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Karampatzakis A, Song CZ, Allsopp LP, Filloux A, Rice SA, Cohen Y, Wohland T, Török P. Probing the internal micromechanical properties of Pseudomonas aeruginosa biofilms by Brillouin imaging. NPJ Biofilms Microbiomes 2017; 3:20. [PMID: 28900539 PMCID: PMC5591272 DOI: 10.1038/s41522-017-0028-z] [Citation(s) in RCA: 23] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/12/2017] [Revised: 08/03/2017] [Accepted: 08/08/2017] [Indexed: 12/17/2022] Open
Abstract
Biofilms are organised aggregates of bacteria that adhere to each other or surfaces. The matrix of extracellular polymeric substances that holds the cells together provides the mechanical stability of the biofilm. In this study, we have applied Brillouin microscopy, a technique that is capable of measuring mechanical properties of specimens on a micrometre scale based on the shift in frequency of light incident upon a sample due to thermal fluctuations, to investigate the micromechanical properties of an active, live Pseudomonas aeruginosa biofilm. Using this non-contact and label-free technique, we have extracted information about the internal stiffness of biofilms under continuous flow. No correlation with colony size was found when comparing the averages of Brillouin shifts of two-dimensional cross-sections of randomly selected colonies. However, when focusing on single colonies, we observed two distinct spatial patterns: in smaller colonies, stiffness increased towards their interior, indicating a more compact structure of the centre of the colony, whereas, larger (over 45 μm) colonies were found to have less stiff interiors. A specialized microscopy technique can monitor biofilm stiffness in a non-destructive manner, yielding insights into biofilm structure and development. The technique, called Brillouin imaging, uses changes in the frequency of light interacting with a substance to reveal fine detail about the material’s mechanical properties. Peter Török and colleagues at Imperial College London, with co-workers in Singapore, used Brillouin imaging to study biofilms of Pseudomonas aeruginosa bacteria at different stages in their life cycle. In young colonies, stiffness increased towards the interior of the biofilm, while mature colonies had less stiff interiors. The older biofilms may therefore have hollow interiors or may have been moving towards a phase of bacterial dispersal from the biofilm state. This non-disruptive method to study mechanical variations within and between living biofilms may help efforts to combat biofilms in clinical, environmental and industrial situations.
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Karampatzakis A, Sankaran J, Kandaswamy K, Rice SA, Cohen Y, Wohland T. Measurement of oxygen concentrations in bacterial biofilms using transient state monitoring by single plane illumination microscopy. Biomed Phys Eng Express 2017. [DOI: 10.1088/2057-1976/aa6db7] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
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Chew SC, Kundukad B, Teh WK, Doyle P, Yang L, Rice SA, Kjelleberg S. Mechanical signatures of microbial biofilms in micropillar-embedded growth chambers. SOFT MATTER 2016; 12:5224-5232. [PMID: 27191395 DOI: 10.1039/c5sm02755a] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/05/2023]
Abstract
Biofilms are surface-attached communities of microorganisms embedded in an extracellular matrix and are essential for the cycling of organic matter in natural and engineered environments. They are also the leading cause of many infections, for example, those associated with chronic wounds and implanted medical devices. The extracellular matrix is a key biofilm component that determines its architecture and defines its physical properties. Herein, we used growth chambers embedded with micropillars to study the net mechanical forces (differential pressure) exerted during biofilm formation in situ. Pressure from the biofilm is transferred to the micropillars via the extracellular matrix, and reduction of major matrix components decreases the magnitude of micropillar deflections. The spatial arrangement of micropillar deflections caused by pressure differences in the different biofilm strains may potentially be used as mechanical signatures for biofilm characterization. Hence, we submit that micropillar-embedded growth chambers provide insights into the mechanical properties and dynamics of the biofilm and its matrix.
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Sule N, Rice SA, Gray SK, Scherer NF. An electrodynamics-Langevin dynamics (ED-LD) approach to simulate metal nanoparticle interactions and motion. OPTICS EXPRESS 2015; 23:29978-29992. [PMID: 26698479 DOI: 10.1364/oe.23.029978] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/05/2023]
Abstract
Understanding the formation of electrodynamically interacting assemblies of metal nanoparticles requires accurate computational methods for determining the forces and propagating trajectories. However, since computation of electromagnetic forces occurs on attosecond to femtosecond timescales, simulating the motion of colloidal nanoparticles on milliseconds to seconds timescales is a challenging multi-scale computational problem. Here, we present a computational technique for performing accurate simulations of laser-illuminated metal nanoparticles. In the simulation, we self-consistently combine the finite-difference time-domain method for electrodynamics (ED) with Langevin dynamics (LD) for the particle motions. We demonstrate the ED-LD method by calculating the 3D trajectories of a single 100-nm-diameter Ag nanoparticle and optical trapping and optical binding of two and three 150-nm-diameter Ag nanoparticles in simulated optical tweezers. We show that surface charge on the colloidal metal nanoparticles plays an important role in their optically driven self-organization. In fact, these simulations provide a more complete understanding of the assembly of different structures of two and three Ag nanoparticles that have been observed experimentally, demonstrating that the ED-LD method will be a very useful tool for understanding the self-organization of optical matter.
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Zhang Q, Shuwen G, Zhang J, Fane AG, Kjelleberg S, Rice SA, McDougald D. Analysis of microbial community composition in a lab-scale membrane distillation bioreactor. J Appl Microbiol 2015; 118:940-53. [PMID: 25604265 PMCID: PMC4409088 DOI: 10.1111/jam.12759] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/19/2014] [Revised: 01/01/2015] [Accepted: 01/11/2015] [Indexed: 12/23/2022]
Abstract
Aims Membrane distillation bioreactors (MDBR) have potential for industrial applications where wastewater is hot or waste heat is available, but the role of micro-organisms in MDBRs has never been determined, and thus was the purpose of this study. Methods and Results Microbial communities were characterized by bacterial and archaeal 16S and eukaryotic 18S rRNA gene tag-encoded pyrosequencing of DNA obtained from sludge. Taxonomy-independent analysis revealed that bacterial communities had a relatively low richness and diversity, and community composition strongly correlated with conductivity, total nitrogen and bound extracellular polymeric substances (EPS). Taxonomy-dependent analysis revealed that Rubrobacter and Caldalkalibacillus were abundant members of the bacterial community, but no archaea were detected. Eukaryotic communities had a relatively high richness and diversity, and both changes in community composition and abundance of the dominant genus, Candida, correlated with bound EPS. Conclusions Thermophilic MDBR communities were comprised of a low diversity bacterial community and a highly diverse eukaryotic community with no archea detected. Communities exhibited low resilience to changes in operational parameters. Specifically, retenatate nutrient composition and concentration was strongly correlated with the dominant species. Significance and Impact of the Study This study provides an understanding of microbial community diversity in an MDBR, which is fundamental to the optimization of reactor performance.
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Seviour T, Doyle LE, Lauw SJL, Hinks J, Rice SA, Nesatyy VJ, Webster RD, Kjelleberg S, Marsili E. Voltammetric profiling of redox-active metabolites expressed by Pseudomonas aeruginosa for diagnostic purposes. Chem Commun (Camb) 2015; 51:3789-92. [DOI: 10.1039/c4cc08590f] [Citation(s) in RCA: 45] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Voltammetric analysis ofPseudomonas aeruginosagrowth cultures unveils the interplay between PQS and phenazines under a potential bias.
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Steinberg PD, Rice SA, Campbell AH, McDougald D, Harder T. Interfaces Between Bacterial and Eukaryotic "Neuroecology". Integr Comp Biol 2011; 51:794-806. [DOI: 10.1093/icb/icr115] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/30/2022] Open
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Abstract
A method of preparation of solid amorphous water is reported, along with a demonstration of the absence of crystalline ice. The samples described are the first to be completely free of contamination with crystalline ice.
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Rice SA, Peden NR, McGlynn S, Morton C. Atypical presentation of infiltrative thyroid dermopathy. Clin Exp Dermatol 2009; 35:56-8. [PMID: 19508564 DOI: 10.1111/j.1365-2230.2008.03109.x] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
A 46-year-old woman with Graves' disease developed infiltrative dermopathy of the thenar eminences. We believe this to be the first reported case of infiltrative dermopathy affecting the thenar eminences, and question whether repetitive occupational injury may have been a contributing factor. There is little published evidence to guide the treatment of infiltrative dermopathy.
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Willcox MDP, Zhu H, Conibear TCR, Hume EBH, Givskov M, Kjelleberg S, Rice SA. Role of quorum sensing by Pseudomonas aeruginosa in microbial keratitis and cystic fibrosis. Microbiology (Reading) 2008; 154:2184-2194. [DOI: 10.1099/mic.0.2008/019281-0] [Citation(s) in RCA: 61] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
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Doty P, McGill BB, Rice SA. THE PROPERTIES OF SONIC FRAGMENTS OF DEOXYRIBOSE NUCLEIC ACID. Proc Natl Acad Sci U S A 2006; 44:432-8. [PMID: 16590216 PMCID: PMC335440 DOI: 10.1073/pnas.44.5.432] [Citation(s) in RCA: 208] [Impact Index Per Article: 11.6] [Reference Citation Analysis] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
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McDougald D, Lin WH, Rice SA, Kjelleberg S. The role of quorum sensing and the effect of environmental conditions on biofilm formation by strains of Vibrio vulnificus. BIOFOULING 2006; 22:133-44. [PMID: 17290858 DOI: 10.1080/08927010600691879] [Citation(s) in RCA: 13] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/13/2023]
Abstract
It has been suggested that Vibrio vulnificus attaches to plankton and algae and is found in large numbers in the environment. Factors affecting attachment, biofilm formation and morphology of V. vulnificus have not been thoroughly investigated. This study evaluated the role of quorum sensing (QS) and environmental conditions on biofilm development of V. vulnificus. It was found that biofilm development by V. vulnificus was affected by nutrient and glucose concentration, but not by NaCl concentration or temperature under the conditions used here. Moreover, biofilm development of a QS mutant strain proceeded rapidly and sloughing occurred earlier than for the isogenic parent strain. There was a significant loss of viability for the QS mutant biofilm early in development. Hence, it is hypothesised that factors regulated by the QS system play a role in proper biofilm development and maintenance of V. vulnificus. Furthermore, it is shown that biofilm development varied among isolates.
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Rice SA, Koh KS, Queck SY, Labbate M, Lam KW, Kjelleberg S. Biofilm formation and sloughing in Serratia marcescens are controlled by quorum sensing and nutrient cues. J Bacteriol 2005; 187:3477-85. [PMID: 15866935 PMCID: PMC1111991 DOI: 10.1128/jb.187.10.3477-3485.2005] [Citation(s) in RCA: 168] [Impact Index Per Article: 8.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
We describe here a role for quorum sensing in the detachment, or sloughing, of Serratia marcescens filamentous biofilms, and we show that nutrient conditions affect the biofilm morphotype. Under reduced carbon or nitrogen conditions, S. marcescens formed a classical biofilm consisting of microcolonies. The filamentous biofilm could be converted to a microcolony-type biofilm by switching the medium after establishment of the biofilm. Similarly, when initially grown as a microcolony biofilm, S. marcescens could be converted back to a filamentous biofilm by increasing the nutrient composition. Under high-nutrient conditions, an N-acyl homoserine lactone quorum-sensing mutant formed biofilms that were indistinguishable from the wild-type biofilms. Similarly, other quorum-sensing-dependent behaviors, such as swarming motility, could be rendered quorum sensing independent by manipulating the growth medium. Quorum sensing was also found to be involved in the sloughing of the filamentous biofilm. The biofilm formed by the bacterium consistently sloughed from the substratum after approximately 75 to 80 h of development. The quorum-sensing mutant, when supplemented with exogenous signal, formed a wild-type filamentous biofilm and sloughed at the same time as the wild type, and this was independent of surfactant production. When we removed the signal from the quorum-sensing mutant prior to the time of sloughing, the biofilm did not undergo significant detachment. Together, the data suggest that biofilm formation by S. marcescens is a dynamic process that is controlled by both nutrient cues and the quorum-sensing system.
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Abstract
There has been much progress in the control of chemical reactions since methods of active control were first proposed by Brumer & Shapiro and by Tannor & Rice ten years ago. This chapter reviews both theoretical and experimental advances in the field. Control schemes based on quantum mechanical interference between competing paths and the manipulation of wave packets with tailored laser pulses are discussed. The theory of optimal control, the limitations of control theory applied to many-body dynamics, and the effects of constraints on the trajectory of the controlled observable are presented. Experimental progress in controlling the population of specific quantum states, in manipulating the dynamics of bound wave packets, and in the control of chemical reactions are reviewed, and current problems in the field are summarized.
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Jortner J, Wilson EG, Rice SA. A Far-Ultraviolet Spectroscopic Study of Xenon Tetrafluoride. J Am Chem Soc 2002. [DOI: 10.1021/ja00889a035] [Citation(s) in RCA: 16] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
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Reichmann ME, Rice SA, Thomas CA, Doty P. A Further Examination of the Molecular Weight and Size of Desoxypentose Nucleic Acid. J Am Chem Soc 2002. [DOI: 10.1021/ja01640a067] [Citation(s) in RCA: 1940] [Impact Index Per Article: 88.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
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Chekmarev DS, Oxtoby DW, Rice SA. Melting of a quasi-two-dimensional metallic system. PHYSICAL REVIEW. E, STATISTICAL, NONLINEAR, AND SOFT MATTER PHYSICS 2001; 63:051502. [PMID: 11414904 DOI: 10.1103/physreve.63.051502] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/19/2000] [Revised: 01/22/2001] [Indexed: 05/23/2023]
Abstract
We analyze the melting of a quasi-two-dimensional metallic system using the results of a series of Monte Carlo simulations of an array of Pb atoms. The system was chosen to model the melting behavior observed for the monolayer of Pb that segregates in the liquid-vapor interface of a dilute Pb in Ga alloy [B. Yang et al., Proc. Natl. Acad. Sci. USA 96, 13 009 (1999)]. Our calculations employed a realistic pair interaction potential between lead pseudoatoms, one that is known to describe accurately the properties of the three-dimensional metal near the melting point. Our results reveal that in the quasi-two-dimensional Pb system melting is a two-stage process which proceeds through formation of a stable intermediate hexatic phase, in agreement with the prediction of the Kosterlitz-Thouless-Halperin-Nelson-Young theory. Both the solid-to-hexatic and the hexatic-to-liquid transitions are found to be first order in our simulations.
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Katz I, Rice SA. On the calculation of the density of localized states in a dense fluid. ACTA ACUST UNITED AC 2001. [DOI: 10.1088/0022-3719/5/11/012] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022]
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Aubert M, Rice SA, Blaho JA. Accumulation of herpes simplex virus type 1 early and leaky-late proteins correlates with apoptosis prevention in infected human HEp-2 cells. J Virol 2001; 75:1013-30. [PMID: 11134315 PMCID: PMC113998 DOI: 10.1128/jvi.75.2.1013-1030.2001] [Citation(s) in RCA: 60] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
We previously reported that a recombinant ICP27-null virus stimulated, but did not prevent, apoptosis in human HEp-2 cells during infection (M. Aubert and J. A. Blaho, J. Virol. 73:2803-2813, 1999). In the present study, we used a panel of 15 recombinant ICP27 mutant viruses to determine which features of herpes simplex virus type 1 (HSV-1) replication are required for the apoptosis-inhibitory activity. Each virus was defined experimentally as either apoptotic, partially apoptotic, or nonapoptotic based on infected HEp-2 cell morphologies, percentages of infected cells with condensed chromatin, and patterns of specific cellular death factor processing. Viruses d27-1, d1-5, d1-2, M11, M15, M16, n504R, n406R, n263R, and n59R are apoptotic or partially apoptotic in HEp-2 cells and severely defective for growth in Vero cells. Viruses d2-3, d3-4, d4-5, d5-6, and d6-7 are nonapoptotic, demonstrating that ICP27 contains a large amino-terminal region, including its RGG box RNA binding domain, which is not essential for apoptosis prevention. Accumulations of viral TK, VP16, and gD but not gC, ICP22, or ICP4 proteins correlated with prevention of apoptosis during the replication of these viruses. Of the nonapoptotic viruses, d4-5 did not produce gC, indicating that accumulation of true late gene products is not necessary for the prevention process. Analyses of viral DNA synthesis in HEp-2 cells indicated that apoptosis prevention by HSV-1 requires that the infection proceeds to the stage in which viral DNA replication takes place. Infections performed in the presence of the drug phosphonoacetic acid confirmed that the process of viral DNA synthesis and the accumulation of true late (gamma(2)) proteins are not required for apoptosis prevention. Based on our results, we conclude that the accumulation of HSV-1 early (beta) and leaky-late (gamma(1)) proteins correlates with the prevention of apoptosis in infected HEp-2 cells.
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McDougald D, Rice SA, Kjelleberg S. SmcR-dependent regulation of adaptive phenotypes in Vibrio vulnificus. J Bacteriol 2001; 183:758-62. [PMID: 11133972 PMCID: PMC94934 DOI: 10.1128/jb.183.2.758-762.2001] [Citation(s) in RCA: 72] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Vibrio vulnificus contains homologues of the V. harveyi luxR and luxS genes. A null mutation in smcR (luxR) resulted in a defect in starvation survival, inhibition of starvation-induced maintenance of culturability that occurs when V. vulnificus is starved prior to low-temperature incubation, and increased expression of stationary-phase phenotypes.
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Gryko J, Rice SA. The structure of the liquid-vapour interface of sodium-caesium alloys. ACTA ACUST UNITED AC 2000. [DOI: 10.1088/0305-4608/12/12/001] [Citation(s) in RCA: 19] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022]
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