Modeling Cell Size Regulation: From Single-Cell-Level Statistics to Molecular Mechanisms and Population-Level Effects

Literature Cited

1. 1.  Adiciptaningrum A, Osella M, Moolman M, Lagomarsino M, Tans S 2015. Stochasticity and homeostasis in the E. coli replication and division cycle. Sci. Rep. 5:18261
   [Google Scholar]
2. 2.  Aldridge B, Fernandez-Suarez M, Heller D, Ambravaneswaran V, Irimia D et al. 2012. Asymmetry and aging of mycobacterial cells lead to variable growth and antibiotic susceptibility. Science 335:100–4
   [Google Scholar]
3. 3.  Amir A. 2014. Cell size regulation in bacteria. Phys. Rev. Lett. 112:208102
   [Google Scholar]
4. 4.  Amir A. 2017. Is cell size a spandrel. eLife 6:e22186
   [Google Scholar]
5. 5.  Banerjee S, Lo K, Daddysman M, Selewa A, Kuntz T et al. 2017. Biphasic growth dynamics control cell division in Caulobacter crescentus. Nat. Microbiol. 2:17116
   [Google Scholar]
6. 6.  Barber F, Ho P, Murray A, Amir A 2017. Details matter: noise and model structure set the relationship between cell size and cell cycle timing. Front. Cell Dev. Biol. 5:92
   [Google Scholar]
7. 6a.  Bowler C, De Martino A, Falciatore A 2010. Diatom cell division in an environmental context. Curr. Opin. Plant Biol. 13:623–30
   [Google Scholar]
8. 7.  Box G, Hunter J, Hunter W 2005. Statistics for Experimenters Hoboken, NJ: Wiley
   [Google Scholar]
9. 8.  Box G, Jenkins G, Reinsel G 1994. Time Series Analysis: Forecasting and Control Upper Saddle River, NJ: Prentice Hall
   [Google Scholar]
10. 9.  Brenner N, Braun E, Yoney A, Susman L, Rotella J, Salman H 2015. Single-cell protein dynamics reproduce universal fluctuations in cell populations. Eur. Phys. J. E 38:102
    [Google Scholar]
11. 10.  Brenner N, Newman C, Osmanovic D, Rabin Y, Salman H, Stein D 2015. Universal protein distributions in a model of cell growth and division. Phys. Rev. E 92:042713
    [Google Scholar]
12. 11.  Campos M, Surotsev I, Kato S, Paintdakhi A, Beltran B et al. 2014. A constant size extension drives bacterial cell size homeostasis. Cell 159:1433–46
    [Google Scholar]
13. 12.  Cooper S, Helmstetter C 1968. Chromosome replication and the division cycle of Escherichia coli B/r. J. Mol. Biol. 31:519–40
    [Google Scholar]
14. 12a.  Deforet M, van Ditmarsch D, Xavier JB 2015. Cell-size homeostasis and the incremental rule in a bacterial pathogen. Biophys. J. 109:521–28
    [Google Scholar]
15. 13.  Donachie W. 1968. Relationship between cell size and time of initiation of DNA replication. Nature 219:1077–79
    [Google Scholar]
16. 14.  Eun Y, Ho P, Kim M, Renner L, LaRussa S et al. 2018. Archaeal cells share common size control with bacteria despite noisier growth and division. Nat. Microbiol. 3:148–54
    [Google Scholar]
17. 15.  Fantes P. 1977. Control of cell size and cycle time in Schizosaccharomyces pombe. J. Cell Sci. 24:51–67
    [Google Scholar]
18. 16.  Gardiner C. 2009. Stochastic Methods: A Handbook for the Natural and Social Sciences Berlin: Springer
    [Google Scholar]
19. 17.  Ghusinga K, Vargas-Garcia C, Singh A 2016. A mechanistic stochastic framework for regulating bacterial cell division. Sci. Rep. 6:30229
    [Google Scholar]
20. 18.  Giometto A, Altermatt F, Carrara F, Maritan A, Rinaldo A 2012. Scaling body size fluctuations. PNAS 110:4646–50
    [Google Scholar]
21. 19.  Godin M, Delgado F, Son S, Grover W, Bryan A et al. 2010. Using buoyant mass to measure the growth of single cells. Nat. Methods 7:387–90
    [Google Scholar]
22. 20.  Grilli J, Osella M, Kennard A, Lagomarsino M 2017. Relevant parameters in models of cell division control. Phys. Rev. E 95:032411
    [Google Scholar]
23. 21.  Harris L, Theriot J 2016. Relative rates of surface and volume synthesis set bacterial cell size. Cell 165:1479–92
    [Google Scholar]
24. 22.  Hashimoto M, Nozoe T, Nakaoka H, Okura R, Akiyoshi S et al. 2016. Noise-driven growth rate gain in clonal cellular populations. PNAS 113:3251–56
    [Google Scholar]
25. 23.  Hill N, Kadoya R, Chattoraj D, Levin P 2012. Cell size and the initiation of DNA replication in bacteria. PLOS Genet 8:e1002549
    [Google Scholar]
26. 24.  Ho P, Amir A 2015. Simultaneous regulation of cell size and chromosome replication in bacteria. Front. Microbiol. 6:662
    [Google Scholar]
27. 25.  Iyer-Biswas S, Crooks G, Scherer N, Dinner A 2014. Universality in stochastic exponential growth. Phys. Rev. Lett. 113:028101
    [Google Scholar]
28. 26.  Iyer-Biswas S, Gudjonson H, Wright C, Riebling J, Dawson E et al. 2016. Bridging the time scales of single-cell and population dynamics. arXiv1611.05149 [q-bio.QM]
29. 27.  Kennard A, Osella M, Javer A, Grilli J, Nghe P et al. 2016. Individuality and universality in the growth-division laws of single E. coli cells. Phys. Rev. E 93:012408
    [Google Scholar]
30. 28.  Kessler D, Burov S 2017. Effective potential for cellular size control. arXiv 1701.01725 [cond-mat.soft]
31. 29.  Koch A. 2001. Bacterial Growth and Form Berlin: Springer
    [Google Scholar]
32. 30.  Koppes L, Meyer M, Oonk H, de Jong M, Nanninga N 1980. Correlation between size and age at different events in the cell division cycle of Escherichia coli. J. Bacteriol. 143:1241–52
    [Google Scholar]
33. 31.  Levins R. 1966. The strategy of model building in population biology. Am. Sci. 54:421–31
    [Google Scholar]
34. 32.  Lin J, Amir A 2017. The effects of stochasticity at the single-cell level and cell size control on the population growth. Cell Syst 5:358–67.e4
    [Google Scholar]
35. 32a.  Lin J, Amir A 2018. Homeostasis of protein and mRNA concentrations in growing cells. bioRxiv:255950
    [Google Scholar]
36. 33.  Logsdon M, Ho P, Papavinasasundaram K, Cokol M, Richardson K et al. 2018. A parallel adder coordinates mycobacterial cell-cycle progression and cell-size homeostasis in the context of asymmetric growth and organization. Curr. Biol. 27:213367–74
    [Google Scholar]
37. 34.  Marantan A, Amir A 2016. Stochastic modeling of cell growth with symmetric or asymmetric division. Phys. Rev. E 94:012405
    [Google Scholar]
38. 35.  Martins B, Tooke A, Thomas P, Locke J 2017. Cell size control driven by the circadian clock and environment in cyanobacteria. bioRxiv183558
39. 36.  Metzl-Raz E, Kafri M, Yaakov G, Soifer I, Gurvich Y, Barkai N 2017. Principles of cellular resource allocation revealed by condition-dependent proteome profiling. eLife 6:e28034
    [Google Scholar]
40. 37.  Mosheiff N, Martins B, Pearl-Mizrahi S, Gruenberger A, Helfrich S et al. 2017. Correlations of single-cell division times with and without periodic forcing. arXiv 1710.00349 [q-bio.CB]
41. 38.  Osella M, Nugent E, Lagomarsino M 2014. Concerted control of Escherichia coli cell division. PNAS 111:3431–35
    [Google Scholar]
42. 39.  Osella M, Tans S, Lagomarsino M 2017. Step by step, cell by cell: quantification of the bacterial cell cycle. Trends. Microbiol. 25:250–56
    [Google Scholar]
43. 40.  Paulsson J. 2005. Models of stochastic gene expression. Phys. Life Rev. 2:157–75
    [Google Scholar]
44. 41.  Powell E. 1956. Growth rate and generation time of bacteria, with special reference to continuous culture. J. Gen. Microbiol. 15:492–511
    [Google Scholar]
45. 42.  Priestley M. 1981. Spectral Analysis and Time Series Cambridge, MA: Academic
    [Google Scholar]
46. 42a.  Robert L, Hoffmann M, Krell N, Aymerich S, Robert J, Doumic M 2014. Division in Escherichia coli is triggered by a size-sensing rather than a timing mechanism. BMC Biol. 1217
    [Google Scholar]
47. 43.  Sandler O, Pearl-Mizrahi S, Weiss N, Agam O, Simon I, Balaban N 2015. Lineage correlations of single cell division time as a probe of cell-cycle dynamics. Nature 519:468–71
    [Google Scholar]
48. 44.  Deleted in proof
49. 45.  Schaechter M, Maaloe O, Kjeldgaard N 1958. Dependency on medium and temperature of cell size and chemical composition during balanced growth of Salmonella typhimurium. J. Gen. Microbiol. 19:592–606
    [Google Scholar]
50. 46.  Scott M, Gunderson C, Mateescu E, Zhang Z, Hwa T 2010. Interdependence of cell growth and gene expression: origins and consequences. Science 330:1099–102
    [Google Scholar]
51. 47.  Soifer I, Robert L, Amir A 2016. Single-cell analysis of growth in budding yeast and bacteria reveals a common size regulation strategy. Curr. Biol. 26:356–61
    [Google Scholar]
52. 48.  Sompayrac L, Maaloe O 1973. Autorepressor model for control of DNA replication. Nat. New Biol. 241:133–35
    [Google Scholar]
53. 49.  Stewart E, Madden R, Paul G, Taddei F 2005. Aging and death in an organism that reproduces by morphologically symmetric division. PLOS Biol 3:e45
    [Google Scholar]
54. 50.  Susman L, Kohram M, Vashistha H, Nechleba J, Salman H, Brenner N 2017. Statistical properties and dynamics of phenotype components in individual bacteria. arXiv 1609.05513 [q-bio.CB]
55. 51.  Taheri-Araghi S, Bradde S, Sauls J, Hill N, Levin P et al. 2015. Cell-size control and homeostasis in bacteria. Curr. Biol. 25:385–91
    [Google Scholar]
56. 52.  Taheri-Araghi S, Brown S, Sauls J, McIntosh D, Jun S 2015. Single-cell physiology. Annu. Rev. Biophys. 44:123–42
    [Google Scholar]
57. 53.  Tanouchi Y, Pai A, Park H, Huang S, Buchler N, You L 2017. Long-term growth data of Escherichia coli at a single-cell level. Sci. Data 4:170036
    [Google Scholar]
58. 54.  Tanouchi Y, Pai A, Park H, Huang S, Stamatov R et al. 2015. A noisy linear map underlies oscillations in cell size and gene expression in bacteria. Nature 523:357–60
    [Google Scholar]
59. 55.  Trueba F, Neijssel O, Woldringh C 1982. Generality of the growth kinetics of the average individual cell in different bacterial populations. J. Bacteriol. 150:1048–55
    [Google Scholar]
60. 56.  Voorn W, Koppes L 1997. Skew or third moment of bacterial generation times. Arch. Microbiol. 169:43–51
    [Google Scholar]
61. 57.  Voorn W, Koppes L, Grover N 1993. Mathematics of cell division in Escherichia coli: comparison between sloppy-size and incremental-size kinetics. Curr. Top. Mol. Gen. 1:187–94
    [Google Scholar]
62. 58.  Wallden M, Fange D, Lundius E, Baltekin O, Elf J 2016. The synchronization of replication and division cycles in individual E. coli cells. Cell 166:729–39
    [Google Scholar]
63. 59.  Wang P, Robert L, Pelletier J, Dang W, Taddei F et al. 2010. Robust growth of Escherichia coli. Curr. Biol. 20:1099–103
    [Google Scholar]
64. 60.  Willis L, Huang K 2017. Sizing up the bacterial cell cycle. Nat. Rev. Microbiol. 15:606–20
    [Google Scholar]
65. 61.  Yu F, Willis L, Chau R, Zambon A, Horowitz M et al. 2017. Long-term microfluidic tracking of coccoid cyanobacterial cells reveals robust control of division timing. BMC Biol 15:11
    [Google Scholar]
66. 62.  Zheng H, Ho P, Jiang M, Tang B, Liu W et al. 2016. Interrogating the Escherichia coli cell cycle by cell dimension perturbations. PNAS 113:15000–5
    [Google Scholar]