FlowMax: A Computational Tool for Maximum Likelihood Deconvolution of CFSE Time Courses

PLoS ONE

Volumn 8, Issue 6, 2013, Pages

  Shokhirev, Maxim Nikolaievich ^a,b   Hoffmann, Alexander ^a,b  

^a UNIVERSITY OF CALIFORNIA   (United States)

^b University of California San Diego   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

B LYMPHOCYTE RECEPTOR; CARBOXYFLUORESCEIN DIACETATE SUCCINIMIDYL ESTER; 5-(6)-CARBOXYFLUORESCEIN DIACETATE SUCCINIMIDYL ESTER; FLUORESCEIN DERIVATIVE; FLUORESCENT DYE; IMMUNOGLOBULIN ENHANCER BINDING PROTEIN; NFKB1 PROTEIN, MOUSE; SUCCINIMIDE DERIVATIVE; TRANSCRIPTION FACTOR REL;

ANIMAL CELL; ARTICLE; B LYMPHOCYTE; B LYMPHOCYTE ACTIVATION; CELL DIVISION; CELL SURVIVAL; COMPUTATIONAL METHODOLOGY; COMPUTER PROGRAM; CONTROLLED STUDY; DATA ANALYSIS; DILUTION; FLUORESCENCE; IMMUNE RESPONSE; INFECTION; KNOCKOUT MOUSE; LYMPHOCYTE PROLIFERATION; LYMPHOCYTE SUBPOPULATION; MAXIMUM LIKELIHOOD METHOD; METHODOLOGY; MOUSE; NOISE; NONHUMAN; PHENOTYPE; QUANTITATIVE ANALYSIS; SAMPLING; ALGORITHM; ANIMAL; BIOLOGICAL MODEL; BIOLOGY; CELL CULTURE; CELL PROLIFERATION; CYTOLOGY; FLOW CYTOMETRY; PHYSIOLOGY; PROCEDURES; SOFTWARE; STAINING; TIME FACTOR;

MUS;

ALGORITHMS; ANIMALS; B-LYMPHOCYTES; CELL PROLIFERATION; CELLS, CULTURED; COMPUTATIONAL BIOLOGY; FLOW CYTOMETRY; FLUORESCEINS; FLUORESCENT DYES; MICE; MICE, KNOCKOUT; MODELS, BIOLOGICAL; NF-KAPPA B P50 SUBUNIT; PROTO-ONCOGENE PROTEINS C-REL; SOFTWARE; STAINING AND LABELING; SUCCINIMIDES; TIME FACTORS;

EID: 84879530893     PISSN: None     EISSN: 19326203     Source Type: Journal    
DOI: 10.1371/journal.pone.0067620     Document Type: Article

References (27)

1. Murphy K, Travers P, Walport M (2007) Janeway's Immunobiology (Immunobiology: The Immune System (Janeway)): Garland Science.
2. Hawkins ED, Turner ML, Dowling MR, van Gend C, Hodgkin PD, (2007) A model of immune regulation as a consequence of randomized lymphocyte division and death times. Proc Natl Acad Sci U S A 104: 5032-5037.
3. Hawkins ED, Markham JF, McGuinness LP, Hodgkin PD, (2009) A single-cell pedigree analysis of alternative stochastic lymphocyte fates. Proc Natl Acad Sci U S A 106: 13457-13462.
4. Subramanian VG, Duffy KR, Turner ML, Hodgkin PD, (2008) Determining the expected variability of immune responses using the cyton model. J Math Biol 56: 861-892.
5. Weston SA, Parish CR, (1990) New fluorescent dyes for lymphocyte migration studies. Analysis by flow cytometry and fluorescence microscopy. J Immunol Methods 133: 87-97.
6. Roeder M (2011) Interpretation of Cellular proliferation Data: Avoid the Panglossian. Cytometry: 95-101.
7. Zilman A, Ganusov VV, Perelson AS (2010) Stochastic models of lymphocyte proliferation and death. PLoS One 5.
8. Miao H, Jin X, Perelson A, Wu H, (2012) Evaluation of Multitype Mathematical Models for CFSE-Labeling Experiment Data. Bull Math Biol 74: 300-326.
9. Hawkins ED, Hommel M, Turner ML, Battye FL, Markham JF, et al. (2007) Measuring lymphocyte proliferation, survival and differentiation using CFSE time-series data. Nat Protoc 2: 2057-2067.
10. De Boer RJ, Ganusov VV, Milutinovic D, Hodgkin PD, Perelson AS, (2006) Estimating lymphocyte division and death rates from CFSE data. Bull Math Biol 68: 1011-1031.
11. Banerjee A, Grumont R, Gugasyan R, White C, Strasser A,et al. (2008) NF-kB1 and c-Rel cooperate to promote the survival of TLR4-activated B cells by neutralizing Bim via distinct mechanisms. Blood: 5063-5073.
12. Pohl T, Gugasyan R, Grumont RJ, Strasser A, Metcalf D,et al. (2002) The combined absence of NF-kB1 and c-Rel reveals that overlapping roles of these transcription factors in the B cell lineage are restricted to the activation and function of mature cells. PNAS: 4514-4519.
13. Hasenauer J, Schittler D, Allgöwer F, (2012) Analysis and Simulation of Division- and Label-Structured Population Models. Bull Math Biol 74: 2692-2732.
14. Hyrien O, Chen R, Zand MS, (2010) An age-dependent branching process model for the analysis of CFSE-labeling experiments. Biol Direct 5: 41.
15. Hyrien O, Zand MS, (2008) A Mixture Model With Dependent Observations for the Analysis of CSFE-Labeling Experiments. Journal of the American Statistical Association 103: 222-239.
16. Banks HT, Sutton KL, Thompson WC, Bocharov G, Doumic M, et al. (2011) A new model for the estimation of cell proliferation dynamics using CFSE data. J Immunol Methods 373: 143-160.
17. Luzyanina T, Roose D, Schenkel T, Sester M, Ehl S, et al. (2007) Numerical modelling of label-structured cell population growth using CFSE distribution data. Theor Biol Med Model 4: 26.
18. Metzger P, Hasenauer J, Allgöwer F. Modeling and analysis of division-, age-, and label structured cell populations. In: Larjo AS, S.; Farhan, M.; Bossert, M.; Yli-Harja, O., editor. TICSP; 2012; Ulm, Germany. Tampere International Center for Signal Processing. 60-63.
19. Rickert RC, Jellusova J, Miletic AV, (2011) Signaling by the tumor necrosis factor receptor superfamily in B-cell biology and disease. Immunol Rev 244: 115-133.
20. Duffy KR, Wellard CJ, Markham JF, Zhou JH, Holmberg R, et al. (2012) Activation-induced B cell fates are selected by intracellular stochastic competition. Science 335: 338-341.
21. Banerjee A, Gugasyan R, McMahon M, Gerondakis S, (2006) Diverse Toll-like receptors utilize Tpl2 to activate extracellular signal-regulated kinase (ERK) in hemopoietic cells. Proc Natl Acad Sci U S A 103: 3274-3279.
22. Babu GR, Jin W, Norman L, Waterfield M, Chang M, et al. (2006) Phosphorylation of NF-kappaB1/p105 by oncoprotein kinase Tpl2: implications for a novel mechanism of Tpl2 regulation. Biochim Biophys Acta 1763: 174-181.
23. Savinova OV, Hoffmann A, Ghosh G, (2009) The Nfkb1 and Nfkb2 Proteins p105 and p100 Function as the Core of High-Molecular-Weight Heterogeneous Complexes. Molecular Cell 34: 591-602.
24. Shih VF-S, Kearns JD, Basak S, Savinova OV, Ghosh G, et al. (2009) Kinetic control of negative feedback regulators of NF-κB/RelA determines their pathogen- and cytokine-receptor signaling specificity. Proceedings of the National Academy of Sciences 106: 9619-9624.
25. Hulspas R, O'Gorman MR, Wood BL, Gratama JW, Sutherland DR, (2009) Considerations for the control of background fluorescence in clinical flow cytometry. Cytometry B Clin Cytom 76: 355-364.
26. Callard R, Hodgkin P, (2007) Modeling T- and B-cell growth and differentiation. Immunological Reviews 216: 119-129.
27. Kirkpatrick S, Gelatt CD Jr, Vecchi MP, (1983) Optimization by simulated annealing. Science 220: 671-680.