1,721,012 research outputs found
Going Beyond Counting First Authors in Author Co-citation Analysis
Get PDFThe present study examines one of the fundamental aspects of author co-citation analysis (ACA) - the way co-citation
counts are defined. Co-citation counting provides the data on which all subsequent statistical analyses and mappings
are based, and we compare ACA results based on two different types of co-citation counting - the traditional type that
only counts the first one among a cited work's authors on the one hand and a non-traditional type that takes into
account the first 5 authors of a cited work on the other hand. Results indicate that the picture produced through this non-traditional author co-citation counting contains more coherent author groups and is therefore considerably clearer. However, this picture represents fewer specialties in the research field being studied than that produced through the traditional first-author co-citation counting when the same number of top-ranked authors is selected and analyzed. Reasons for these effects are discussed
Variations on the Author
Get PDF“Variations on the Author” discusses two of Eduardo Coutinho’s recent films (Um Dia na Vida, from 2010, and Últimas Conversas, posthumously released in 2015) and their contribution to the general question of documentary authorship. The director’s filmography is characterized by a consistent yet self-effacing form of authorial self-inscription: Coutinho often features as an interviewer that rather than express opinions propels discourses; an interviewer that is good at listening. This mode of self-inscription characterizes him as an author who is not expressive but who is nonetheless markedly present on the screen. In Um Dia na Vida, however, Coutinho is completely absent form the image, while Últimas Conversas, on the contrary, includes a confessional prologue that moves the director from the margins to the center of his films. This article examines the ways in which these works stand out in the filmography of a director who offers new insights into the notion of cinematic authorship
Appropriate Similarity Measures for Author Cocitation Analysis
Get PDFWe provide a number of new insights into the methodological discussion about author cocitation analysis. We first argue that the use of the Pearson correlation for measuring the similarity between authors’ cocitation profiles is not very satisfactory. We then discuss what kind of similarity measures may be used as an alternative to the Pearson correlation. We consider three similarity measures in particular. One is the well-known cosine. The other two similarity measures have not been used before in the bibliometric literature. Finally, we show by means of an example that our findings have a high practical relevance.information science;Pearson correlation;cosine;similarity measure;author cocitation analysis
Dynamics of active surfaces
Get PDFMechano-chemical processes in biological systems play an important role during the morphogenesis of cells and tissues. In particular, they are responsible for the dynamic organisation of active stress, which itself results from non-equilibrium processes and leads to flows and deformations of material. The generation of active stress often occurs in thin biological structures, such as the cellular cortex or epithelial tissues, which motivates the theoretical concept of an active surface. In this thesis, we study the dynamics of curved and deforming active surfaces. More specifically, we are interested in the dynamics of mechano-chemical processes on these surfaces, as well as in their interaction with the surface shape and external forces.
To study the interplay of mechano-chemical processes with shape changes of the material, we consider the fully self-organised shape dynamics using the theory of active fluids on deforming surfaces. We then develop a numerical approach to solve the corresponding force and torque balance equations. We further examine how the stability of surface shapes is affected by mechano-chemical processes. We show that the tight coupling between chemical processes and surface mechanics gives rise to the spontaneous generation of specific surface shapes, to shape oscillations and to directed surface flows that resemble peristaltic motion.
In the following part, we explore the mechano-chemical self-organisation of active fluids on fixed surfaces, focussing on mechanical interactions with surrounding material. We introduce a description in which active surface flows set a surrounding passive fluid into motion. We then study two scenarios. First, inspired by the cellular cortex and its interactions with the cytoplasm, we consider a fluid that is enclosed by the surface. We find that mechanical interactions with the surrounding passive fluid enable an isotropic active surface to spontaneously generate patterns with polar asymmetry and to form a contractile ring in a fully self-organised fashion. Second, we consider the case where the passive fluid surrounds the active surface on the outside. This description leads to the model of a microswimmer, which is characterised by an onset of motion due to spontaneous symmetry breaking on the active surface.
Most biological materials are viscoelastic, such that they show viscous and elastic responses if mechanical stress is applied on different time scales. In the final part of this thesis, we therefore consider a surface whose response to self-organised active stress is described by a Maxwell model. We identify a minimal time scale for the relaxation of elastic stress, beyond which spatio-temporal, mechano-chemical oscillations on the surface can spontaneously emerge.
In summary, we identify and characterise in this thesis various processes that result from the self-organisation of active surfaces. The underlying coupling between surface mechanics and a chemical organisation of stress in the material represents a key feature of morphogenetic processes in biology. Furthermore, we develop several numerical approaches that will enable to study alternative constitutive relations of active surfaces in the future. Overall, we contribute theoretical insights and numerical tools to further the understanding of the emerging spatial organisation and shape generation of active surfaces.Mechanochemische Prozesse spielen eine wichtige Rolle für die Morphogenese von biologischen Zellen und Geweben. Sie sind insbesondere verantwortlich für die dynamische Organisation von aktiver mechanischer Spannung, welche Nicht-Gleichgewichtsprozessen entstammt und zu Flüssen und Verformungen von Material führt. Aktive mechanische Spannung wird häufig in dünnen biologischen Strukturen erzeugt, wie zum Beispiel dem Zellkortex oder dem Epithelgewebe, was die Einführung von aktiven Flächen als theoretisches Konzept motiviert. In der vorliegenden Arbeit untersuchen wir die Dynamik von gekrümmten und sich verformenden aktiven Flächen. Dabei interessieren wir uns insbesondere für die Dynamik mechanochemischer Prozesse auf diesen Flächen, sowie für deren Wechselwirkung mit der Flächenform und externen Kräften.
Zur Untersuchung der Wechselwirkung zwischen mechanochemischen Prozessen und Flächenverformungen nutzen wir die hydrodynamische Theorie aktiver Fluide auf sich verformenden Flächen und betrachten eine vollständig selbstorganisierte Flächendynamik. Wir entwickeln eine Methode zur Bestimmung numerischer Lösungen des Kräfte- und Drehmomentgleichgewichts auf Flächen und untersuchen wie die Stabilität von Flächenformen durch mechanochemische Prozesse beeinflusst wird. Wir zeigen, dass die enge Kopplung zwischen chemischen Prozessen und der Mechanik von Flächen zur spontanen Erzeugung spezifischer Formen, zu Formoszillationen und zu gerichteten Flüssen führt, welche eine peristaltische Bewegung nachbilden.
Im Folgenden untersuchen wir die mechanochemische Selbstorganisation aktiver Fluide auf festen Flächen und betrachten mechanische Wechselwirkungen mit umgebendem Material. Dazu beschreiben wir ein umgebendes passives Fluid, welches durch aktive Flüsse auf der Fläche in Bewegung versetzt wird. Im Rahmen dieser Beschreibung untersuchen wir zwei Szenarien. Inspiriert durch die Wechselwirkung des Zellkortex mit dem Zytoplasma, betrachten wir zuerst ein Fluid, welches durch die Fläche eingeschlossen wird. Wir zeigen, dass die mechanische Wechselwirkung einer isotropen, aktiven Fläche mit dem umgebenden Fluid es ermöglicht, Muster mit einer polaren Asymmetrie, sowie einen kontraktilen Ring spontan und selbstorganisiert zu bilden. Danach betrachten wir ein passives Fluid, welches die Fläche außen umgibt. Diese Beschreibung führt zu einem Modell für einen Mikroschwimmer, welcher durch eine spontane Symmetriebrechung auf der aktiven Fläche beginnt sich durch das passive Fluid zu bewegen.
Die meisten biologischen Materialien verhalten sich viskoelastisch, sodass deren mechanische Antwort je nach Zeitskala einer applizierten mechanischen Spannung viskos und elastisch ausfallen kann. Im abschließenden Teil dieser Arbeit betrachten wir daher eine Fläche, deren mechanische Antwort auf aktive Spannung durch ein Maxwell-Modell beschrieben wird. Wir bestimmen eine minimale Zeitskala für die Relaxation von elastischer Spannung, welche das spontane Einsetzen räumlich-zeitlicher Oszillationen aktiver mechanischer Spannung kennzeichnet.
Zusammengefasst identifizieren und charakterisieren wir in dieser Arbeit eine Reihe von Prozessen, welche der Selbstorganisation aktiver Flächen entspringen. Die zugrundeliegende Kopplung zwischen der Mechanik von Flächen und einer chemischen Organisation aktiver mechanischer Spannung stellen ein Schlüsselprinzip morphogenetischer Vorgänge in der Biologie dar. Zusätzlich entwickeln wir eine Reihe numerischer Methoden, welche es in Zukunft erlauben weitere Beschreibungen aktiver Flächen zu untersuchen. Damit trägt diese Arbeit neue theoretische Einsichten und numerische Algorithmen zur Verbesserung des Verständnisses der emergenten räumlichen Organisation und Formerzeugung aktiver Flächen bei
Dispelling the Myths Behind First-author Citation Counts
Get PDFWe conducted a full-scale evaluative citation analysis study of scholars in the XML research field to explore just how different from each other author rankings resulting from different citation counting methods actually are, and to demonstrate the capability of emerging data and tools on the Web in supporting more realistic citation counting methods. Our results contest some common arguments for the continued
use of first-author citation counts in the evaluation of scholars, such as high correlations between author rankings by first-author citation counts and other citation
counting methods, and high costs of using more realistic citation counting methods that are not well-supported by the ISI databases. It is argued that increasingly available digital full text research papers make it possible for citation analysis studies to go beyond what the ISI databases have directly supported and to employ more
sophisticated methods
A Single Molecule Perspective on Protein-DNA Condensates
Get PDFBiomolecular condensates are dynamic intracellular structural units or distinct reaction spaces that can form by condensation of their constituents from the cytoplasm or the nucleoplasm. It is generally not clear yet, how dynamic, continuum-like condensate properties relevant for large-scale intracellular organisation emerge from the interplay of proteins and nucleic acids on the level of few individual molecules. With this work, we expand the portfolio of methods to investigate the role of protein-nucleic acid interactions in biomolecular condensates by introducing optical tweezers-based mechanical micromanipulation of single DNA molecules combined with confocal fluorescence microscopy to the field. We used this approach to characterise how the two landmark proteins1 Fused in Sarcoma and Heterochromatin Protein 1 form condensates with single DNA molecules. Fused in Sarcoma (FUS) is a key protein for various aspects of the nucleic acid metabolism and evidence is accumulating that biomolecular condensation is crucial for both, its physiological functions and its role in pathological aggregate formation. In this thesis, we directly visualised the formation of FUS condensates with single molecules of ssDNA and dsDNA. We showed that the formation of these microcondensates is based on nucleic acid scaffolding. We explored their mechanical properties and found that the mechanical tension that (FUS dsDNA) condensates can withstand or exert is in the range below 2 pN. We further demonstrated that already on this fundamental scale and with limited amounts of constituent molecules, dynamic properties like shape relaxations, reminiscent of viscoelastic materials, can emerge. Heterochromatin Protein 1 (HP1) is a prototypic chromatin organising factor that is in particular involved in the formation of dynamically compacted heterochromatin domains. HP1 forms biomolecular condensates and compacts DNA strands in vitro. In this work, we measured the influence of HP1 on the
mechanical properties of individual DNA molecules and demonstrated the response of HP1-DNA condensates to different environmental conditions. We contributed a methodological framework to characterise viscoelastic-like systems on the single molecule level.
Taken together, our optical tweezers-based approach revealed structural and mechanical properties of prototypic protein-DNA condensates and hence helped to elucidate mechanisms underlying their formation in unprecedented spatiotemporal and mechanical detail. We anticipate that this method can become a valuable tool to investigate how large-scale intracellular organisation based on protein-nucleic acid condensation emerges from interactions between individual building blocks
Elucidating the mechanism of AP axis alignment in the C. elegans embryo
No full textDevelopment of a single-cell embryo into an adult multi-cellular organism features the establishment of upto three anatomical body axes - anteroposterior, dorsoventral and left-right. It has been observed in many organisms that these body axes can consistently orient relative with respect to the geometric features of the embryo in many organisms. One such example is observed in the model organism Caenorhabditis elegans (C. elegans), where the Anteroposterior (AP) axis coincides with the geometric long axis of the ellipsoidal embryo -- the shape being imposed by the surrounding eggshell. In C. elegans, the Anteroposterior axis is established at the one-cell stage via its polarization by PAR polarity proteins. This cell polarization proceeds via a self-organized mechanochemical feedback between the PAR proteins and mechanical flows in the actomyosin cortex, resulting in the formation of two mutually exclusive domains of Anterior PAR and Posterior PAR proteins on the cortex denoting the future anterior and posterior end of the embryo -- and thus establishing the Anteroposterior axis. The initial orientation of the Anteroposterior axis is determined by the site of sperm entry at fertilization. However, the nascent Anteroposterior axis that forms after fertilization is observed to actively re-orient -- indicated by the movement of the PAR domains and concurrent migration (here termed posteriorisation) of the sperm-donated male pronucleus -- such that it aligns with the long axis of the ellipsoidal embryo, if it is not already aligned. In effect, the site of sperm entry only determines which half of the embryo becomes the posterior half of the embryo. This phenomenon of active re-orientation of the Anteroposterior axis, that ensures that the Anteroposterior axis aligns with the long axis of the embryo, is termed Anteroposterior axis alignment. The work described in this thesis investigates the mechanism of this Anteroposterior axis alignment in the C. elegans embryo.
Anterior-directed flows in the actomyosin cortex observed during Anteroposterior axis establishment have also been found to be essential for Anteroposterior axis alignment. In this thesis, two possible mechanisms of Anteroposterior axis alignment are considered, both of which are consequences of these cortical flows. Cortical flows at the embryo surface can drive flows in the bulk cytoplasm in the embryo, generating cytoplasmic flows which point towards the sperm-donated male pronucleus as it posteriorises. Previous studies have proposed that these cytoplasmic flows could push onto the male pronucleus, and due to the ellipsoidal geometry of the embryo, drive it towards the closest tip of the embryo. This proposed mechanism is referred to as the cytoplasmic flow-dependent mechanism in this thesis. Another mechanism proposed in this thesis postulates that the reorientation of the Anteroposterior axis occurs via the repositioning of the pseudocleavage furrow. The pseudocleavage furrow is a contractile ring-like structure that forms at the boundary of the two PAR domains during Anteroposterior axis establishment. The pseudocleavage furrow forms as a result of compressive alignment of actin filaments in the actomyosin cortex due to cortical flows. In cases where the Anteroposterior axis is not aligned with the long axis of the embryo, the pseudocleavage furrow is
not perpendicular to the long axis of the embryo. In such cases, active anisotropic stresses generated in the actomyosin cortex could force the rotation of the pseudocleavage furrow akin to an elastic rubber-band on an ellipsoid, and cause the Anteroposterior axis to re-orient towards the long axis of the embryo. This proposed mechanism is referred to as the pseudocleavage furrow-dependent mechanism in this thesis.
This thesis investigates the role played by the two mechanisms in Anteroposterior axis alignment. This is accomplished in the following way: a theoretical model of the Anteroposterior axis alignment is introduced, consisting of a description of the actomyosin cortex as an active nematic fluid present on the 2D surface of a fixed ellipsoid representing the embryo. This description of the cortex incorporates both the cytoplasmic flow-dependent mechanism and the pseudocleavage furrow-dependent mechanism. RNAi experiments in the C. elegans embryo that remove the pseudocleavage furrow, in conjuction with numerical simulations using the theoretical model, show that the pseudocleavage furrow-dependent mechanism is the predominant mechanism that drives Anteroposterior axis alignment, while cytoplasmic flow-dependent mechanism plays only a minor role. RNAi experiments that modify the geometry of the C. elegans embryo -- specifically, generate rounder embyros -- show that embryo geometry can influence the rate of re-orientation of the Anteroposterior axis during Anteroposterior axis alignment -- with slower Anteroposterior axis alignment in rounder embryos. Such an relation between embryo geometry and Anteroposterior axis alignment is found to be consistent with pseudocleavage furrow-dependent mechanism, both via predictions made using the theoretical model and using a simplified effective model of a contractile ring (or elastic rubber-band) on a fixed ellipsoid.
Altogether, the work presented in this thesis shows Anteroposterior axis alignment observed in the C. elegans embryo is driven primarily by the anisotropic stresses in the actomyosin cortex that generate the pseudocleavage furrow. The work here also shows that the Anteroposterior axis alignment process is sensitive to the geometry of the embryo. In effect, active mechanical flows in the actomyosin cortex translate the ellipsoidal geometry of the embryo into a robust orientation of the Anteroposterior axis of the C. elegans embryo. Mechanical flows such as these are not exclusive to C. elegans, nor are specific orientations of the body axes with respect to the embryo geometry. The results in this thesis thus point towards a possibly general role of the interactions between mechanical flows and embryo geometry to properly orient the body axes of the developing embryos of many multi-cellular organisms.:Contents
Abbreviations iii
Abstract iv
1 Introduction 1
1.1 Cytoskeleton 3
1.1.1 Main constituents of the cytoskeleton 3
1.1.2 Actomyosin cortex 7
1.2 Hydrodynamic theory of active fluids 8
1.2.1 Conservation Laws 9
1.2.2 Continuously broken symmetries 11
1.2.3 Irreversible thermodynamics of active fluids 13
1.2.4 Constitutive equations of active nematic fluids 19
1.3 C. elegans as a model organism 21
1.3.1 Early embryogenesis in C. elegans 22
1.4 AP axis establishment in C. elegans 24
1.4.1 PAR polarity system . 24
1.4.2 Mechanism of AP axis establishment 26
1.4.3 AP axis alignment 27
1.5 Overview 29
2 A theoretical model for AP axis alignment 30
2.1 A model of AP axis establishment in C. elegans 30
2.1.1 Turing-like system for PAR polarity system 31
2.1.2 Active isotropic description of actomyosin cortex 33
2.1.3 Guiding cues for AP axis establishment 34
2.1.4 Full model of AP axis establishment in [1] 35
2.2 A model of pseudocleavage furrow formation in C. elegans 36
2.2.1 Dynamics of Actin alignment 37
2.2.2 Active stress generated by alignment of actin filaments 38
2.3 A model of AP axis alignment in C. elegans 39
2.3.1 A thin film active nematic description of the cortex 40
2.3.2 Description of the Cytoplasm and Male pronucleus 46
2.3.3 Numerical simulations of the theoretical model 48
3 Materials and Methods 52
3.1 Culture conditions, strains and worm handling 52
3.2 Genetic perturbations by RNAi 53
3.3 Time-lapse microscopy 53
3.4 Image analysis 54
3.4.1 Pre-processing 54
3.4.2 Tracking posteriorisation of the male pronucleus 56
3.4.3 Measuring cortical flows 66
3.4.4 Measuring cytoplasmic flows 67
3.5 Data analysis 67
4 Experimental investigation of AP axis alignment 71
4.1 Characterising AP axis alignment in unperturbed embryos 71
4.2 Cortical flows are required for AP axis alignment 76
4.3 Role of Pseudocleavage furrow in AP axis alignment 83
4.3.1 Removing Pseudocleavage furrow via RNAi 83
4.3.2 Comparing numerical simulations to experimental results 88
4.4 Role of embryo geometry in AP axis alignment 99
4.4.1 Rounder embryos show slower AP axis alignment 99
4.4.2 Relation between embryo geometry and AP axis alignment 108
4.5 Additional experiments 118
4.5.1 Exploring relation between embryo geometry and AP axis alignment in ima-3 RNAi embryos 118
4.5.2 Are pseudocleavage furrow-dependent and cytoplasmic flow-dependent mechanisms sufficient to explain AP axis alignment? 121
4.5.3 Role of microtubules in AP axis alignment 127
5 Conclusions and Outlook 134
Appendix 139
Bibliography 142
List of publications 156
Acknowledgements 15
Elucidating the mechanism of AP axis alignment in the C. elegans embryo
No full textDevelopment of a single-cell embryo into an adult multi-cellular organism features the establishment of upto three anatomical body axes - anteroposterior, dorsoventral and left-right. It has been observed in many organisms that these body axes can consistently orient relative with respect to the geometric features of the embryo in many organisms. One such example is observed in the model organism Caenorhabditis elegans (C. elegans), where the Anteroposterior (AP) axis coincides with the geometric long axis of the ellipsoidal embryo -- the shape being imposed by the surrounding eggshell. In C. elegans, the Anteroposterior axis is established at the one-cell stage via its polarization by PAR polarity proteins. This cell polarization proceeds via a self-organized mechanochemical feedback between the PAR proteins and mechanical flows in the actomyosin cortex, resulting in the formation of two mutually exclusive domains of Anterior PAR and Posterior PAR proteins on the cortex denoting the future anterior and posterior end of the embryo -- and thus establishing the Anteroposterior axis. The initial orientation of the Anteroposterior axis is determined by the site of sperm entry at fertilization. However, the nascent Anteroposterior axis that forms after fertilization is observed to actively re-orient -- indicated by the movement of the PAR domains and concurrent migration (here termed posteriorisation) of the sperm-donated male pronucleus -- such that it aligns with the long axis of the ellipsoidal embryo, if it is not already aligned. In effect, the site of sperm entry only determines which half of the embryo becomes the posterior half of the embryo. This phenomenon of active re-orientation of the Anteroposterior axis, that ensures that the Anteroposterior axis aligns with the long axis of the embryo, is termed Anteroposterior axis alignment. The work described in this thesis investigates the mechanism of this Anteroposterior axis alignment in the C. elegans embryo.
Anterior-directed flows in the actomyosin cortex observed during Anteroposterior axis establishment have also been found to be essential for Anteroposterior axis alignment. In this thesis, two possible mechanisms of Anteroposterior axis alignment are considered, both of which are consequences of these cortical flows. Cortical flows at the embryo surface can drive flows in the bulk cytoplasm in the embryo, generating cytoplasmic flows which point towards the sperm-donated male pronucleus as it posteriorises. Previous studies have proposed that these cytoplasmic flows could push onto the male pronucleus, and due to the ellipsoidal geometry of the embryo, drive it towards the closest tip of the embryo. This proposed mechanism is referred to as the cytoplasmic flow-dependent mechanism in this thesis. Another mechanism proposed in this thesis postulates that the reorientation of the Anteroposterior axis occurs via the repositioning of the pseudocleavage furrow. The pseudocleavage furrow is a contractile ring-like structure that forms at the boundary of the two PAR domains during Anteroposterior axis establishment. The pseudocleavage furrow forms as a result of compressive alignment of actin filaments in the actomyosin cortex due to cortical flows. In cases where the Anteroposterior axis is not aligned with the long axis of the embryo, the pseudocleavage furrow is
not perpendicular to the long axis of the embryo. In such cases, active anisotropic stresses generated in the actomyosin cortex could force the rotation of the pseudocleavage furrow akin to an elastic rubber-band on an ellipsoid, and cause the Anteroposterior axis to re-orient towards the long axis of the embryo. This proposed mechanism is referred to as the pseudocleavage furrow-dependent mechanism in this thesis.
This thesis investigates the role played by the two mechanisms in Anteroposterior axis alignment. This is accomplished in the following way: a theoretical model of the Anteroposterior axis alignment is introduced, consisting of a description of the actomyosin cortex as an active nematic fluid present on the 2D surface of a fixed ellipsoid representing the embryo. This description of the cortex incorporates both the cytoplasmic flow-dependent mechanism and the pseudocleavage furrow-dependent mechanism. RNAi experiments in the C. elegans embryo that remove the pseudocleavage furrow, in conjuction with numerical simulations using the theoretical model, show that the pseudocleavage furrow-dependent mechanism is the predominant mechanism that drives Anteroposterior axis alignment, while cytoplasmic flow-dependent mechanism plays only a minor role. RNAi experiments that modify the geometry of the C. elegans embryo -- specifically, generate rounder embyros -- show that embryo geometry can influence the rate of re-orientation of the Anteroposterior axis during Anteroposterior axis alignment -- with slower Anteroposterior axis alignment in rounder embryos. Such an relation between embryo geometry and Anteroposterior axis alignment is found to be consistent with pseudocleavage furrow-dependent mechanism, both via predictions made using the theoretical model and using a simplified effective model of a contractile ring (or elastic rubber-band) on a fixed ellipsoid.
Altogether, the work presented in this thesis shows Anteroposterior axis alignment observed in the C. elegans embryo is driven primarily by the anisotropic stresses in the actomyosin cortex that generate the pseudocleavage furrow. The work here also shows that the Anteroposterior axis alignment process is sensitive to the geometry of the embryo. In effect, active mechanical flows in the actomyosin cortex translate the ellipsoidal geometry of the embryo into a robust orientation of the Anteroposterior axis of the C. elegans embryo. Mechanical flows such as these are not exclusive to C. elegans, nor are specific orientations of the body axes with respect to the embryo geometry. The results in this thesis thus point towards a possibly general role of the interactions between mechanical flows and embryo geometry to properly orient the body axes of the developing embryos of many multi-cellular organisms.:Contents
Abbreviations iii
Abstract iv
1 Introduction 1
1.1 Cytoskeleton 3
1.1.1 Main constituents of the cytoskeleton 3
1.1.2 Actomyosin cortex 7
1.2 Hydrodynamic theory of active fluids 8
1.2.1 Conservation Laws 9
1.2.2 Continuously broken symmetries 11
1.2.3 Irreversible thermodynamics of active fluids 13
1.2.4 Constitutive equations of active nematic fluids 19
1.3 C. elegans as a model organism 21
1.3.1 Early embryogenesis in C. elegans 22
1.4 AP axis establishment in C. elegans 24
1.4.1 PAR polarity system . 24
1.4.2 Mechanism of AP axis establishment 26
1.4.3 AP axis alignment 27
1.5 Overview 29
2 A theoretical model for AP axis alignment 30
2.1 A model of AP axis establishment in C. elegans 30
2.1.1 Turing-like system for PAR polarity system 31
2.1.2 Active isotropic description of actomyosin cortex 33
2.1.3 Guiding cues for AP axis establishment 34
2.1.4 Full model of AP axis establishment in [1] 35
2.2 A model of pseudocleavage furrow formation in C. elegans 36
2.2.1 Dynamics of Actin alignment 37
2.2.2 Active stress generated by alignment of actin filaments 38
2.3 A model of AP axis alignment in C. elegans 39
2.3.1 A thin film active nematic description of the cortex 40
2.3.2 Description of the Cytoplasm and Male pronucleus 46
2.3.3 Numerical simulations of the theoretical model 48
3 Materials and Methods 52
3.1 Culture conditions, strains and worm handling 52
3.2 Genetic perturbations by RNAi 53
3.3 Time-lapse microscopy 53
3.4 Image analysis 54
3.4.1 Pre-processing 54
3.4.2 Tracking posteriorisation of the male pronucleus 56
3.4.3 Measuring cortical flows 66
3.4.4 Measuring cytoplasmic flows 67
3.5 Data analysis 67
4 Experimental investigation of AP axis alignment 71
4.1 Characterising AP axis alignment in unperturbed embryos 71
4.2 Cortical flows are required for AP axis alignment 76
4.3 Role of Pseudocleavage furrow in AP axis alignment 83
4.3.1 Removing Pseudocleavage furrow via RNAi 83
4.3.2 Comparing numerical simulations to experimental results 88
4.4 Role of embryo geometry in AP axis alignment 99
4.4.1 Rounder embryos show slower AP axis alignment 99
4.4.2 Relation between embryo geometry and AP axis alignment 108
4.5 Additional experiments 118
4.5.1 Exploring relation between embryo geometry and AP axis alignment in ima-3 RNAi embryos 118
4.5.2 Are pseudocleavage furrow-dependent and cytoplasmic flow-dependent mechanisms sufficient to explain AP axis alignment? 121
4.5.3 Role of microtubules in AP axis alignment 127
5 Conclusions and Outlook 134
Appendix 139
Bibliography 142
List of publications 156
Acknowledgements 15
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