding affinity and specificity for individual MMPs. TIMP-3 is unique in that it inhibits not only MMPs, but also several ADAM (a disintegrin and metalloproteinase) and ADAMTS (ADAM with thrombospondin motifs) metalloproteinases. Inhibition of the latter groups of metalloproteinases, as exemplified with ADAMTS-4 (aggrecanase 1), requires additional structural elements in TIMP-3 that have not yet been identified. Knowledge of the structural basis of the inhibitory action of TIMPs will facilitate the design of selective TIMP variants for investigating the biological roles of specific MMPs and for developing therapeutic interventions for MMP-associated diseases.

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