Model-based extension of high-throughput to high-content data

BMC Systems Biology

Volumn 4, Issue , 2010, Pages

  Pfeifer, Andrea C ^a,b   Kaschek, Daniel ^c   Bachmann, Julie ^a   Klingmüller, Ursula ^a,b   Timmer, Jens ^c  

^a GERMAN CANCER RESEARCH CENTER   (Germany)

^b UNIVERSITY OF HEIDELBERG   (Germany)

^c UNIVERSITY OF FREIBURG   (Germany)

Author keywords

[No Author keywords available]

Indexed keywords

EUKARYOTA;

STAT5 PROTEIN;

ACTIVE TRANSPORT; ANIMAL; ARTICLE; BIOLOGICAL MODEL; CALIBRATION; CELL NUCLEUS; CELL SIZE; CELL STRAIN 3T3; FLOW CYTOMETRY; FLUORESCENCE RECOVERY AFTER PHOTOBLEACHING; METABOLISM; METHODOLOGY; MICROSCOPY; MOUSE; SINGLE CELL ANALYSIS; SYSTEMS BIOLOGY; TIME;

ACTIVE TRANSPORT, CELL NUCLEUS; ANIMALS; CALIBRATION; CELL NUCLEUS; CELL SIZE; FLOW CYTOMETRY; FLUORESCENCE RECOVERY AFTER PHOTOBLEACHING; MICE; MICROSCOPY; MODELS, BIOLOGICAL; NIH 3T3 CELLS; SINGLE-CELL ANALYSIS; STAT5 TRANSCRIPTION FACTOR; SYSTEMS BIOLOGY; TIME FACTORS;

EID: 77955187803     PISSN: None     EISSN: 17520509     Source Type: Journal    
DOI: 10.1186/1752-0509-4-106     Document Type: Article

References (31)

1. Sigal A, Milo R, Cohen A, Geva-Zatorsky N, Klein Y, Liron Y, Rosenfeld N, Danon T, Perzov N, Alon U. Variability and memory of protein levels in human cells. Nature 2006, 444(7119):643-646. 10.1038/nature05316, 17122776.
2. Spencer SL, Gaudet S, Albeck JG, Burke JM, Sorger PK. Non-genetic origins of cell-to-cell variability in TRAIL-induced apoptosis. Nature 2009, 459(7245):428-432. 10.1038/nature08012, 2858974, 19363473.
3. Halter M, Elliott JT, Hubbard JB, Tona A, Plant AL. Cell volume distributions reveal cell growth rates and division times. J Theor Biol 2009, 257:124-130. 10.1016/j.jtbi.2008.10.031, 19068221.
4. Diercks A, Kostner H, Ozinsky A. Resolving cell population heterogeneity: real-time PCR for simultaneous multiplexed gene detection in multiple single-cell samples. PLoS One 2009, 4(7):e6326. 10.1371/journal.pone.0006326, 2711328, 19633712.
5. Masujima T. Live single-cell mass spectrometry. Anal Sci 2009, 25(8):953-960. 10.2116/analsci.25.953, 19667470.
6. Lapainis T, Rubakhin SS, Sweedler JV. Capillary electrophoresis with electrospray ionization mass spectrometric detection for single-cell metabolomics. Anal Chem 2009, 81(14):5858-5864. 10.1021/ac900936g, 2810313, 19518091.
7. Pepperkok R, Ellenberg J. High-throughput fluorescence microscopy for systems biology. Nat Rev Mol Cell Biol 2006, 7(9):690-696. 10.1038/nrm1979, 16850035.
8. George T, Morrissey P, Cui C, Singh S, Fitzgerald-Bocarsly P. Measurement of cytoplasmic to nuclear translocation. Curr Protoc Cytom 2009,
9. Pfeifer AC, Timmer J, Klingmüller U. Systems biology of JAK/STAT signalling. Essays Biochem 2008, 45:109-120. 10.1042/BSE0450109, 18793127.
10. Meyer T, Begitt A, Lödige I, van Rossum M, Vinkemeier U. Constitutive and IFN-gamma-induced nuclear import of STAT1 proceed through independent pathways. EMBO J 2002, 21(3):344-354. 10.1093/emboj/21.3.344, 125830, 11823427.
11. Bhattacharya S, Schindler C. Regulation of Stat3 nuclear export. J Clin Invest 2003, 111(4):553-559. 151917, 12588893.
12. Pranada AL, Metz S, Herrmann A, Heinrich PC, Müller-Newen G. Real time analysis of STAT3 nucleocytoplasmic shuttling. J Biol Chem 2004, 279(15):15114-15123. 10.1074/jbc.M312530200, 14701810.
13. Liu L, McBride KM, Reich NC. STAT3 nuclear import is independent of tyrosine phosphorylation and mediated by importin-alpha3. Proc Natl Acad Sci USA 2005, 102(23):8150-8155. 10.1073/pnas.0501643102, 1149424, 15919823.
14. Zeng R, Aoki Y, Yoshida M, ichi Arai K, Watanabe S. Stat5B shuttles between cytoplasm and nucleus in a cytokine-dependent and -independent manner. J Immunol 2002, 168(9):4567-4575.
15. Iyer J, Reich NC. Constitutive nuclear import of latent and activated STAT5a by its coiled coil domain. FASEB J 2008, 22(2):391-400. 10.1096/fj.07-8965com, 17846080.
16. Marg A, Shan Y, Meyer T, Meissner T, Brandenburg M, Vinkemeier U. Nucleocytoplasmic shuttling by nucleoporins Nup153 and Nup214 and CRM1-dependent nuclear export control the subcellular distribution of latent Stat1. J Cell Biol 2004, 165(6):823-833. 10.1083/jcb.200403057, 2172394, 15210729.
17. Meyer T, Marg A, Lemke P, Wiesner B, Vinkemeier U. DNA binding controls inactivation and nuclear accumulation of the transcription factor Stat1. Genes Dev 2003, 17(16):1992-2005. 10.1101/gad.268003, 196254, 12923054.
18. Swameye I, Müller TG, Timmer J, Sandra O, Klingmüller U. Identification of nucleocytoplasmic cycling as a remote sensor in cellular signaling by databased modeling. Proc Natl Acad Sci USA 2003, 100(3):1028-1033. 10.1073/pnas.0237333100, 298720, 12552139.
19. Axelrod D, Koppel DE, Schlessinger J, Elson E, Webb WW. Mobility measurement by analysis of fluorescence photobleaching recovery kinetics. Bio-phys J 1976, 16(9):1055-69.
20. Sprague BL, McNally JG. FRAP analysis of binding: proper and fitting. Trends Cell Biol 2005, 15(2):84-91. 10.1016/j.tcb.2004.12.001, 15695095.
21. Das B, Resnick SI. QQ - Plots, Random Sets and Data from a Heavy Tailed Distribution. Stochastic Models 2008, 24:103.
22. Reich NC, Liu L. Tracking STAT nuclear traffic. Nat Rev Immunol 2006, 6(8):602-612. 10.1038/nri1885, 16868551.
23. Ma J, Cao X. Regulation of Stat3 nuclear import by importin alpha5 and importin alpha7 via two different functional sequence elements. Cell Signal 2006, 18(8):1117-1126. 10.1016/j.cellsig.2005.06.016, 16298512.
24. Kawashima T, Bao YC, Minoshima Y, Nomura Y, Hatori T, Hori T, Fukagawa T, Fukada T, Takahashi N, Nosaka T, Inoue M, Sato T, Kukimoto-Niino M, Shirouzu M, Yokoyama S, Kitamura T. A Rac GTPase-activating protein, MgcRacGAP, is a nuclear localizing signal-containing nuclear chaperone in the activation of STAT transcription factors. Mol Cell Biol 2009, 29(7):1796-1813. 10.1128/MCB.01423-08, 2655612, 19158271.
25. Timney BL, Tetenbaum-Novatt J, Agate DS, Williams R, Zhang W, Chait BT, Rout MP. Simple kinetic relationships and nonspecific competition govern nuclear import rates in vivo. J Cell Biol 2006, 175(4):579-593. 10.1083/jcb.200608141, 2064595, 17116750.
26. Kopito RB, Elbaum M. Reversibility in nucleocytoplasmic transport. Proceedings of the National Academy of Sciences 2007, 104(31):12743-12748.
27. Hawley TS, Hawley RG. Flow Cytometry Protocols (Methods in Moldecular Biology). 2004, Humana Press.
28. Köster M, Frahm T, Hauser H. Nucleocytoplasmic shuttling revealed by FRAP and FLIP technologies. Curr Opin Biotechnol 2005, 16:28-34. 10.1016/j.copbio.2004.11.002, 15722012.
29. Ketteler R, Glaser S, Sandra O, Martens UM, Klingmüller U. Enhanced transgene expression in primitive hematopoietic progenitor cells and embryonic stem cells efficiently transduced by optimized retroviral hybrid vectors. Gene Ther 2002, 9(8):477-487. 10.1038/sj.gt.3301653, 11948372.
30. Rasband W. ImageJ 1997 - 2009. , http://rsb.info.nih.gov/ij
31. Glynn E. FCSExtract. 2006, , http://research.stowers-institute.org/efg/ScientificSoftware/Utility/FCSExtract/index.htm