Cover Page
The handle http://hdl.handle.net/1887/57789 holds various files of this Leiden University dissertation
Author: Pomp, Wim
Title: Physics implications of shape on biological function
Date: 2017-12-05
Physics Implications of Shape on Biological Function
PROEFSCHRIFT
ter verkrijging van
de graad van Doctor aan de Universiteit Leiden, op gezag van Rector Magnificus prof. mr. C. J. J. M. Stolker,
volgens besluit van het College voor Promoties te verdedigen op dinsdag 5 december 2017
klokke 12:30 uur
door
Wim Pomp
geboren te Rotterdam in 1988
Promotor: Prof. dr. T. Schmidt Co-promotor: Dr. L. Giomi
Promotiecommissie: Prof. dr. G. J. Schütz (TU Wien, Wenen, Oostenrijk) Prof. dr. C. Storm (TU Eindhoven)
Prof. dr. A. M. Dogterom Prof. dr. E. R. Eliel Prof. dr. H. Schiessel
The cover shows an artist’s impression of the work described in this thesis.
Generously drawn in pencil by: Valeriya Pervova (Валерия Сергеевна Перво- ва).
Casimir PhD Series, Delft-Leiden, 2017-41 ISBN 978-90-8593-325-0
An electronic version of this thesis can be found at https://openaccess.leidenuniv.nl
Het onderzoek beschreven in dit proefschrift is onderdeel van het wetenschap- pelijke programma van de Stichting voor Fundamenteel Onderzoek der Materie (FOM) (tegenwoordig NWO-I), die financieel wordt gesteund door de Neder-
landse organisatie voor Wetenschappelijk Onderzoek (NWO).
“If a man never contradicts himself, the reason must be that he virtually never says anything at all.”
Erwin Schrödinger
Contents
1 Introduction 1
1.1 About shape and biology . . . 2
1.2 Biology . . . 2
1.2.1 Synapse . . . 2
1.2.2 Membrane . . . 4
1.2.3 Cytoskeleton . . . 5
1.3 Microscopy . . . 6
1.3.1 Super resolution . . . 6
1.3.2 Confocal microscopy . . . 7
1.4 Outline of this thesis . . . 8
2 Retention of neuronal receptors induced by spine-morphology 17 2.1 Introduction . . . 18
2.2 Results . . . 19
2.2.1 Mimetic system of the synaptic spine . . . 19
2.2.2 Diffusion constant . . . 22
2.2.3 Escape rate . . . 23
2.2.4 Dependence of escape rate on GUV radius . . . 24
2.2.5 Dependence of the escape rate on tube length . . . 26
2.3 Discussion & Conclusion . . . 26
2.4 Acknowledgements . . . 29
2.5 Materials and Methods . . . 29
2.5.1 GUV preparation . . . 29
2.5.2 Receptor mimicry . . . 30
2.5.3 Imaging . . . 30
2.5.4 Particle tracking . . . 30
2.5.5 Escape rate . . . 31
2.6 Supplementary information . . . 31
CONTENTS
2.6.1 Angular average of the escape rate . . . 31
2.6.2 Diffusion constants . . . 33
2.6.3 Tube Radius . . . 34
3 Control of membrane mechanics by light-induced lipid oxida- tion 39 3.1 Introduction . . . 40
3.2 Results . . . 41
3.2.1 Light-induced phase separation . . . 41
3.2.2 Lipid oxidation and phase separation depends on fluo- rophore concentration and illumination intensity . . . . 43
3.2.3 Light-induced shape fluctuations . . . 47
3.2.4 Sub-diffraction tracking of the GUV perimeter . . . 48
3.2.5 Mechanical properties of the membrane througout phase separation . . . 50
3.3 Discussion & Conclusion . . . 53
3.4 Materials and Methods . . . 57
3.4.1 GUV preparation . . . 57
3.4.2 Imaging . . . 58
3.4.3 Image Analysis . . . 58
4 Cytoskeletal anisotropy controls geometry and forces of adher- ent cells 63 4.1 Introduction . . . 64
4.2 Model . . . 64
4.3 The actin cytoskeleton is anisotropic . . . 66
4.4 Discussion & Conclusion . . . 70
4.5 Materials & Methods . . . 70
4.5.1 Cell culture and fluorescent labeling . . . 70
4.5.2 Micropillar arrays . . . 71
4.5.3 Imaging . . . 71
4.5.4 Image analysis . . . 71
4.5.5 Ellipse fitting . . . 72
4.5.6 Force analysis . . . 72
4.6 Supplementary data . . . 74
5 Reconstruction of an αvβ3 phenotype in α5β1 expressing cells on Rho-kinase down regulation 81 5.1 Introduction . . . 82
5.2 Results . . . 83
CONTENTS
5.2.1 Force Analysis . . . 83 5.2.2 Change in cell spreading on inhibition of the actin-myosin
contractility . . . 86 5.2.3 Change in cell shape on inhibition of actin-myosin con-
tractility . . . 87 5.2.4 Change in traction forces on inhibition of the actin-
myosin contractility . . . 88 5.3 Discussion & Conclusion . . . 95 5.4 Materials & Methods . . . 96
Summary 103
Samenvatting 107
Publications 111
Curriculum Vitae 113
Acknowledgements 115
