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Subject of study: Cilia and flagella are slender appendages of eukaryotic cells. They are actively bending structures and display regular bending waves. These active flagellar bending waves drive fluid flows on cell surfaces like in the case of the ciliated trachea or propels single cell micro-swimmers like sperm or alga. Objective: The axoneme is the evolutionarily conserved mechanical apparatus within cilia and flagella. It is comprised of a cylindrical arrangement of microtubule doublets, which are the elastic elements and dyneins, which are the force generating elements in the axonemal structure. Dyneins collectively bend the axoneme and must be specifically regulated to generate symmetric and highly asymmetric waveforms. In this thesis, I address the question of the molecular origin of the asymmetric waveform and test different theoretical descriptions for motor regulation. Approach: I introduce the isolated and reactivated Chlamydomonas axoneme as an experimental model for the symmetric and asymmetric flagellar beat. This system allows to study the beat in a controlled and cell free environment. I use high-speed microscopy to record shapes with high spatial and temporal resolution. Through image analysis and shape parameterization I extract a minimal set of parameters that describe the flagellar waveform. Using Chlamydomonas, I make use of different structural and motor mutants to study their effect on the shape in different reactivation conditions. Although the isolated axoneme system has many advantages compared to the cell-bound flagellum, to my knowledge, it has not been characterized yet. Results: I present a shape parameterization of the asymmetric beat using Fourier decomposition methods and find, that the asymmetric waveform can be understood as a sinusoidal beat around a circular arc. This reveals the similarities of the two different beat types: the symmetric and the asymmetric beat. I investigate the origin of the beat-asymmetry and find evidence for a specific dynein motor to be responsible for the asymmetry. I furthermore find experimental evidence for a strong sliding restriction at the basal end of the axoneme, which is important to establish a static bend. In collaboration with P. Sartori and F. Jülicher, I compare theoretical descriptions of different motor control mechanisms and find that a curvature controlled motor-regulation mechanism describes the experimental data best. We furthermore find, that in the dynamic case an additional sliding restriction at the base is unnecessary. By comparing the waveforms of intact cells and isolated reactivated axonemes, I reveal the effect of hydrodynamic loading, and the influence of boundary conditions on the shape of the beating flagella.

Subject of study: Cilia and flagella are slender appendages of eukaryotic cells. They are actively bending structures and display regular bending waves. These active flagellar bending waves drive fluid flows on cell surfaces like in the case of the ciliated trachea or propels single cell micro-swimmers like sperm or alga. Objective: The axoneme is the evolutionarily conserved mechanical apparatus within cilia and flagella. It is comprised of a cylindrical arrangement of microtubule doublets, which are the elastic elements and dyneins, which are the force generating elements in the axonemal structure. Dyneins collectively bend the axoneme and must be specifically regulated to generate symmetric and highly asymmetric waveforms. In this thesis, I address the question of the molecular origin of the asymmetric waveform and test different theoretical descriptions for motor regulation. Approach: I introduce the isolated and reactivated Chlamydomonas axoneme as an experimental model for the symmetric and asymmetric flagellar beat. This system allows to study the beat in a controlled and cell free environment. I use high-speed microscopy to record shapes with high spatial and temporal resolution. Through image analysis and shape parameterization I extract a minimal set of parameters that describe the flagellar waveform. Using Chlamydomonas, I make use of different structural and motor mutants to study their effect on the shape in different reactivation conditions. Although the isolated axoneme system has many advantages compared to the cell-bound flagellum, to my knowledge, it has not been characterized yet. Results: I present a shape parameterization of the asymmetric beat using Fourier decomposition methods and find, that the asymmetric waveform can be understood as a sinusoidal beat around a circular arc. This reveals the similarities of the two different beat types: the symmetric and the asymmetric beat. I investigate the origin of the beat-asymmetry and find evidence for a specific dynein motor to be responsible for the asymmetry. I furthermore find experimental evidence for a strong sliding restriction at the basal end of the axoneme, which is important to establish a static bend. In collaboration with P. Sartori and F. Jülicher, I compare theoretical descriptions of different motor control mechanisms and find that a curvature controlled motor-regulation mechanism describes the experimental data best. We furthermore find, that in the dynamic case an additional sliding restriction at the base is unnecessary. By comparing the waveforms of intact cells and isolated reactivated axonemes, I reveal the effect of hydrodynamic loading, and the influence of boundary conditions on the shape of the beating flagella.:Contents 1 Introduction. . . . . . . . .. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 3 1.1 Biology of Cilia and Flagella . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 3 1.1.1 The dimensions of flagellated micro-swimmers . . . . . . . . . . . . . . . . . 4 1.1.2 The symmetric and the asymmetric beat . . . . . . . . .. . . . . . . . . . . . 5 1.1.3 Chlamydomonas reinhardtii as a flagella model . . . . . . . . . . 5 1.2 The axoneme is the internal structure in eukaryotic cilia and flagella . . 6 1.3 Structure and function of microtubules and dyneins . . . . . . . . . . . 9 1.3.1 Microtubules: The structural elements in the axoneme . . . . . . 9 1.3.2 Dyneins: The force generators that drive the axonemal beat . . . 10 1.3.3 The asymmetries in the axoneme and consequences for the beat 17 1.4 Axonemal waveform models and mechanisms: from sliding to bending to beating . . . . . . . . . . . . . . 20 1.5 Geometrical representation and parameterization of the axonemal beat . . . . . . . . . . . . . . . 23 2 Questions addressed in this thesis . . . . . . . . . . . . . . 27 3 Material and Methods . . . . . . . . . . . . . . 29 3.1 Chlamydomonas cells: Axoneme preparation and motility assays . . . . 29 3.1.1 Culturing of Chlamydomonas reinhardtii cells . . . . . . . . . . . 29 3.1.2 Isolation, demembranation and storage of axonemes . . . . . . . 33 3.1.3 Reactivation of axonemes in controlled conditions . . . . . . . . . 35 3.1.4 Axoneme gliding assay using kinesin 1 . . . . . . . . . . . . . . . 36 3.2 Imaging and image processing . . . . . . . . . . . . . . . . . . . . . . . . 38 3.2.1 High-speed imaging of the flagella and axonemes . . . . . . . . . 38 3.2.2 Precise tracking of isolated axonemes and the flagella of cells . . 42 3.2.3 High throughput frequency evaluation of isolated axonemes . . . 47 3.2.4 Beat frequency characterization of the reactivated WT axoneme . . . . . . . . . . . . . . 49 4 Results and Discussion . . . . . . . . . . . . . . 53 4.1 The beat of the axoneme propagates from base to tip . . . . . . . . . . . 53 4.1.1 TEM study reveals no sliding at the base of a bend axoneme . . 53 4.1.2 The direction of wave propagation is directly determined from the reactivation of polarity marked axonemes . . . . . . . . . . 57 4.1.3 Summary . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 60 4.2 The asymmetric beat is the superposition of a static semi-circular arc and a sinusoidal beat . . . . . . .. . . . . . . . . . . . . . . . . 61 4.2.1 The waveform is parameterized by Fourier decomposition in time . . . . . . . . . . . . . . 61 4.2.2 The 0th and 1st Fourier modes describe the axonemal waveform . . . . . . . . . . . . . . 65 4.2.3 General dependence of shape parameters on axoneme length and beat frequency. . . . . . . . . . . . . . . . . . . . . . . . . . . . . 68 4.2.4 The isolated axoneme is a good model for the intact flagellum . .. . . . . . . . . . . . . . 71 4.2.5 Summary: . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 76 4.3 The circular motion is a consequence of the axonemal waveform . . . . . . . . . . . . . . . . . . . 79 4.3.1 Hydrodynamic relations for small amplitude waves explain the relation between swimming and shape of axonemes . . . . 79 4.3.2 The swimming path can be reconstructed using shape information and a hydrodynamic model . . . . . . . . . . . . . . . . 83 4.3.3 Motor mutations alter the direction of rotation of reactivated axonemes. . . . . . . . . . . . . . . . . . . . . . . . 84 4.3.4 Summary: . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 87 4.4 The molecular origin of the circular mean shape. . . . . . . . . . . . . . 89 4.4.1 Motor Mutations do not abolish the mean shape, a structural mutation does . . . . . . . . . . . . . . . . . . . . . . . . . . . . 89 4.4.2 The axoneme is straight in absence of ATP but bend at low ATP concentrations. . . . . . . . . . . . . . . . . . . . . . . . . . . . . 93 4.4.3 Viscous load decreases the mean curvature . . . . . . . . . . . . 99 4.4.4 Summary: . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 100 4.5 Curvature-dependent dynein activation accounts for the shape of the beat of the isolated axoneme . . . . . . . . . . . . . . . . 103 5 Conclusions and Outlook . . . . . . . . . . . . . . . . 109 5.1 Summary of the results . . . . . . . . . . . . . . . . . . . . . . . . . . . 109 5.2 Future directions . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 110 Abbreviations . . . . . . . . . . . . . . . . 111 List of figures . . . . . . . . . . . . . . . . 116 List of tables . . . . . . . . . . . . . . . . 118 Bibliography

Made available in DSpace on 2014-06-11T19:26:05Z (GMT). No. of bitstreams: 0 Previous issue date: 2011-07-29Bitstream added on 2014-06-13T20:14:37Z : No. of bitstreams: 1 pereira_llv_me_sjrp.pdf: 1182871 bytes, checksum: 6053df49fe569dc60c6513fafdffaa9d (MD5) / No presente trabalho verificamos que os testículos possuem morfologias diferentes podendo ser arredondados, arredondados/espiralados ou alongados/espiralados. Com relação à morfometria das células em prófase I, B. micantulum e R. zela foram as que apresentaram as menores células, G. f. flavus foi a que apresentou maior tamanho e R. c. crassifemur e M. brasiliensis apresentaram tamanho intermediário. A avaliação da espermatogênese nos permitiu concluir que as características observadas são semelhantes às das outras espécies de Heteroptera, descritas na literatura, diferindo apenas com relação à morfologia dos testículos, o número de cromossomos e o sistema cromossômico do sexo. A análise das ultraestruturas observadas durante a espermatogênese de Gelastocoris flavus flavus e Martarega uruguayensis mostraram a presença de várias mitocôndrias pequenas e uniformemente distribuidas pelo citoplasma em células em profase I, de ambas espécies, que foram se unindo formando o complexo mitocondrial, que possui no seu interior as mitocôndrias enoveladas, posteriormente este complexo mitocondrial se divide em duas estruturas denominadas derivados mitocondriais, que se dispõem bilateralmente ao axonema. O axonema dessas espécies possui o padrão de 9+9+2. A formação do acrossomo inicia-se nos primeiros estágios da espermiogênese sendo composto de muitas vesículas acrossomais que se unem formando uma única estrutura, sendo observada regiões e algumas estruturas mais coradas em seu interior. Basicamente o processo de espermiogênese não diferiu entre as duas espécies analisadas / In this study, we found different morphologies for testes of the Heteroptera species Belostoma anurum, B. micantulum, Gelastocoris angulatus, G. flavus flavus, Rheumatobates crassifemur crassifemur, Buenoa amnigenus, B. unguis, Martarega brasiliensis, M. membranacea, M. uruguayensis, Rhagovelia tenuipes and R. zela. They can by round, round/spiral and elongated/spiral. The size of prophase I cells also varied, being the smallest ones detected in B. micantulum and R. zela, the largest in G. f. flavus, and the intermediate in R. c. crassifemur and M. brasiliensis. The analyses of spermatogenesis allowed us to conclude that, in the studied species, the features are similar to those of other previously described Heteroptera species, differing only as to the testicular morphology, the chromosome number, and the sex chromosome system. Ultrastructural analysis of the spermatogenesis showed several small mitochondrias evenly distributed throughout the cytoplasm, in cells at prophase I of G. f. flavus and M. uruguayensis. The small mitochondrias joined to form the mitochondrial complex. Later, this mitochondrial complex divided into two structures called mitochondrial derivatives, located bilaterally to the axoneme. The axoneme of these species showed the flagellar pattern 9+9+2. The acrosome started to be formed in the early stages of spermiogenesis, being composed of many acrosome vesicles that join to form a single structure. Some regions within this structure were more strongly stained. Basically the process of spermiogenesis did not differ between the species G. f. flavus and M. uruguayensis

Les structures treillis constituées d’un nombre important de barres sont largement utilisées, notamment en génie civil. L’étude par éléments finis de telles structures se révèle très coûteuse dès que la maille répétitive du treillis est complexe. Il s’avère intéressant de réduire la taille du problème en définissant un milieu continu équivalent. L’objectif de la première partie de ce travail est de proposer, en se plaçant dans le cadre des méthodes d’homogénéisation des milieux périodiques, une poutre de Timoshenko équivalente à une structure périodique dont l’une des dimension est grande par rapport aux deux autres. Une des originalités réside dans l’étude de cellules de base non symétriques. Par ailleurs, on s’intéresse à la prise en compte de déformations libres (par exemple, d’origine thermique) apparaissant à l’échelle microscopique. La seconde partie est consacrée à l’étude de la structure axonémale du flagelle et des cils vibratiles. Il s’agit de proposer et valider un modèle pour cette structure biomécanique complexe et d’appliquer ensuite la méthode d’homogénéisation proposée / Lattice structures are widely used, especially in civil engineering. The finite element analysis of such structures might require a consequent amount of computational time when the periodical mesh of this lattice is complex. Defining an equivalent continuous medium in order to reduce the size of the problem appears to be interesting. The aim of the first part of this document is to apply a homogenization method in order to find a Timoshenko beam model macroscopically equivalent to a slender structure which is periodical in the longitudinal direction. One of the unusual aspects tackled reside in the study of structures with periodical cells having a longitudinal asymmetry. In addition, the case of periodical structures with free deformation (e.g. thermal dilatation) at microscopic scale is dealt. The second part is consecrated to the study of the axonemal structure of the biological cell flagella and Cilia. A shorten version of the axonemal structure is studied at first and homogenized afterward

No description available.

Orientador: Mary Massumi Itoyama / Banca: Fernanda Cristina Alcantara dos Santos / Banca: Sandra Regina de Carvalho Marchesin / Resumo: No presente trabalho verificamos que os testículos possuem morfologias diferentes podendo ser arredondados, arredondados/espiralados ou alongados/espiralados. Com relação à morfometria das células em prófase I, B. micantulum e R. zela foram as que apresentaram as menores células, G. f. flavus foi a que apresentou maior tamanho e R. c. crassifemur e M. brasiliensis apresentaram tamanho intermediário. A avaliação da espermatogênese nos permitiu concluir que as características observadas são semelhantes às das outras espécies de Heteroptera, descritas na literatura, diferindo apenas com relação à morfologia dos testículos, o número de cromossomos e o sistema cromossômico do sexo. A análise das ultraestruturas observadas durante a espermatogênese de Gelastocoris flavus flavus e Martarega uruguayensis mostraram a presença de várias mitocôndrias pequenas e uniformemente distribuidas pelo citoplasma em células em profase I, de ambas espécies, que foram se unindo formando o complexo mitocondrial, que possui no seu interior as mitocôndrias enoveladas, posteriormente este complexo mitocondrial se divide em duas estruturas denominadas derivados mitocondriais, que se dispõem bilateralmente ao axonema. O axonema dessas espécies possui o padrão de 9+9+2. A formação do acrossomo inicia-se nos primeiros estágios da espermiogênese sendo composto de muitas vesículas acrossomais que se unem formando uma única estrutura, sendo observada regiões e algumas estruturas mais coradas em seu interior. Basicamente o processo de espermiogênese não diferiu entre as duas espécies analisadas / Abstract: In this study, we found different morphologies for testes of the Heteroptera species Belostoma anurum, B. micantulum, Gelastocoris angulatus, G. flavus flavus, Rheumatobates crassifemur crassifemur, Buenoa amnigenus, B. unguis, Martarega brasiliensis, M. membranacea, M. uruguayensis, Rhagovelia tenuipes and R. zela. They can by round, round/spiral and elongated/spiral. The size of prophase I cells also varied, being the smallest ones detected in B. micantulum and R. zela, the largest in G. f. flavus, and the intermediate in R. c. crassifemur and M. brasiliensis. The analyses of spermatogenesis allowed us to conclude that, in the studied species, the features are similar to those of other previously described Heteroptera species, differing only as to the testicular morphology, the chromosome number, and the sex chromosome system. Ultrastructural analysis of the spermatogenesis showed several small mitochondrias evenly distributed throughout the cytoplasm, in cells at prophase I of G. f. flavus and M. uruguayensis. The small mitochondrias joined to form the mitochondrial complex. Later, this mitochondrial complex divided into two structures called mitochondrial derivatives, located bilaterally to the axoneme. The axoneme of these species showed the flagellar pattern 9+9+2. The acrosome started to be formed in the early stages of spermiogenesis, being composed of many acrosome vesicles that join to form a single structure. Some regions within this structure were more strongly stained. Basically the process of spermiogenesis did not differ between the species G. f. flavus and M. uruguayensis / Mestre

Cilia and flagella are hair-like appendages of eukaryotic cells. They are actively bending structures that exhibit regular beat patterns and thereby play an important role in many different circumstances where motion on a cellular level is required. Most dramatic is the effect of nodal cilia whose vortical motion leads to a fluid flow that is directly responsible for establishing the left-right axis during embryological development in many vertebrate species, but examples range from the propulsion of single cells, such as the swimming of sperm, to the transport of mucus along epithelial cells, e.g. in the ciliated trachea. Cilia and flagella contain an evolutionary highly conserved structure called the axoneme, whose characteristic architecture is based on a cylindrical arrangement of elastic filaments (microtubules). In the presence of a chemical fuel (ATP), molecular motors (dynein) exert shear forces between neighbouring microtubules, leading to a bending of the axoneme through structural constraints. We address the following two questions: How can these organelles generate regular oscillatory beat patterns in the absence of a biochemical signal regulating the activity of the force generating elements? And how can the beat patterns be so different for apparently very similar structures? We present a theoretical description of the axonemal structure as an actively bending elastic cylinder, and show that in such a system bending waves emerge from a non-oscillatory state via a dynamic instability. The corresponding beat patterns are solutions to a set of coupled partial differential equations presented herein.