메뉴 건너뛰기




Volumn 8, Issue 10, 2013, Pages

Novel Multiscale Modeling Tool Applied to Pseudomonas aeruginosa Biofilm Formation

Author keywords

[No Author keywords available]

Indexed keywords

NITRATE; OXYGEN;

EID: 84885795974     PISSN: None     EISSN: 19326203     Source Type: Journal    
DOI: 10.1371/journal.pone.0078011     Document Type: Article
Times cited : (60)

References (33)
  • 1
    • 84880559564 scopus 로고    scopus 로고
    • Multiscale Computational Models of Complex Biological Systems
    • doi:10.1146/annurev-bioeng-071811-150104
    • Walpole J, Papin JA, Peirce SM, (2013) Multiscale Computational Models of Complex Biological Systems. Annu Rev Biomed Eng, 15: 137-154. doi:10.1146/annurev-bioeng-071811-150104. PubMed: 23642247.
    • (2013) Annu Rev Biomed Eng , vol.15 , pp. 137-154
    • Walpole, J.1    Papin, J.A.2    Peirce, S.M.3
  • 2
    • 80755141377 scopus 로고    scopus 로고
    • Ensuring Congruency in Multiscale Modeling: Towards Linking Agent Based and Continuum Biomechanical Models of Arterial Adaptation
    • Hayenga HN, Thorne BC, Peirce SM, Humphrey JD, (2012) Ensuring Congruency in Multiscale Modeling: Towards Linking Agent Based and Continuum Biomechanical Models of Arterial Adaptation. Ann Biomed Eng, 39: 2669-2682. PubMed: 21809144.
    • (2012) Ann Biomed Eng , vol.39 , pp. 2669-2682
    • Hayenga, H.N.1    Thorne, B.C.2    Peirce, S.M.3    Humphrey, J.D.4
  • 3
    • 84859418664 scopus 로고    scopus 로고
    • Toward a multi-scale computational model of arterial adaptation in hypertension: verification of a multi-cell agent based model
    • Thorne BC, Hayenga HN, Humphrey JD, Peirce SM, (2011) Toward a multi-scale computational model of arterial adaptation in hypertension: verification of a multi-cell agent based model. Front Physiology, 2: 20.
    • (2011) Front Physiology , vol.2 , pp. 20
    • Thorne, B.C.1    Hayenga, H.N.2    Humphrey, J.D.3    Peirce, S.M.4
  • 7
    • 77951096659 scopus 로고    scopus 로고
    • NetLogo meets R: Linking agent-based models with a toolbox for their analysis
    • doi:10.1016/j.envsoft.2010.02.008
    • Thiele JC, Grimm V, (2010) NetLogo meets R: Linking agent-based models with a toolbox for their analysis. Environ Model Softw, 25: 972-974. doi:10.1016/j.envsoft.2010.02.008.
    • (2010) Environ Model Softw , vol.25 , pp. 972-974
    • Thiele, J.C.1    Grimm, V.2
  • 9
    • 38049172599 scopus 로고    scopus 로고
    • Multiscale computational analysis of Xenopus laevis morphogenesis reveals key insights of systems-level behavior
    • doi:10.1186/1752-0509-1-46
    • Robertson SH, Smith CK, Langhans AL, McLinden SE, Oberhardt MA, et al. (2007) Multiscale computational analysis of Xenopus laevis morphogenesis reveals key insights of systems-level behavior. BMC Systems Biol, 1: 46. doi:10.1186/1752-0509-1-46. PubMed: 17953751.
    • (2007) BMC Systems Biol , vol.1 , pp. 46
    • Robertson, S.H.1    Smith, C.K.2    Langhans, A.L.3    McLinden, S.E.4    Oberhardt, M.A.5
  • 10
    • 84875894038 scopus 로고    scopus 로고
    • TypA is involved in virulence, antimicrobial resistance and biofilm formation in Pseudomonas aeruginosa
    • doi:10.1186/1471-2180-13-77
    • Neidig A, Yeung AT, Rosay T, Tettmann B, Strempel N, et al. (2013) TypA is involved in virulence, antimicrobial resistance and biofilm formation in Pseudomonas aeruginosa. BMC Microbiol, 13: 77. doi:10.1186/1471-2180-13-77. PubMed: 23570569.
    • (2013) BMC Microbiol , vol.13 , pp. 77
    • Neidig, A.1    Yeung, A.T.2    Rosay, T.3    Tettmann, B.4    Strempel, N.5
  • 11
    • 67249099362 scopus 로고    scopus 로고
    • Pseudomonas aeruginosa biofilms in the respiratory tract of cystic fibrosis patients
    • doi:10.1002/ppul.21011
    • Bjarnsholt T, Jensen PØ, Fiandaca MJ, Pedersen J, Hansen CR, et al. (2009) Pseudomonas aeruginosa biofilms in the respiratory tract of cystic fibrosis patients. Pediatr Pulmonol, 44: 547-558. doi:10.1002/ppul.21011. PubMed: 19418571.
    • (2009) Pediatr Pulmonol , vol.44 , pp. 547-558
    • Bjarnsholt, T.1    Jensen, PØ.2    Fiandaca, M.J.3    Pedersen, J.4    Hansen, C.R.5
  • 12
    • 0035450553 scopus 로고    scopus 로고
    • Quantitative cellular automaton model for biofilms
    • doi:10.1061/(ASCE)0733-9372(2001)127:9(782)
    • Pizarro G, Griffeath D, Noguera D, (2001) Quantitative cellular automaton model for biofilms. Environ Eng, 127: 782-789. doi:10.1061/(ASCE)0733-9372(2001)127:9(782).
    • (2001) Environ Eng , vol.127 , pp. 782-789
    • Pizarro, G.1    Griffeath, D.2    Noguera, D.3
  • 14
    • 41149163825 scopus 로고    scopus 로고
    • Genome-scale metabolic network analysis of the opportunistic pathogen Pseudomonas aeruginosa PAO1
    • doi:10.1128/JB.01583-07
    • Oberhardt MA, Puchałka J, Fryer KE, Martins dos Santos VAP, Papin JA, (2008) Genome-scale metabolic network analysis of the opportunistic pathogen Pseudomonas aeruginosa PAO1. J Bacteriol, 190: 2790-2803. doi:10.1128/JB.01583-07. PubMed: 18192387.
    • (2008) J Bacteriol , vol.190 , pp. 2790-2803
    • Oberhardt, M.A.1    Puchałka, J.2    Fryer, K.E.3    Martins dos Santos, V.A.P.4    Papin, J.A.5
  • 16
    • 77957837882 scopus 로고    scopus 로고
    • Metabolic network analysis of Pseudomonas aeruginosa during chronic cystic fibrosis lung infection
    • doi:10.1128/JB.00900-10
    • Oberhardt MA, Goldberg JB, Hogardt M, Papin JA, (2010) Metabolic network analysis of Pseudomonas aeruginosa during chronic cystic fibrosis lung infection. J Bacteriol, 192: 5534-5548. doi:10.1128/JB.00900-10. PubMed: 20709898.
    • (2010) J Bacteriol , vol.192 , pp. 5534-5548
    • Oberhardt, M.A.1    Goldberg, J.B.2    Hogardt, M.3    Papin, J.A.4
  • 17
    • 0037372799 scopus 로고    scopus 로고
    • Diffusion in Biofilm
    • doi:10.1128/JB.185.5.1485-1491.2003
    • Stewart PS, (2003) Diffusion in Biofilm. J Bacteriol, 185(5):: 1485-1491. doi:10.1128/JB.185.5.1485-1491.2003. PubMed: 12591863.
    • (2003) J Bacteriol , vol.185 , pp. 1485-1491
    • Stewart, P.S.1
  • 18
    • 34347258175 scopus 로고    scopus 로고
    • Quantitative prediction of cellular metabolism with constraint-based models: the COBRA Toolbox
    • doi:10.1038/nprot.2007.99
    • Becker SA, Feist AM, Mo ML, Hannum G, Palsson BØ, et al. (2007) Quantitative prediction of cellular metabolism with constraint-based models: the COBRA Toolbox. Nat Protoc, 2: 727-738. doi:10.1038/nprot.2007.99. PubMed: 17406635.
    • (2007) Nat Protoc , vol.2 , pp. 727-738
    • Becker, S.A.1    Feist, A.M.2    Mo, M.L.3    Hannum, G.4    Palsson, BØ.5
  • 19
    • 84885580876 scopus 로고    scopus 로고
    • Optimizer Gurobi, Houston TX, Inc
    • Optimizer Gurobi, Houston TX (2013) Gurobi Optimization, Inc.
    • (2013) Gurobi Optimization
  • 21
    • 0036708443 scopus 로고    scopus 로고
    • Dynamic flux balance analysis of diauxic growth in Escherichia coli
    • doi:10.1016/S0006-3495(02)73903-9
    • Mahadevan R, Edwards JS, Doyle FJ, (2002) Dynamic flux balance analysis of diauxic growth in Escherichia coli. Biophys J, 83: 1331-1340. doi:10.1016/S0006-3495(02)73903-9. PubMed: 12202358.
    • (2002) Biophys J , vol.83 , pp. 1331-1340
    • Mahadevan, R.1    Edwards, J.S.2    Doyle, F.J.3
  • 22
    • 0031710092 scopus 로고    scopus 로고
    • Spatial physiological heterogeneity in Pseudomonas aeruginosa biofilm is determined by oxygen availability
    • Xu KD, Stewart PS, Xia F, Huang CT, McFeters GA, (1998) Spatial physiological heterogeneity in Pseudomonas aeruginosa biofilm is determined by oxygen availability. Appl Environ Microbiol, 64: 4035-4039. PubMed: 9758837.
    • (1998) Appl Environ Microbiol , vol.64 , pp. 4035-4039
    • Xu, K.D.1    Stewart, P.S.2    Xia, F.3    Huang, C.T.4    McFeters, G.A.5
  • 23
    • 77957950357 scopus 로고    scopus 로고
    • Anaerobic adaptation in Pseudomonas aeruginosa: definition of the Anr and Dnr regulons
    • Trunk K, Benkert B, Quäck N, Münch R, Scheer M, et al. (2010) Anaerobic adaptation in Pseudomonas aeruginosa: definition of the Anr and Dnr regulons. Environ Microbiol, 12: 1719-1733. PubMed: 20553552.
    • (2010) Environ Microbiol , vol.12 , pp. 1719-1733
    • Trunk, K.1    Benkert, B.2    Quäck, N.3    Münch, R.4    Scheer, M.5
  • 24
    • 3042536089 scopus 로고    scopus 로고
    • Oxygen limitation contributes to antibiotic tolerance of Pseudomonas aeruginosa in biofilms
    • doi:10.1128/AAC.48.7.2659-2664.2004
    • Borriello G, Werner E, Roe F, (2004) Oxygen limitation contributes to antibiotic tolerance of Pseudomonas aeruginosa in biofilms. Antimicrob Agents Chemother, 48: 2659-2664. doi:10.1128/AAC.48.7.2659-2664.2004. PubMed: 15215123.
    • (2004) Antimicrob Agents Chemother , vol.48 , pp. 2659-2664
    • Borriello, G.1    Werner, E.2    Roe, F.3
  • 25
    • 59349120148 scopus 로고    scopus 로고
    • Gene expression characteristics of a cystic fibrosis epidemic strain of Pseudomonas aeruginosa during biofilm and planktonic growth
    • doi:10.1111/j.1574-6968.2008.01472.x
    • Manos J, Arthur J, Rose B, Bell S, Tingpej P, et al. (2009) Gene expression characteristics of a cystic fibrosis epidemic strain of Pseudomonas aeruginosa during biofilm and planktonic growth. FEMS Microbiol Lett, 292: 107-114. doi:10.1111/j.1574-6968.2008.01472.x. PubMed: 19222585.
    • (2009) FEMS Microbiol Lett , vol.292 , pp. 107-114
    • Manos, J.1    Arthur, J.2    Rose, B.3    Bell, S.4    Tingpej, P.5
  • 26
    • 67149137783 scopus 로고    scopus 로고
    • Role of gluconic acid production in the regulation of biocontrol traits of Pseudomonas fluorescens CHA0
    • doi:10.1128/AEM.00295-09
    • De Werra P, Péchy-Tarr M, Keel C, Maurhofer M, (2009) Role of gluconic acid production in the regulation of biocontrol traits of Pseudomonas fluorescens CHA0. Appl Environ Microbiol, 75: 4162-4174. doi:10.1128/AEM.00295-09. PubMed: 19376896.
    • (2009) Appl Environ Microbiol , vol.75 , pp. 4162-4174
    • De Werra, P.1    Péchy-Tarr, M.2    Keel, C.3    Maurhofer, M.4
  • 27
    • 80052631835 scopus 로고    scopus 로고
    • iDynoMiCS: next-generation individual-based modelling of biofilms
    • doi:10.1111/j.1462-2920.2011.02414.x
    • Lardon LA, Merkey BV, Martins S, Dötsch A, Picioreanu C, et al. (2011) iDynoMiCS: next-generation individual-based modelling of biofilms. Environ Microbiol, 13: 2416-2434. doi:10.1111/j.1462-2920.2011.02414.x. PubMed: 21410622.
    • (2011) Environ Microbiol , vol.13 , pp. 2416-2434
    • Lardon, L.A.1    Merkey, B.V.2    Martins, S.3    Dötsch, A.4    Picioreanu, C.5
  • 28
    • 80052630416 scopus 로고    scopus 로고
    • Growth dependence of conjugation explains limited plasmid invasion in biofilms: an individual-based modelling study
    • doi:10.1111/j.1462-2920.2011.02535.x
    • Merkey BV, Lardon LA, Seoane JM, Kreft J-U, Smets BF, (2011) Growth dependence of conjugation explains limited plasmid invasion in biofilms: an individual-based modelling study. Environ Microbiol, 13: 2435-2452. doi:10.1111/j.1462-2920.2011.02535.x. PubMed: 21906217.
    • (2011) Environ Microbiol , vol.13 , pp. 2435-2452
    • Merkey, B.V.1    Lardon, L.A.2    Seoane, J.M.3    Kreft, J.-U.4    Smets, B.F.5
  • 29
    • 80054724505 scopus 로고    scopus 로고
    • Viability and Resilience of a Bacterial Biofilm Individual-Based Model
    • Mabrouk N, Mathias J, Deffuant G, (2011) Viability and Resilience of a Bacterial Biofilm Individual-Based Model, In: Deffuant G, Gilbert N, eds., Viability and Resilience of Complex Systems.
    • (2011) Viability and Resilience of Complex Systems
    • Deffuant, G.1    Gilbert, N.2
  • 30
    • 77953619760 scopus 로고    scopus 로고
    • Bacteria can form interconnected microcolonies when a self-excreted product reduces their surface motility: evidence from individual-based model simulations
    • doi:10.1007/s12064-009-0078-8
    • Mabrouk N, Deffuant G, Tolker-Nielsen T, Lobry C, (2010) Bacteria can form interconnected microcolonies when a self-excreted product reduces their surface motility: evidence from individual-based model simulations. Theory Biosci, 129: 1-13. doi:10.1007/s12064-009-0078-8. PubMed: 19946800.
    • (2010) Theory Biosci , vol.129 , pp. 1-13
    • Mabrouk, N.1    Deffuant, G.2    Tolker-Nielsen, T.3    Lobry, C.4
  • 31
    • 84877924096 scopus 로고    scopus 로고
    • The problem of pattern and scale in ecology: what have we learned in 20 years?
    • doi:10.1111/ele.12048
    • Chave J, (2013) The problem of pattern and scale in ecology: what have we learned in 20 years? Ecol Lett, 16: 4-16. doi:10.1111/ele.12048. PubMed: 23351093.
    • (2013) Ecol Lett , vol.16 , pp. 4-16
    • Chave, J.1
  • 32
    • 84883507704 scopus 로고    scopus 로고
    • Using Pattern-oriented Modeling (POM) to Cope with Uncertainty in Multi-scale Agent-based Models of Land Change
    • doi:10.1111/tgis.12012
    • Magliocca NR, Ellis EC, (2013) Using Pattern-oriented Modeling (POM) to Cope with Uncertainty in Multi-scale Agent-based Models of Land Change. Trans GIS. doi:10.1111/tgis.12012.
    • (2013) Trans GIS
    • Magliocca, N.R.1    Ellis, E.C.2
  • 33
    • 84871242406 scopus 로고    scopus 로고
    • An empirical study on human mobility and its agent-based modeling
    • doi:10.1088/1742-5468/2012/11/P11024
    • Jia T, Jiang B, Carling K, Bolin M, Ban Y, (2012) An empirical study on human mobility and its agent-based modeling. J Statistical Mechanics. doi:10.1088/1742-5468/2012/11/P11024.
    • (2012) J Statistical Mechanics
    • Jia, T.1    Jiang, B.2    Carling, K.3    Bolin, M.4    Ban, Y.5


* 이 정보는 Elsevier사의 SCOPUS DB에서 KISTI가 분석하여 추출한 것입니다.