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Volumn 14, Issue SUPPL7, 2013, Pages

Quasi-cellular systems: Stochastic simulation analysis at nanoscale range

Author keywords

[No Author keywords available]

Indexed keywords

BIOCHEMICAL REACTIONS; EXPERIMENTAL APPROACHES; FLUORESCENCE EMISSION; FLUORESCENCE SIGNALS; INITIAL CONCENTRATION; QUANTITATIVE PARAMETERS; SPECIES CONCENTRATION; STOCHASTIC SIMULATIONS;

EID: 84887196015     PISSN: None     EISSN: 14712105     Source Type: Journal    
DOI: 10.1186/1471-2105-14-S7-S7     Document Type: Article
Times cited : (22)

References (35)
  • 1
    • 0035905809 scopus 로고    scopus 로고
    • Synthesizing life
    • 10.1038/35053176, 11201752
    • Szostak JW, Bartel DP, Luisi PL. Synthesizing life. Nature 2001, 409(6818):387-390. 10.1038/35053176, 11201752.
    • (2001) Nature , vol.409 , Issue.6818 , pp. 387-390
    • Szostak, J.W.1    Bartel, D.P.2    Luisi, P.L.3
  • 2
    • 33846108255 scopus 로고    scopus 로고
    • Towards synthesis of a minimal cell
    • 9140d519-fc79-e312-0a8a-bfb7cec33a4e, 1681520, 16924266
    • Forster A, Church G. Towards synthesis of a minimal cell. Molecular systems biology 2006, 2((9140d519-fc79-e312-0a8a-bfb7cec33a4e):45. 1681520, 16924266.
    • (2006) Molecular systems biology , vol.2 , pp. 45
    • Forster, A.1    Church, G.2
  • 3
    • 81855192773 scopus 로고    scopus 로고
    • Compartmentalized reactions as a case of soft-matter biotechnology: synthesis of proteins and nucleic acids inside lipid vesicles
    • Stano P, Carrara P, Kuruma Y, Pereira de Souza T, Luisi PL. Compartmentalized reactions as a case of soft-matter biotechnology: synthesis of proteins and nucleic acids inside lipid vesicles. Journal of Materials Chemistry 2011, 21(47):18887-18902.
    • (2011) Journal of Materials Chemistry , vol.21 , Issue.47 , pp. 18887-18902
    • Stano, P.1    Carrara, P.2    Kuruma, Y.3    Pereira de Souza, T.4    Luisi, P.L.5
  • 4
    • 31344455122 scopus 로고    scopus 로고
    • Approaches to semi-synthetic minimal cells: a review
    • e975186c-6d35-e5a8-7236-239c98c5ea6f
    • Luisi P, Ferri F, Stano P. Approaches to semi-synthetic minimal cells: a review. Naturwissenschaften 2006, 93(e975186c-6d35-e5a8-7236-239c98c5ea6f):1-14.
    • (2006) Naturwissenschaften , vol.93 , pp. 1-14
    • Luisi, P.1    Ferri, F.2    Stano, P.3
  • 5
    • 0000615462 scopus 로고
    • Oparin's Reactions Revisited: Enzymic Synthesis of Poly(adenylic acid) in Micelles and Self-Reproducing Vesicles
    • Walde P, Goto A, Monnard P-A, Wessicken M, Luisi PL. Oparin's Reactions Revisited: Enzymic Synthesis of Poly(adenylic acid) in Micelles and Self-Reproducing Vesicles. Journal of the American Chemical Society 1994, 116(17):7541-7547.
    • (1994) Journal of the American Chemical Society , vol.116 , Issue.17 , pp. 7541-7547
    • Walde, P.1    Goto, A.2    Monnard, P.-A.3    Wessicken, M.4    Luisi, P.L.5
  • 6
    • 0029379613 scopus 로고
    • Polymerase chain reaction in liposomes
    • 10.1016/1074-5521(95)90031-4, 9383474
    • Oberholzer T, Albrizio M, Luisi PL. Polymerase chain reaction in liposomes. Chemistry & biology 1995, 2(10):677-682. 10.1016/1074-5521(95)90031-4, 9383474.
    • (1995) Chemistry & biology , vol.2 , Issue.10 , pp. 677-682
    • Oberholzer, T.1    Albrizio, M.2    Luisi, P.L.3
  • 7
    • 0033517038 scopus 로고    scopus 로고
    • Protein expression in liposomes
    • 10.1006/bbrc.1999.0404, 10425171
    • Oberholzer T, Nierhaus KH, Luisi PL. Protein expression in liposomes. Biochem Biophys Res Commun 1999, 261(2):238-241. 10.1006/bbrc.1999.0404, 10425171.
    • (1999) Biochem Biophys Res Commun , vol.261 , Issue.2 , pp. 238-241
    • Oberholzer, T.1    Nierhaus, K.H.2    Luisi, P.L.3
  • 9
    • 59249084001 scopus 로고    scopus 로고
    • A synthetic biology approach to the construction of membrane proteins in semi-synthetic minimal cells
    • 10.1016/j.bbamem.2008.10.017, 19027713
    • Kuruma Y, Stano P, Ueda T, Luisi PL. A synthetic biology approach to the construction of membrane proteins in semi-synthetic minimal cells. Biochimica et biophysica acta 2009, 1788(2):567-574. 10.1016/j.bbamem.2008.10.017, 19027713.
    • (2009) Biochimica et biophysica acta , vol.1788 , Issue.2 , pp. 567-574
    • Kuruma, Y.1    Stano, P.2    Ueda, T.3    Luisi, P.L.4
  • 10
    • 77952821785 scopus 로고    scopus 로고
    • Cellular compartment model for exploring the effect of the lipidic membrane on the kinetics of encapsulated biochemical reactions
    • 10.1021/la904569m, 20131804
    • Sunami T, Hosoda K, Suzuki H, Matsuura T, Yomo T. Cellular compartment model for exploring the effect of the lipidic membrane on the kinetics of encapsulated biochemical reactions. Langmuir : the ACS journal of surfaces and colloids 2010, 26(11):8544-8595. 10.1021/la904569m, 20131804.
    • (2010) Langmuir : the ACS journal of surfaces and colloids , vol.26 , Issue.11 , pp. 8544-8595
    • Sunami, T.1    Hosoda, K.2    Suzuki, H.3    Matsuura, T.4    Yomo, T.5
  • 11
    • 62649157858 scopus 로고    scopus 로고
    • Quantitative study of the structure of multilamellar giant liposomes as a container of protein synthesis reaction
    • Hosoda K, Sunami T, Kazuta Y, Matsuura T. Quantitative study of the structure of multilamellar giant liposomes as a container of protein synthesis reaction. Langmuir 2008, 24(23).
    • (2008) Langmuir , vol.24 , Issue.23
    • Hosoda, K.1    Sunami, T.2    Kazuta, Y.3    Matsuura, T.4
  • 12
    • 70349554688 scopus 로고    scopus 로고
    • Time-resolved tracking of a minimum gene expression system reconstituted in giant liposomes
    • 10.1002/cbic.200900205, 19533718
    • Saito H, Kato Y, Le Berre M, Yamada A, Inoue T, Yosikawa K, Baigl D. Time-resolved tracking of a minimum gene expression system reconstituted in giant liposomes. Chembiochem 2009, 10(10):1640-1643. 10.1002/cbic.200900205, 19533718.
    • (2009) Chembiochem , vol.10 , Issue.10 , pp. 1640-1643
    • Saito, H.1    Kato, Y.2    Le Berre, M.3    Yamada, A.4    Inoue, T.5    Yosikawa, K.6    Baigl, D.7
  • 14
    • 80053595736 scopus 로고    scopus 로고
    • Spontaneous Crowding of Ribosomes and Proteins inside Vesicles: A Possible Mechanism for the Origin of Cell Metabolism
    • (2c6f5d5a-f6b1-7d40-4922-239c9858e542)
    • Pereira de Souza T, Steiniger F, Stano P, Fahr A, Luisi P. Spontaneous Crowding of Ribosomes and Proteins inside Vesicles: A Possible Mechanism for the Origin of Cell Metabolism. Chembiochem : a European journal of chemical biology 2011, (2c6f5d5a-f6b1-7d40-4922-239c9858e542).
    • (2011) Chembiochem : a European journal of chemical biology
    • Pereira de Souza, T.1    Steiniger, F.2    Stano, P.3    Fahr, A.4    Luisi, P.5
  • 15
    • 0034904102 scopus 로고    scopus 로고
    • Cell-free translation reconstituted with purified components
    • (28f9cb18-d3a3-328d-ae54-239c98cdc21d)
    • Shimizu Y, Inoue A, Tomari Y, Suzuki T. Cell-free translation reconstituted with purified components. Nature 2001, (28f9cb18-d3a3-328d-ae54-239c98cdc21d).
    • (2001) Nature
    • Shimizu, Y.1    Inoue, A.2    Tomari, Y.3    Suzuki, T.4
  • 16
    • 34548049283 scopus 로고    scopus 로고
    • Question 7: New Aspects of Interactions Among Vesicles
    • 10.1007/s11084-007-9086-1, 17610045
    • Stano P. Question 7: New Aspects of Interactions Among Vesicles. Origins of Life and Evolution of Biospheres 2007, 37(4):439-444. 10.1007/s11084-007-9086-1, 17610045.
    • (2007) Origins of Life and Evolution of Biospheres , vol.37 , Issue.4 , pp. 439-444
    • Stano, P.1
  • 17
    • 84861794330 scopus 로고    scopus 로고
    • Semi-synthetic minimal cells as a tool for biochemical ICT
    • 10.1016/j.biosystems.2012.01.002, 22261641
    • Stano P, Rampioni G, Carrara P, Damiano L, Leoni L, Luisi PL. Semi-synthetic minimal cells as a tool for biochemical ICT. Bio Systems 2012, 109(1):24-34. 10.1016/j.biosystems.2012.01.002, 22261641.
    • (2012) Bio Systems , vol.109 , Issue.1 , pp. 24-34
    • Stano, P.1    Rampioni, G.2    Carrara, P.3    Damiano, L.4    Leoni, L.5    Luisi, P.L.6
  • 18
    • 65549091378 scopus 로고    scopus 로고
    • The Minimal Size of Liposome-Based Model Cells Brings about a Remarkably Enhanced Entrapment and Protein Synthesis
    • aaece635-437c-a62d-75d9-239c9855d981
    • Pereira de Souza T, Stano P, Luisi PL. The Minimal Size of Liposome-Based Model Cells Brings about a Remarkably Enhanced Entrapment and Protein Synthesis. ChemBioChem 2009, 10(aaece635-437c-a62d-75d9-239c9855d981).
    • (2009) ChemBioChem , vol.10
    • Pereira de Souza, T.1    Stano, P.2    Luisi, P.L.3
  • 19
    • 80053595736 scopus 로고    scopus 로고
    • Spontaneous Crowding of Ribosomes and Proteins inside Vesicles: A Possible Mechanism for the Origin of Cell Metabolism
    • 2c6f5d5a-f6b1-7d40-4922-239c9858e542
    • Pereira de Souza P, Steiniger F, Stano P, Fahr A, Luisi PL. Spontaneous Crowding of Ribosomes and Proteins inside Vesicles: A Possible Mechanism for the Origin of Cell Metabolism. ChemBioChem 2011, 12(2c6f5d5a-f6b1-7d40-4922-239c9858e542).
    • (2011) ChemBioChem , vol.12
    • Pereira de Souza, P.1    Steiniger, F.2    Stano, P.3    Fahr, A.4    Luisi, P.L.5
  • 20
    • 84864932428 scopus 로고    scopus 로고
    • Stochastic simulations of minimal cells: the Ribocell model
    • 10.1186/1471-2105-13-S4-S10, 3303737, 22536956
    • Mavelli F. Stochastic simulations of minimal cells: the Ribocell model. BMC bioinformatics 2012, 13(Suppl 4):S10. 10.1186/1471-2105-13-S4-S10, 3303737, 22536956.
    • (2012) BMC bioinformatics , vol.13 , Issue.SUPPL 4
    • Mavelli, F.1
  • 21
    • 84864953372 scopus 로고    scopus 로고
    • Characterization of the emergent properties of a synthetic quasi-cellular system
    • 3434441, 22536976
    • Lazzerini-Ospri L, Stano P, Luisi P, Marangoni R. Characterization of the emergent properties of a synthetic quasi-cellular system. BMC bioinformatics 2012, 13:S9. 3434441, 22536976.
    • (2012) BMC bioinformatics , vol.13
    • Lazzerini-Ospri, L.1    Stano, P.2    Luisi, P.3    Marangoni, R.4
  • 22
    • 34249950625 scopus 로고    scopus 로고
    • Stochastic simulation of chemical kinetics
    • 10.1146/annurev.physchem.58.032806.104637, 17037977
    • Gillespie DT. Stochastic simulation of chemical kinetics. Annual review of physical chemistry 2007, 58:35-55. 10.1146/annurev.physchem.58.032806.104637, 17037977.
    • (2007) Annual review of physical chemistry , vol.58 , pp. 35-55
    • Gillespie, D.T.1
  • 23
    • 33748921584 scopus 로고    scopus 로고
    • Stochastic simulations of homogeneous chemically reacting systems
    • Mavelli F, Piotto S. Stochastic simulations of homogeneous chemically reacting systems. Journal of Molecular Structure: THEOCHEM 2006, 771(1-3):55-64.
    • (2006) Journal of Molecular Structure: THEOCHEM , vol.771 , Issue.1-3 , pp. 55-64
    • Mavelli, F.1    Piotto, S.2
  • 24
    • 0017030517 scopus 로고
    • A general method for numerically simulating the stochastic time evolution of coupled chemical reactions
    • Gillespie DT. A general method for numerically simulating the stochastic time evolution of coupled chemical reactions. Journal of Computational Physics 1976, 22(4):403-434.
    • (1976) Journal of Computational Physics , vol.22 , Issue.4 , pp. 403-434
    • Gillespie, D.T.1
  • 25
    • 79955117238 scopus 로고    scopus 로고
    • Stochastic sequence-level model of coupled transcription and translation in prokaryotes
    • 79563a14-1272-feb7-481d-85b1f894f09e, 3113936, 21521517
    • Mäkelä J, Lloyd-Price J, Yli-Harja O, Ribeiro A. Stochastic sequence-level model of coupled transcription and translation in prokaryotes. BMC bioinformatics 2011, 12(79563a14-1272-feb7-481d-85b1f894f09e):121. 3113936, 21521517.
    • (2011) BMC bioinformatics , vol.12 , pp. 121
    • Mäkelä, J.1    Lloyd-Price, J.2    Yli-Harja, O.3    Ribeiro, A.4
  • 26
    • 84860443532 scopus 로고    scopus 로고
    • Experiment and mathematical modeling of gene expression dynamics in a cell-free system
    • b372eb93-1286-890c-a0d2-94e985aa0a47
    • Stogbauer T, Windhanger L, Zimmer R, Radler JO. Experiment and mathematical modeling of gene expression dynamics in a cell-free system. Integrative Biology 2012, 4(b372eb93-1286-890c-a0d2-94e985aa0a47).
    • (2012) Integrative Biology , vol.4
    • Stogbauer, T.1    Windhanger, L.2    Zimmer, R.3    Radler, J.O.4
  • 27
    • 0030928859 scopus 로고    scopus 로고
    • Nuclease activity of T7 RNA polymerase and the heterogeneity of transcription elongation complexes
    • 10.1074/jbc.272.13.8644, 9079696
    • Sastry SS, Ross BM. Nuclease activity of T7 RNA polymerase and the heterogeneity of transcription elongation complexes. The Journal of biological chemistry 1997, 272(13):8644-8652. 10.1074/jbc.272.13.8644, 9079696.
    • (1997) The Journal of biological chemistry , vol.272 , Issue.13 , pp. 8644-8652
    • Sastry, S.S.1    Ross, B.M.2
  • 28
    • 0024405193 scopus 로고
    • Codon usage determines translation rate in Escherichia coli
    • 10.1016/0022-2836(89)90260-X, 2474074
    • Sorensen MA, Kurland CG, Pedersen S. Codon usage determines translation rate in Escherichia coli. Journal of molecular biology 1989, 207(2):365-377. 10.1016/0022-2836(89)90260-X, 2474074.
    • (1989) Journal of molecular biology , vol.207 , Issue.2 , pp. 365-377
    • Sorensen, M.A.1    Kurland, C.G.2    Pedersen, S.3
  • 30
    • 75549087930 scopus 로고    scopus 로고
    • BioNumbers--the database of key numbers in molecular and cell biology
    • Database, 10.1093/nar/gkp889, 2808940, 19854939
    • Milo R, Jorgensen P, Moran U, Weber G, Springer M. BioNumbers--the database of key numbers in molecular and cell biology. Nucleic acids research 2010, 38(Database):D750-753. 10.1093/nar/gkp889, 2808940, 19854939.
    • (2010) Nucleic acids research , vol.38
    • Milo, R.1    Jorgensen, P.2    Moran, U.3    Weber, G.4    Springer, M.5
  • 31
    • 0942298127 scopus 로고    scopus 로고
    • Promoter binding, initiation, and elongation by bacteriophage T7 RNA polymerase. A single-molecule view of the transcription cycle
    • Skinner GM, Baumann CG, Quinn DM, Molloy JE, Hoggett JG. Promoter binding, initiation, and elongation by bacteriophage T7 RNA polymerase. A single-molecule view of the transcription cycle. The Journal of biological chemistry 2004, 279(5):3239-3244.
    • (2004) The Journal of biological chemistry , vol.279 , Issue.5 , pp. 3239-3244
    • Skinner, G.M.1    Baumann, C.G.2    Quinn, D.M.3    Molloy, J.E.4    Hoggett, J.G.5
  • 32
    • 33846820156 scopus 로고    scopus 로고
    • A model for protein translation: polysome self-organization leads to maximum protein synthesis rates
    • 10.1529/biophysj.106.087825, 1779991, 17098800
    • Zouridis H, Hatzimanikatis V. A model for protein translation: polysome self-organization leads to maximum protein synthesis rates. Biophys J 2007, 92(3):717-730. 10.1529/biophysj.106.087825, 1779991, 17098800.
    • (2007) Biophys J , vol.92 , Issue.3 , pp. 717-730
    • Zouridis, H.1    Hatzimanikatis, V.2
  • 33
    • 0030854708 scopus 로고    scopus 로고
    • Physical interference between Escherichia coli RNA polymerase molecules transcribing in tandem enhances abortive synthesis and misincorporation
    • 10.1093/nar/25.13.2640, 146789, 9185576
    • Kubori T, Shimamoto N. Physical interference between Escherichia coli RNA polymerase molecules transcribing in tandem enhances abortive synthesis and misincorporation. Nucleic acids research 1997, 25(13):2640-2647. 10.1093/nar/25.13.2640, 146789, 9185576.
    • (1997) Nucleic acids research , vol.25 , Issue.13 , pp. 2640-2647
    • Kubori, T.1    Shimamoto, N.2
  • 34
    • 58249090246 scopus 로고    scopus 로고
    • The native 3D organization of bacterial polysomes
    • 10.1016/j.cell.2008.11.016, 19167328
    • Brandt F, Etchells SA, Ortiz JO, Elcock AH, Hartl FU, Baumeister W. The native 3D organization of bacterial polysomes. Cell 2009, 136(2):261-271. 10.1016/j.cell.2008.11.016, 19167328.
    • (2009) Cell , vol.136 , Issue.2 , pp. 261-271
    • Brandt, F.1    Etchells, S.A.2    Ortiz, J.O.3    Elcock, A.H.4    Hartl, F.U.5    Baumeister, W.6
  • 35
    • 70349761555 scopus 로고    scopus 로고
    • Chemical approaches to synthetic biology
    • 10.1016/j.copbio.2009.08.004, 19729295
    • Chiarabelli C, Stano P, Luisi PL. Chemical approaches to synthetic biology. Current opinion in biotechnology 2009, 20(4):492-497. 10.1016/j.copbio.2009.08.004, 19729295.
    • (2009) Current opinion in biotechnology , vol.20 , Issue.4 , pp. 492-497
    • Chiarabelli, C.1    Stano, P.2    Luisi, P.L.3


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