Browsing by Department "Center for Nonlinear Dynamics"
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Item Asymmetry and Inequity in the Inheritance of a Bacterial Adhesive(New Journal of Physics, 2016-04) Cooley, Benjamin J.; Dellos-Nolan, Sheri; Dhamani, Numa; Todd, Ross; Waller, William; Wozniak, Daniel; Gordon, Vernita D.; Gordon, Vernita D.Pseudomonas aeruginosa is an opportunistic human pathogen that forms biofilm infections in a wide variety of contexts. Biofilms initiate when bacteria attach to a surface, which triggers changes in gene expression leading to the biofilm phenotype.Wehave previously shown, for the P. aeruginosa lab strain PAO1, that the self-produced polymer Psl is the most dominant adhesive for attachment to the surface but that another self-produced polymer, Pel, controls the geometry of attachment of these rod-shaped bacteria—strains that make Psl but not Pel are permanently attached to the surface but adhere at only one end (tilting up off the surface), whereas wild-type bacteria that make both Psl and Pel are permanently attached and lie down flat with very little or no tilting (Cooley et al 2013 Soft Matter 9 3871–6). Here we show that the change in attachment geometry reflects a change in the distribution of Psl on the bacterial cell surface. Bacteria that make Psl and Pel have Psl evenly coating the surface, whereas bacteria that make only Psl have Psl concentrated at only one end.Weshow that Psl can act as an inheritable, epigenetic factor. Rod-shaped P. aeruginosa grows lengthwise and divides across the middle.Wefind that asymmetry in the distribution of Psl on a parent cell is reflected in asymmetry between siblings in their attachment to the surface. Thus, Pel not only promotes P. aeruginosa lying downItem Bacteria Use Type IV Pili to Walk Upright and Detach from Surfaces(Science, 2010-10) Gibiansky, Maxsim L.; Conrad, Jacinta C.; Jin, Fan; Gordon, Vernita D.; Motto, Dominick A.; Mathewson, Margie A.Bacterial biofilms are structured multicellular communities involved in a broad range of infections. Knowing how free-swimming bacteria adapt their motility mechanisms near surfaces is crucial for understanding the transition between planktonic and biofilm phenotypes. By translating microscopy movies into searchable databases of bacterial behavior, we identified fundamental type IV pili–driven mechanisms for Pseudomonas aeruginosa surface motility involved in distinct foraging strategies. Bacteria stood upright and “walked” with trajectories optimized for two-dimensional surface exploration. Vertical orientation facilitated surface detachment and could influence biofilm morphology.Item A Dynamical Systems Approach to Spiral Wave Dynamics(1994-09) Barkley, Dwight; Kevrekidis, Ioannis G.; Barkley, DwightA simple system of five nonlinear ordinary differential equations is shown to reproduce many dynamical features of spiral waves in two-dimensional excitable media.Item Lagrangian Based Methods for Coherent Structure Detection(2015-09) Allshouse, Michael R.; Peacock, Thomas; Allshouse, Michael R.There has been a proliferation in the development of Lagrangian analytical methods for detecting coherent structures in fluid flow transport, yielding a variety of qualitatively different approaches. We present a review of four approaches and demonstrate the utility of these methods via their application to the same sample analytic model, the canonical double-gyre flow, highlighting the pros and cons of each approach. Two of the methods, the geometric and probabilistic approaches, are well established and require velocity field data over the time interval of interest to identify particularly important material lines and surfaces, and influential regions, respectively. The other two approaches, implementing tools from cluster and braid theory, seek coherent structures based on limited trajectory data, attempting to partition the flow transport into distinct regions. All four of these approaches share the common trait that they are objective methods, meaning that their results do not depend on the frame of reference used. For each method, we also present a number of example applications ranging from blood flow and chemical reactions to ocean and atmospheric flows. (C) 2015 AIP Publishing LLC.Item A Low-Cost, Hands-on Module to Characterize Antimicrobial Compounds Using an Interdisciplinary, Biophysical Approach(PLoS Biology, 2015-01) Kaushik, Karishma S.; Kessel, Ashley; Ratnayeke, Nalin; Gordon, Vernita D.We have developed a hands-on experimental module that combines biology experiments with a physics-based analytical model in order to characterize antimicrobial compounds. To understand antibiotic resistance, participants perform a disc diffusion assay to test the antimicrobial activity of different compounds and then apply a diffusion-based analytical model to gain insights into the behavior of the active antimicrobial component. In our experience, this module was robust, reproducible, and cost-effective, suggesting that it could be implemented in diverse settings such as undergraduate research, STEM (science, technology, engineering, and math) camps, school programs, and laboratory training workshops. By providing valuable interdisciplinary research experience in science outreach and education initiatives, this module addresses the paucity of structured training or education programs that integrate diverse scientific fields. Its low-cost requirements make it especially suitable for use in resource-limited settings.Item Membrane Adhesion and the Formation of Heterogeneities: Biology, Biophysics, and Biotechnology(Physical Chemistry Chemical Physics, 2015-03) Gordon, Vernita D.; O'Halloran, T. J.; Shindell, O.; Gordon, Vernita D.; O'Halloran, T. J.; Shindell, O.Membrane adhesion is essential to many vital biological processes. Sites of membrane adhesion are often associated with heterogeneities in the lipid and protein composition of the membrane. These heterogeneities are thought to play functional roles by facilitating interactions between proteins. However, the causal links between membrane adhesion and membrane heterogeneities are not known. Here we survey the state of the field and indicate what we think are understudied areas ripe for development.Item The Pseudomonas Aeruginosa PSL Polysaccharide is a Social but Non-Cheatable Trait in Biofilms(bioRxiv, 2016-05) Irie, Yasuhiko; Roberts, Aled E. L.; Kragh, Kasper N.; Gordon, Vernita D.; Hutchison, Jamie; Allen, Rosalind J.; Bjarnsholt, Thomas; West, Stuart A.; Diggle, Stephen P.; Gordon, Vernita D.Extracellular polysaccharides are compounds secreted by microorganisms into the surrounding environment and which are important for surface attachment and maintaining structural integrity within biofilms. They have been suggested to be metabolically costly to produce, and because they are secreted, to act as co-operative shared resources within biofilm communities. These assumptions have, however, not been experimentally well-examined. Here we empirically test the cooperative nature of the PSL polysaccharide, which is crucial for the formation of biofilms in Pseudomonas aeruginosa. We show that: (1) PSL provides population level benefits in biofilms, for both growth and antibiotic tolerance; (2) the benefits of PSL production are social and are shared with other cells; (3) the benefits of PSL production appear to be preferentially directed towards cells which produce PSL; (4) cells which do not produce PSL are unable to successfully exploit cells which produce PSL. Taken together, this suggests that PSL is a social but relatively non-exploitable trait, and that growth within biofilms selects for PSL-producing strains, even when multiple strains can interact (low relatedness). The growth and proliferative success of many bacteria, including human pathogens, depends upon their ability to form biofilms in their respective environmental niches. Biofilms are multicellular three dimensional biomass structures, held together by extracellular matrix molecules that encapsulate cells and cause them to aggregate. These extracellular polysaccharides (EPS) which are secreted by the bacteria, typically function as adhesins that are used to attach to a surface and to maintain the three-dimensional biofilm structure, and sometimes aid in protection against a variety of stresses, including dehydration, antibiotics, and predators. The production of EPS represents a problem from an evolutionary perspective 3, because it appears to be a type of co-operative behaviour that can potentially provide a benefit to all cells in the community, and not just to those that produce EPS. Consequently, the question arises: “what prevents the invasion of potential cheats that do not produce EPS?”. A possible solution to this problem is that EPS production may not be an exploitable co32 operative trait. Xavier & Foster showed, in an individual based simulation, that if the production of EPS facilitated growth into areas where nutrient availability was greater, then EPS producing lineages could spatially smother and outcompete non-producers. In this case, EPS production was costly, but the benefits were preferentially provided to nearby cells, which were likely to be EPS-producing clone mates. Some empirical support for this particular mechanism has been demonstrated in Vibrio cholerae, where it has been shown that EPS producing lineages are able to displace non-producers. In addition, EPS producers in V. cholerae are also able to share other secreted public goods with each other, which provides another benefit that is preferentially directed towards other EPS producers. However, the generality of these explanations for the evolutionary stability of EPS production remains unclear, and the work on V. cholerae represents the only empirical study to measure the social costs and benefits of EPS production. In addition, EPS produced by other bacterial species can vary greatly in both their chemical structure and the biological roles they play within biofilms. Furthermore, many species produce more than one type of EPS that are sometimes but not necessarily co-regulated. This means that there may be differences in the social nature of different types of EPS, and for different bacterial species. Pseudomonas aeruginosa is an opportunistic pathogen that causes various biofilm infections such as chronic respiratory infections of cystic fibrosis, keratitis, and chronic wound infections. P. aeruginosa is known to produce at least three different types of EPS as major components of its biofilm matrix: alginate, PEL, and PSL polysaccharides. Alginate production is inversely regulated with PSL and is not expressed to high levels in the majority of non-CF isolates. In contrast, PSL is expressed in most P. aeruginosa natural and clinical isolates. PSL is a crucial adhesive scaffolding component of the biofilm matrix, promoting both cell-to-cell interactions and surface attachment. Here we test the social nature of PSL and find that (1) PSL production is not metabolically costly to P. aeruginosa cells; (2) PSL+ strains are significantly fitter than PSL- strains in mixed culture biofilms and PSL- strains cannot act as social cheats; (3) the benefit of producing PSL is enhanced when there are many PSL- cells present; (4) biofilms containing a high proportion of PSL- cells are more susceptible to antibiotics; (5) relatedness in biofilms does not matter since PSL+ strains are favoured in conditions of high and low relatedness. More generally we highlight that not all components of the biofilm matrix should be considered as shared resources.Item Refining Finite-Time Lyapunov Exponent Ridges and the Challenges of Classifying Them(2015-08) Allshouse, Michael R.; Peacock, Thomas; Allshouse, Michael R.While more rigorous and sophisticated methods for identifying Lagrangian based coherent structures exist, the finite-time Lyapunov exponent (FTLE) field remains a straightforward and popular method for gaining some insight into transport by complex, time-dependent two-dimensional flows. In light of its enduring appeal, and in support of good practice, we begin by investigating the effects of discretization and noise on two numerical approaches for calculating the FTLE field. A practical method to extract and refine FTLE ridges in two-dimensional flows, which builds on previous methods, is then presented. Seeking to better ascertain the role of a FTLE ridge in flow transport, we adapt an existing classification scheme and provide a thorough treatment of the challenges of classifying the types of deformation represented by a FTLE ridge. As a practical demonstration, the methods are applied to an ocean surface velocity field data set generated by a numerical model. (C) 2015 AIP Publishing LLC.Item Rhombic Patterns: Broken Hexagonal Symmetry(1993-10) Ouyang, Qi; Gunaratne, Gemunu H.; Swinney, Harry L.; Ouyang, Qi; Swinney, Harry L.Landau-Ginzburg equations derived to conserve two-dimensional spatial symmetries lead to the prediction that rhombic arrays with characteristic angles slightly differ from 60 degrees should form in many systems. Beyond the bifurcation from the uniform state to patterns, rhombic patterns are linearly stable for a band of angles near the 60 degrees angle of regular hexagons. Experiments conducted on a reaction-diffusion system involving a chlorite-iodide-malonic acid reaction yield rhombic patterns in good accord with the theory.Item Role of Multicellular Aggregates in Biofilm Formation(American Society for Microbiology, 2016-03) Kragh, Kasper N.; Hutchison, Jaime B.; Melaugh, Gavin; Rodesney, Chris; Roberts, Aled E. L.; Irie, Yasuhiko; Jensen, Peter O.; Diggle, Stephen P.; Allen, Rosalind J.; Gordon, Vernita D.; Bjarnsholt, Thomas; Gordon, Vernita D.In traditional models of in vitro biofilm development, individual bacterial cells seed a surface, multiply, and mature into multicellular, three-dimensional structures. Much research has been devoted to elucidating the mechanisms governing the initial attachment of single cells to surfaces. However, in natural environments and during infection, bacterial cells tend to clump as multicellular aggregates, and biofilms can also slough off aggregates as a part of the dispersal process. This makes it likely that biofilms are often seeded by aggregates and single cells, yet how these aggregates impact biofilm initiation and development is not known. Here we use a combination of experimental and computational approaches to determine the relative fitness of single cells and preformed aggregates during early development of Pseudomonas aeruginosa biofilms. We find that the relative fitness of aggregates depends markedly on the density of surrounding single cells, i.e., the level of competition for growth resources. When competition between aggregates and single cells is low, an aggregate has a growth disadvantage because the aggregate interior has poor access to growth resources. However, if competition is high, aggregates exhibit higher fitness, because extending vertically above the surface gives cells at the top of aggregates better access to growth resources. Other advantages of seeding by aggregates, such as earlier switching to a biofilm-like phenotype and enhanced resilience toward antibiotics and immune response, may add to this ecological benefit. Our findings suggest that current models of biofilm formation should be reconsidered to incorporate the role of aggregates in biofilm initiation.Item Shaping the Growth Behaviour of Biofilms Initiated from Bacterial Aggregates(PLoS ONE, 2016-03) Melaugh, Gavin; Hutchison, Jamie; Kragh, Kasper N.; Irie, Yasuhiko; Roberts, Aled E. L.; Bjarnsholt, Thomas; Diggle, Stephen P.; Gordon, Vernita D.; Allen, Rosalind J.; Gordon, Vernita D.; Gordon, Vernita D.Bacterial biofilms are usually assumed to originate from individual cells deposited on a surface. However, many biofilm-forming bacteria tend to aggregate in the planktonic phase so that it is possible that many natural and infectious biofilms originate wholly or partially from pre-formed cell aggregates. Here, we use agent-based computer simulations to investigate the role of pre-formed aggregates in biofilm development. Focusing on the initial shape the aggregate forms on the surface, we find that the degree of spreading of an aggregate on a surface can play an important role in determining its eventual fate during biofilm development. Specifically, initially spread aggregates perform better when competition with surrounding unaggregated bacterial cells is low, while initially rounded aggregates perform better when competition with surrounding unaggregated cells is high. These contrasting outcomes are governed by a trade-off between aggregate surface area and height. Our results provide new insight into biofilm formation and development, and reveal new factors that may be at play in the social evolution of biofilm communities.Item Shiver me timbers: Pulsatile Contractility in Model Tissues(Proceedings of the National Academy of Sciences of the U. S. A., 2011-08) Gordon, Vernita D.; Gordon, Vernita D.Cells self-assemble and differentiate to form functional structures. This theme is ubiquitous throughout multicellular life and happens all along an organism's lifespan, from embryogenesis to tissue maintenance in a mature adult. Understanding how cells interact to form functional structures is a fundamental challenge in biology and biophysics; characterizing and targeting interactions such that they can be used for regenerative or therapeutic purposes is a major goal in bioengineering and medicine. In PNAS, Guevorkian et al. (1) study a multicellular aggregate that serves as a model tissue. Through experiments and analytical and numerical modeling, they find that small clusters of cells can respond to an externally imposed stretching force by pulsed contractions, which they dub “shivering” (1). The pulsatile nature of this response results from a threshold value of deformation required to trigger contractility; if the applied deformation is appropriately sized, contraction can reduce the deformation such that it then falls below the threshold value, causing the contraction to stop and then restart if the deformation continues. This active thresholded response constitutes an important potential class of interaction for sensitively shaping tissues.Item Singly Flagellated Pseudomonas Aeruginosa Chemotaxes Efficiently by Unbiased Motor Regulation(American Society for Microbiology, 2016-04) Cai, Qiuxian; Li, Zhaojun; Ouyang, Qi; Gordon, Vernita D.; Gordon, Vernita D.Pseudomonas aeruginosa is an opportunistic human pathogen that has long been known to chemotax. More recently, it has been established that chemotaxis is an important factor in the ability of P. aeruginosa to make biofilms. Genes that allow P. aeruginosa to chemotax are homologous with genes in the paradigmatic model organism for chemotaxis, Escherichia coli. However, P. aeruginosa is singly flagellated and E. coli has multiple flagella. Therefore, the regulation of counterclockwise/ clockwise flagellar motor bias that allows E. coli to efficiently chemotax by runs and tumbles would lead to inefficient chemotaxis by P. aeruginosa, as half of a randomly oriented population would respond to a chemoattractant gradient in the wron sense. How P. aeruginosa regulates flagellar rotation to achieve chemotaxis is not known. Here, we analyze the swimming trajectories of single cells in microfluidic channels and the rotations of cells tethered by their flagella to the surface of a variableenvironment flow cell. We show that P. aeruginosa chemotaxes by symmetrically increasing the durations of both counterclockwise and clockwise flagellar rotations when swimming up the chemoattractant gradient and symmetrically decreasing rotation durations when swimming down the chemoattractant gradient. Unlike the case for E. coli, the counterclockwise/clockwise bias stays constant for P. aeruginosa. We describe P. aeruginosa’s chemotaxis using an analytical model for symmetric motor regulation. We use this model to do simulations that show that, given P. aeruginosa’s physiological constraints on motility, its distinct, symmetric regulation of motor switching optimizes chemotaxis.Item Solid-Like Domains in Mixed Lipid Bilayers: Effect of Membrane Lamellarity and Transition Pathway(Advances in Planar Lipid Bilayers and Liposomes, 2014) Gordon, Vernita D.; Beales, Paul A.; Shearman, Gemma C.; Zhao, Zhijun; Seddon, John M.; Poon, Wilson C. K.; Egelhaaf, Stefan U.We present optical observations of phase separation in mixed model membranes in the form of giant unilamellar vesicles. These observations are compared to the phase behavior of lipid mixtures, which we determined by X-ray scattering and differential scanning calorimetry or extracted from the existing literature. The domain properties are affected not only by the bulk phase behavior but also by the membrane lamellarity and phase transition pathways. These observations have important implications for how phase behavior determined by bulk methods using dense, multilamellar lipid bilayers are linked to phase separation in giant, unilamellar lipid bilayers as observed by microscopy.Item Specific Adhesion of Membranes Simultaneously Supports Dual Heterogeneities in Lipids and Proteins(Physical Chemistry Chemical Physics, 2015-03) Shindell, O.; Mica, N.; Ritzer, M.; Gordon, Vernita D.; Gordon, Vernita D.; Gordon, Vernita D.; Shindell, O.Membrane adhesion is a vital component of many biological processes. Heterogeneities in lipid and protein composition are often associated with the adhesion site. These heterogeneities are thought to play functional roles in facilitating signalling. Here we experimentally examine this phenomenon using model membranes made of a mixture of lipids that is near a phase boundary at room temperature. Non-adherent model membranes are in a well-mixed, disordered-fluid lipid phase indicated by homogeneous distribution of a fluorescent dye that is a marker for the fluid-disordered (Ld) phase. We specifically adhere membranes to a flat substrate bilayer using biotin–avidin binding. Adhesion produces two types of coexisting heterogeneities: an ordered lipid phase that excludes binding proteins and the fluorescent membrane dye, and a disordered lipid phase that is enriched in both binding proteins and membrane dye compared with the non-adhered portion of the same membrane. Thus, a single type of adhesion interaction (biotin–avidin binding), in an initially-homogeneous system, simultaneously stabilizes both ordered-phase and disordered-phase heterogeneities that are compositionally distinct from the non-adhered portion of the vesicle. These heterogeneities are long-lived and unchanged upon increased temperature.Item Specific Adhesion of Membranes Simultaneously Supports Dual Heterogeneities in Lipids and Proteins(Physical Chemistry Chemical Physics, 2015-03) Shindell, O.; Mica, N.; Ritzer, M.; Gordon, Vernita D.Membrane adhesion is a vital component of many biological processes. Heterogeneities in lipid and protein composition are often associated with the adhesion site. These heterogeneities are thought to play functional roles in facilitating signalling. Here we experimentally examine this phenomenon using model membranes made of a mixture of lipids that is near a phase boundary at room temperature. Non-adherent model membranes are in a well-mixed, disordered-fluid lipid phase indicated by homogeneous distribution of a fluorescent dye that is a marker for the fluid-disordered (Ld) phase. We specifically adhere membranes to a flat substrate bilayer using biotin–avidin binding. Adhesion produces two types of coexisting heterogeneities: an ordered lipid phase that excludes binding proteins and the fluorescent membrane dye, and a disordered lipid phase that is enriched in both binding proteins and membrane dye compared with the non-adhered portion of the same membrane. Thus, a single type of adhesion interaction (biotin–avidin binding), in an initially-homogeneous system, simultaneously stabilizes both ordered-phase and disordered-phase heterogeneities that are compositionally distinct from the non-adhered portion of the vesicle. These heterogeneities are long-lived and unchanged upon increased temperature.Item Tobramycin and Bicarbonate Synergise to Kill Planktonic Pseudomonas Aeruginosa, but Antagonise to Promote Biofilm Survival(Nature Partner Journals, 2016-05) Kaushik, Karishma S.; Stolhandske, Jake; Shindell, Orrin; Smyth, Hugh D.; Gordon, Vernita D.; Gordon, Vernita D.Increasing antibiotic resistance and the declining rate at which new antibiotics come into use create a need to increase the efficacy of existing antibiotics. The aminoglycoside tobramycin is standard-of-care for many types of Pseudomonas aeruginosa infections, including those in the lungs of cystic fibrosis (CF) patients. P. aeruginosa is a nosocomial and opportunistic pathogen that, in planktonic form, causes acute infections and, in biofilm form, causes chronic infections. Inhaled bicarbonate has recently been proposed as a therapy to improve antimicrobial properties of the CF airway surface liquid and viscosity of CF mucus. Here we measure the effect of combining tobramycin and bicarbonate against P. aeruginosa, both lab strains and CF clinical isolates. Bicarbonate synergises with tobramycin to enhance killing of planktonic bacteria. In contrast, bicarbonate antagonises with tobramycin to promote better biofilm growth. This suggests caution when evaluating bicarbonate as a therapy for CF lungs infected with P. aeruginosa biofilms. We analyse tobramycin and bicarbonate interactions using an interpolated surface methodology to measure the dose–response function. These surfaces allow more accurate estimation of combinations yielding synergy and antagonism than do standard isobolograms. By incorporating predictions based on Loewe additivity theory, we can consolidate information on a wide range of combinations that produce a complex dose–response surface, into a single number that measures the net effect. This tool thus allows rapid initial estimation of the potential benefit or harm of a therapeutic combination. Software code is freely made available as a resource for the community.Item Torque And Optical Traps(2008-12) Ibeneche, C.; Ibeneche, ChiezeOptical traps are an important tool for research in the field of single molecule biophysics. Recent advances in optical trapping have extended their functionality from simple linear manipulation and measurement of forces, to now the ability to rotate objects and measure torques. This mini review summarizes these recent developments of the optical trap as a tool to apply and measure torque in biophysical applications.Item Transition to Chemical Turbulence(1991-12) Ouyang, Q.; Swinney, Harry L.; Ouyang, Q.; Swinney, Harry L.Experiments have been conducted on Turing-type chemical spatial patterns and their variants in a quasi-two-dimensional open spatial reactor with a chlorite-iodide-malonic acid reaction. A variety of stationary spatial structures-hexagons, stripes, and mixed states-were observed, and transitions to these states were studied. For conditions beyond those corresponding to the emergence of patterns, a transition was observed from stationary spatial patterns to chemical turbulence, which is marked by a continuous motion of the pattern within a domain and of the grain boundaries between domains. The transition to chemical turbulence was analyzed by measuring the correlation length, the average pattern speed, and the total length of the domain boundaries. The emergence of chemical turbulence is accompanied by a large increase in the defects in the pattern, which suggests that this is an example of defect-mediated turbulence.