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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] [What about the content of this article? (0)] [Affiliation(s)] [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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Affiliation(s)
- A Karampatzakis
- Centre for BioImaging Sciences, National University of Singapore, Singapore, 117557 Singapore.,NUS Graduate School for Integrative Sciences and Engineering, National University of Singapore, Singapore, 117557 Singapore.,Blackett Laboratory, Department of Physics, Imperial College London, Prince Consort Road, London, SW7 2BZ United Kingdom
| | - C Z Song
- Blackett Laboratory, Department of Physics, Imperial College London, Prince Consort Road, London, SW7 2BZ United Kingdom
| | - L P Allsopp
- Imperial College London, Department of Life Sciences, MRC Centre for Molecular Bacteriology and Infection, South Kensington Campus, Flowers Building, SW7 2AZ London, United Kingdom
| | - A Filloux
- Imperial College London, Department of Life Sciences, MRC Centre for Molecular Bacteriology and Infection, South Kensington Campus, Flowers Building, SW7 2AZ London, United Kingdom
| | - S A Rice
- Singapore Centre for Environmental Life Sciences Engineering and the School of Biological Sciences, Nanyang Technological University Singapore, Singapore, 637551 Singapore
| | - Y Cohen
- Singapore Centre for Environmental Life Sciences Engineering and the School of Biological Sciences, Nanyang Technological University Singapore, Singapore, 637551 Singapore
| | - T Wohland
- Centre for BioImaging Sciences, National University of Singapore, Singapore, 117557 Singapore.,NUS Graduate School for Integrative Sciences and Engineering, National University of Singapore, Singapore, 117557 Singapore.,Department of Biological Sciences and Department of Chemistry, National University of Singapore, Singapore, 117346 Singapore
| | - P Török
- Blackett Laboratory, Department of Physics, Imperial College London, Prince Consort Road, London, SW7 2BZ United Kingdom
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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] [What about the content of this article? (0)] [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] [What about the content of this article? (0)] [Affiliation(s)] [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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Affiliation(s)
- S C Chew
- Singapore Centre for Environmental Life Sciences Engineering (SCELSE), Nanyang Technological University, Singapore.
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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. Opt 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] [What about the content of this article? (0)] [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] [What about the content of this article? (0)] [Affiliation(s)] [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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Affiliation(s)
- Q Zhang
- Advanced Environmental Biotechnology Centre, Nanyang Environment and Water Research Institute, Nanyang Technological University, Singapore City, Singapore; School of Biological Sciences, Nanyang Technological University, Singapore City, Singapore
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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] [What about the content of this article? (0)] [Affiliation(s)] [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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Affiliation(s)
- T. Seviour
- Singapore Centre on Environmental Life Sciences Engineering
- Nanyang Technological University
- Singapore
| | - L. E. Doyle
- Singapore Centre on Environmental Life Sciences Engineering
- Nanyang Technological University
- Singapore
- Interdisciplinary Graduate School
- Nanyang Technological University
| | - S. J. L. Lauw
- School of Physical & Mathematical Sciences
- Nanyang Technological University
- Singapore
| | - J. Hinks
- Singapore Centre on Environmental Life Sciences Engineering
- Nanyang Technological University
- Singapore
| | - S. A. Rice
- Singapore Centre on Environmental Life Sciences Engineering
- Nanyang Technological University
- Singapore
| | - V. J. Nesatyy
- Singapore Centre on Environmental Life Sciences Engineering (SCELSE)
- National University of Singapore
- Singapore
- Singapore
| | - R. D. Webster
- School of Physical & Mathematical Sciences
- Nanyang Technological University
- Singapore
| | - S. Kjelleberg
- Singapore Centre on Environmental Life Sciences Engineering
- Nanyang Technological University
- Singapore
- School of Biotechnology and Biomolecular Sciences and Centre for Marine Bio-Innovation
- The University of New South Wales
| | - E. Marsili
- Singapore Centre on Environmental Life Sciences Engineering
- Nanyang Technological University
- Singapore
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Affiliation(s)
- S A Rice
- Department of Dermatology, Royal Free Hospital, London NW3 2QG, UK.
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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] [What about the content of this article? (0)] [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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Affiliation(s)
- D S Olander
- Department of Chemistry, The University of Chicago, Chicago, Illinois 60637
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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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Affiliation(s)
- S A Rice
- Department of Dermatology, Stirling Royal Infirmary, Stirling, UK
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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] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Affiliation(s)
- M. D. P. Willcox
- Vision CRC, Sydney, Australia
- Institute for Eye Research, Sydney, Australia
- School of Optometry and Vision Science, University of New South Wales, Sydney, NSW 2052, Australia
| | - H. Zhu
- Vision CRC, Sydney, Australia
- Institute for Eye Research, Sydney, Australia
- School of Optometry and Vision Science, University of New South Wales, Sydney, NSW 2052, Australia
| | - T. C. R. Conibear
- Vision CRC, Sydney, Australia
- School of Optometry and Vision Science, University of New South Wales, Sydney, NSW 2052, Australia
| | - E. B. H. Hume
- Vision CRC, Sydney, Australia
- Institute for Eye Research, Sydney, Australia
- School of Optometry and Vision Science, University of New South Wales, Sydney, NSW 2052, Australia
| | - M. Givskov
- BioScience and Technology, The Technical University of Denmark, DK-2800 Lyngby, Denmark
| | - S. Kjelleberg
- School of Biotechnology and Biomolecular Sciences and The Centre for Marine Bio-Innovation, University of New South Wales, Sydney, NSW 2052, Australia
| | - S. A. Rice
- School of Biotechnology and Biomolecular Sciences and The Centre for Marine Bio-Innovation, University of New South Wales, Sydney, NSW 2052, Australia
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Affiliation(s)
- P Doty
- DEPARTMENT OF CHEMISTRY, HARVARD UNIVERSITY, CAMBRIDGE MASSACHUSETTS
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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] [What about the content of this article? (0)] [Affiliation(s)] [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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Affiliation(s)
- D McDougald
- School of Biotechnology and Biomolecular Sciences, University of New South Wales, Sydney, Australia
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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] [What about the content of this article? (0)] [Affiliation(s)] [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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Affiliation(s)
- S A Rice
- The Centre for Marine Biofouling and Bio-Innovation, The University of New South Wales, Sydney, NSW 2052 Australia
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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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Affiliation(s)
- R J Gordon
- Department of Chemistry (m/c 111), University of Illinois at Chicago, 845 W Taylor Street, Chicago, IL 60607-7061, USA.
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Chekmarev DS, Oxtoby DW, Rice SA. Melting of a quasi-two-dimensional metallic system. Phys Rev E Stat Nonlin Soft Matter Phys 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] [What about the content of this article? (0)] [Affiliation(s)] [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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Affiliation(s)
- D S Chekmarev
- Department of Chemistry and The James Franck Institute, The University of Chicago, Chicago, Illinois 60637, USA
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Affiliation(s)
- S A Rice
- James Franck Institute, University of Chicago, Illinois 60637, USA.
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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] [What about the content of this article? (0)] [Affiliation(s)] [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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Affiliation(s)
- M Aubert
- Department of Microbiology, Mount Sinai School of Medicine, New York, New York 10029, USA
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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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Affiliation(s)
- D McDougald
- School of Microbiology and Immunology, The University of New South Wales, Sydney, New South Wales, 2052, Australia
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Lin B, Yu J, Rice SA. Direct measurements of constrained brownian motion of an isolated sphere between two walls. Phys Rev E Stat Phys Plasmas Fluids Relat Interdiscip Topics 2000; 62:3909-19. [PMID: 11088911 DOI: 10.1103/physreve.62.3909] [Citation(s) in RCA: 155] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/22/1999] [Revised: 06/02/2000] [Indexed: 11/07/2022]
Abstract
We report the results of direct measurements, using video microscopy in combination with optical tweezers, of constrained diffusion of an isolated uncharged PMMA sphere in a density-matched fluid confined between two parallel flat walls. Our experimental methodology allows us to study the hindered diffusion of the sphere as an explicit function of its distance from the walls, without interference from sedimentation or from electrostatic interaction between the particle and the walls. The measured diffusion coefficients are used to test the predictions of the wall drag effect predicted by several approximate theoretical analyses. We find a quantitative agreement with the behavior predicted using a hydrodynamic analysis that independently superimposes the wall drag effects arising from each wall. Our results imply, indirectly, that neglect of multiple interactions with the colloid sphere of the perturbations of the pressure and velocity fields induced by each wall leads to an underestimate of the influence of the wall on the drag force experienced by the particle.
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Affiliation(s)
- B Lin
- The James Franck Institute, The University of Chicago, Chicago, Illinois 60637, USA
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Abstract
Invertebrate interspecific developmental patterns can be highly variable and, taxonomically, are considered only weakly constrained. Intraspecifically, some invertebrate species possess multiple developmental modes-a condition known as poecilogony. Closer examination of most putative poecilogenous species, however, has not supported poecilogony, but rather has uncovered hidden or cryptic species. The polychaete Streblospio benedicti is a well-known, poecilogenous species found along the coast of North America. We collected mitochondrial cytochrome subunit I DNA sequence data from 88 individuals taken from 11 locations along the Atlantic, Gulf, and Pacific Coasts of the United States to provide a phylogenetic framework from which to interpret intraspecific variation in larval life history and brooding structure morphology in this species. Our results are consistent with a recent revision of the species into two separate species: S. benedicti, a pouched brooding form distributed along the Atlantic and Pacific Coasts, and S. gynobranchiata, a branchiate brooding form in the Gulf of Mexico. Contrary to the redescription, S. benedicti is paraphyletic because the pouched brooding population in Vero Beach, Florida shows strong genetic affinity with Gulf of Mexico populations (S. gynobranchiata). However, S. benedicti is a true poecilogenous species, with both lecithotrophic and planktotrophic individuals possessing identical mitochondrial DNA haplotypes. Crossbreeding experiments further support the molecular phylogeny with reproductive isolation demonstrated between, but not within, the major phylogenetic clades consistent with the previously described species. The genetic break near Vero Beach, Florida, corresponds to a well-known phylogeographic boundary, but the estimated time of separation for the Streblospio spp., approximately 10 million years before present, predates all other known phylogeographic subdivisions in this area. This suggests that biogeographic sundering in this region is a recurrent event. Divergence times within the major Streblospio spp. clades are recent and indicate that changes in larval life history as well as brooding structure morphology are highly plastic and can evolve rapidly.
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Affiliation(s)
- S R Schulze
- University of South Florida, Department of Biology, Tampa 33620, USA.
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Bunnell SM, Rice SA. The conserved carboxyl-terminal half of herpes simplex virus type 1 regulatory protein ICP27 is dispensable for viral growth in the presence of compensatory mutations. J Virol 2000; 74:7362-74. [PMID: 10906189 PMCID: PMC112256 DOI: 10.1128/jvi.74.16.7362-7374.2000] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
ICP27 is an essential herpes simplex virus type 1 (HSV-1) immediate-early protein that regulates viral gene expression by poorly characterized mechanisms. Previous data suggest that its carboxyl (C)-terminal portion is absolutely required for productive viral infection. In this study, we isolated M16R, a second-site revertant of a viral ICP27 C-terminal mutant. M16R harbors an intragenic reversion, as demonstrated by the fact that its cloned ICP27 allele can complement the growth of an HSV-1 ICP27 deletion mutant. DNA sequencing demonstrated that the intragenic reversion is a frameshift alteration in a homopolymeric run of C residues at codons 215 to 217. This results in the predicted expression of a truncated, 289-residue molecule bearing 72 novel C-terminal residues derived from the +1 reading frame. Consistent with this, M16R expresses an ICP27-related molecule of the predicted size in the nuclei of infected cells. Transfection-based viral complementation assays confirmed that the truncated, frameshifted protein can partially substitute for ICP27 in the context of viral infection. Surprisingly, its novel C-terminal residues are required for this activity. To see if the frameshift mutation is all that is required for M16R's viability, we re-engineered the M16R ICP27 allele and inserted it into a new viral background, creating the HSV-1 mutant M16exC. An additional mutant, exCd305, was constructed which possesses the frameshift in the context of an ICP27 gene with the C terminus deleted. We found that both M16exC and exCd305 are nonviable in Vero cells, suggesting that one or more extragenic mutations are also required for the viability of M16R. Consistent with this interpretation, we isolated two viable derivatives of exCd305 which grow productively in Vero cells despite being incapable of encoding the C-terminal portion of ICP27. Studies of viral DNA synthesis in mutant-infected cells indicated that the truncated, frameshifted ICP27 protein can enhance viral DNA replication. In summary, our results demonstrate that the C-terminal portion of ICP27, conserved widely in herpesviruses and previously believed to be absolutely essential, is dispensable for HSV-1 lytic replication in the presence of compensatory genomic mutations.
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Affiliation(s)
- S M Bunnell
- Department of Biochemistry, University of Alberta, Edmonton, Alberta, Canada T6G 2H7
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Abstract
Herpes simplex virus (HSV) ICP27 is an essential and multifunctional regulator of viral gene expression that modulates RNA splicing, polyadenylation, and nuclear export. We have previously reported that ICP27 causes the cytoplasmic accumulation of unspliced alpha-globin pre-mRNA. Here we examined the effects of a series of ICP27 mutations that alter important functional regions of the protein on the processing and nuclear transport of alpha-globin and HSV ICP0 RNA. The results demonstrate that ICP27 mutants that are impaired for growth in noncomplementing cells, including mutants in the N- and C-terminal regions, are defective in the accumulation of alpha-globin pre-mRNA. Unexpectedly, several mutants that are competent to repress the expression of reporter genes in transient transfection assays failed to accumulate unspliced RNA, implying that different mechanisms are responsible for transrepression and pre-mRNA accumulation. Several mutants caused a marked increase in the length and heterogeneity of the alpha-globin mRNA poly(A) tail, suggesting that ICP27 may directly or indirectly affect the regulation of poly(A) polymerase. ICP27 was also required for the accumulation of multiple ICP0 intron-bearing transcripts, but this effect displayed a mutational sensitivity profile different from that of accumulation of unspliced alpha-globin RNA. Moreover, unlike spliced and unspliced alpha-globin RNAs, which were efficiently exported to the cytoplasm, spliced and intron-containing ICP0 transcripts were predominantly nuclear in localization, and ICP27 was not required for nuclear retention of the spliced message. We propose that these transcript- and ICP27 allele-specific differences may be explained by the presence of a strong cis-acting ICP27 response element in the alpha-globin transcript.
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Affiliation(s)
- K S Ellison
- Department of Medical Microbiology and Immunology, University of Alberta, Edmonton, Alberta, Canada T6G 2H7
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Rice SA, McDougald D, Kjelleberg S. Vibrio vulnificus: a physiological and genetic approach to the viable but nonculturable response. J Infect Chemother 2000; 6:115-20. [PMID: 11810549 DOI: 10.1007/pl00012150] [Citation(s) in RCA: 27] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/04/1999] [Accepted: 02/07/2000] [Indexed: 11/29/2022]
Abstract
In this review, we focus on studies of the viable but nonculturable response (VBNC) of Vibrio vulnificus, a significant and aggressive human pathogen, as a model system for the general understanding of the VBNC response. This response is characterized physiologically as the inability to culture an organism on media that normally supports its growth, and yet those cells retain indicators of metabolic activity. Implicit in this definition is that it may be possible to return or resuscitate VBNC cells to active division on laboratory media. Since its original description in 1985, the VBNC response has been recognized in a range of bacteria. Study of the VBNC response has traditionally focused on physiological methods aimed at demonstrating that VBNC cells are indeed viable but have a specific block that prevents them from dividing on laboratory media, and such study has attempted to identify conditions that unequivocally demonstrate the resuscitation of VBNC cells. With the advent of molecular genetics, VBNC studies have begun to focus on genetics as a means to determine whether there are specific genes or regulatory pathways responsible for the development of the VBNC response. Thus, by combining information from physiological and genetic experiments, it is hoped that it can be determined whether the VBNC response represents a genetically programmed physiological adaptation similar to sporulation and outgrowth or whether VBNC represents the slow loss of function on the way to cellular death.
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Affiliation(s)
- S A Rice
- The School of Microbiology and Immunology, The University of New South Wales, Sydney 2052, Australia
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McDougald D, Rice SA, Kjelleberg S. The marine pathogen Vibrio vulnificus encodes a putative homologue of the Vibrio harveyi regulatory gene, luxR: a genetic and phylogenetic comparison. Gene 2000; 248:213-21. [PMID: 10806366 DOI: 10.1016/s0378-1119(00)00117-7] [Citation(s) in RCA: 42] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
Abstract
Vibrio vulnificus is an opportunistic pathogen that exhibits numerous virulence factors, including the secretion of a zinc metalloprotease and the production of a capsule. We have cloned and sequenced a gene from V. vulnificus that is a homologue of the positive transcriptional regulator, luxR, of the lux operon in Vibrio harveyi. This gene encodes a putative, single complete open reading frame designated smcR, which shares greater than 75% nucleotide identity with luxR of V. harveyi. The deduced amino acid sequence of the putative SmcR protein is more than 90% identical and 95% similar to that of LuxR of V. harveyi, suggesting that V. vulnificus possesses a member of the family of signal-response genes recently described in Vibrio cholerae and in Vibrio parahaemolyticus. Our data also demonstrate that, in addition to V. vulnificus, all six Vibrio spp. tested contained genes that hybridized with the luxR probe. We also present evidence that this regulatory protein was inherited from a common ancestor, and that the gene is ancient and widespread in marine Vibrio spp.
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Affiliation(s)
- D McDougald
- School of Microbiology and Immunology, The University of New South Wales, Sydney, Australia
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Manefield M, Harris L, Rice SA, de Nys R, Kjelleberg S. Inhibition of luminescence and virulence in the black tiger prawn (Penaeus monodon) pathogen Vibrio harveyi by intercellular signal antagonists. Appl Environ Microbiol 2000; 66:2079-84. [PMID: 10788385 PMCID: PMC101458 DOI: 10.1128/aem.66.5.2079-2084.2000] [Citation(s) in RCA: 162] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Expression of luminescence in the Penaeus monodon pathogen Vibrio harveyi is regulated by an intercellular quorum sensing mechanism involving the synthesis and detection of two signaling molecules, one of which is N-hydroxy butanoyl-L-homoserine lactone and the other of which is uncharacterized. Indirect evidence has suggested that virulence, associated with a toxic extracellular protein, and luminescence in V. harveyi are coregulated. In this study the effects of an acylated homoserine lactone antagonist produced by the marine alga Delisea pulchra on luminescence and toxin production in a virulent strain of V. harveyi were analyzed. Luminescence and toxin production were both inhibited by the signal antagonist at concentrations that had no impact on growth. Toxin production was found to be prematurely induced in V. harveyi cultures incubated in a 10% conditioned medium. Additionally, a significant reduction in the toxicity of concentrated supernatant extracts from V. harveyi cultures incubated in the presence of the signal antagonist, as measured by in vivo toxicity assays in mice and prawns, was observed. These results suggest that intercellular signaling antagonists have potential utility in the control of V. harveyi prawn infections.
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Affiliation(s)
- M Manefield
- School of Microbiology and Immunology, James Cook University of North Queensland, Townsville, Australia.
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Karnchanaphanurach P, Lin B, Rice SA. Melting transition in a quasi-two-dimensional colloid suspension: influence of the colloid-colloid interaction. Phys Rev E Stat Phys Plasmas Fluids Relat Interdiscip Topics 2000; 61:4036-4044. [PMID: 11088195 DOI: 10.1103/physreve.61.4036] [Citation(s) in RCA: 23] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/22/1999] [Indexed: 05/23/2023]
Abstract
We report the results of a study, using digital video microscopy, of the melting transition in a quasi-two-dimensional suspension of uncharged silica spheres. This system was chosen to further test the dependence of the two-dimensional melting transition on the functional form of the colloid-colloid interaction. Our experimental data show that the solid phase undergoes a first order transition directly to the liquid phase. The system studied yields no evidence of the existence of a hexatic phase interpolating between the solid and liquid phases in the melting process.
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Affiliation(s)
- P Karnchanaphanurach
- James Franck Institute and The Department of Chemistry, The University of Chicago, Chicago, Illinois 60637, USA
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Zangi R, Rice SA. Nature of the transition from two- to three-dimensional ordering in a confined colloidal suspension. Phys Rev E Stat Phys Plasmas Fluids Relat Interdiscip Topics 2000; 61:660-670. [PMID: 11046309 DOI: 10.1103/physreve.61.660] [Citation(s) in RCA: 31] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/23/1999] [Indexed: 05/23/2023]
Abstract
We report the results of extensive molecular dynamics simulations of solid-to-solid transitions in two- to six-layer colloidal suspensions confined between two smooth parallel walls. The studies are designed to elucidate the ordered particle packings that interpolate between the structures of two- and three-dimensional crystals in a confined space. At a fixed density per layer, as the wall separation increases we find a sequence of stable phases, each characterized by uniform amplitude buckling along the normal to the layer planes. The buckling is coupled to an in-plane ordering transition. The buckled phases alternate with phases whose structures contain only parallel planes of particles. The relative densities of the positively and negatively displaced particles in a buckled layer, the in-plane structures, and the behavior with respect to increasing wall separation of the split density distribution that characterizes a buckled layer, clearly identify these layers as intermediates in the reconstructive transformations ntriangle up-->(n+1) square that occur when the character of the constrained space evolves from being two dimensional to being three dimensional (triangle up denotes layers with hexagonal packing symmetry, while square denotes layers with square packing symmetry). The two transitions, ntriangle up-->n-buckled-->(n+1) square, are found to be first order.
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Affiliation(s)
- R Zangi
- Department of Chemistry and The James Franck Institute, The University of Chicago, Chicago, Illinois 60637, USA
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Zangi R, Rice SA. Hexagonal to square lattice conversion in bilayer systems. Phys Rev E Stat Phys Plasmas Fluids Relat Interdiscip Topics 2000; 61:671-681. [PMID: 11046310 DOI: 10.1103/physreve.61.671] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/06/1999] [Indexed: 05/23/2023]
Abstract
We report the results of extensive molecular dynamics simulations of the reconstructive hexagonal to square lattice conversion in bilayer colloid systems. Two types of interparticle potential were used to represent the colloid-colloid interactions in the suspension. One potential, due to Marcus and Rice, is designed to describe the interaction of sterically stabilized colloid particles. This potential has a term that represents the attraction between colloid particles when there is incipient overlap between the stabilizing brushes on their surfaces, a (soft repulsion) term that represents the entropy cost associated with interpenetration of the stabilizing brushes, and a term that represents core-core repulsion. The other potential we used is an almost hard core repulsion with continuous derivatives. Our results clearly show that the character of the reconstructive hexagonal to square lattice conversion in bilayer colloid systems is potential dependent. For a system with colloid-colloid interactions of the Marcus-Rice type, the packing of particles in the square array exhibits a large interlayer lattice spacing, with the particles located at the minima of the attractive well. In this case the hexagonal to square lattice transition is first order. For a system with hard core colloid-colloid interactions there are two degenerate stable intermediate phases, linear and zigzag rhombic, that are separated from the square lattice by strong first order transitions, and from the hexagonal lattice by either weak first or second order transitions.
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Affiliation(s)
- R Zangi
- Department of Chemistry and The James Franck Institute, The University of Chicago, Chicago, Illinois 60637, USA
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Yang B, Gidalevitz D, Li D, Huang Z, Rice SA. Two-dimensional freezing in the liquid-vapor interface of a dilute Pb:Ga alloy. Proc Natl Acad Sci U S A 1999; 96:13009-11. [PMID: 10557263 PMCID: PMC23890 DOI: 10.1073/pnas.96.23.13009] [Citation(s) in RCA: 16] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
We report the results of x-ray reflectivity and grazing incidence x-ray diffraction studies of the liquid-vapor interface of a dilute alloy of Pb in Ga over the temperature range of 23-76 degrees C. Our data show that the liquid-vapor interface of this alloy is stratified for several atomic diameters into the bulk liquid and that a monolayer of Pb forms the outermost stratum of the interface. Over the temperature range of 23-56 degrees C, the monolayer of Pb is in an ordered hexagonal phase. At about 58 degrees C, this monolayer undergoes a first-order transition to a hexatic phase, which remains stable to 76 degrees C. An analogy between the observed transition and the first-order melting transition in a one-component classical plasma is suggested.
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Affiliation(s)
- B Yang
- Department of Chemistry and The James Franck Institute, University of Chicago, Chicago, IL 60637, USA
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Marcus AH, Schofield J, Rice SA. Experimental observations of non-Gaussian behavior and stringlike cooperative dynamics in concentrated quasi-two-dimensional colloidal liquids. Phys Rev E Stat Phys Plasmas Fluids Relat Interdiscip Topics 1999; 60:5725-36. [PMID: 11970468 DOI: 10.1103/physreve.60.5725] [Citation(s) in RCA: 132] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/03/1999] [Indexed: 11/07/2022]
Abstract
We report, from direct observation of particle trajectories as a function of time, the presence of stringlike cooperative motion in a quasi-two-dimensional liquid. We have used digital video microscopy to study the equilibrium dynamics of suspensions of sterically stabilized uncharged poly(methylmethacrylate) spheres confined in a thin glass cell. Our experiments reveal the existence, in semidilute and dense liquid states, of a transition in the qualitative dynamical behavior of the system. At short times particles undergo unhindered Brownian motion, at intermediate times they undergo uncorrelated binary collisions, and at long times these one-particle self-diffusive modes are coupled to collective longitudinal acoustic modes of the fluid, the signature of which is local fluctuating domains of enhanced particle mobility. We study the properties of these domains by examining the density dependence of the van Hove self-correlation function and its deviation from Gaussian behavior. We observe that periods of non-Gaussian behavior correlate precisely with the timing of events involved in the relaxation of "caged" particles and their nearest neighbors. In contrast with relaxation processes in supercooled liquids, the lifetime of dynamical heterogeneities in a dissipative colloidal suspension is found to shift towards shorter time scales with increasing particle density. During time periods for which a quasi-two-dimensional system follows Gaussian behavior, we observe that, as predicted by Cichocki and Felderhof [J. Phys. Condens. Matter 6, 7287 (1994)], the time dependence of the evolution of the effective diffusion coefficient from its short time to its long time value has the form (ln t)/t. This last finding is true for all observed particle densities. To our knowledge, these results are the first experimental verification of the existence of microscopic cooperativity and the predicted temporal evolution of the diffusion coefficient for Brownian motion in concentrated quasi-two-dimensional liquids.
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Affiliation(s)
- A H Marcus
- Department of Chemistry and Materials Science Institute, University of Oregon, Eugene, Oregon 97403, USA
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Rice SA, Givskov M, Steinberg P, Kjelleberg S. Bacterial signals and antagonists: the interaction between bacteria and higher organisms. J Mol Microbiol Biotechnol 1999; 1:23-31. [PMID: 10941781] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/17/2023] Open
Abstract
It is now well established that bacteria communicate through the secretion and uptake of small diffusable molecules. These chemical cues, or signals, are often used by bacteria to coordinate phenotypic expression and this mechanism of regulation presumably provides them with a competitive advantage in their natural environment. Examples of coordinated behaviors of marine bacteria which are regulated by signals include swarming and exoprotease production, which are important for niche colonisation or nutrient acquisition (e.g. protease breakdown of substrate). While the current focus on bacterial signalling centers on N-Acylated homoserine lactones, the quorum sensing signals of gram-negative bacteria, these are not the only types of signals used by bacteria. Indeed, there appears to be many other types of signals produced by bacteria and it also appears that a bacterium may use multiple classes of signals for phenotypic regulation. Recent work in the area of marine microbial ecology has led to the observation that some marine eukaryotes secrete their own signals which compete with the bacterial signals and thus inhibit the expression of bacterial signalling phenotypes. This type of molecular mimicry has been well characterised for the interaction of marine prokaryotes with the red alga, Delisea pulchra.
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Affiliation(s)
- S A Rice
- The School of Microbiology and Immunology, The University of New South Wales, Sydney, Australia
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Long MC, Leong V, Schaffer PA, Spencer CA, Rice SA. ICP22 and the UL13 protein kinase are both required for herpes simplex virus-induced modification of the large subunit of RNA polymerase II. J Virol 1999; 73:5593-604. [PMID: 10364308 PMCID: PMC112617 DOI: 10.1128/jvi.73.7.5593-5604.1999] [Citation(s) in RCA: 106] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Herpes simplex virus type 1 (HSV-1) infection alters the phosphorylation of the large subunit of RNA polymerase II (RNAP II), resulting in the depletion of the hypophosphorylated and hyperphosphorylated forms of this polypeptide (known as IIa and IIo, respectively) and induction of a novel, alternatively phosphorylated form (designated IIi). We previously showed that the HSV-1 immediate-early protein ICP22 is involved in this phenomenon, since induction of IIi and depletion of IIa are deficient in cells infected with 22/n199, an HSV-1 ICP22 nonsense mutant (S. A. Rice, M. C. Long, V. Lam, P. A. Schaffer, and C. A. Spencer, J. Virol. 69:5550-5559, 1995). However, depletion of IIo still occurs in 22/n199-infected cells. This suggests either that another viral gene product affects the RNAP II large subunit or that the truncated ICP22 polypeptide encoded by 22/n199 retains residual activity which leads to IIo depletion. To distinguish between these possibilities, we engineered an HSV-1 ICP22 null mutant, d22-lacZ, and compared it to 22/n199. The two mutants are indistinguishable in their effects on the RNAP II large subunit, suggesting that an additional viral gene product is involved in altering RNAP II. Two candidates are UL13, a protein kinase which has been implicated in ICP22 phosphorylation, and the virion host shutoff (Vhs) factor, the expression of which is positively regulated by ICP22 and UL13. To test whether UL13 is involved, a UL13-deficient viral mutant, d13-lacZ, was engineered. This mutant was defective in IIi induction and IIa depletion, displaying a phenotype very similar to that of d22-lacZ. In contrast, a Vhs mutant had effects that were indistinguishable from wild-type HSV-1. Therefore, UL13 but not the Vhs function plays a role in modifying the RNAP II large subunit. To study the potential role of UL13 in viral transcription, we carried out nuclear run-on transcription analyses in infected human embryonic lung cells. Infections with either UL13 or ICP22 mutants led to significantly reduced amounts of viral genome transcription at late times after infection. Together, our results suggest that ICP22 and UL13 are involved in a common pathway that alters RNAP II phosphorylation and that in some cell lines this change promotes viral late transcription.
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Affiliation(s)
- M C Long
- Departments of Biochemistry, University of Alberta, Edmonton, Alberta, Canada T6G 2H7
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Gidalevitz D, Huang Z, Rice SA. Urease and hexadecylamine-urease films at the air-water interface: an x-ray reflection and grazing incidence x-ray diffraction study. Biophys J 1999; 76:2797-802. [PMID: 10233095 PMCID: PMC1300250 DOI: 10.1016/s0006-3495(99)77433-3] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/21/2022] Open
Abstract
We report the results of surface x-ray scattering measurements performed on urease and hexadecylamine-urease films at the air-aqueous solution interface. It is demonstrated that although hexadecylamine does not form a stable monolayer on the pure aqueous surface, it does self-assemble into a stable, well-organized structure when spread on top of a urease film at the air-water interface. It is also likely that protein and hexadecylamine domains coexist at the interface.
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Affiliation(s)
- D Gidalevitz
- The James Franck Institute, The University of Chicago, Chicago, Illinois 60637, USA
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Abstract
We report the results of x-ray reflectivity measurements of thin films formed by different water-soluble proteins at the air-aqueous solution interface. It is demonstrated that glucose oxidase, alcohol dehydrogenase, and urease molecules denaturate at the air-aqueous solution interface to form 8- to 14-A-thick peptide sheets. X-ray reflectivity data indicate that the spreading of a lipid monolayer at the aqueous solution surface before protein injection does not prevent proteins from unfolding. On the other hand, crosslinking of proteins results in intact enzyme layers at the subphase surface. A model that involves interaction of glucose oxidase molecules with a phospholipid monolayer is proposed. In this model, an observed decrease of the lipid electron density in the protein presence is explained in terms of "holes" in the monolayer film caused by protein molecule adsorption.
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Affiliation(s)
- D Gidalevitz
- The James Franck Institute, The University of Chicago, Chicago, IL 60637, USA
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Abstract
ICP27 is an essential herpes simplex virus type 1 (HSV-1) nuclear protein which regulates viral early and late genes during infection. The exact mechanism by which ICP27 modulates viral gene expression is unknown, but considerable evidence suggests that it functions posttranscriptionally. In this study, we have asked whether ICP27, like some other viral and cellular posttranscriptional regulatory proteins, shuttles between the nuclear and cytoplasmic compartments of the cell. Using an interspecies heterokaryon assay, we demonstrate that ICP27, but not the HSV-1 nuclear proteins ICP4 or ICP8, is an efficient shuttling protein. ICP27's shuttling ability does not depend on viral infection or other HSV-1 proteins, as it shuttles even when transiently expressed in uninfected cells. To understand the importance of shuttling for ICP27's regulatory functions, we examined several mutant forms of ICP27 to see whether they exhibited altered shuttling. We identified three ICP27 mutations which partially disrupt shuttling, as well as one mutation, M15, which completely abrogates this activity. The M15 mutation alters residues 465 and 466 near the carboxyl terminus of ICP27 and was previously shown to inactivate ICP27's ability to induce certain viral late mRNAs. These results suggest that ICP27's nuclear shuttling activity is involved in its viral late gene activation function.
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Affiliation(s)
- W E Mears
- Department of Biochemistry, University of Alberta, Edmonton, Canada.
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Abstract
We examined and contrasted morning reports at two hospitals, university and community, that have a pediatric residency program. Patient diagnoses assigned at morning report were compared with final diagnoses to assess disease categories discussed and the value of including outpatient follow-up in this educational forum. Data were obtained during morning reports for 6 months by chief residents at university and private community hospitals. Pertinent history, physical examination, and laboratory and radiologic findings were recorded and were assigned a tentative morning report diagnosis based on morning report discussion. Cases were then reviewed at discharge and at 6 months to determine final diagnoses. At the university hospital, 58% of the cases were undiagnosed before presentation at morning report. Of those cases, 23% were assigned a diagnosis at morning report that differed from the final diagnosis. Similarly, at the private community hospital, 28% of cases were undiagnosed before presentation at morning report. Of those cases, 73% were assigned a diagnosis that differed from the final diagnosis. We conclude that the provision of follow-up at morning report is important for maximizing resident education.
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Affiliation(s)
- L L Barton
- Department of Pediatrics, University of Arizona, Tucson, USA
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Abstract
Lytic infection of mammalian cells with herpes simplex virus type 1 (HSV-1) results in rapid repression of host gene expression and selective activation of the viral genome. This transformation in gene expression is thought to involve repression of host transcription and diversion of the host RNA polymerase (RNAP II) transcription machinery to the viral genome. However, the extent of virus-induced host transcription repression and the mechanisms responsible for these major shifts in transcription specificities have not been examined. To determine how HSV-1 accomplishes repression of host RNAP II transcription, we assayed transcription patterns on several cellular genes in cells infected with mutant and wild-type HSV-1. Our results suggest that HSV-1 represses RNAP II transcription on most cellular genes. However, each cellular gene we examined responds differently to the transcription repressive effects of virus infection, both quantitatively and with respect to the involvement of viral gene products. Virus-induced shutoff of host RNAP II transcription requires expression of multiple immediate-early genes. In contrast, expression of delayed-early and late genes and viral DNA replication appear to contribute little to repression of host cell RNAP II transcription. Modification of RNAP II to the intermediately phosphorylated (II(I)) form appears unlinked to virus-induced repression of host cell transcription. However, full repression of host transcription is correlated with depletion of the hyperphosphorylated (IIO) form of RNAP II.
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Affiliation(s)
- C A Spencer
- Department of Biochemistry, University of Alberta, Edmonton, Canada
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Lampson BC, Rice SA. Repetitive sequences found in the chromosome of the myxobacterium Nannocystis exedens are similar to msDNA: a possible retrotransposition event in bacteria. Mol Microbiol 1997; 23:813-23. [PMID: 9157251 DOI: 10.1046/j.1365-2958.1997.2671627.x] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/04/2023]
Abstract
The first reverse transcriptase (RT) to be found in a prokaryotic cell is encoded by an element called a retron which resides in the chromosome of many different bacteria. In addition, all retrons code for a functionally obscure RNA-DNA satellite molecule called msDNA. msDNA is synthesized from an RNA template by the retron-encoded RT. An unusual retron element is described here from the myxobacterium Nannocystis exedens. This retron does not appear to have a typical RT gene in close proximity (1 kb) to the gene msd (which encodes the DNA strand of msDNA). The gene msr (which encodes the RNA strand of msDNA) appears to be duplicated and flanks both sides of the msd gene. Also discovered throughout the chromosome of this bacterium is a set of repeated sequences related to msDNA. These repeat sequences match only part of the sequences of msDNA and may have become incorporated into the chromosome of this bacterium by reverse transcription.
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Affiliation(s)
- B C Lampson
- Department of Microbiology, University of Tennessee, Knoxville 37996-0845, USA
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Abstract
ICP27 is an essential herpes simplex virus type 1 nuclear regulatory protein that is required for efficient viral gene expression. Although the mechanism by which ICP27 regulates genes is unknown, a variety of evidence suggests that it functions posttranscriptionally, and recent studies indicate that it is an RNA-binding protein. Previously, we noted that a short arginine- and glycine-rich sequence in ICP27 (residues 138 to 152) is similar to an RGG box motif, a putative RNA-binding determinant found in a number of cellular proteins (W. Mears, V. Lam, and S. Rice, J. Virol. 69:935-947, 1995). In the present study, we have further investigated ICP27's association with RNA and examined the role of the RGG box in RNA binding. We find that ICP27 binds efficiently to RNA homopolymers composed of poly(G) and weakly to poly(U) RNA homopolymers. Poly(G) binding activity maps to the N-terminal 189 residues of ICP27 and requires the RGG box sequence. Using a northwestern blotting assay, we demonstrate that the RGG box alone (residues 140 to 152) can mediate RNA binding when attached to a heterologous protein. As many cellular RGG box proteins are methylated on arginine residues, we also investigated the in vivo methylation status of ICP27. Our results demonstrate that ICP27 is methylated in herpes simplex virus-infected cells. Methylation is dependent on the presence of the RGG box, suggesting that one or more arginine residues in the RGG box sequence are modified. These data demonstrate that ICP27 displays the characteristics of an RGG box-type RNA-binding protein.
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Affiliation(s)
- W E Mears
- Department of Biochemistry, University of Alberta, Edmonton, Canada
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Lees-Miller SP, Long MC, Kilvert MA, Lam V, Rice SA, Spencer CA. Attenuation of DNA-dependent protein kinase activity and its catalytic subunit by the herpes simplex virus type 1 transactivator ICP0. J Virol 1996; 70:7471-7. [PMID: 8892865 PMCID: PMC190814 DOI: 10.1128/jvi.70.11.7471-7477.1996] [Citation(s) in RCA: 148] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/02/2023] Open
Abstract
The DNA-dependent protein kinase (DNA-PK) is involved in several fundamental nuclear processes, including DNA double-strand break repair, V(D)J recombination, and transcription by RNA polymerases I and II. In this study, we show that infection of mammalian cells with herpes simplex virus type 1 attenuates DNA-PK activity by specifically depleting the p350/DNA-PKcs catalytic subunit. The half-life of the p350/DNA-PKcs protein decreases from greater than 24 h to less than 4 h following infection. The depletion of DNA-PK activity and p350/DNA-PKcs abundance is dependent on expression of the viral immediate-early protein ICP0. As ICP0 acts as a promoter-independent transactivator of gene expression, these data suggest that ICP0 may function by directly or indirectly targeting the p350/DNA-PKcs subunit of DNA-PK, thereby altering the inhibitory effects of DNA-PK on RNA polymerase II transcription.
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Affiliation(s)
- S P Lees-Miller
- Department of Biological Sciences, University of Calgary, Alberta, Canada
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Marcus AH, Rice SA. Observations of First-Order Liquid-to-Hexatic and Hexatic-to-Solid Phase Transitions in a Confined Colloid Suspension. Phys Rev Lett 1996; 77:2577-2580. [PMID: 10061989 DOI: 10.1103/physrevlett.77.2577] [Citation(s) in RCA: 48] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/23/2023]
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Barton LL, Villar RG, Rice SA. Neonatal group B streptococcal vertebral osteomyelitis. Pediatrics 1996; 98:459-61. [PMID: 8784377] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [MESH Headings] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 02/02/2023] Open
Affiliation(s)
- L L Barton
- Department of Pediatrics Steele Memorial Children's Research Center University of Arizona, Tucson 85724, USA
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Marcus AH, Lin B, Rice SA. Self-diffusion in dilute quasi-two-dimensional hard sphere suspensions: Evanescent wave light scattering and video microscopy studies. Phys Rev E Stat Phys Plasmas Fluids Relat Interdiscip Topics 1996; 53:1765-1776. [PMID: 9964438 DOI: 10.1103/physreve.53.1765] [Citation(s) in RCA: 20] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/22/2023]
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