Skeletal muscle consists of an extremely regular organization of myofibers that are specialized in contraction. Development and maintenance of skeletal muscle function depends on the precise organization of sarcomeric contractile proteins that consist the myofibrils. Impaired or delayed myofibrillogenesis has been identified as the primary pathological mechanism of many skeletal muscle myopathies. Several members of the Kelch family of proteins have been implicated in skeletal muscle development and diseases, and mutations in these proteins have resulted in perturbations in the ubiquitin proteasome system (UPS), which is the primary means of proteasomal degradation in eukaryotes. In particular, KLHL41 of the BTB-BACK Kelch family is primarily expressed in skeletal muscle and has been identified as a regulator of the skeletal muscle differentiation process that results in the normal development and functioning of mature skeletal muscles. KLHL41 acts as a substrate-specific adaptor for Cullin 3 (Cul3) E3 ubiquitin ligase, implicating the role/s of KLHL41 in proteasomal ubiquitination processes in skeletal muscle. Recent studies have determined that the degradation of nebulin-related anchoring protein (NRAP), which was found to interact with KLHL41, is a critical process in skeletal myofibril maturation that is caused by KLHL41-mediated ubiquitination of the NRAP protein. Through this study, it was further confirmed that KLHL41 changes in localization as maturation occurs, which may provide insight into the mechanism of its functions in myofibril maturation. In addition, the study found that KLHL41 promotes the critical process of nebulin-related anchoring protein (NRAP) degradation. Lastly, mutations in the KLHL41, which are known to cause Nemaline Myopathy (NM) in patients, were modeled in murine C2C12 myoblasts to gain a greater understanding of how KLHL41 mutations may affect protein stability and Cul3 E3 ubiquitin ligase activity. Overall, the findings of this thesis support the critical role of KLHL41 in the formation of mature myofibrils, and provides insight into how deficiency of KLHL41 contributes to a disease state through regulation of the CUL3 protein complex. / 2022-06-30T00:00:00Z

Myofibrillogenesis is a complex process, which involves assembly of hundreds of structural proteins in a highly ordered manner to form the contractile structural unit of muscle, the sarcomere. Several myopathic conditions reported in humans are caused due to abnormal myofibrillogenesis owing to mutations in the genes coding for many of these structural proteins. These myopathies have highly variable clinical features and time of onset. Since their aetiology is poorly understood, it becomes imperative to have a model system to study the muscle defects. Present study proposes to employ the Indirect Flight Muscle (IFM) system in Drosophila melanogaster as a model to analyse the development/onset of some of these myopathies and resulting pathophysiology. We have carried out a systematic study on mutations in two major proteins of the sarcomere, actin and myosin, to understand the pathophysiology associated with the disease conditions and in turn gain insights into the process of myofibrillogenesis. To verify whether the human muscle phenotypes are observed in flies, we analysed the IFM for functional and structural defects categorised by the presence of aberrant sarcomeric structures. An important question that we have addressed is whether mutants of the Drosophila IFM recapitulate human conditions and whether it can serve as a good genetic model to study the developmental mechanisms of the human skeletal myopathies in vivo. Mutations of the human ACTA1 skeletal actin gene produce seven congenital myopathies – actin myopathy, nemaline rod myopathy, intranuclear rod myopathy, congenital fibre type disproportion, congenital myopathy with core-like areas, cap disease and zebra body myopathy. Four known mutations in Act88F—a Drosophila homologue of ACTA1—occur at the same actin residues mutated in ten ACTA1 nemaline mutations, A138D/P, R256H/L, G268C/D/R/S and R372C/S. These Act88F mutants were examined for muscle phenotypes with nemaline structures. Mutant homozygotes show phenotypes ranging from lack of myofibrils to almost normal sarcomeres at eclosion. Whereas, heterozygotes do allow myofibrillar assembly to certain extent; however, atypical structures are seen adjacent to normal sarcomeres. Aberrant Z disc-like structures and serial Z disc arrays, ‘zebra bodies’, are observed in homozygotes and heterozygotes of all the four Act88F mutants. The electron-dense structures observed in electron micrographs show homologies to human nemaline bodies/rods, but are much smaller than those typically found in the human myopathy. A possible mechanism for the ‘zebra bodies’ is proposed based on this study. Analysis of IFM at early developmental stages shows that in three of the mutants, there is an abnormal myofibril assembly leading to malformed sarcomeres mirrored in the adult stages. In one of the Act88F mutants, normal myofibrils are seen post-eclosion but the IFM show activity dependant progression of muscle degeneration. All the Act88F mutants produce dominant disruption of muscle structure and function which cannot be rescued even by three copies of the wild type Act88F gene implying that the mutants are strong antimorphs. Myosin myopathies are a group of human muscle diseases with heterogeneous clinical features and are caused by mutations in the skeletal muscle myosin heavy chain. We identified two chemical mutagen generated flightless mutants, Ifm(2)RU1 and ifm(2)RU2 that map closely to myosin heavy chain gene (Mhc) region. Since there are no structural proteins predicted in the mapped region, it was likely that these two are Mhc mutations. We show that Ifm(2)RU1 and ifm(2)RU2 are indeed Mhc mutations and the molecular aberrations affect amino acid residues present in the myosin rod region. Human muscle myosin heavy chain (MyHC) mutations that cause Laing early onset distal myopathy and myosin storage myopathy occur in this domain of the protein. Even though mutations lie in the same region of myosin rod, Ifm(2)RU1 is semidominant, whereas ifm(2)RU2 is recessive. Both the mutants show IFM defects and the presence of abnormal myofibrils. Mutant myofibrillar structures can be rescued with an additional wild type Mhc gene copy. However, the restored myofibrillar structure is incapable of rescuing the flight ability of mutants. The muscle phenotypes are due to defects in thick filament assembly which manifest from the early stages of sarcomere development. The MHC protein rod region is an α-helix that forms coiled-coils which further self assemble to form thick filaments or aggregates as observed in in vitro conditions. Biophysical and biochemical analyses reveal that the coiled-coil structure of mutant rods is not affected, however the thermodynamic stability is altered in ifm(2)RU2 mutation. Interestingly, rod aggregate size and stability are not affected in mutant rods. The Drosophila MHC mutant rods were studied along with four MHC mutant rods that harbour human rod mutations to compare the molecular consequences. The Drosophila mutations do not hamper the rod structure and assembly. Therefore, the defects may arise due to altered interactions with myosin rod binding proteins. Flightin is an extensively studied myosin rod binding protein. The amount and phosphorylation status of flightin are an extremely sensitive measure of thick filament assembly. Flightin phosphorylation is affected in the mutants suggesting a functional dependence on MHC and it also indicates MHC instability. In the light of the work done, we have assessed the mutations with respect to their structure-functional implications. The acto-myosin interactions responsible for the defects are also discussed. Formation of unusual myofibrillar structures are analysed with regards to the process of myofibrillogenesis. An understanding of this entire process with the information available from IFM is reviewed in detail. The work so far has helped in understanding the manifestation of myopathies at tissue/cellular levels with insights into the plausible mechanisms of origin of the disease phenotypes. Myopathic condition may arise due to developmental or functional defects. For therapeutic considerations, the fly provides a simple test to inspect the effects of adding extra copies of the wild type gene. We conclude that the Drosophila IFM provide a good model system for the study of human ACTA1 and MyHC myopathies.

Muscle development involves concerted action of a repertoire of mechanisms governing myoblast proliferation, migration, fusion and differentiation. Subsequently, there are cellular events administrating proper muscle function and maintenance of muscle integrity. Chapter 1 covers what is known about muscle development, building up of mass and maintenance in vertebrates and Drosophila, highlighting the myogenic programs and factors that play a role in them. The formation of vertebrate skeletal muscles can be recapitulated in Drosophila indirect flight muscles (IFMs), making IFMs an interesting model to dissect and understand the mechanisms of muscle development and maintenance. The cellular and developmental events that occur during IFM development have been discussed in detail along with their genetic control which encompasses both cell autonomous and cell non-autonomous mechanisms. The fly resources and tools used for experimentations have been described in Chapter 2. One of the hallmark events during muscle development is myoblast fusion. Myoblasts are kept in undifferentiated state until they fuse through a balanced action of anti-differentiation and pro-differentiation factors. The swarming myoblasts are in semi-differentiated state and just prior to fusion should exit cell cycle to achieve terminal differentiation. The mechanisms of cyclin/CDK complexes and their regulation via CKI (CDK inhibitor) are known in a cell. However, tissue specific factors exerting additional control on molecules that participate in cell cycle have been proposed but have not been shown in vivo. Chapter 3 uncovers a novel role played by the transcription factor, Erect wing (Ewg) in IFM development and patterning. Despite the fact that Ewg is known to express in fusing myoblasts and nuclei of developing IFMs and has long been used as a nuclear marker for IFMs, the mechanism(s) behind Ewg‟s function has remained enigmatic. Historical perspective of Ewg has been presented in Chapter 1. One set of IFMs; dorsal longitudinal muscles (DLMs) require larval templates for their formation and the other set; dorsal ventral muscles (DVMs) form de novo. Chapter 3 shows that Ewg is required in a spatio-temporal fashion to initiate myoblast fusion process. In the absence of Ewg, the number of fusion events in a given time is reduced. In addition de novo fusion is observed in the region of DLM development just like DVM and overall IFM development is delayed resulting in an aberrant adult IFM pattern. Genetic studies undertaken reveal a requirement for Ewg in exerting a temporal control on myoblast fusion. This is achieved by down-regulating Cyclin E levels, as a result of which the myoblasts exit cell cycle at G1/S stage. Through this study the proposal for DLM development and pattern has been put forth as follows: i) appropriate progression of DLM development commences on synchronous exit of myoblasts from cell cycle. This function is facilitated by Ewg expression in fusing myoblasts assisting symmetrical DLM formation in hemithoraces. ii) DLM pattern of six muscles in each hemithorax is dependent on template survival which requires fusion of enough myoblasts and further subsequent fusion events to support the splitting of three larval templates or presumptive DLM. The muscles that develop should preserve their structural integrity for efficient functional output. Muscles perform extensive activities warranting high energy requirements. IFMs are widely utilised for thorax movements that aid flight. IFMs are exclusively oxidative in nature with upto 40% mass contributed by large mitochondria themselves. Chapter 4 describes yet another novel finding for Ewg function in IFM maintenance. Vertebrate homolog of Ewg is nuclear respiratory factor 1 (NRF1) known for its role in mitochondrial biogenesis. This prompted an investigation on the role of Ewg, if any, in mitochondrial function and IFM maintenance. In this chapter, Ewg null adult IFMs are shown to undergo degeneration. Mitochondria in these muscles show rounder and smaller phenotype. Mitochondria morphology is traced throughout Drosophila pupal DLM development and extensive fusion is observed in last one-fourth of pupal phase. In Ewg null condition transcripts of Opa1-like required for inner mitochondrial membrane fusion is found to be absent, suggesting lack of mitochondrial fusion behind the smaller mitochondrial morphology. This emerged as an intriguing problem since Ewg expression follows until sarcomerogenesis (formation of sarcomeres) initiates at mid pupal stage. Developmentally extending Ewg‟s expression beyond mid pupal stage is not observed to increase Opa1-like levels pointing an indirect regulation by Ewg. However, Opa1-like knock-down beyond mid pupal stage is not observed to result in any muscle or flight defect. It is thus proposed that Ewg expression early during muscle development helps to up-regulate Opa1-like levels needed to support mitochondrial growth and fusion. In addition, this chapter provides additional data on requirement of Opa1-like for maintenance of mitochondrial as well as muscle integrity. This is the first ever report of tissue specific temporal regulation of Opa1-like by Ewg. Chapter 3 and Chapter 4 conclude spatially segregated functional requirements of Ewg which are also mechanistically distinct. Expression in fusing myoblasts channelizes fusing myoblasts to exit cell cycle and undergo timely fusion saving the larval template, subsequent fusion assists template splitting thus forming the appropriate adult DLM pattern. On the other hand expression until mid pupal stage up-regulates Opa1-like expression, facilitating mitochondrial fusion during the late pupal stage. This as a result helps maintain structural integrity of muscles in the adult. Vertebrate skeletal muscle contains multiple muscle fibres that provide appropriate mass and size to muscles. As DLM share similarity in development to that of the vertebrate skeletal muscle, DLM organisation is studied to get insights into the mechanisms which regulate the process. Chapter 5 discusses role of nuclear number and nuclear activity in determining the DLM organisation. In order to alter nuclear number, myoblast population is reduced to amounts lesser than that of the wild type and to alter nuclear activity, two nuclear encoded genes Opa1-like and Marf , involved in inner and outer mitochondrial membrane fusion respectively have been knocked down in IFMs. First, the DLM organisation is established by comparing it to the vertebrate skeletal muscle organisation. This organisation is affected on lowering the number of myoblasts destined to fuse and form IFMs, without affecting the differentiation. On the other hand, when nuclear encoded mitochondrial fusion genes are knocked down, not only DLM organisation but their differentiation is also affected. A proposal for achieving DLM organisation has been presented which should also apply to vertebrate skeletal muscle given their developmental similarity. In conclusion, the studies decipher a novel mechanism by which a transcription factor, Ewg exerts a temporal control on myoblast fusions directly influencing progression of DLM formation, and thereby, symmetry and pattern. Moreover, Ewg is also shown here to regulate mitochondrial fusion during later pupal stages helping muscles to attain greater function and maintain structural integrity. Discovery of such regulatory mechanisms controlling mitochondrial dynamics in vertebrates can open up new avenues to understand and design new therapeutic approaches to tackle mitochondrial diseases. Additionally, myoblast fusion and hence myonuclear number and their efficient functioning are shown to be important determinants of muscle organisation. This has further implications in understanding and using stem cell science in dystrophic or atrophic or ageing related muscle loss and therapy.

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