Angiosperm sexual reproduction is unique and remarkable. Unlike for other living organisms, fertilisation involves the fusion of two sperm cells to two cell types of female gametophyte, the egg and central cell. This fertilization process is called double fertilisation. Fusion of the egg and the sperm yields a zygote whereas the interaction of the central cell and the sperm gives the nutritive endosperm. This fertilization process has been studied extensively for many years. However, despite these studies, relatively little is known at the molecular level about either of the plant gametes. This is primarily due to the difficulties in plant gamete isolation. Both plant gametes reside within enclosed tissues, pollen grains and embryo sacs. In this study, sperm isolation techniques were successfully developed for Brassica oleracea and Arabidopsis thaliana which ultimately utilised fluorescence-activated cell sorting (FACS) to obtain pure cell samples. Proteomic studies utilising two-dimensional protein electrophoresis and mass spectrometry (MS) were carried out on both semi-purified and FACS-purified sperm cells. In parallel with the proteomic studies a bioinformatics approach was taken which used sperm transcriptome data of maize, Plumbago zeylanica, rice and tobacco to identify homologues in Arabidopsis. Transcriptional analyses, RT-PCR and GFP translational fusion experiments were used to investigate these Arabidopsis sperm cell-expressed gene candidates. As a result, two sperm cell-expressed genes (At1g10090 and At5g39650) were identified and these are being analysed to confirm their functions in the reproductive process. Moreover, the sperm cell-expressed gene candidates derived from the bioinformatics were also screened for roles in plant reproduction by a reverse genetics approach (Arabidopsis T-DNA insertion mutagenesis plant screening) and eight genes were identified. In addition, for the first time, sperm cell size dimorphism was identified for Arabidopsis in this study utilising a GFP-labelled sperm line and confocal microscopy. Overall the techniques for sperm cell-expressed gene candidate selection were proven to be effective and will certainly facilitate further sperm cell-specific gene identification studies. Further the Arabidopsis sperm purification technique successfully developed in this project will surely be useful for any plant sperm cell studies in the future.

The ubiquitin-proteasomal system which is the major pathway for intracellular protein degradation is also involved in sperm quality control in the mammalian epididymis. Defective sperm become surface- ubiquitinated during epididymal passage. The level of sperm surface ubiquitination negatively correlates with their quality. Hypothetically it is possible that after fertilization, highly ubiquitinated sperm, naturally present in mammalian ejaculates, would be actively recognized by oocyte (probably via 26S proteasomal complex). Subsequent partial or total sperm degradation should negatively affect the development of the potentially defective embryo. In this study, we examined the effect of sperm ubiquitination on the early embryonic development in pig (Sus scrofa f. domestica) using the method of intracytoplasmic sperm injection (ICSI). In vitro embryonic development to the blastocyst stage after ICSI was comparable with other laboratories. In this study, no significant difference was observed in the formation of pronuclei between oocytes fertilized by lower and highly ubiquitinated sperm cells. On the other hand, significantly better embryonic development to the blastocyst stage was observed in oocytes fertilized by sperm with lower surface ubiquitination (17 %) compared with oocytes fertilized by highly...

Orientador: Fabiana Ferreira Souza / Resumo: As proteínas dos fluido e células do sitema reprodutor são constantes objetos de estudo, a fim de elucidar eventos fisiológicos e buscar biomarcadores das funções reprodutivas, facilitando a escolha de reprodutores. Em vista disso, este estudo objetivou caracterizar as proteínas dos espermatozoides do ejaculado e da cauda do epidídimo, do plasma seminal e do fluido epididimário de touros. Foram utilizados 10 touros adultos da raça Brangus. O sêmen foi colhido por eletroejaculação e, posteriormente os machos foram orquiectomizados para a colheita dos espermatozoides e fluido do epidídimo. As células do ejaculado e da cauda do epidídimo foram analisadas subjetivamente após a colheita, e o plasma seminal e fluido do epidídimo foram separados por centrifugação. Então, as amostras foram preparadas para a espectrometria de massas (ESI-QTof MS/MS), com um pool de cada grupo. A concentração de proteínas totais não diferiu entre os grupos. Foram encontradas 67 e 66 proteínas nos espermatozoides do ejaculado e da cauda do epidídimo, e 20 e 16 no plasma seminal e líquido epididimário, respectivamente. Além disso, 52 proteínas foram comuns entre os espermatozoides obtidos do ejaculado e epidídimo, e 9 entre o plasma seminal e fluido epididimário. Atividade catalítica foi a principal função molecular nas células espermáticas; já no plasma seminal foi de ligação e no fluido epididimário, atividade catalítica. As proteínas que se destacaram foram: 14-3-3 protein zeta/delta, A-kinase anchor ... (Resumo completo, clicar acesso eletrônico abaixo) / Mestre

L'infertilité masculine est une préoccupation croissante dans les sociétés modernes. Parmi les différentes causes d'infertilités masculines, certaines ont une origine génétique. C'est le cas de la globozoospermie de type I, une infertilité sévère caractérisée par la production exclusive des spermatozoïdes ayant une tête ronde et sans acrosome. Cette pathologie présente un phénotype complexe associant à l'absence de l'acrosome, des défauts de compaction nucléaire, des lésions de l'ADN et une déficience d'activation ovocytaire.Récemment notre équipe a montré que le gène DPY19L2 est impliqué dans 60 à 80% des cas de globozoospermie de type I et représente donc la cause majeure de la globozoospermie de type I chez l'homme. La fonction de la protéine étant complètement inconnue au moment de l'identification du gène DPY19L2, nous avons alors réalisée une étude fondamentale sur les mécanismes moléculaires expliquant la pathogénie moléculaire de cette maladie et avons démontré, grâce à l'utilisation du modèle des souris KO pour le gène Dpy19l2, que la protéine est localisée dans la membrane nucléaire interne et est nécessaire à l'ancrage de l'acrosome sur l'enveloppe nucléaire. Dans le but d'identifier d'autres acteurs impliqués dans l'attachement de l'acrosome au noyau spermatique, nous nous sommes intéressés à l'étude de la protéine Sun5 de l'enveloppe nucléaire interne située en regard de l'acrosome qui pouvait être un partenaire de Dpy19l2. On a trouvé que les deux protéines n'étaient pas des partenaires puisque Sun5 était, contrairement à ce qui a été décrit dans la littérature, du côté postérieur opposé à l'acrosome. En deuxième temps, nous nous sommes intéressés à la compréhension des principales causes moléculaires de l'absence de fécondation ou du très faible taux de réussite lors d'ICSI réalisées avec des spermatozoïdes globozoospermiques.Pour ce faire, nous avons recherché la protéine PLC ζ, le principal facteur spermatique activateur de l'ovocyte, dans les spermatozoïdes humains provenant de patients délétés pour le gène DPY19L2 et murins (de souris KO Dpy19l2-/-) et avons montré qu'effectivement cette protéine est absente tant chez les patients que dans le modèle d'étude murin. Nous avons également réalisé une étude comparative des principales étapes de la compaction du génome spermatique entre les souris mâles WT et Dpy19l2-/- et nous avons montré que la compaction du génome des spermatozoïdes globozoospermiques était défectueuse avec un défaut de protamination et une rétention des histones. Ainsi, la déficience en PLC ζ, les défauts de compaction et le taux élevé de fragmentation de l'ADN sont susceptibles d'expliquer l'échec de la fécondation après ICSI, et le développement très réduit des embryons issus des patients déficients pour le gène DPY19L2 ainsi que des souris Dpy19l2-/-. La compréhension de cette physiopathologie devrait permettre la proposition de nouvelles stratégies thérapeutiques permettant d'améliorer le taux du développement embryonnaire en AMP. / Male infertility is a growing concern in modern societies. Among the various causes of male factor infertility, some have a genetic origin. This is the case of type I globozoospermia, a severe infertility characterized by the presence in the ejaculate of a majority of round spermatozoa devoid of acrosome. This pathology presents a complex phenotype associating to the absence of the acrosome, sperm nuclear compaction defects, DNA damage and failure in egg activation.Recently our team identified the DPY19L2 gene as responsible for a large majority of pure globozoospermia cases (>80%) and therefore represents the major cause of type I globozoospermia in humans. The function of the protein was completely unknown at the time of identification of DPY19L2 gene, we then performed a fundamental study of the molecular mechanisms underlying the molecular pathogenesis of the disease and have shown, through the use of knockout mice model for the Dpy19l2 gene, that the protein is localized in the inner nuclear membrane and is necessary for the anchoring of the acrosome to the nuclear envelope. In order to characterize new actors of acrosome attachment, we assessed the importance of Sun5 (also called Spag4l) in acrosome attachment which was previously shown to be expressed in NE of spermatogenic cells, facing the acrosome and that could be a partner of Dpy19l2. Interestingly we demonstrate that Sun5 and Dpy19l2 are not partners and that Sun5, is not as initially reported, facing the acrosome but is in fact excluded from this zone. We were also interested in understanding the main molecular causes of the poor fertilization ability or the very low success rate in ICSI when performed with globozoospermics sperm.Therefore we have searched the PLC ζ protein, the sperm factor thought to induce the Ca2+ oscillations responsible for egg activation, in human spermatozoa from patients with DPY19L2 deleted gene and in murine spermatozoa from Dpy19l2 Knock-Out mice and showed that actually this protein is absent both in patients and in KO mice. We also made a comparative study of the main stages of genome compaction of sperm from both WT and Dpy19l2 KO mice and we showed that Dpy19l2 deficient sperm displays defective genome condensation and DNA alterations. Thus, PLC ζ deficiency, the compaction defects and the high rate of DNA fragmentation may explain the failure of fertilization after ICSI, and the poor development of embryos from patients deficient for the gene DPY19L2 as well as Dpy19l2 KO mice.Understanding the physiopathology of globozoospermia should allow the proposal of new therapeutic strategies that improves the rate of embryonic development in ART.

Durante o processo de criopreservação de sêmen, os espermatozóides sofrem alguns danos que resultam na diminuição da fertilidade deste. O presente estudo foi realizado a fim de avaliar o efeito da utilização, combinada de duas curvas de congelamento com dois diluentes comerciais sobre a criopreservação de sêmen eqüino. Foram analisados 20 ejaculados. As amostras foram avaliadas, pela motilidade progressiva e total do sêmen pós-descongelamento e pela integridade e funcionalidade da membrana dos espermatozóides. A combinação entre curva automatizada e Botu- Crio® apresentou as maiores médias, nas análises de motilidade total (55,53%) e progressiva (17,25%), após o descongelamento. O diluente Botu-Crio® ,isoladamente, apresentou também os melhores resultados quando foram realizadas as análises de integridade (CFDA/PI) e funcionalidade de membrana pelo teste hiposmótico. / During semen cryopreservation, sperm cells were submitted to some deleterious events leading to membrane damage which result in fertility decrease. This study was designed to compare the effects of two freezing techniques (conventional and automated), their freezing rates and the use of two commercial extenders as cryoprotectants (FR-5® and Botu-Crio®) on the total and progressive motility, integrity and functionality of spermatic membranes during the cryopreservation of equine semen. Twenty ejaculates were analyzed. The total and progressive motility of fresh and postthawing semen samples were evaluated by the patterns assays. The function of plasmatic membrane was measured by the hipoosmotic swelling test. The integrity of plasmatic membrane was evaluated using CFDA/PI fluorescent probes. There were significant differences between the two freezing techniques and/or between cryoprotectants for all assessed parameters. The combined used between Botu-Crio® and automated curves showed better results in total and progressive post-thawing motility. The extender Botu-Crio®, alone, showed better results in order to preserve the membrane integrity and function.

Durante o processo de criopreservação de sêmen, os espermatozóides sofrem alguns danos que resultam na diminuição da fertilidade deste. O presente estudo foi realizado a fim de avaliar o efeito da utilização, combinada de duas curvas de congelamento com dois diluentes comerciais sobre a criopreservação de sêmen eqüino. Foram analisados 20 ejaculados. As amostras foram avaliadas, pela motilidade progressiva e total do sêmen pós-descongelamento e pela integridade e funcionalidade da membrana dos espermatozóides. A combinação entre curva automatizada e Botu- Crio® apresentou as maiores médias, nas análises de motilidade total (55,53%) e progressiva (17,25%), após o descongelamento. O diluente Botu-Crio® ,isoladamente, apresentou também os melhores resultados quando foram realizadas as análises de integridade (CFDA/PI) e funcionalidade de membrana pelo teste hiposmótico. / During semen cryopreservation, sperm cells were submitted to some deleterious events leading to membrane damage which result in fertility decrease. This study was designed to compare the effects of two freezing techniques (conventional and automated), their freezing rates and the use of two commercial extenders as cryoprotectants (FR-5® and Botu-Crio®) on the total and progressive motility, integrity and functionality of spermatic membranes during the cryopreservation of equine semen. Twenty ejaculates were analyzed. The total and progressive motility of fresh and postthawing semen samples were evaluated by the patterns assays. The function of plasmatic membrane was measured by the hipoosmotic swelling test. The integrity of plasmatic membrane was evaluated using CFDA/PI fluorescent probes. There were significant differences between the two freezing techniques and/or between cryoprotectants for all assessed parameters. The combined used between Botu-Crio® and automated curves showed better results in total and progressive post-thawing motility. The extender Botu-Crio®, alone, showed better results in order to preserve the membrane integrity and function.

Durante o processo de criopreservação de sêmen, os espermatozóides sofrem alguns danos que resultam na diminuição da fertilidade deste. O presente estudo foi realizado a fim de avaliar o efeito da utilização, combinada de duas curvas de congelamento com dois diluentes comerciais sobre a criopreservação de sêmen eqüino. Foram analisados 20 ejaculados. As amostras foram avaliadas, pela motilidade progressiva e total do sêmen pós-descongelamento e pela integridade e funcionalidade da membrana dos espermatozóides. A combinação entre curva automatizada e Botu- Crio® apresentou as maiores médias, nas análises de motilidade total (55,53%) e progressiva (17,25%), após o descongelamento. O diluente Botu-Crio® ,isoladamente, apresentou também os melhores resultados quando foram realizadas as análises de integridade (CFDA/PI) e funcionalidade de membrana pelo teste hiposmótico. / During semen cryopreservation, sperm cells were submitted to some deleterious events leading to membrane damage which result in fertility decrease. This study was designed to compare the effects of two freezing techniques (conventional and automated), their freezing rates and the use of two commercial extenders as cryoprotectants (FR-5® and Botu-Crio®) on the total and progressive motility, integrity and functionality of spermatic membranes during the cryopreservation of equine semen. Twenty ejaculates were analyzed. The total and progressive motility of fresh and postthawing semen samples were evaluated by the patterns assays. The function of plasmatic membrane was measured by the hipoosmotic swelling test. The integrity of plasmatic membrane was evaluated using CFDA/PI fluorescent probes. There were significant differences between the two freezing techniques and/or between cryoprotectants for all assessed parameters. The combined used between Botu-Crio® and automated curves showed better results in total and progressive post-thawing motility. The extender Botu-Crio®, alone, showed better results in order to preserve the membrane integrity and function.

The present habilitation thesis in theoretical biological physics addresses two central dynamical processes in cells and organisms: (i) active motility and motility control and (ii) self-organized pattern formation. The unifying theme is the nonlinear dynamics of biological function and its robustness in the presence of strong fluctuations, structural variations, and external perturbations. We theoretically investigate motility control at the cellular scale, using cilia and flagella as ideal model system. Cilia and flagella are highly conserved slender cell appendages that exhibit spontaneous bending waves. This flagellar beat represents a prime example of a chemo-mechanical oscillator, which is driven by the collective dynamics of molecular motors inside the flagellar axoneme. We study the nonlinear dynamics of flagellar swimming, steering, and synchronization, which encompasses shape control of the flagellar beat by chemical signals and mechanical forces. Mechanical forces can synchronize collections of flagella to beat at a common frequency, despite active motor noise that tends to randomize flagellar synchrony. In Chapter 2, we present a new physical mechanism for flagellar synchronization by mechanical self-stabilization that applies to free-swimming flagellated cells. This new mechanism is independent of direct hydrodynamic interactions between flagella. Comparison with experimental data provided by experimental collaboration partners in the laboratory of J. Howard (Yale, New Haven) confirmed our new mechanism in the model organism of the unicellular green alga Chlamydomonas. Further, we characterize the beating flagellum as a noisy oscillator. Using a minimal model of collective motor dynamics, we argue that measured non-equilibrium fluctuations of the flagellar beat result from stochastic motor dynamics at the molecular scale. Noise and mechanical coupling are antagonists for flagellar synchronization. In addition to the control of the flagellar beat by mechanical forces, we study the control of the flagellar beat by chemical signals in the context of sperm chemotaxis. We characterize a fundamental paradigm for navigation in external concentration gradients that relies on active swimming along helical paths. In this helical chemotaxis, the direction of a spatial concentration gradient becomes encoded in the phase of an oscillatory chemical signal. Helical chemotaxis represents a distinct gradient-sensing strategy, which is different from bacterial chemotaxis. Helical chemotaxis is employed, for example, by sperm cells from marine invertebrates with external fertilization. We present a theory of sensorimotor control, which combines hydrodynamic simulations of chiral flagellar swimming with a dynamic regulation of flagellar beat shape in response to chemical signals perceived by the cell. Our theory is compared to three-dimensional tracking experiments of sperm chemotaxis performed by the laboratory of U. B. Kaupp (CAESAR, Bonn). In addition to motility control, we investigate in Chapter 3 self-organized pattern formation in two selected biological systems at the cell and organism scale, respectively. On the cellular scale, we present a minimal physical mechanism for the spontaneous self-assembly of periodic cytoskeletal patterns, as observed in myofibrils in striated muscle cells. This minimal mechanism relies on the interplay of a passive coarsening process of crosslinked actin clusters and active cytoskeletal forces. This mechanism of cytoskeletal pattern formation exemplifies how local interactions can generate large-scale spatial order in active systems. On the organism scale, we present an extension of Turing’s framework for self-organized pattern formation that is capable of a proportionate scaling of steady-state patterns with system size. This new mechanism does not require any pre-pattering clues and can restore proportional patterns in regeneration scenarios. We analytically derive the hierarchy of steady-state patterns and analyze their stability and basins of attraction. We demonstrate that this scaling mechanism is structurally robust. Applications to the growth and regeneration dynamics in flatworms are discussed (experiments by J. Rink, MPI CBG, Dresden). / Das Thema der vorliegenden Habilitationsschrift in Theoretischer Biologischer Physik ist die nichtlineare Dynamik funktionaler biologischer Systeme und deren Robustheit gegenüber Fluktuationen und äußeren Störungen. Wir entwickeln hierzu theoretische Beschreibungen für zwei grundlegende biologische Prozesse: (i) die zell-autonome Kontrolle aktiver Bewegung, sowie (ii) selbstorganisierte Musterbildung in Zellen und Organismen. In Kapitel 2, untersuchen wir Bewegungskontrolle auf zellulärer Ebene am Modelsystem von Zilien und Geißeln. Spontane Biegewellen dieser dünnen Zellfortsätze ermöglichen es eukaryotischen Zellen, in einer Flüssigkeit zu schwimmen. Wir beschreiben einen neuen physikalischen Mechanismus für die Synchronisation zweier schlagender Geißeln, unabhängig von direkten hydrodynamischen Wechselwirkungen. Der Vergleich mit experimentellen Daten, zur Verfügung gestellt von unseren experimentellen Kooperationspartnern im Labor von J. Howard (Yale, New Haven), bestätigt diesen neuen Mechanismus im Modellorganismus der einzelligen Grünalge Chlamydomonas. Der Gegenspieler dieser Synchronisation durch mechanische Kopplung sind Fluktuationen. Wir bestimmen erstmals Nichtgleichgewichts-Fluktuationen des Geißel-Schlags direkt, wofür wir eine neue Analyse-Methode der Grenzzykel-Rekonstruktion entwickeln. Die von uns gemessenen Fluktuationen entstehen mutmaßlich durch die stochastische Dynamik molekularen Motoren im Innern der Geißeln, welche auch den Geißelschlag antreiben. Um die statistische Physik dieser Nichtgleichgewichts-Fluktuationen zu verstehen, entwickeln wir eine analytische Theorie der Fluktuationen in einem minimalen Modell kollektiver Motor-Dynamik. Zusätzlich zur Regulation des Geißelschlags durch mechanische Kräfte untersuchen wir dessen Regulation durch chemische Signale am Modell der Chemotaxis von Spermien-Zellen. Dabei charakterisieren wir einen grundlegenden Mechanismus für die Navigation in externen Konzentrationsgradienten. Dieser Mechanismus beruht auf dem aktiven Schwimmen entlang von Spiralbahnen, wodurch ein räumlicher Konzentrationsgradient in der Phase eines oszillierenden chemischen Signals kodiert wird. Dieser Chemotaxis-Mechanismus unterscheidet sich grundlegend vom bekannten Chemotaxis-Mechanismus von Bakterien. Wir entwickeln eine Theorie der senso-motorischen Steuerung des Geißelschlags während der Spermien-Chemotaxis. Vorhersagen dieser Theorie werden durch Experimente der Gruppe von U.B. Kaupp (CAESAR, Bonn) quantitativ bestätigt. In Kapitel 3, untersuchen wir selbstorganisierte Strukturbildung in zwei ausgewählten biologischen Systemen. Auf zellulärer Ebene schlagen wir einen einfachen physikalischen Mechanismus vor für die spontane Selbstorganisation von periodischen Zellskelett-Strukturen, wie sie sich z.B. in den Myofibrillen gestreifter Muskelzellen finden. Dieser Mechanismus zeigt exemplarisch auf, wie allein durch lokale Wechselwirkungen räumliche Ordnung auf größeren Längenskalen in einem Nichtgleichgewichtssystem entstehen kann. Auf der Ebene des Organismus stellen wir eine Erweiterung der Turingschen Theorie für selbstorganisierte Musterbildung vor. Wir beschreiben eine neue Klasse von Musterbildungssystemen, welche selbst-organisierte Muster erzeugt, die mit der Systemgröße skalieren. Dieser neue Mechanismus erfordert weder eine vorgegebene Kompartimentalisierung des Systems noch spezielle Randbedingungen. Insbesondere kann dieser Mechanismus proportionale Muster wiederherstellen, wenn Teile des Systems amputiert werden. Wir bestimmen analytisch die Hierarchie aller stationären Muster und analysieren deren Stabilität und Einzugsgebiete. Damit können wir zeigen, dass dieser Skalierungs-Mechanismus strukturell robust ist bezüglich Variationen von Parametern und sogar funktionalen Beziehungen zwischen dynamischen Variablen. Zusammen mit Kollaborationspartnern im Labor von J. Rink (MPI CBG, Dresden) diskutieren wir Anwendungen auf das Wachstum von Plattwürmern und deren Regeneration in Amputations-Experimenten.

The present habilitation thesis in theoretical biological physics addresses two central dynamical processes in cells and organisms: (i) active motility and motility control and (ii) self-organized pattern formation. The unifying theme is the nonlinear dynamics of biological function and its robustness in the presence of strong fluctuations, structural variations, and external perturbations. We theoretically investigate motility control at the cellular scale, using cilia and flagella as ideal model system. Cilia and flagella are highly conserved slender cell appendages that exhibit spontaneous bending waves. This flagellar beat represents a prime example of a chemo-mechanical oscillator, which is driven by the collective dynamics of molecular motors inside the flagellar axoneme. We study the nonlinear dynamics of flagellar swimming, steering, and synchronization, which encompasses shape control of the flagellar beat by chemical signals and mechanical forces. Mechanical forces can synchronize collections of flagella to beat at a common frequency, despite active motor noise that tends to randomize flagellar synchrony. In Chapter 2, we present a new physical mechanism for flagellar synchronization by mechanical self-stabilization that applies to free-swimming flagellated cells. This new mechanism is independent of direct hydrodynamic interactions between flagella. Comparison with experimental data provided by experimental collaboration partners in the laboratory of J. Howard (Yale, New Haven) confirmed our new mechanism in the model organism of the unicellular green alga Chlamydomonas. Further, we characterize the beating flagellum as a noisy oscillator. Using a minimal model of collective motor dynamics, we argue that measured non-equilibrium fluctuations of the flagellar beat result from stochastic motor dynamics at the molecular scale. Noise and mechanical coupling are antagonists for flagellar synchronization. In addition to the control of the flagellar beat by mechanical forces, we study the control of the flagellar beat by chemical signals in the context of sperm chemotaxis. We characterize a fundamental paradigm for navigation in external concentration gradients that relies on active swimming along helical paths. In this helical chemotaxis, the direction of a spatial concentration gradient becomes encoded in the phase of an oscillatory chemical signal. Helical chemotaxis represents a distinct gradient-sensing strategy, which is different from bacterial chemotaxis. Helical chemotaxis is employed, for example, by sperm cells from marine invertebrates with external fertilization. We present a theory of sensorimotor control, which combines hydrodynamic simulations of chiral flagellar swimming with a dynamic regulation of flagellar beat shape in response to chemical signals perceived by the cell. Our theory is compared to three-dimensional tracking experiments of sperm chemotaxis performed by the laboratory of U. B. Kaupp (CAESAR, Bonn). In addition to motility control, we investigate in Chapter 3 self-organized pattern formation in two selected biological systems at the cell and organism scale, respectively. On the cellular scale, we present a minimal physical mechanism for the spontaneous self-assembly of periodic cytoskeletal patterns, as observed in myofibrils in striated muscle cells. This minimal mechanism relies on the interplay of a passive coarsening process of crosslinked actin clusters and active cytoskeletal forces. This mechanism of cytoskeletal pattern formation exemplifies how local interactions can generate large-scale spatial order in active systems. On the organism scale, we present an extension of Turing’s framework for self-organized pattern formation that is capable of a proportionate scaling of steady-state patterns with system size. This new mechanism does not require any pre-pattering clues and can restore proportional patterns in regeneration scenarios. We analytically derive the hierarchy of steady-state patterns and analyze their stability and basins of attraction. We demonstrate that this scaling mechanism is structurally robust. Applications to the growth and regeneration dynamics in flatworms are discussed (experiments by J. Rink, MPI CBG, Dresden).:1 Introduction 10 1.1 Overview of the thesis 10 1.2 What is biological physics? 12 1.3 Nonlinear dynamics and control 14 1.3.1 Mechanisms of cell motility 16 1.3.2 Self-organized pattern formation in cells and tissues 28 1.4 Fluctuations and biological robustness 34 1.4.1 Sources of fluctuations in biological systems 34 1.4.2 Example of stochastic dynamics: synchronization of noisy oscillators 36 1.4.3 Cellular navigation strategies reveal adaptation to noise 39 2 Selected publications: Cell motility and motility control 56 2.1 “Flagellar synchronization independent of hydrodynamic interactions” 56 2.2 “Cell body rocking is a dominant mechanism for flagellar synchronization” 57 2.3 “Active phase and amplitude fluctuations of the flagellar beat” 58 2.4 “Sperm navigation in 3D chemoattractant landscapes” 59 3 Selected publications: Self-organized pattern formation in cells and tissues 60 3.1 “Sarcomeric pattern formation by actin cluster coalescence” 60 3.2 “Scaling and regeneration of self-organized patterns” 61 4 Contribution of the author in collaborative publications 62 5 Eidesstattliche Versicherung 64 6 Appendix: Reprints of publications 66 / Das Thema der vorliegenden Habilitationsschrift in Theoretischer Biologischer Physik ist die nichtlineare Dynamik funktionaler biologischer Systeme und deren Robustheit gegenüber Fluktuationen und äußeren Störungen. Wir entwickeln hierzu theoretische Beschreibungen für zwei grundlegende biologische Prozesse: (i) die zell-autonome Kontrolle aktiver Bewegung, sowie (ii) selbstorganisierte Musterbildung in Zellen und Organismen. In Kapitel 2, untersuchen wir Bewegungskontrolle auf zellulärer Ebene am Modelsystem von Zilien und Geißeln. Spontane Biegewellen dieser dünnen Zellfortsätze ermöglichen es eukaryotischen Zellen, in einer Flüssigkeit zu schwimmen. Wir beschreiben einen neuen physikalischen Mechanismus für die Synchronisation zweier schlagender Geißeln, unabhängig von direkten hydrodynamischen Wechselwirkungen. Der Vergleich mit experimentellen Daten, zur Verfügung gestellt von unseren experimentellen Kooperationspartnern im Labor von J. Howard (Yale, New Haven), bestätigt diesen neuen Mechanismus im Modellorganismus der einzelligen Grünalge Chlamydomonas. Der Gegenspieler dieser Synchronisation durch mechanische Kopplung sind Fluktuationen. Wir bestimmen erstmals Nichtgleichgewichts-Fluktuationen des Geißel-Schlags direkt, wofür wir eine neue Analyse-Methode der Grenzzykel-Rekonstruktion entwickeln. Die von uns gemessenen Fluktuationen entstehen mutmaßlich durch die stochastische Dynamik molekularen Motoren im Innern der Geißeln, welche auch den Geißelschlag antreiben. Um die statistische Physik dieser Nichtgleichgewichts-Fluktuationen zu verstehen, entwickeln wir eine analytische Theorie der Fluktuationen in einem minimalen Modell kollektiver Motor-Dynamik. Zusätzlich zur Regulation des Geißelschlags durch mechanische Kräfte untersuchen wir dessen Regulation durch chemische Signale am Modell der Chemotaxis von Spermien-Zellen. Dabei charakterisieren wir einen grundlegenden Mechanismus für die Navigation in externen Konzentrationsgradienten. Dieser Mechanismus beruht auf dem aktiven Schwimmen entlang von Spiralbahnen, wodurch ein räumlicher Konzentrationsgradient in der Phase eines oszillierenden chemischen Signals kodiert wird. Dieser Chemotaxis-Mechanismus unterscheidet sich grundlegend vom bekannten Chemotaxis-Mechanismus von Bakterien. Wir entwickeln eine Theorie der senso-motorischen Steuerung des Geißelschlags während der Spermien-Chemotaxis. Vorhersagen dieser Theorie werden durch Experimente der Gruppe von U.B. Kaupp (CAESAR, Bonn) quantitativ bestätigt. In Kapitel 3, untersuchen wir selbstorganisierte Strukturbildung in zwei ausgewählten biologischen Systemen. Auf zellulärer Ebene schlagen wir einen einfachen physikalischen Mechanismus vor für die spontane Selbstorganisation von periodischen Zellskelett-Strukturen, wie sie sich z.B. in den Myofibrillen gestreifter Muskelzellen finden. Dieser Mechanismus zeigt exemplarisch auf, wie allein durch lokale Wechselwirkungen räumliche Ordnung auf größeren Längenskalen in einem Nichtgleichgewichtssystem entstehen kann. Auf der Ebene des Organismus stellen wir eine Erweiterung der Turingschen Theorie für selbstorganisierte Musterbildung vor. Wir beschreiben eine neue Klasse von Musterbildungssystemen, welche selbst-organisierte Muster erzeugt, die mit der Systemgröße skalieren. Dieser neue Mechanismus erfordert weder eine vorgegebene Kompartimentalisierung des Systems noch spezielle Randbedingungen. Insbesondere kann dieser Mechanismus proportionale Muster wiederherstellen, wenn Teile des Systems amputiert werden. Wir bestimmen analytisch die Hierarchie aller stationären Muster und analysieren deren Stabilität und Einzugsgebiete. Damit können wir zeigen, dass dieser Skalierungs-Mechanismus strukturell robust ist bezüglich Variationen von Parametern und sogar funktionalen Beziehungen zwischen dynamischen Variablen. Zusammen mit Kollaborationspartnern im Labor von J. Rink (MPI CBG, Dresden) diskutieren wir Anwendungen auf das Wachstum von Plattwürmern und deren Regeneration in Amputations-Experimenten.:1 Introduction 10 1.1 Overview of the thesis 10 1.2 What is biological physics? 12 1.3 Nonlinear dynamics and control 14 1.3.1 Mechanisms of cell motility 16 1.3.2 Self-organized pattern formation in cells and tissues 28 1.4 Fluctuations and biological robustness 34 1.4.1 Sources of fluctuations in biological systems 34 1.4.2 Example of stochastic dynamics: synchronization of noisy oscillators 36 1.4.3 Cellular navigation strategies reveal adaptation to noise 39 2 Selected publications: Cell motility and motility control 56 2.1 “Flagellar synchronization independent of hydrodynamic interactions” 56 2.2 “Cell body rocking is a dominant mechanism for flagellar synchronization” 57 2.3 “Active phase and amplitude fluctuations of the flagellar beat” 58 2.4 “Sperm navigation in 3D chemoattractant landscapes” 59 3 Selected publications: Self-organized pattern formation in cells and tissues 60 3.1 “Sarcomeric pattern formation by actin cluster coalescence” 60 3.2 “Scaling and regeneration of self-organized patterns” 61 4 Contribution of the author in collaborative publications 62 5 Eidesstattliche Versicherung 64 6 Appendix: Reprints of publications 66