Publikationsserver der Universitätsbibliothek Marburg

Titel:Dynamics and Structure of Cellular Aggregation
Autor:Bitter, Patrick
Weitere Beteiligte: Lenz, Peter (Prof. Dr.)
Veröffentlicht:2015
URI:https://archiv.ub.uni-marburg.de/diss/z2015/0211
URN: urn:nbn:de:hebis:04-z2015-02111
DOI: https://doi.org/10.17192/z2015.0211
DDC: Physik
Titel (trans.):Dynamik und Struktur zellulärer Aggregation
Publikationsdatum:2015-09-17
Lizenz:https://rightsstatements.org/vocab/InC-NC/1.0/

Dokument

Schlagwörter:
Quantitative Biology, Quantitative Biologie, Flokkulation, Mathematische Modellierung, Flocculation, Mathematical Modelling

Summary:
This work provides new insights into the dynamics and structure of cellular aggregation. Starting from cell motility which is necessary to get the cells into close proximity it presents new tools for visualization, analysis and modeling of aggregation processes. While a lot of work has been done in the field of microbial and amoeboid motility, there is a lack in theoretical understanding of mammalian cell motion, especially concerning directed migration stirred by external cues. To close this gap I developed a two-dimensional generic model based on mechanical cell-substrate interactions. This model facilitates the discrete nature of the motion cycle of mammalian cells by a randomized growth of protrusions and their retraction depending on the strength of an external cue. This model is capable of reproducing most experimental observations, especially the behavior at sharp changes in strength of the external cues, and provides an explanation for the attachment of the lagging cell pole as it increases the efficiency of gradient sensing. Furthermore, I introduce new experimental methods to visualize and analytical toolkits to analyze the structure of the highly irregular cell aggregates. These approaches were tested in two example cases: the two dimensional aggregation of mouse embryonic fibroblast (MEF)cells and the flocculation of S. cerevisiae mediated by the sugar-dependent adhesion protein Flo5. While it was possible to achieve temporal information of the MEF cell aggregation, the flocculation of S. cerevisiae is not accessible in this way. The time-lapse microscopy series indicate a subdivision of MEF cell aggregation into a spreading and a contraction phase. In addition, the data shows that there is a dependency of the aggregate’s structure on its size with a sharp transition from a linear dependency to a constant structure. The three-dimensional imaging of immobilized flocs using a confocal laser scanning microscope provided information about the structural properties of yeast flocs. The most important findings are that the flocs are self similar fractal structures and that cheater cells, i.e. cells that do not produce the necessary binding proteins but benefit from the altruistic behavior of producing cells, are largely underprivileged in the process. This indicates that, even though flo5 does not qualify as a “green beard gene” by definition, the benefits of the resulting altruistic behavior are strongly shifted in favor of the producing cells by the aggregation mechanism.

Bibliographie / References

  1. Sarah L. Veatch, Benjamin B. Machta, Sarah A. Shelby, Ethan N. Chiang, David A. Holowka and Barbara A. Baird. 'Correlation Functions Quantify Super-Resolution Images and Esti- mate Apparent Clustering Due to Over-Counting'. PLoS ONE, 7(2):e31457 (2012). 49
  2. George J Todaro and Howard Green. 'Quantitative studies of the growth of mouse embryo cells in culture and their development into established lines'. J. Cell Biol., 17(2):299–313 (1963). 9, 43
  3. David Sloan Wilson and Edward O Wilson. 'Rethinking the theoretical foundation of sociobi- ology'. The Quarterly review of biology, 82(4):327–348 (2007). 1 BIBLIOGRAPHY Fred Winston, Catherine Dollard and Stephanie L Ricupero-Hovasse. Yeast, 11(1):53–55 (1995). 91, 92
  4. M J Tindall, P K Maini, S L Porter and J P Armitage. 'Overview of mathematical approaches used to model bacterial chemotaxis II: bacterial populations.' Bulletin of mathematical biology, 70(6):1570–607 (2008a). 4, 14, 18
  5. DS Gray, Joe Tien and CS Chen. 'Repositioning of cells by mechanotaxis on surfaces with micropatterned Young's modulus'. J. Biomed. Mater. Res., 66:605–614 (2003). 4, 5, 6, 14, 24
  6. Kinneret Keren and Julie A. Theriot. 'Biophysical Aspects of Actin-Based Cell Motility in Fish Epithelial Keratocytes'. In Peter Lenz, editor, 'Cell Motility', (2008). 5, 6, 24
  7. Herbert Levine and Wouter-Jan Rappel. 'Directed Motility and Dictyostelium Aggregation'.
  8. Anita Häcker. 'A mathematical model for mesenchymal and chemosensitive cell dynamics'.
  9. William D Hamilton. 'The genetical evolution of social behaviour. I'. Journal of theoretical biology, 7(1):1–16 (1964a). 3
  10. John C Zak, Michael R Willig, Daryl L Moorhead and Howard G Wildman. 'Functional di- versity of microbial communities: a quantitative approach'. Soil Biology and Biochemistry, 26(9):1101–1108 (1994). 3
  11. J Victor Small and Guenter P Resch. 'The comings and goings of actin: coupling protrusion and retraction in cell motility'. Current opinion in cell biology, 17(5):517–523 (2005). 5, 20
  12. Tomas Linder and Claes M Gustafsson. 'Molecular phylogenetics of ascomycotal adhesins— a novel family of putative cell-surface adhesive proteins in fission yeasts'. Fungal genetics and biology, 45(4):485–497 (2008). 12, 44 BIBLIOGRAPHY E. M. Purcell. 'Life at low Reynolds number'. American Journal of Physics, 45(1):3–11 (1977). 4, 5, 13, 16, 18
  13. A. Gerisch and M. a. J. Chaplain. 'Mathematical modelling of cancer cell invasion of tissue: local and non-local models and the effect of adhesion.' Journal of theoretical biology, 250(4):684–704 (2008). 5, 7, 14, 25
  14. A. R. Leach. Molecular Modelling: Principles and Applications. Pearson Education, second edition Auflage (2001). ISBN 0-582-38210-6. 55
  15. Anandwardhan A Hardikar, Bernice Marcus-Samuels, Elizabeth Geras-Raaka, Bruce M Raaka and Marvin C Gershengorn. 'Human pancreatic precursor cells secrete FGF2 to BIBLIOGRAPHY stimulate clustering into hormone-expressing islet-like cell aggregates'. Proceedings of the National Academy of Sciences, 100(12):7117–7122 (2003). 2, 9, 43, 73
  16. Bryan C Thorne, Alexander M Bailey and Shayn M Peirce. 'Combining experiments with multi-cell agent-based modeling to study biological tissue patterning'. Briefings in bioin- formatics, 8(4):245–257 (2007). 54
  17. TA Witten Jr. and Leonard M Sander. 'Diffusion-limited aggregation, a kinetic critical phe- nomenon'. Physical review letters, 47(19):1400 (1981). 9, 42, 79, 80, 87, 120
  18. AJ Koch and Hans Meinhardt. 'Biological pattern formation: from basic mechanisms to com- plex structures'. Reviews of modern physics, 66(4):1481 (1994). 9, 42
  19. Matthias Leinweber, Patrick Bitter, Stefan Brueckner, Hans-Ulrich Moesch, Peter Lenz and Bernd Freisleben. 'GPU-Based Simulation of Yeast Cell Flocculation'. In 'Parallel, Dis- tributed and Network-Based Processing (PDP), 2014 22nd Euromicro International Confer- ence on', Seiten 601–608. IEEE (2014). 2, 55, 69
  20. Jean-Luc Legras, Didier Merdinoglu, Jean Cornuet and Francis Karst. 'Bread, beer and wine: Saccharomyces cerevisiae diversity reflects human history'. Molecular ecology, 16(10):2091–2102 (2007). 11
  21. Kevin J Verstrepen and Frans M Klis. 'Flocculation, adhesion and biofilm formation in yeasts'. Molecular microbiology, 60(1):5–15 (2006). 12, 44
  22. David C Queller, Eleonora Ponte, Salvatore Bozzaro and Joan E Strassmann. 'Single- gene greenbeard effects in the social amoeba Dictyostelium discoideum'. Science, 299(5603):105–106 (2003). 3
  23. Shigeru Kondo and Takashi Miura. 'Reaction-diffusion model as a framework for understand- ing biological pattern formation'. Science, 329(5999):1616–1620 (2010). 8, 41
  24. B Rubinstein, K Jacobson and A Mogilner. 'Multiscale two-dimensional modeling of a motile simple-shaped cell'. Multiscale Modeling & Simulation, 3(2):413–439 (2005). 7, 25
  25. Ciyou Zhu, Richard H Byrd, Peihuang Lu and Jorge Nocedal. 'Algorithm 778: L-BFGS-B: Fortran subroutines for large-scale bound-constrained optimization'. ACM Transactions on Mathematical Software (TOMS), 23(4):550–560 (1997). 81
  26. V Govindasamy, VS Ronald, AN Abdullah, KR Ganesan Nathan, ZAC Ab Aziz, M Abdullah, S Musa, NH Abu Kasim and RR Bhonde. 'Differentiation of dental pulp stem cells into islet-like aggregates'. Journal of dental research, 90(5):646–652 (2011). 2, 9, 43, 73
  27. Robert Tarjan. 'Depth-first search and linear graph algorithms'. SIAM journal on computing, 1(2):146–160 (1972). 52 BIBLIOGRAPHY Martin Thanbichler and Lucy Shapiro. 'MipZ, a Spatial Regulator Coordinating Chromosome Segregation with Cell Division in< i> Caulobacter'. Cell, 126(1):147–162 (2006). 8, 41
  28. Tamas Vicsek. 'Pattern formation in diffusion-limited aggregation'. Phys. Rev. Lett., 53(24):2281 (1984). 9, 42
  29. Eduardo V Soares. 'Flocculation in Saccharomyces cerevisiae: a review'. Journal of applied microbiology, 110(1):1–18 (2011). 12, 43, 114, 123
  30. Christopher P Toret, Michael V D'Ambrosio, Ronald D Vale, Michael A Simon and W James Nelson. 'A genome-wide screen identifies conserved protein hubs required for cadherin- mediated cell–cell adhesion'. The Journal of cell biology, 204(2):265–279 (2014). 10, 43
  31. Daniel Zicha, Graham A. Dunn and Alastair F. Brown. 'A new direct-viewing chemotaxis chamber.' Journal of cell science, 99:769–75 (1991). 40, 118
  32. Todd B Reynolds and Gerald R Fink. 'Bakers' yeast, a model for fungal biofilm formation'. Science, 291(5505):878–881 (2001). 11
  33. Tony Yeung, Penelope C Georges, Lisa a Flanagan, Beatrice Marg, Miguelina Ortiz, Makoto Funaki, Nastaran Zahir, Wenyu Ming, Valerie Weaver and Paul a Janmey. 'Effects of sub- strate stiffness on cell morphology, cytoskeletal structure, and adhesion.' Cell motility and the cytoskeleton, 60(1):24–34 (2005). 6, 24
  34. Gespräche, Diskussionen und Hilfestellungen bei der Erstellung meiner Dissertation sehr geholfen haben: Kristof Beck, Alexander Orlov, Konstanze Bandmann Tobias Kreilos, Hannes Versicherung Die vorliegende Dissertation wurde von mir selbst und ohne fremde Hilfe verfasst. Es wurden keine anderen als die in ihr angegebenen Quellen oder Hilfsmittel benutzt. Alle vollständigen oder sinngemäß übernommenen Zitate wurden als solche gekennzeichnet und die Dissertation wurde in der vorliegenden oder einer ähnlichen Form noch bei keiner anderen in-oder aus- ländischen Hochschule anlässlich eines Promotionsgesuchs oder zu anderen Prüfungszwecken eingereicht. Marburg, 17.12.2014
  35. Richard O Hynes. 'Integrins: a family of cell surface receptors'. Cell, 48(4):549–554 (1987). 10, 43
  36. Richard O Hynes. 'Integrins: versatility, modulation, and signaling in cell adhesion'. Cell, 69(1):11–25 (1992). 10, 43
  37. M. Griebel, G. Zumbusch, S. Knapek and A. Caglar. Numerische Simulation in der Molekül- dynamik. Springer-Verlag (2004). ISBN 3-540-41856-3. 55, 56, 57
  38. LA Hohl and WV Cruess. 'Observations on certain film forming yeasts'. Zentr. Bakteriol. Parasitenk., Abt. II, 101:65–78 (1939). 11
  39. Patrick Bitter Erklärung Ich habe vor diesem Promotionsversuch keinen weiteren Versuch unternommen. Marburg, 17.12.2014
  40. Eric Jones, Travis E. Oliphant, Pearu Peterson et al. 'SciPy: Open source scientific tools for Python' (2001). 81
  41. Alan Mathison Turing. 'The chemical basis of morphogenesis'. Philosophical Transactions of the Royal Society of London. Series B, Biological Sciences, 237(641):37–72 (1952). 8, 41
  42. M. Roderfeld, S. Matern and E. Roeb. 'Konfokale Laserscanning-Mikroskopie: Der Blick in die Zelle'. Dtsch Med Wochenschr, 128:2539–2542 (2003). ISSN 0012-0472. 93
  43. Joyce Y. Wong, Alan Velasco, Padmavathy Rajagopalan and Quynh Pham. 'Directed Move- ment of Vascular Smooth Muscle Cells on Gradient-Compliant Hydrogels †'. Langmuir, 19(5):1908–1913 (2003). 5, 14
  44. Joan E Strassmann, Yong Zhu and David C Queller. 'Altruism and social cheating in the social amoeba Dictyostelium discoideum'. Nature, 408(6815):965–967 (2000). 3
  45. Severino Zara, Alan T Bakalinsky, Giacomo Zara, Giorgia Pirino, Maria Antonietta Demontis and Marilena Budroni. 'FLO11-based model for air-liquid interfacial biofilm formation by Saccharomyces cerevisiae'. Applied and Environmental microbiology, 71(6):2934–2939 (2005). 11
  46. Robert S Sikorski and Philip Hieter. 'A system of shuttle vectors and yeast host strains designed for efficient manipulation of DNA in Saccharomyces cerevisiae.' Genetics, 122(1):19–27 (1989). 92
  47. Drazen Raucher and Michael P. Sheetz. 'Characteristics of a Membrane Reservoir Buffering Membrane Tension'. Biophysical journal, 77:1992–2002 (1999). 33
  48. Muhammad H Zaman, Roger D Kamm, Paul Matsudaira and Douglas a Lauffenburger. 'Com- putational model for cell migration in three-dimensional matrices.' Biophysical journal, 89(2):1389–97 (2005). 6, 7, 24, 25
  49. Tatyana M. Svitkina, Elena A. Bulanova, Oleg Y. Chaga, Danijela M. Vignjevic, Shin-ichiro Kojima, Jury M. Vasiliev and Gary G. Borisy. 'Mechanism of filopodia initiation by reor- ganization of a dendritic network'. The Journal of cell biology, 160(3):409–421 (2003).
  50. Yuhai Tu, Thomas S Shimizu and Howard C. Berg. 'Modeling the chemotactic response of Escherichia coli to time-varying stimuli'. Proceedings of the National Academy of Sciences of the United States of America, 105(39):14855–14860 (2008). 18
  51. Scott Smukalla, Marina Caldara, Nathalie Pochet, Anne Beauvais, Stephanie Guadagnini, Chen Yan, Marcelo D Vinces, An Jansen, Marie Christine Prevost, Jean-Paul Latgé et al. 'FLO1 Is a Variable Green Beard Gene that Drives Biofilm-like Cooperation in Budding Yeast'. Cell, 135(4):726–737 (2008). 90, 104, 105, 114, 123
  52. Alexander E Smith, Zhibing Zhang, Colin R Thomas, Kennith E Moxham and Anton PJ Mid- delberg. 'The mechanical properties of Saccharomyces cerevisiae'. Proceedings of the National Academy of Sciences, 97(18):9871–9874 (2000). 66
  53. Eric Theveneau, Lorena Marchant, Sei Kuriyama, Mazhar Gull, Barbara Moepps, Maddy Parsons and Roberto Mayor. 'Collective Chemotaxis Requires Contact-Dependent Cell Polarity'. Developmental Cell, 19:39–53 (2010). 6, 24, 26, 118
  54. Maik Veelders, Stefan Brückner, Dimitri Ott, Carlo Unverzagt, Hans-Ulrich Mösch and Lars- Oliver Essen. 'Structural basis of flocculin-mediated social behavior in yeast'. Proceedings of the National Academy of Sciences, 107(52):22511–22516 (2010). 12
  55. Inbal Hecht, Monica L Skoge, Pascale G Charest, Eshel Ben-Jacob, Richard a Firtel, William F Loomis, Herbert Levine and Wouter-Jan Rappel. 'Activated membrane patches guide chemotactic cell motility.' PLoS computational biology, 7(6):e1002044 (2011). 22, 23, 39
  56. Anna Huttenlocher and Alan Rick Horwitz. 'Integrins in cell migration.' Cold Spring Harbor perspectives in biology, 3(9):a005074 (2011). 5, 6, 14, 24
  57. Ida Rishal, Naaman Kam, Rotem Ben-Tov Perry, Vera Shinder, Elizabeth Fisher, Giampietro Schiavo and Mike Fainzilber. 'A motor-driven mechanism for cell-length sensing'. Cell reports, 1(6):608–616 (2012). 60
  58. William R. Holmes and Leah Edelstein-Keshet. 'A comparison of Computational Models for Eukaryotic Cell Shape And Motility'. PLoS computational biology, 8(12) (2012). 6, 25
  59. Herbert Levine and Wouter-Jan Rappel. 'The physics of eukaryotic chemotaxis.' Physics today, 66(2) (2013). 20, 22, 23, 125
  60. Joseph Schlessinger, Yoram Shechter, Mark C Willingham and Ira Pastan. 'Direct visualiza- tion of binding, aggregation, and internalization of insulin and epidermal growth factor on living fibroblastic cells'. Proceedings of the National Academy of Sciences, 75(6):2659– 2663 (1978). 9, 43
  61. Léa Trichet, Jimmy Le Digabel, Rhoda J Hawkins, Sri Ram Krishna Vedula, Mukund Gupta, Claire Ribrault, Pascal Hersen, Raphaël Voituriez and Benoît Ladoux. 'Evidence of a large- Bibliography scale mechanosensing mechanism for cellular adaptation to substrate stiffness.' Proceed- ings of the National Academy of Sciences of the United States of America, 109(18):6933–8 (2012). 6, 25
  62. Lewis Wolpert. 'Positional information and the spatial pattern of cellular differentiation'. Journal of theoretical biology, 25(1):1–47 (1969). 8, 41, 73
  63. D a Lauffenburger and a F Horwitz. 'Cell migration: a physically integrated molecular pro- cess.' Cell, 84(3):359–69 (1996). 6, 7, 24, 25, 35
  64. Anne J Ridley, Martin a Schwartz, Keith Burridge, Richard a Firtel, Mark H Ginsberg, Gary Borisy, J Thomas Parsons and Alan Rick Horwitz. 'Cell migration: integrating signals from front to back.' Science (New York, N.Y.), 302(5651):1704–9 (2003). 6, 24, 35
  65. Kevin J Verstrepen, Todd B Reynolds and Gerald R Fink. 'Origins of variation in the fungal cell surface'. Nature Reviews Microbiology, 2(7):533–540 (2004). 12, 44


* Das Dokument ist im Internet frei zugänglich - Hinweise zu den Nutzungsrechten