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Volumn 110, Issue 3, 2013, Pages 812-826

Cell mass and cell cycle dynamics of an asynchronous budding yeast population: Experimental observations, flow cytometry data analysis, and multi-scale modeling

Author keywords

Cell cycle; Flow cytometry; Multiscale modeling; Population balance model (PBM); Saccharomyces cerevisiae; Standardized data analysis; Total protein content

Indexed keywords

BATCH CULTIVATION; CELL BEHAVIORS; CELL CULTIVATION; CELL CYCLE; CELL MASS; CELL POPULATIONS; CELL SIZE; CO-EXISTING; EXPERIMENTAL OBSERVATION; HETEROGENEOUS POPULATIONS; MATHEMATICAL DESCRIPTIONS; MECHANISTIC MODELS; MICROBIAL CULTIVATION; MICROBIAL POPULATIONS; MODEL PREDICTION; MULTI-SCALE MODELING; MULTISCALE MODELS; PHENOTYPIC TRAITS; POPULATION BALANCE MODELS; TOTAL PROTEIN; UNSTRUCTURED MODEL;

EID: 84872673703     PISSN: 00063592     EISSN: 10970290     Source Type: Journal    
DOI: 10.1002/bit.24749     Document Type: Article
Times cited : (28)

References (51)
  • 1
    • 20444407493 scopus 로고    scopus 로고
    • Alberghina L, Westerhoff HV, editors, Berlin/Heidelberg: Springer-Verlag.
    • Alberghina L, Westerhoff HV, editors. 2005. Systems biology, Vol. 13. Berlin/Heidelberg: Springer-Verlag.
    • (2005) Systems biology , vol.13
  • 2
    • 0031858093 scopus 로고    scopus 로고
    • Control by nutrients of growth and cell cycle progression in budding yeast, analyzed by double-tag flow cytometry
    • Alberghina L, Smeraldi C, Ranzi BM, Porro D. 1998. Control by nutrients of growth and cell cycle progression in budding yeast, analyzed by double-tag flow cytometry. J Bacteriol 180: 3864-3872.
    • (1998) J Bacteriol , vol.180 , pp. 3864-3872
    • Alberghina, L.1    Smeraldi, C.2    Ranzi, B.M.3    Porro, D.4
  • 3
    • 33747174575 scopus 로고    scopus 로고
    • Microbial cell individuality and the underlying sources of heterogeneity
    • Avery SV. 2006. Microbial cell individuality and the underlying sources of heterogeneity. Nat Rev Micro 4: 577-587.
    • (2006) Nat Rev Micro , vol.4 , pp. 577-587
    • Avery, S.V.1
  • 4
    • 18244376808 scopus 로고    scopus 로고
    • Homeostatic adjustment and metabolic remodeling in glucose-limited yeast cultures
    • Brauer MJ, Saldanha AJ, Dolinski K, Botstein D. 2005. Homeostatic adjustment and metabolic remodeling in glucose-limited yeast cultures. Mol Biol Cell 16: 2503-2517.
    • (2005) Mol Biol Cell , vol.16 , pp. 2503-2517
    • Brauer, M.J.1    Saldanha, A.J.2    Dolinski, K.3    Botstein, D.4
  • 6
    • 17644413178 scopus 로고    scopus 로고
    • Sfp1 is involved in cell size modulation in respiro-fermentative growth conditions
    • Cipollina C, Alberghina L, Porro D, Vai M. 2005. Sfp1 is involved in cell size modulation in respiro-fermentative growth conditions. Yeast 22: 385-399.
    • (2005) Yeast , vol.22 , pp. 385-399
    • Cipollina, C.1    Alberghina, L.2    Porro, D.3    Vai, M.4
  • 7
    • 33846073419 scopus 로고    scopus 로고
    • Towards understanding of the complex structure of growing yeast populations
    • Cipollina C, Vai M, Porro D, Hatzis C. 2007. Towards understanding of the complex structure of growing yeast populations. J Biotechnol 128: 393-402.
    • (2007) J Biotechnol , vol.128 , pp. 393-402
    • Cipollina, C.1    Vai, M.2    Porro, D.3    Hatzis, C.4
  • 8
    • 0029832083 scopus 로고    scopus 로고
    • Flow cytometry and cell sorting of heterogeneous microbial populations: The importance of single-cell analyses
    • Davey H, Kell D. 1996. Flow cytometry and cell sorting of heterogeneous microbial populations: The importance of single-cell analyses. Microbiol Rev 60: 641-696.
    • (1996) Microbiol Rev , vol.60 , pp. 641-696
    • Davey, H.1    Kell, D.2
  • 9
    • 34548168571 scopus 로고    scopus 로고
    • The effects of molecular noise and size control on variability in the budding yeast cell cycle
    • Di Talia S, Skotheim JM, Bean JM, Siggia ED, Cross FR. 2007. The effects of molecular noise and size control on variability in the budding yeast cell cycle. Nature 448: 947-951.
    • (2007) Nature , vol.448 , pp. 947-951
    • Di Talia, S.1    Skotheim, J.M.2    Bean, J.M.3    Siggia, E.D.4    Cross, F.R.5
  • 12
    • 84855932783 scopus 로고    scopus 로고
    • A novel population balance model to investigate the kinetics of in vitro cell proliferation: Part I. Model development
    • Fadda S, Cincotti A, Cao G. 2012a. A novel population balance model to investigate the kinetics of in vitro cell proliferation: Part I. Model development. Biotech Bioeng 109: 772-781.
    • (2012) Biotech Bioeng , vol.109 , pp. 772-781
    • Fadda, S.1    Cincotti, A.2    Cao, G.3
  • 13
    • 84855932783 scopus 로고    scopus 로고
    • A novel population balance model to investigate the kinetics of in vitro cell proliferation: Part II-Numerical solution, parameters' determination and model outcomes
    • Fadda S, Cincotti A, Cao G. 2012b. A novel population balance model to investigate the kinetics of in vitro cell proliferation: Part II-Numerical solution, parameters' determination and model outcomes. Biotech Bioeng 109: 772-781.
    • (2012) Biotech Bioeng , vol.109 , pp. 772-781
    • Fadda, S.1    Cincotti, A.2    Cao, G.3
  • 14
    • 0037394192 scopus 로고    scopus 로고
    • Population balance equations for cell and microbial cultures revisited
    • Fredrickson AG. 2003. Population balance equations for cell and microbial cultures revisited. AIChE J 49: 1050-1059.
    • (2003) AIChE J , vol.49 , pp. 1050-1059
    • Fredrickson, A.G.1
  • 15
    • 49949137115 scopus 로고
    • Statistics and dynamics of procaryotic cell populations
    • Fredrickson AG, Ramkrishna D, Tsuchiya HM. 1967. Statistics and dynamics of procaryotic cell populations. Math Biosci 1: 327-374.
    • (1967) Math Biosci , vol.1 , pp. 327-374
    • Fredrickson, A.G.1    Ramkrishna, D.2    Tsuchiya, H.M.3
  • 18
    • 33745184700 scopus 로고    scopus 로고
    • Morphologically-structured models of growing budding yeast populations
    • Hatzis C, Porro D. 2006. Morphologically-structured models of growing budding yeast populations. J Biotechnol 124: 420-438.
    • (2006) J Biotechnol , vol.124 , pp. 420-438
    • Hatzis, C.1    Porro, D.2
  • 19
    • 0028990631 scopus 로고
    • Multistaged corpuscular models of microbial growth: Monte Carlo simulations
    • Hatzis C, Srienc F, Fredrickson AG. 1995. Multistaged corpuscular models of microbial growth: Monte Carlo simulations. Biosystems 36: 19-35.
    • (1995) Biosystems , vol.36 , pp. 19-35
    • Hatzis, C.1    Srienc, F.2    Fredrickson, A.G.3
  • 20
    • 0032989750 scopus 로고    scopus 로고
    • Flow cytometric investigation of heterogeneous copper-sensitivity in asynchronously grown Saccharomyces cerevisiae
    • Howlett NG, Avery SV. 1999. Flow cytometric investigation of heterogeneous copper-sensitivity in asynchronously grown Saccharomyces cerevisiae FEMS Microbiol Lett 176: 379-386.
    • (1999) FEMS Microbiol Lett , vol.176 , pp. 379-386
    • Howlett, N.G.1    Avery, S.V.2
  • 21
    • 10344222155 scopus 로고    scopus 로고
    • How cells coordinate growth and division
    • Jorgensen P, Tyers M. 2004. How cells coordinate growth and division. Curr Biol 14: R1014-R1027.
    • (2004) Curr Biol , vol.14
    • Jorgensen, P.1    Tyers, M.2
  • 22
    • 0037135134 scopus 로고    scopus 로고
    • Systematic identification of pathways that couple cell growth and division in yeast
    • Jorgensen P, Nishikawa JL, Breitkreutz B-J, Tyers M. 2002. Systematic identification of pathways that couple cell growth and division in yeast. Science 297: 395-400.
    • (2002) Science , vol.297 , pp. 395-400
    • Jorgensen, P.1    Nishikawa, J.L.2    Breitkreutz, B.-J.3    Tyers, M.4
  • 23
    • 0029869390 scopus 로고    scopus 로고
    • Differential response to UV stress and DNA damage during the yeast replicative life span
    • Kale SP, Jazwinski SM. 1996. Differential response to UV stress and DNA damage during the yeast replicative life span. Dev Genet 18: 154-160.
    • (1996) Dev Genet , vol.18 , pp. 154-160
    • Kale, S.P.1    Jazwinski, S.M.2
  • 24
    • 77956064697 scopus 로고    scopus 로고
    • Multi-scale modeling of heterogeneities in mammalian cell culture processes
    • Karra S, Sager B, Karim MN. 2010. Multi-scale modeling of heterogeneities in mammalian cell culture processes. Ind Eng Chem Res 49: 7990-8006.
    • (2010) Ind Eng Chem Res , vol.49 , pp. 7990-8006
    • Karra, S.1    Sager, B.2    Karim, M.N.3
  • 25
    • 0030128282 scopus 로고    scopus 로고
    • On the solution of population balance equations by discretization-i. A fixed pivot technique
    • Kumar S, Ramkrishna D. 1996. On the solution of population balance equations by discretization-i. A fixed pivot technique. Chem Eng Sci 51: 1311-1332.
    • (1996) Chem Eng Sci , vol.51 , pp. 1311-1332
    • Kumar, S.1    Ramkrishna, D.2
  • 27
    • 0031149205 scopus 로고    scopus 로고
    • Solutions of population balance models based on a successive generations approach
    • Liou J-J, Srienc F, Fredrickson AG. 1997. Solutions of population balance models based on a successive generations approach. Chem Eng Sci 52: 1529-1540.
    • (1997) Chem Eng Sci , vol.52 , pp. 1529-1540
    • Liou, J.-J.1    Srienc, F.2    Fredrickson, A.G.3
  • 28
    • 35348835362 scopus 로고    scopus 로고
    • A population balance model describing the cell cycle dynamics of myeloma cell cultivation
    • Liu Y-H, Bi J-X, Zeng A-P, Yuan J-Q. 2007. A population balance model describing the cell cycle dynamics of myeloma cell cultivation. Biotechnol Prog 23: 1198-1209.
    • (2007) Biotechnol Prog , vol.23 , pp. 1198-1209
    • Liu, Y.-H.1    Bi, J.-X.2    Zeng, A.-P.3    Yuan, J.-Q.4
  • 30
    • 0032838485 scopus 로고    scopus 로고
    • Numerical solution of a mass structured cell population balance model in an environment of changing substrate concentration
    • Mantzaris NV, Liou J-J, Daoutidis P, Srienc F. 1999. Numerical solution of a mass structured cell population balance model in an environment of changing substrate concentration. J Biotechnol 71: 157-174.
    • (1999) J Biotechnol , vol.71 , pp. 157-174
    • Mantzaris, N.V.1    Liou, J.-J.2    Daoutidis, P.3    Srienc, F.4
  • 31
    • 0035890846 scopus 로고    scopus 로고
    • Numerical solution of multi-variable cell population balance models: i. Finite difference methods
    • Mantzaris NV, Daoutidis P, Srienc F. 2001. Numerical solution of multi-variable cell population balance models: i. Finite difference methods. Comp Chem Eng 25: 1411-1440.
    • (2001) Comp Chem Eng , vol.25 , pp. 1411-1440
    • Mantzaris, N.V.1    Daoutidis, P.2    Srienc, F.3
  • 32
    • 0037039537 scopus 로고    scopus 로고
    • Nonlinear productivity control using a multi-staged cell population balance model
    • Mantzaris NV, Srienc F, Daoutidis P. 2002. Nonlinear productivity control using a multi-staged cell population balance model. Chem Eng Sci 57: 1-14.
    • (2002) Chem Eng Sci , vol.57 , pp. 1-14
    • Mantzaris, N.V.1    Srienc, F.2    Daoutidis, P.3
  • 33
    • 77950627389 scopus 로고    scopus 로고
    • Origin and analysis of microbial population heterogeneity in bioprocesses
    • Müller S, Harms H, Bley T. 2010. Origin and analysis of microbial population heterogeneity in bioprocesses. Curr Opin Biotechnol 21: 100-113.
    • (2010) Curr Opin Biotechnol , vol.21 , pp. 100-113
    • Müller, S.1    Harms, H.2    Bley, T.3
  • 34
    • 10444225385 scopus 로고    scopus 로고
    • Comparison and pitfalls of different discretised solution methods for population balance models: A simulation study
    • Nopens I, Beheydt D, Vanrolleghem PA. 2005. Comparison and pitfalls of different discretised solution methods for population balance models: A simulation study. Comp Chem Eng 29: 367-377.
    • (2005) Comp Chem Eng , vol.29 , pp. 367-377
    • Nopens, I.1    Beheydt, D.2    Vanrolleghem, P.A.3
  • 35
    • 58949087904 scopus 로고    scopus 로고
    • Celebrating a milestone in population balance modeling
    • Nopens I, Briesen H, Ducoste J. 2009. Celebrating a milestone in population balance modeling. Chem Eng Sci 64: 627.
    • (2009) Chem Eng Sci , vol.64 , pp. 627
    • Nopens, I.1    Briesen, H.2    Ducoste, J.3
  • 36
    • 0029294029 scopus 로고
    • Tracking of individual cell cohorts in asynchronous Saccharomyces cerevisiae populations
    • Porro D, Srienc F. 1995. Tracking of individual cell cohorts in asynchronous Saccharomyces cerevisiae populations. Biotechnol Prog 11: 342-347.
    • (1995) Biotechnol Prog , vol.11 , pp. 342-347
    • Porro, D.1    Srienc, F.2
  • 37
    • 0346849875 scopus 로고    scopus 로고
    • Glucose metabolism and cell size in continuous cultures of Saccharomyces cerevisiae
    • Porro D, Brambilla L, Alberghina L. 2003. Glucose metabolism and cell size in continuous cultures of Saccharomyces cerevisiae FEMS Microb Lett 229: 165-171.
    • (2003) FEMS Microb Lett , vol.229 , pp. 165-171
    • Porro, D.1    Brambilla, L.2    Alberghina, L.3
  • 38
    • 60849101063 scopus 로고    scopus 로고
    • Analysis and modeling of growing budding yeast populations at the single cell level
    • Porro D, Vai M, Vanoni M, Alberghina L, Hatzis C. 2009. Analysis and modeling of growing budding yeast populations at the single cell level. Cytometry 75A: 114-120.
    • (2009) Cytometry , vol.75 A , pp. 114-120
    • Porro, D.1    Vai, M.2    Vanoni, M.3    Alberghina, L.4    Hatzis, C.5
  • 39
    • 0036716747 scopus 로고    scopus 로고
    • Checking cell size in yeast
    • Rupeš I. 2002. Checking cell size in yeast. Trends Genet 18: 479-485.
    • (2002) Trends Genet , vol.18 , pp. 479-485
    • Rupeš, I.1
  • 40
    • 4344685444 scopus 로고    scopus 로고
    • Nutritional homeostasis in batch and steady-state culture of yeast
    • Saldanha AJ, Brauer MJ, Botstein D. 2004. Nutritional homeostasis in batch and steady-state culture of yeast. Mol Biol Cell 15: 4089-4104.
    • (2004) Mol Biol Cell , vol.15 , pp. 4089-4104
    • Saldanha, A.J.1    Brauer, M.J.2    Botstein, D.3
  • 41
    • 80052319096 scopus 로고    scopus 로고
    • Bistability versus bimodal distributions in gene regulatory processes from population balance
    • Shu C-C, Chatterjee A, Dunny G, Hu W-S, Ramkrishna D. 2011. Bistability versus bimodal distributions in gene regulatory processes from population balance. PLoS Comput Biol 7: e1002140.
    • (2011) PLoS Comput Biol , vol.7
    • Shu, C.-C.1    Chatterjee, A.2    Dunny, G.3    Hu, W.-S.4    Ramkrishna, D.5
  • 42
    • 84855450639 scopus 로고    scopus 로고
    • Modeling of gene regulatory processes by population-mediated signaling: New applications of population balances
    • Shu C-C, Chatterjee A, Hu W-S, Ramkrishna D. 2012. Modeling of gene regulatory processes by population-mediated signaling: New applications of population balances. Chem Eng Sci 70: 188-199.
    • (2012) Chem Eng Sci , vol.70 , pp. 188-199
    • Shu, C.-C.1    Chatterjee, A.2    Hu, W.-S.3    Ramkrishna, D.4
  • 43
    • 33748306378 scopus 로고    scopus 로고
    • A coupled single cell-population model for mammalian cell cultures
    • Sidoli FR, Asprey SP, Mantalaris A. 2006. A coupled single cell-population model for mammalian cell cultures. Ind Eng Chem Res 45: 5801-5811.
    • (2006) Ind Eng Chem Res , vol.45 , pp. 5801-5811
    • Sidoli, F.R.1    Asprey, S.P.2    Mantalaris, A.3
  • 44
    • 0022736565 scopus 로고
    • Growth of Saccharomyces cerevisiae is controlled by its limited respiratory capacity: Formulation and verification of a hypothesis
    • Sonnleitner B, Käppeli O. 1986. Growth of Saccharomyces cerevisiae is controlled by its limited respiratory capacity: Formulation and verification of a hypothesis. Biotechnol Bioeng 28: 927-937.
    • (1986) Biotechnol Bioeng , vol.28 , pp. 927-937
    • Sonnleitner, B.1    Käppeli, O.2
  • 45
    • 0242437869 scopus 로고    scopus 로고
    • Cell cycle- and age-dependent activation of sod1p drives the formation of stress resistant cell subpopulations within clonal yeast cultures
    • Sumner ER, Avery AM, Houghton JE, Robins RA, Avery SV. 2003. Cell cycle- and age-dependent activation of sod1p drives the formation of stress resistant cell subpopulations within clonal yeast cultures. Mol Microbiol 50: 857-870.
    • (2003) Mol Microbiol , vol.50 , pp. 857-870
    • Sumner, E.R.1    Avery, A.M.2    Houghton, J.E.3    Robins, R.A.4    Avery, S.V.5
  • 46
    • 0035902599 scopus 로고    scopus 로고
    • Intrinsic noise in gene regulatory networks
    • Thattai M, van Oudenaarden A. 2001. Intrinsic noise in gene regulatory networks. Proc Natl Acad Sci 98: 8614-8619.
    • (2001) Proc Natl Acad Sci , vol.98 , pp. 8614-8619
    • Thattai, M.1    van Oudenaarden, A.2
  • 47
    • 0021071243 scopus 로고
    • Structural heterogeneity in populations of the budding yeast Saccharomyces cerevisiae
    • Vanoni M, Vai M, Popolo L, Alberghina L. 1983. Structural heterogeneity in populations of the budding yeast Saccharomyces cerevisiae J Bacteriol 156: 1282-1291.
    • (1983) J Bacteriol , vol.156 , pp. 1282-1291
    • Vanoni, M.1    Vai, M.2    Popolo, L.3    Alberghina, L.4
  • 49
    • 0026710123 scopus 로고
    • Effect of benzoic acid on metabolic fluxes in yeasts: A continuous-culture study on the regulation of respiration and alcoholic fermentation
    • Verduyn C, Postma E, Scheffers WA, Van Dijken JP. 1992. Effect of benzoic acid on metabolic fluxes in yeasts: A continuous-culture study on the regulation of respiration and alcoholic fermentation. Yeast 8: 501-517.
    • (1992) Yeast , vol.8 , pp. 501-517
    • Verduyn, C.1    Postma, E.2    Scheffers, W.A.3    Van Dijken, J.P.4
  • 50
    • 84891558594 scopus 로고    scopus 로고
    • Aging and the survival of quiescent and non-quiescent cells in yeast stationary-phase cultures
    • Breitenbach M, Jazwinski SM, Laun P, editors., Vol. 57. Dordrecht: Springer Netherlands.
    • Werner-Washburne M, Roy S, Davidson GS. 2011. Aging and the survival of quiescent and non-quiescent cells in yeast stationary-phase cultures. In: Breitenbach M, Jazwinski SM, Laun P, editors. Aging research in yeast, Vol. 57. Dordrecht: Springer Netherlands. p 123-143.
    • (2011) Aging research in yeast , pp. 123-143
    • Werner-Washburne, M.1    Roy, S.2    Davidson, G.S.3
  • 51
    • 72449171935 scopus 로고    scopus 로고
    • Growth landscape formed by perception and import of glucose in yeast
    • Youk H, van Oudenaarden A. 2009. Growth landscape formed by perception and import of glucose in yeast. Nature 462: 875-880.
    • (2009) Nature , vol.462 , pp. 875-880
    • Youk, H.1    van Oudenaarden, A.2


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