A three-dimensional computer model analysis of three hypothetical biofilm detachment mechanisms

Three hypothetical mechanisms of detachment were incorporated into a three-dimensional computer model of biofilm development. The model integrated processes of substrate utilization, substrate diffusion, growth, cell advection, and detachment in a cellular automata framework. The purpose of this investigation was to characterize each of the mechanisms with respect to four criteria: the resulting biofilm structure, the existence of a steady state, the propensity for sloughing events, and the dynamics during starvation. The three detachment mechanisms analyzed represented various physical and biological influences hypothesized to affect biofilm detachment. The first invoked the concept of fluid shear removing biomass that protrudes far above the surface and is therefore subjected to relatively large drag forces. The second pathway linked detachment to changes in the local availability of a nutrient. The third pathway simulated an erosive process in which individual cells are lost from the surface of a biofilm cell cluster. The detachment mechanisms demonstrated diverse behaviors with respect to the four analysis criteria. The height-dependant mechanism produced flat, steady state biofilms that lacked sloughing events. Detachment based on substrate limitation produced significant sloughing events. The resulting biofilm structures included distinct, hollow clusters separated by channels. The erosion mechanism produced neither a non-zero steady state nor sloughing events. A mechanism combining all three-detachment mechanisms produced mushroom-like structures. The dynamics of biofilm decay during starvation were distinct for each detachment mechanism. These results show that detachment is a critical determinant of biofilm structure and of the dynamics of biofilm accumulation and loss.     

The metabolically active subpopulation in Pseudomonas aeruginosa biofilms survives exposure to membrane-targeting antimicrobials via distinct molecular mechanisms

Biofilms are reported to be inherently refractory toward antimicrobial attack and, therefore, cause problems in industrial and medical settings. Pseudomonas aeruginosa biofilms contain subpopulations that exhibit high metabolic activity and subpopulations that exhibit low metabolic activity. We have found that membrane-targeting antimicrobials such as colistin, EDTA, SDS, and chlorhexidine specifically kill the inactive subpopulation in P.?aeruginosa biofilms, whereas the active subpopulation survives exposure to these compounds. Because treatment of P.?aeruginosa biofilms with the membrane-targeting compounds colistin, EDTA, SDS, and chlorhexidine resulted in the same spatial distribution of live and dead bacteria, we investigated whether tolerance to these compounds originated from the same molecular mechanisms. Development of colistin-tolerant subpopulations was found to depend on the pmr genes encoding lipopolysaccharide modification enzymes, as well as on the mexAB-oprM, mexCD-oprJ, and muxABC-opmB genes encoding antimicrobial efflux pumps, but does not depend on the mexPQ-opmE efflux pump genes. Development of chlorhexidine-tolerant subpopulations was found to depend on the mexCD-oprJ genes, but does not depend on the pmr, mexAB-oprM, mexPQ-opmE, or muxABC-opmB genes. Tolerance to SDS and EDTA in P. aeruginosa biofilms is linked to metabolically active cells, but does not depend on the pmr, mexAB, mexCD, mexPQ, or muxABC genes. Our data suggest that the active subpopulation in P.?aeruginosa biofilms is able to adapt to exposure to membrane-targeting agents through the use of different genetic determinants, dependent on the specific membrane-targeting compound.     

A hypothetical synaptic-neural-behavioral model of operant learning

Biological Cybernetics -     

Drag production mechanisms of filamentous biofilms

Abstract

Biofilms were grown on smooth acrylic surfaces for nominal incubation times of three, five, and ten weeks in a flow loop at the University of Michigan. The biofilm covered surfaces were exposed to the turbulent flow in a high-aspect ratio, fully developed channel flow facility at height-based Reynolds numbers from Re_H ≈ 5,000 to 30,000. Measurements of the pressure drop along each fouled upper surface revealed that the friction drag increased from approximately 10% to 400%. The wide range in drag penalty was linked to variations in flow speed, the average thickness of the biofilms, and the level of film coverage over each surface through scaling parameters and empirical correlations. Rigid replicas of select biofilms were produced from time-averaged laser scans collected while the biofilm was subjected to flow. These rigid biofilm replicas experienced roughly half the drag increase of their compliant counterparts with the increase in friction spanning roughly 50% to 200%.     

A computer graphics model of frog gamma-crystallin based on the three-dimensional structure of calf gamma-II crystallin

Molecular models for Rana gamma-1 and gamma-2 crystallins have been constructed using computer graphics on the basis of the protein primary structure derived from the complementary DNA sequence and the three-dimensional structure of calf gamma-II crystallin that has been defined at high resolution by X-ray analysis. The models show that the cores of the two domains are conserved as hydrophobic, with the polypeptide chain arranged as a four Greek-key motif structure. Although many lysines replace arginines at equivalent positions in mammalian proteins, the Rana crystallins also have an extensive series of ion pairs on their surface; these are strongly implicated in their function as stable structural molecules, which are highly conserved in the evolution of the vertebrate eye lens.     

A television/computer three-dimensional surface shape measurement system

An optical scanner is described which has been designed primarily for the measurement of human back shape. A projector and television camera were mounted together in a box which could rotate about a horizontal axis. The projector shone a horizontal plane of light, which was viewed at an angle from below by the television camera, linked directly to a minicomputer. The shape of the line of light formed by the plane as it fell on an object, together with a knowledge of the geometry of the system, enabled three-dimensional coordinates of points on the line to be calculated. A record of a surface shape was built up by scanning the object in about 2 s. Calibration of the system was achieved by scanning an object of known dimensions. Sets of algorithms are described which derive geometric parameters from the calibration scan and which sort surface shape coordinates, outline them and detect special markers from the surface shape scan. The accuracy of measurement exceeded the design aim of +/- 3 mm in each axis within a volume of 400 mm x 500 mm x 300 mm.     

A three-dimensional homology model of the O-acetylserine sulfhydrylase-B from Salmonella typhimurium

O-acetylserine sulfhydrylase (OASS) catalyzes the last step in the cysteine biosynthetic pathway in enteric bacteria and plants. The overall pathway involves the substitution of the beta-acetoxy group of O-acetyl-L-serine with inorganic bisulfide. Two isozymes are present in S. typhimurium, the A- and B-isozymes, expressed under aerobic and anaerobic conditions, respectively. No crystal structure is presently available for the B-isozyme. Kinetic data indicate the catalytic mechanism of OASS-B is ping-pong, as found for the A-isozyme, but kinetic parameters and substrate specificity differ. In order to estimate whether structural differences may be responsible for the kinetic differences, a homology model was built using the structure of OASS-A as the template for the OASS-B model. The beta-subunit of tryptophan synthase and cystathionine beta-synthase were used for comparison. Differences between the OASS-A structure and the homology model for OASS-B are discussed.     

A computer model of evolutionary optimization

Molecular evolution is viewed as a typical combinatorial optimization problem. We analyse a chemical reaction model which considers RNA replication including correct copying and point mutations together with hydrolytic degradation and the dilution flux of a flow reactor. The corresponding stochastic reaction network is implemented on a computer in order to investigate some basic features of evolutionary optimization dynamics. Characteristic features of real molecular systems are mimicked by folding binary sequences into unknotted two-dimensional structures. Selective values are derived from these molecular 'phenotypes' by an evaluation procedure which assigns numerical values to different elements of the secondary structure. The fitness function obtained thereby contains nontrivial long-range interactions which are typical for real systems. The fitness landscape also reveals quite involved and bizarre local topologies which we consider also representative of polynucleotide replication in actually occurring systems. Optimization operates on an ensemble of sequences via mutation and natural selection. The strategy observed in the simulation experiments is fairly general and resembles closely a heuristic widely applied in operations research areas. Despite the relative smallness of the system--we study 2000 molecules of chain length v = 70 in a typical simulation experiment--features typical for the evolution of real populations are observed as there are error thresholds for replication, evolutionary steps and quasistationary sequence distributions. The relative importance of selectively neutral or almost neutral variants is discussed quantitatively. Four characteristic ensemble properties, entropy of the distribution, ensemble correlation, mean Hamming distance and diversity of the population, are computed and checked for their sensitivity in recording major optimization events during the simulation.     

A fluid dynamics model of the growth of phototrophic biofilms

A system of nonlinear hyperbolic partial differential equations is derived using mixture theory to model the formation of biofilms. In contrast with most of the existing models, our equations have a finite speed of propagation, without using artificial free boundary conditions. Adapted numerical scheme will be described in detail and several simulations will be presented in one and more space dimensions in the particular case of cyanobacteria biofilms. Besides, the numerical scheme we present is able to deal in a natural and effective way with regions where one of the phases is vanishing.     

A hypothetical model of the flavodoxin-tetraheme cytochrome c3 complex of sulfate-reducing bacteria

A hypothetical model of the flavodoxin-tetraheme cytochrome c3 electron-transfer complex from the sulfate-reducing bacterium Desulfovibrio vulgaris has been constructed by using interactive computer graphics based on electrostatic potential field calculations and previous NMR experiments. Features of the proposed complex are (1) van der Waals contact between the flavin mononucleotide prosthetic group of flavodoxin and one heme of the cytochrome, (2) unique complementarity of electrostatic fields between the region surrounding this heme and the region surrounding the exposed portion of the flavin mononucleotide group of flavodoxin, and (3) no steric interferences between the two polypeptide chains in the complex. This complex is consistent with all structural and spectroscopic data available.     

A computer model of the house-environment system

An energy-flow computer model of a house is developed which can be made to simulate the changes in temperature of a simple physical model during the 24-hr day. By adjusting parameters (albedo, sun's angles, conduction coefficients, wall dimensions, window dimensions, house orientation, internal heating or air-conditioning, insolation) the computer model is easily altered. It is presumably an easier model to experiment with than physical models. Experimentation with the computer model by architects should help them to maximize useful and minimize detrimental aspects of the external climate in the design of houses.

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Zusammenfassung Ein Energiefluss Computer-Modell eines Hauses wird beschrieben, das zur Simulierung der Veränderungen in der Temperatur eines einfachen physikalischen Models während eines 24-Stunden Tages benutzt werden kann. Das Computer-Modell lässt sich leicht durch Anpassung der Parameter (Albedo, Sonnenstand, Leitungskoeffizient, Dimensionen der Wände und Fenster, Stellung des Hauses, Heizung oder Luftkonditionierung) verändern. Man kann damit vermutlich leichter experimentieren als mit physikalischen Modellen. Es sollte Architekten beim Entwurf von Häusern helfen, um wertvolle Aspekte des äusseren Klimas maximal auszunutzen und nachteilige auszuschalten.

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Resume On décrit ici un modèle, utilisable sur ordinateur, du flux d'énergie à l'intérieur d'une maison. Ce modèle permet de simuler les modifications de température d'un immeuble aux conditions physiques simples pendant les 24 heures de la journée. Ce modèle peut être modifié facilement en adaptant les paramètres (albédo, hauteur du soleil, coefficient de conductibilité, dimensions des parois et des fenêtres, orientation de l'immeuble, chauffage ou conditionnement de l'air). Il est plus facile d'expérimenter par cette méthode qu'en utilisant des modèles uniquement physiques. Cette nouvelle méthode devrait aider les architectes dans l'établissement de plans de maisons, en leur apportant de précieuses valeurs provenant du climat extérieur et en leur évitant par là même bien des déboires.

     

A three-dimensional model of an anti-lysozyme antibody

The primary amino acid structure of the lysozyme-binding antibody, HyHEL-10, as determined by amino acid and nucleotide sequencing was utilized to construct a scale model of the Fv (variable region domain of immunoglobulin) using energy-minimized torsional angles of the McPC603 Fv as a prototype template. This model was in turn used as a template for generating a computer-built set of co-ordinates, which were subjected to a total of 600 steps of Adopted Basis Newton-Raphson energy minimizations using the program CHARMM. Only minimal shifts of the backbone (root-mean-square 0.76 A) were required to give an energetically stable structure with a favorable van der Waals' energy. Several notable features were evident from both the scale model and the energy-minimized computer model: (1) the shape of the antibody combining region is that of a very shallow concavity approximately 20 A X 25 A; (2) the concavity is acidic and non-hydrophobic and is bordered by hydrophobic segments; (3) the lower portion of the combining site is dominated by a cluster of tyrosine residues over the L3 and H2 areas; (4) a somatic mutation encoded by the J region of the heavy chain (JH) may contribute significantly to the complementarity of heavy chain H3 to the epitope on hen egg white lysozyme. In addition, the space-filling energy-minimized model revealed that residue 49L, a framework residue, was prominently exposed and accessible in the center of the combining-site concavity. The model suggests that variation in length of complementarity-determining regions may function not only to change directly the shape of the antibody combining site, but may also influence indirectly the nature of the antibody surface by changing the accessibility of residues not usually involved in antigen binding.     

A computer model of pancreatic islet glycolysis

We have modeled an experiment with perifused pancreatic islet cells using our BIOSSIM language. The experiment and the resulting model are concerned with glucose uptake and glycolysis by the beta-cells of pancreatic islets. Although glycolysis appears to be involved in insulin release, we do not have enough information to represent insulin release in detail. The rapid entry of glucose into the beta-cell is promoted by a carrier having a very high tissue capacity. Phosphorylation of glucose by the low affinity enzyme glucokinase appears to be limiting for glycolysis. The effects of several hexose diphosphate activators of phosphofructokinase are modeled. Model behavior is described. The kinetic parameters of the enzyme submodels are given. Because of the difficulties of preparing large amounts of experimental material, information on pancreatic islet metabolism is limited. This model is a plausible explanation of the experimental results. Recent work on the genetically engineered glucose transporter and glucokinase is discussed.     

A simple in vitro model for growth control of bacterial biofilms

The perfused biofilm fermenter was found to be unsuitable for the long-term culture and growth rate control of Staphylococcus aureus and Pseudomonas aeruginosab biofilms. In a simplified approach, biofilms of these organisms were grown within Sorbarod filter plugs which were perfused with culture medium. Pseudo-steady states were established which were stable over several days at which the growth rate of the biofilm was reproducible, measurable and significantly slower than in broth culture. Environmental scanning electron microscopy of dissected Sorbarods demonstrated an association of cells with the surfaces of individual cellulose fibres, and growth characteristic of biofilms. Relatively high cell numbers recovered from the Sorbarod model facilitated biochemical investigations of biofilm populations and cells released spontaneously from them.
SDS-PAGE demonstrated significant differences between the protein profiles of biofilm and eluted populations, which include, in Staph. aureus , the repression of a 48 kDa protein and increased expression of a 21 kDa protein relative to planktonic controls cultured at equivalent growth rates. The paper demonstrates the suitability of the approach for the culture of biofilm samples which are suitable for biochemical analysis.     

A simple in vitro model for growth control of bacterial biofilms

The perfused biofilm fermenter was found to be unsuitable for the long-term culture and growth rate control of Staphylococcus aureus and Pseudomonas aeruginosa biofilms. In a simplified approach, biofilms of these organisms were grown within Sorbarod filter plugs which were perfused with culture medium. Pseudo-steady states were established which were stable over several days at which the growth rate of the biofilm was reproducible, measurable and significantly slower than in broth culture. Environmental scanning electron microscopy of dissected Sorbarods demonstrated an association of cells with the surfaces of individual cellulose fibres, and growth characteristic of biofilms. Relatively high cell numbers recovered from the Sorbarod model facilitated biochemical investigations of biofilm populations and cells released spontaneously from them. SDS-PAGE demonstrated significant differences between the protein profiles of biofilm and eluted populations, which include, in Staph. aureus, the repression of a 48 kDa protein and increased expression of a 21 kDa protein relative to planktonic controls cultured at equivalent growth rates. The paper demonstrates the suitability of the approach for the culture of biofilm samples which are suitable for biochemical analysis.