Understanding multimodal biological decisions from single cell and population dynamics

Wiley Interdisciplinary Reviews: Systems Biology and Medicine

Volumn 4, Issue 4, 2012, Pages 385-399

  Selvarajoo, Kumar ^a  

^a KEIO UNIVERSITY   (Japan)

Author keywords

[No Author keywords available]

Indexed keywords

CELL DNA; MESSENGER RNA; MITOCHONDRIAL PROTEIN; TOLL LIKE RECEPTOR 4; TOM40 PROTEIN; UNCLASSIFIED DRUG;

CELL FATE; CELL FUNCTION; CELL POPULATION; CELL STIMULATION; CONFOCAL LASER MICROSCOPY; ESCHERICHIA COLI; FLUORESCENCE CORRELATION SPECTROSCOPY; FLUORESCENCE IN SITU HYBRIDIZATION; GENE EXPRESSION; HUMAN; MACROPHAGE; MICROENVIRONMENT; MOLECULAR DYNAMICS; NONHUMAN; PHENOTYPE; PHENOTYPIC VARIATION; POPULATION DYNAMICS; REVIEW; SINGLE CELL ANALYSIS;

ANIMALS; BACILLUS SUBTILIS; BACTERIAL PROTEINS; CELLS, CULTURED; HUMANS; IMMUNITY, INNATE; MACROPHAGES; MODELS, BIOLOGICAL; NONLINEAR DYNAMICS; STOCHASTIC PROCESSES; TOLL-LIKE RECEPTOR 4; TRANSCRIPTION FACTORS;

EID: 84862562689     PISSN: 19395094     EISSN: 1939005X     Source Type: Journal    
DOI: 10.1002/wsbm.1175     Document Type: Review

References (112)

1. Pollack JR, Perou CM, Alizadeh AA, Eisen MB, Pergamenschikov A, Williams CF, Jeffrey SS, Botstein D, Brown PO. Genome-wide analysis of DNA copy-number changes using cDNA microarrays. Nat Genet 1999, 23:41-46.
2. Anderson NL, Anderson NG. Proteome and proteomics: new technologies, new concepts, and new words. Electrophoresis 1998, 19:1853-1861.
3. Weckwerth W. Metabolomics in systems biology. Annu Rev Plant Biol 2003, 54:669-689.
4. Kitano H. Biological robustness. Nat Rev Genet 2004, 5:826-837.
5. Barabási AL, Bonabeau E. Scale-free networks. Sci Am 2003, 288:60-69.
6. Barabási AL, Oltvai ZN. Network biology: understanding the cell's functional organization. Nat Rev Genet 2004, 5:101-113.
7. Hartwell LH, Hopfield JJ, Leibler S, Murray AW. From molecular to modular cell biology. Nature 1999, 402:C47-C52.
8. Ravasz E, Somera AL, Mongru DA, Oltvai ZN, Barabasi AL. Hierarchical organization of modularity in metabolic networks. Science 297, 2002:1551-1555.
9. Rao CV, Arkin AP. Control motifs for intracellular regulatory networks. Annu Rev Biomed Eng 2001, 3:391-419.
10. Bennett MR, Hasty J. Systems biology: genome rewired. Nature 2008, 452:824-825.
11. Ishii N, Nakahigashi K, Baba T, Robert M, Soga T, Kanai A, Hirasawa T, Naba M, Hirai K, Hoque A, et al. Multiple high-throughput analyses monitor the response of E. coli to perturbations. Science 2007, 316:593-597.
12. Barkai N, Leibler S. Robustness in simple biochemical networks. Nature 1997, 387:913-917.
13. Alon U, Surette MG, Barkai N, Leibler S. Robustness in bacterial chemotaxis. Nature 1999, 397:168-171.
14. Stromberg SP, Carlson J. Robustness and fragility in immunosenescence. PLoS Comput Biol 2006, 2:e160.
15. Lemoine FJ, Degtyareva NP, Lobachev K, Petes TD. Chromosomal translocations in yeast induced by low levels of DNA polymerase a model for chromosome fragile sites. Cell, 2005, 120:587-598.
16. Carlson JM, Doyle J. Complexity and robustness. Proc Natl Acad Sci U S A 2002, 99:2538-2545.
17. Albert R, Jeong H, Barabasi AL. Error and attack tolerance of complex networks. Nature 2000, 406:378-382.
18. Yu H, Kim PM, Sprecher E, Trifonov V, Gerstein M. The importance of bottlenecks in protein networks: correlation with gene essentiality and expression dynamics. PLoS Comput Biol 2007, 3:e59.
19. Selvarajoo K, Takada Y, Gohda J, Helmy M, Akira S, Tomita M, Tsuchiya M, Inoue J, Matsuo K. Signaling flux redistribution at toll-like receptor pathway junctions. PLoS One 2008, 3:e3430.
20. Helmy M, Gohda J, Inoue J, Tomita M, Tsuchiya M, Selvarajoo K. Predicting novel features of toll-like receptor 3 signaling in macrophages. PLoS One 2009, 4:e4661.
21. Piras V, Hayashi K, Tomita M, Selvarajoo K. Enhancing apoptosis in TRAIL-resistant cancer cells using fundamental response rules. Sci Rep 2011, 1:144.
22. Selvarajoo K, Tomita M, Tsuchiya M. Can complex cellular processes be governed by simple linear rules? J Bioinform Comput Biol 2009, 7:243-268.
23. Selvarajoo K. Macroscopic law of conservation revealed in the population dynamics of Toll- like receptor signaling. Cell Commun Signal 2011, 9:9.
24. Fong SS, Palsson BØ. Metabolic gene-deletion strains of Escherichia coli evolve to computationally predicted growth phenotypes. Nat Genet 2004, 36:1056-1058.
25. Ma J, Zhang X, Ung CY, Chen YZ, Li B. Metabolic network analysis revealed distinct routes of deletion effects between essential and non-essential genes. Mol Biosyst 2012, 8:1179-1186.
26. Saadatpour A, Wang RS, Liao A, Liu X, Loughran TP, Albert I, Albert R. Dynamical and structural analysis of a T cell survival network identifies novel candidate therapeutic targets for large granular lymphocyte leukemia. PLoS Comput Biol 2011, 7:e1002267.
27. Krishna S, Semsey S, Sneppen K. Combinatorics of feedback in cellular uptake and metabolism of small molecules. Proc Natl Acad Sci U S A 2007, 104: 20815-20819.
28. Bruex A, Kainkaryam RM, Wieckowski Y, Kang YH, Bernhardt C, Xia Y, Zheng X, Wang JY, Lee MM, Benfey P, et al. A gene regulatory network for root epidermis cell differentiation in Arabidopsis. PLoS Genet 2012, 8:e1002446.
29. Reynolds SM, Käll L, Riffle ME, Bilmes JA, Noble WS. Transmembrane topology and signal peptide prediction using dynamic bayesian networks. PLoS Comput Biol 2008, 4:e1000213.
30. Templer RH, Ces O. New frontiers in single-cell analysis. J R Soc Interface 2008, 5:S111-S112.
31. Li GW, Xie XS. Central dogma at the single-molecule level in living cells. Nature 2011, 475:308-315.
32. Sagues F, Sancho JM, Garcia-Ojalvo J. Spatiotemporal order out of noise. Rev Mod Phys 2007, 79:829-882.
33. Franaszek M, Simiu E. Stochastic resonance: a chaotic dynamics approach. Phys Rev E Stat Phys 1996, 54:1298-1304.
34. Losick R, Desplan C. Stochasticity and cell fate. Science 2008, 320:65-68.
35. Zernicka-Goetz M, Huang S. Stochasticity versus determinism in development: a false dichotomy? Nat Rev Genet 2010, 11:743-744.
36. Sumner ER, Avery SV. Phenotypic heterogeneity: differential stress resistance among individual cells of the yeast Saccharomyces cerevisiae. Microbiology 2002, 148:345-351.
37. Brock A, Chang H, Huang S. Non-genetic heterogeneity-a mutation-independent driving force for the somatic evolution of tumours. Nat Rev Genet 2009, 10:336-342.
38. Chen JH, Ozanne SE, Hales CN. Heterogeneity in premature senescence by oxidative stress correlates with differential DNA damage during the cell cycle. DNA Repair 2005, 4:1140-1148.
39. Wong AH, Gottesman II, Petronis A. Phenotypic differences in genetically identical organisms: the epigenetic perspective. Hum Mol Genet 2005, 14: R11-R18.
40. Delbruck M. Statistical fluctuations in autocatalytic reactions. J Chem Phys 1940, 8:120-124.
41. Ellis EL, Delbruck M. The growth of bacteriophage. J Gen Physiol 1939, 22:365-384.
42. Schrödinger E. What is Life? Cambridge: Cambridge University Press, 1944.
43. Spudich JL, Koshland DE Jr. Non-genetic individuality: chance in the single cell. Nature 1976, 262: 467-471.
44. Smith ZD, Nachman I, Regev A, Meissner A. Dynamic single-cell imaging of direct reprogramming reveals an early specifying event. Nat Biotechnol 2010, 28: 521-526.
45. Marquer C, Lévêque-Fort S, Potier MC. Determination of lipid raft partitioning of fluorescently-tagged probes in living cells by fluorescence correlation spectroscopy (FCS). J Vis Exp 2012, 62:3513.
46. Ji Z, Zhang L. Chromosomics: detection of numerical and structural alterations in all 24 human chromosomes simultaneously using a novel OctoChrome FISH assay. J Vis Exp 2012, 60:3619.
47. Renda A, Nashmi R. Spectral confocal imaging of fluorescently tagged nicotinic receptors in knock-in mice with chronic nicotine administration. J Vis Exp 2012, 60:3516.
48. Hukasova E, Silva Cascales H, Kumar SR, Lindqvist A. Monitoring kinase and phosphatase activities through the cell cycle by ratiometric FRET. J Vis Exp 2012, 59:3410.
49. Suhling K, Levitt JA, Chung PH, Kuimova MK, Yahioglu G. Fluorescence lifetime imaging of molecular rotors in living cells. J Vis Exp 2012, 60:2925.
50. Nissim-Rafinia M, Meshorer E. Photobleaching assays (FRAP & FLIP) to measure chromatin protein dynamics in living embryonic stem cells. J Vis Exp 2011, 52:2696.
51. Huang Y, Agrawal B, Clark PA, Williams JC, Kuo JS. Evaluation of cancer stem cell migration using compartmentalizing microfluidic devices and live cell imaging. J Vis Exp 2011, 58:3297.
52. Elowitz MB, Levine AJ, Siggia ED, Swain PS. Stochastic gene expression in a single cell. Science 2002, 297:1183-1186.
53. Ozbudak EM, Thattai M, Kurtser I, Grossman AD, van Oudenaarden A. Regulation of noise in the expression of a single gene. Nat Genet 2002, 31:69-73.
54. Raser JM, O'Shea EK. Control of stochasticity in eukaryotic gene expression. Science 2004, 304:1811-1814.
55. Bar-Even A, Paulsson J, Maheshri N, Carmi M, O'Shea E, Pilpel Y, Barkai N. Noise in protein expression scales with natural protein abundance. Nat Genet 2006, 38:636-643.
56. Chang HH, Hemberg M, Barahona M, Ingber DE, Huang S. Transcriptome-wide noise controls lineage choice in mammalian progenitor cells. Nature 2008, 453:544-547.
57. Verstrepen L, Bekaert T, Chau TL, Tavernier J, Chariot A, Beyaert R. TLR-4, IL-1R and TNF-R signaling to NF-kappaB: variations on a common theme. Cell Mol Life Sci 2008, 65:2964-2978.
58. van den Berg B, Ellis RJ, Dobson CM. Effects of macromolecular crowding on protein folding and aggregation. EMBO J 1999, 18:6927-6933.
59. Zhou HX, Rivas G, Minton AP. Macromolecular crowding and confinement: biochemical, biophysical, and potential physiological consequences. Annu Rev Biophys 2008, 37:375-397.
60. Hall D, Hoshino M. Effects of macromolecular crowding on intracellular diffusion from a single particle perspective. Biophys Rev 2010, 2:39-53.
61. Ando T, Skolnick J. Crowding and hydrodynamic interactions likely dominate in vivo macromolecular motion. Proc Natl Acad Sci U S A 2010, 107:18457-18462.
62. Dehmelt L, Bastiaens PIH. Spatial organization of intracellular communication: insights from imaging. Nat Rev Mol Cell Biol 2010, 11:440-452.
63. Kuzmenko A, Tankov S, English BP, Tarassov I, Tenson T, Kamenski P, Elf J, Hauryliuk V. Single molecule tracking fluorescence microscopy in mitochondria reveals highly dynamic but confined movement of Tom40. Sci Rep 2011, 1:195.
64. Lukas C, Falck J, Bartkova J, Bartek J, Lukas J. Distinct spatiotemporal dynamics of mammalian checkpoint regulators induced by DNA damage. Nat Cell Biol 2003, 5:255-260.
65. Feinberg AP, Irizarry RA. Evolution in health and medicine Sackler colloquium: stochastic epigenetic variation as a driving force of development, evolutionary adaptation, and disease. Proc Natl Acad Sci U S A 2010, 107:1757-1764.
66. Swain PS, Elowitz MB, Siggia ED. Intrinsic and extrinsic contributions to stochasticity in gene expression. Proc Natl Acad Sci U S A 2002, 99:12795-12800.
67. Ozbudak EM, Thattai M, Kurtser I, Grossman AD, van Oudenaarden A. Regulation of noise in the expression of a single gene. Nat Genet 2002, 31:69-73.
68. Blake WJ, KAErn M, Cantor CR, Collins JJ. Noise in eukaryotic gene expression. Nature 2003, 422:633-637.
69. Dubnau D. Genetic competence in Bacillus subtilis. Microbiol Rev 1991, 55:395-424.
70. Hamoen LW, Venema G, Kuipers OP. Controlling competence in Bacillus subtilis: shared use of regulators. Microbiology 2003, 149:9-17.
71. Maamar H, Raj A, Dubnau D. Noise in gene expression determines cell fate in Bacillus subtilis. Science 2007, 317:526-529.
72. Mettetal JT, van Oudenaarden A. Necessary noise. Science 2007, 317:463-464.
73. To TL, Maheshri N. Noise can induce bimodality in positive transcriptional feedback loops without bistability. Science 2010, 327:1142-1145.
74. Raj A, Rifkin SA, Andersen E, van Oudenaarden A. Variability in gene expression underlies incomplete penetrance. Nature 2010, 463:913-918.
75. Burga A, Casanueva MO, Lehner B. Predicting mutation outcome from early stochastic variation in genetic interaction partners. Nature 2011, 480:250-253.
76. Avery SV. Cell individuality: the bistability of competence development. Trends Microbiol 2005, 13:459-462.
77. Perkins TJ, Swain PS. Strategies for cellular decision-making. Mol Syst Biol 2009, 5:326.
78. Xavier JB. Social interaction in synthetic and natural microbial communities. Mol Syst Biol 2011, 7:483.
79. Jullien J, Pasque V, Halley-Stott RP, Miyamoto K, Gurdon JB. Mechanisms of nuclear reprogramming by eggs and oocytes: a deterministic process? Nat Rev Mol Cell Biol 2011, 12:453-459.
80. Gupta PB, Fillmore CM, Jiang G, Shapira SD, Tao K, Kuperwasser C, Lander ES. Stochastic state transitions give rise to phenotypic equilibrium in populations of cancer cells. Cell 2011, 146:633-644.
81. Huang S, Eichler G, Bar-Yam Y, Ingber DE. Cell fates as high-dimensional attractor states of a complex gene regulatory network. Phys Rev Lett 2005, 94:128701.
82. Guo Y, Eichler GS, Feng Y, Ingber DE, Huang S. Towards a holistic, yet gene-centered analysis of gene expression profiles: a case study of human lung cancers. J Biomed Biotechnol 2006, 2006:69141.
83. Huang S, Ernberg I, Kauffman S. Cancer attractors: a systems view of tumors from a gene network dynamics and developmental perspective. Semin Cell Dev Biol 2009, 20:869-876.
84. Tsuchiya M, Piras V, Choi S, Akira S, Tomita M, Giuliani A, Selvarajoo K. Emergent genome-wide control in wild-type and genetically mutated lipopolysaccarides-stimulated macrophages. PLoS One 2009, 4:e4905.
85. Tsuchiya M, Selvarajoo K, Piras V, Tomita M, Giuliani A. Local and global responses in complex gene regulation networks. Physica A 2009, 388:1738-1746.
86. Nilsson R, Bajic VB, Suzuki H, di Bernardo D, Björkegren J, Katayama S, Reid JF, Sweet MJ, Gariboldi M, Carninci P, et al. Transcriptional network dynamics in macrophage activation. Genomics 2006, 88:133-142.
87. Rajapakse I, Perlman MD, Scalzo D, Kooperberg C, Groudine M, Kosak ST. The emergence of lineage-specific chromosomal topologies from coordinate gene regulation. Proc Natl Acad Sci U S A 2009, 106: 6679-6684.
88. Poincaré H. Les méthodes nouvelles de la méchanique céleste. vol III. Paris: Gauthiers, 1899.
89. Lorenz E. The Essence of Chaos. The Jessie and John Danz Lecture Series. Seattle, WA: University of Washington Press, 1995.
90. Lorenz E. Deterministic nonperiodic flow. J Atmos Sci 1963, 20:130-148.
91. Liebovitch LS, Scheurle D. Two lessons from fractals and chaos. Complexity 2000, 5:34-43.
92. Gleick J. Chaos: Making a New Science. London: Penguin (Non-Classics), 1987.
93. Chaudry A. Stem cell bioengineering, 2004
94. Nicolis C, Nicolis G. Stochastic aspects of climatic transitions-additive fluctuations. Tellus B 1981, 33:225-237.
95. Benzi R, Parisi G, Sutera A, Vulpiani A. Stochastic resonance in climatic change. Tellus B 1982, 34:10-16.
96. Benzi R. Stochastic resonance in complex systems. J Stat Mech 2009, 1:1052.
97. Gammaitoni L, Hänggi P, Jung P, Marchesoni F. Stochastic resonance. Rev Mod Phys 1998, 70: 1223-1287.
98. Longtin A. Stochastic resonance in neuron models. J Stat Phys 1993, 70:309-327.
99. Hodgkin A, Huxley A. A quantitative description of membrane current and its application to conduction and excitation in nerve. J Physiol 1952, 117:500-544.
100. Suzuki N, Furusawa C, Kaneko K. Oscillatory protein expression dynamics endows stem cells with robust differentiation potential. PLoS One 2011, 6:e27232.
101. Lander AD, Gokoffski KK, Wan FY, Nie Q, Calof AL. Cell lineage and the logic of proliferative control. PLoS Biol 2009, 7:e1000015.
102. Kirouac DC, Madlambayan GJ, Yu M, Sykes EA, Ito C, Zandstra PW. Cell-cell interaction networks regulate blood stem and progenitor cell fate. Mol Syst Biol 2009, 5:293.
103. McAdams HH, Arkin A. Stochastic mechanisms in gene expression. Proc Natl Acad Sci U S A 1997, 94:814-819.
104. Rao CV, Wolf DM, Arkin AP. Control, exploitation and tolerance of intracellular noise. Nature 2002, 420:231-237.
105. Capp JP. Stochastic gene expression, disruption of tissue averaging effects and cancer as a disease of development. Bioessays 2005, 27:1277-1285.
106. Hornung G, Barkai N. Noise propagation and signaling sensitivity in biological networks: a role for positive feedback. PLoS Comput Biol 2008, 4:e8.
107. Ribrault C, Sekimoto K, Triller A. From the stochasticity of molecular processes to the variability of synaptic transmission. Nat Rev Neurosci 2011, 12:375-387.
108. Lee HH, Molla MN, Cantor CR, Collins JJ. Bacterial charity work leads to population-wide resistance. Nature 2010, 467:82-85.
109. Danø S, Madsen MF, Sørensen PG. Quantitative characterization of cell synchronization in yeast. Proc Natl Acad Sci U S A 2007, 104:12732-12736.
110. Axmacher N, Mormann F, Fernández G, Elger CE, Fell J. Memory formation by neuronal synchronization. Brain Res Rev 2006, 52:170-182.
111. Vázquez-Laslop N, Lee H, Neyfakh AA. Increased persistence in Escherichia coli caused by controlled expression of toxins or other unrelated proteins. J Bacteriol 2006, 188:3494-3497.
112. Stroeymeyt N, Franks NR, Giurfa M. Knowledgeable individuals lead collective decisions in ants. J Exp Biol 2011, 214:3046-3054.