Mathematical modeling is an important tool in improving the understanding of complex biological processes. However, mathematical models are often faced with challenges that arise due to the limited knowledge of the underlying biological processes and the high number of parameters for which exact values are unknown. The method of generalized modeling is an alternative modeling approach that aims to address these challenges by extracting information about stability and bifurcations of classes of models while making only minimal assumptions on the specific functional forms of the model. This is achieved by a direct parameterization of the Jacobian in the steady state, introducing a set of generalized parameters which have a biological interpretation. In this thesis, the method of generalized modeling is extended and applied to different problems from cell biology. In the first part, we extend the method to include also the higher derivatives at the steady state. This allows an analysis of the normal form of bifurcations and thereby a more specific description of the nearby dynamics. In models of gene-regulatory networks, it is shown that the extended method can be applied to better characterize oscillatory systems and to detect bistable dynamics. In the second part, we investigate mathematical models of bone remodeling, a process that renews the human skeleton constantly. We investigate the connection between structural properties of mathematical models and the stability of steady states in different models. We find that the dynamical system operates from a stable steady state that is situated in the vicinity of bifurcations where stability can be lost, potentially leading to diseases of bone. In the third part of this thesis, models of the MAPK signal transduction pathway are analyzed. Since mathematical models for this system include a high number of parameters, statistical methods are employed to analyze stability and bifurcations. Thereby, the parameters with a strong influence on the stability of steady states are identified. By an analysis of the bifurcation structure of the MAPK cascade, it is found that a combination of multiple layers in a cascade-like way allows for additional types of dynamic behavior such as oscillations and chaos. In summary, this thesis shows that generalized modeling is a fruitful alternative modeling approach for various types of systems in cell biology. / Mathematische Modelle stellen ein wichtiges Hilfmittel zur Verbesserung des Verständnisses komplexer biologischer Prozesse dar. Sie stehen jedoch vor Schwierigkeiten, wenn wenig über die zugrundeliegende biologischen Vorgänge bekannt ist und es eine große Anzahl von Parametern gibt, deren exakten Werte unbekannt sind. Die Methode des Verallgemeinerten Modellierens ist ein alternativer Modellierungsansatz mit dem Ziel, diese Schwierigkeiten dadurch anzugehen, dass dynamische Informationen über Stabilität und Bifurkationen aus Klassen von Modellen extrahiert werden, wobei nur minimale Annahmen über die spezifischen funktionalen Formen getätigt werden. Dies wird erreicht durch eine direkte Parametrisierung der Jacobimatrix im Gleichgewichtszustand, bei der neue, verallgemeinerte Parameter eingeführt werden, die eine biologische Interpretation besitzen. In dieser Arbeit wird die Methode des Verallgemeinerten Modellierens erweitert und auf verschiedene zellbiologische Probleme angewandt. Im ersten Teil wird eine Erweiterung der Methode vorgestellt, bei der die Analyse höherer Ableitungen im Gleichgewichtszustand integriert wird. Dies erlaubt die Bestimmung der Normalform von Bifurkationen und hierdurch eine spezifischere Beschreibung der Dynamik in deren Umgebung. In Modellen für genregulatorische Netzwerke wird gezeigt, dass die so erweiterte Methode zu einer besseren Charakterisierung oszillierender Systeme sowie zur Erkennung von Bistabilität verwendet werden kann. Im zweiten Teil werden mathematische Modelle zur Knochenremodellierung untersucht, einem Prozess der das menschliche Skelett kontinuierlich erneuert. Wir untersuchen den Zusammenhang zwischen strukturellen Eigenschaften verschiedener Modelle und der Stabilität von Gleichgewichtszuständen. Wir finden, dass das dynamische System von einem stabilen Zustand operiert, in dessen Nähe Bifurkationen existieren, welche das System destabilisieren und so potentiell Knochenkranheiten verursachen können. Im dritten Teil werden Modelle für den MAPK Signaltransduktionsweg analysiert. Da mathematische Modelle für dieses System eine hohe Anzahl von Parametern beinhalten, werden statistische Methoden angewandt zur Analyse von Stabilität und Bifurkationen. Zunächst werden Parameter mit einem starken Einfluss auf die Stabilität von Gleichgewichtszuständen identifizert. Durch eine Analyse der Bifurkationsstruktur wird gezeigt, dass eine kaskadenartige Kombination mehrerer Ebenen zu zusätzliche Typen von Dynamik wie Oszillationen und Chaos führt. Zusammengefasst zeigt diese Arbeit, dass Verallgemeinertes Modellieren ein fruchtbarer alternativer Modellierungsansatz für verschiedene zellbiologische Probleme ist.

The FYVE domain is a lipid binding domain found in approximately 27 different mammalian proteins. It specifically interacts with the lipid, PI(3)P, which is enriched on early endosomes. Consequently, many FYVE domain-containing proteins localize to the endosome, however the ability of FYVE domains to target to endosomal membranes is variable, despite high sequence conservation. Here we describe the structural requirements necessary for endosomal localization and liposome avidity. As FYVE domains are lipid binding domain, many FYVE domain-containing proteins have been implicated in membrane trafficking. We performed an RNAi screen of FYVE domain-containing proteins to identify general regulators of endocytosis in Caenorhabditis elegans. In this screen, we identified the EEA1, a known regulator of endocytosis and two novel genes: WDF2 and KIAA1643. Initial characterization of WDF2 suggest that its function is conserved in humans. Of all the FYVE domain-containing proteins, we have been particularly interested in SARA (Smad Anchor for Receptor Activation); a protein implicated in the TGFβ signaling pathway. This protein contains a binding domain for the TGFβ mediated transcription factor, Smad2/3, and a FYVE domain. It was the presence of the FYVE domain, an endosomal targeting signal, in SARA that lead us to hypothesize that endocytosis might be a necessary step in TGFβ signaling. SARA localizes to the early endosome; the TGFβ receptors also internalize into these endosome. When this internalization is prohibited, there is correlative decrease in Smad2/3 phosphorylation, Smad2 nuclear translocation and TGFβ mediated transcription. Overexpression of a dominant negative SARA construct and SARA siRNA oligonucleotides inhibit TGFβ signaling. We conclude that TGFβ receptor signaling to Smad2/3 occurs on the endosome and this signaling requires SARA. Receptor mediated endocytosis has been classically thought of as an important mechanism for attenuating signaling pathways. We have redefined the role of endocytosis to include the necessary and positive regulation of specific signaling pathways. We have also extended our insights into the biological role of the endosome as a compartment specialized for the assembly and propagation of specific extracellular signals.

Cytokinesis is the final event of the cell division cycle and results in physical and irreversible separation of a mother cell into two daughter cells. Cytokinesis must only occur after chromosomes have segregated during mitosis to ensure each daughter cell receives the proper complement of genetic material. Failure to execute normal cytokinesis can result in aneuploidy and/or polyploidy, a hallmark of many cancers. Cytokinesis occurs mechanically through constriction of an actin-myosin based contractile ring, while initiation of ring constriction is temporally and spatially mediated by complex signaling networks. It is absolutely crucial that cytokinesis is tightly coordinated with the cell cycle in order to preserve the fidelity of cell division. We hypothesized that to achieve such tight control of cytokinesis, cells may utilize both promotional and inhibitory signals, however how cells maintained this control was poorly understood. The goal of this thesis was to characterize how cells regulate signaling of cytokinesis, both positively and negatively, during cell division using the fission yeast Schizosaccharomyces pombe as a model organism. Two approaches were employed. (1) We first sought to characterize the positive timing mechanism that signals cytokinesis though a detailed investigation of Sid1p, a protein kinase essential for activation of ring constriction. (2) Secondly, we sought to define how cells negatively regulate cytokinesis through investigation of Dma1p, a spindle checkpoint protein implicated in inhibition of cytokinesis. Our results reveal a conserved signaling network, termed the Septation Initiation Network (SIN), of which Sid1p is an intermediate component, that controls temporal and spatial regulation of cytokinesis. We found Sid1p is additionally controlled by Cyclin Dependent Kinase activity, uncovering an important link between mitotic events and initiation of cytokinesis. Furthermore, we found that aberrant SIN activation can override a microtubule-damage-induced spindle checkpoint arrest. This effect is counteracted by Dma1p, which normally inhibits the SIN during checkpoint activation to preserve cell viability until damage is repaired. We conclude that signaling cytokinesis is tightly coordinated with mitosis in S. pombe by positive signals acting through Sid1p and the SIN, and under certain conditions, negative signals acting through Dma1p. Considering the conservation of cell cycle regulators in the eukaryotic kingdom, it is likely that similar mechanisms to control cytokinesis exist in humans.

Evaluating our environment by deciding what is beneficial or harmful, pleasant or punishing is a part of our daily lives. Seeking pleasure and avoiding pain is a common trait all mobile organisms exhibit and understanding how rewarding stimuli are represented in the brain remains a major goal of neuroscience. Studying reward learning in the fruit fly, Drosophila melanogaster has enabled us to better understand the complex neural circuit mechanisms involved in reward processing in the brain. By conditioning flies with sugars of differing nutritional properties, we determined that flies trained with sweet but non-nutritive sugars formed robust short-term memory (STM), but not long-term memory (LTM). However, flies conditioned with a sweet and nutritious sugar or a sweet non-nutritious sugar supplemented with a tasteless nutritious compound, formed robust 24 hour LTM. These findings led us to propose a model of parallel reinforcement pathways for appetitive olfactory conditioning in the fly, in which both sweet taste and nutrient value contribute to appetitive long-term memory. We followed this line of research by examining the neural circuitry in the fly brain that represents these parallel reward pathways. We found that the biogenic amine octopamine (OA) only represents the reinforcing effects of sweet taste. Stimulation of OA neurons could replace sugar in olfactory conditioning to form appetitive STM. Surprisingly, implanting memory with OA was dependent on dopamine (DA) signaling, which although being long associated with reward in mammals, was previously linked with punishment in flies. We found that OA-reinforced memory functions through the α-adrenergic OAMB receptor in a novel subset of rewarding DA neurons that innervate the mushroom body (MB). The rewarding population of DA neurons is required for sweet and nutrient reinforced memory suggesting they may integrate both signals to drive appetitive LTM formation. In addition, OA implanted memory requires concurrent modulation of negatively reinforcing DA neurons through the β-adrenergic OCTβ2R receptor. These data provide a new layered reward model in Drosophila in which OA modulates distinct populations of both positive and negative coding DA neurons. Therefore, the reinforcement system in flies is more similar to that of mammals than previously thought.

Neuronal nicotinic acetylcholine receptors (nAChRs) are involved in a plethora of fundamental biological processes ranging from muscle contraction to the formation of memories. The studies described in this work focus on the transcriptional regulation of the CHRNB4 gene, which encodes the ß4 subunit of neuronal nAChRs. We previously identified a regulatory sequence (5´– CCACCCCT –3´), or “CA box”, critical for CHRNB4 promoter activity in vitro. Here I report transcription factor interaction at the CA box along with an in vivo analysis of CA box transcriptional activity. My data indicate that Sp1, Sp3, Sox10 and c-Jun interact with the CHRNB4 CA box in the context of native chromatin. Using an in vivo transgenic approach in mice, I demonstrated that a 2.3-kb fragment of the CHRNB4 promoter region, containing the CA box, is capable of directing cell-type specific expression of a reporter gene to many of the brain regions that endogenously express the CHRNB4 gene. Site-directed mutagenesis was used to test the hypothesis that the CA box is critical for CHRNB4 promoter activity in vivo. Transgenic animals were generated in which LacZ expression is driven by a mutant form of the CA box. Reporter gene expression was not detected in any tissue or cell type at ED18.5. Similarly, I observed dramatically reduced reporter gene expression at PD30 when compared to wild type transgenic animals, indicating that the CA box is an important regulatory feature of the CHRNB4 promoter. ChIP analysis of brain tissue from mutant transgenic animals demonstrated that CA box mutation results in decreased interaction of the transcription factor Sp1 with the CHRNB4 promoter. I have also investigated transcription factor interaction at the CHRNB4 promoter CT box, (5´– ACCCTCCCCTCCCCTGTAA –3´) and demonstrated that hnRNP K interacts with the CHRNB4 promoter in an olfactory bulb derived cell line. Surprisingly, siRNA experiments demonstrated that hnRNP K knockdown has no impact on CHRNA5, CHRNA3 or CHRNB4 gene expression. Interestingly, knockdown of the transcription factor Purα results in significant decreases in CHRNA5, CHRNA3 and CHRNB4 mRNA levels. These data indicate that Purα can act to enhance expression of the clustered CHRNA5, CHRNA3 and CHRNB4 genes. Together, these results contribute to a more thorough understanding of the transcriptional regulatory mechanisms underlying expression of the CHRNB4 as well as the CHRNA5 and CHRNA3 genes, critical components of cholinergic signal transduction pathways in the nervous system.

Motile microorganisms navigate through their environment using special molecular machinery in order to sense gradients of various signals: chemotaxis (reactions to chemical compounds) and phototaxis (to light) sensory cascades. Transmembrane receptors play a central role in these cascades as they receive input signals and transmit them inside the cell, where they modulate activity of the kinases CheA, which are tightly bound to their cytoplasmic domains. CheA further phosphorylates the response regulator protein CheY, which regulates the flagella. At the same time, CheA phosphorylates and, by means of this, activates another response regulator, CheB, which, along with the constantly active CheR protein, catalyzes two opposite reactions: methylation and demethylation of the specific glutamic acid residues located at the cytoplasmic domain of the receptors. The latter reactions establish the adaptation mechanism, which allows microbes to sense in a very broad range of the input signal intensities. Many functional, structural and dynamical aspects of the signal propagation through the prokaryotic receptors as well as a mechanism of the signal amplification remain still unclear. In the present thesis we have used various techniques of computational biophysics, chiefly molecular dynamics (MD) simulations, in order to approach these problems. In Chapter 3, we have carried out MD simulations of the isolated linker domain (HAMP) from the E. coli Tsr chemoreceptor. The MD simulations revealed highly dynamical nature of this domain, which allows for interconversion between several metastable states. These metastable states feature a number of structural and dynamical properties, which were previously reported for HAMP domains of various receptors obtained from different organisms. It allowed us to reconcile numerous experimental data and to hypothesize that different HAMP domains share similar mechanism of their action. In Chapter 4, we have performed MD simulations of the whole cytoplasmic domain of the Tsr chemoreceptor. The simulations revealed a mechanism for the inter-domain coupling between the HAMP domain and a part of the cytoplasmic domain adjacent to the HAMP, the adaptation subdomain, by means of the regulated unfolding of a short linker region termed the stutter. Also, we have found that the reversible methylation/demethylation of the cytoplasmic domain affects its flexibility and symmetry. Altogether, these findings suggest a mechanism of signal propagation at the level of an individual chemoreceptor dimer. In Chapter 5, we have built a model of the trimer-of-dimers of the archaeal phototaxis receptor complex (NpSRII:NpHtrII). Subsequent MD simulations revealed an important role of dynamics in signal transduction and, potentially, in the kinase activation. In Chapter 6, we have reconstructed a whole transmembrane lattice formed by the NpSRII:NpHtrII complexes. The concave shape of the obtained lattice naturally explains polar localization of the receptor arrays in prokaryotic cells. At the same time, additional MD simulations of an individual unit of this lattice (a dimer of the photosensor) revealed global motional modes in its transmembrane region, which presumably co-occur with its activation and can spread across the tightly packed transmembrane arrays allowing for the signal amplification.

No description available.

Die Familie der G-Protein-gekoppelten Rezeptoren (GPCRs) bildet die größte Gruppe von Membranrezeptoren im menschlichen Organismus. Für viele GPCRs sind bisher die physiologischen Funktionen nicht bekannt. Das biologische Verständnis der Funktionen im menschlichen Organismus dieser sogenannten „orphan“ GPCRs (oGPCRs) hat, aufgrund möglicher kausaler Beteiligung an der Pathogenese von Erkrankungen sowie deren therapeutische Beeinflussbarkeit, hohe medizinische Relevanz. Die GPCRs der P2Y12-ähnliche Rezeptorgruppe besitzen eine große physiologische Bedeutung bei der Thrombozytenaggregation und der Induktion der Migration von immunokompetenten Zellen in Schädigungsgebiete. Der ADP-Rezeptor P2Y12 kann durch verschiedene pharmakologische Wirkstoffe beeinflusst werden, was bereits klinisch-therapeutisch genutzt wird. Diese Gruppe von GPCRs enthält jedoch auch Mitglieder, deren Funktionen völlig unbekannt sind. Einer dieser oGPCRs ist der GPR34. Ziel dieser Arbeit war es, mittels verschiedener in-vitro-Methoden und anhand eines GPR34-defizienten Mausstamms die physiologische Relevanz dieses P2Y12-ähnlichen Rezeptors zu analysieren. Dazu wurde ein GPR34-Knockout-Mausmodell etabliert. Die GPR34-Defizienz hatte keinen wesentlichen Einfluss auf die Entwicklung, Morphologie, das Wachstum oder die Fertilität bei Mäusen. Die Ergebnisse aus Immunisierungs– und Infektionsstudien zeigten jedoch, dass dieser evolutionär hoch konservierte Rezeptor eine wichtige Funktion in der Feinkontrolle der zellulären Immunabwehr ausübt. Neben einer verstärkten Antwort im Delayed-type Hypersensitivity (DTH)-Test war die Abwehr einer Cryptococcus-Infektion in diesem GPR34-defizienten Tiermodell beeinträchtigt. Signifikant erhöhte Zytokinspiegel nach Antigen- bzw. Pathogenexposition deuteten auf eine gestörte Immunregulation in GPR34-defizienten Mäusen hin. Weiterführende Untersuchungen sollten sich der Identifizierung des endogenen Agonisten und der Funktion des GPR34 bei der Koordinierung der zellulären Immunreaktion widmen.

<p>Oncogenic mutations in KRAS are present in approximately 95% of patients diagnosed with pancreatic ductal adenocarcinoma (<b>PDAC</b>) and are considered the initiating event during the development of pancreatic intraepithelial neoplasia (<b>PanIN</b>) precursor lesions. While it is well established that KRAS mutations can drive the initiation of pancreatic oncogenesis, the effects of oncogenic KRAS signaling on regulation of phosphatases during this process is not fully appreciated. Protein Phosphatase 2A (<b>PP2A</b>) has been implicated in suppressing KRAS-driven cellular transformation. However, low PP2A activity is observed in PDAC cells compared to non-transformed cells, suggesting that suppression of PP2A activity is an important step in the overall development of PDAC. In the current study, we demonstrate that KRASG12D induces the expression of both Cancerous Inhibitor of PP2A (<b>CIP2A</b>), an endogenous inhibitor of PP2A activity, and the PP2A target, c-MYC. Consistent with these findings, KRASG12D sequestered the specific PP2A subunit responsible for c-MYC degradation, B56a, away from the active PP2A holoenzyme in a CIP2A-dependent manner. During PDAC initiation <i>in vivo</i>, knockout of B56a promoted KRASG12D tumorigenesis by accelerating acinar-to-ductal metaplasia (<b>ADM</b>) and the formation of PanIN lesions. The process of ADM was attenuated <i>ex vivo</i> in response to pharmacological re-activation of PP2A utilizing direct small molecule activators of PP2A (<b>SMAP</b>s). Together, the results of this study suggest that suppression of PP2A-B56a through KRAS signaling can promote Myc-driven initiation of pancreatic tumorigenesis.</p>

<p>The PRLs are a subfamily of dual specificity phosphatases that appear to play important roles in oncogenesis. Much of the current understanding of PRL function has been either correlative, and deduced from observed PRL overexpression in pathological conditions, or from in vitro analysis of signaling pathways following PRL deletion or overexpression. Such studies, necessitated by the general lack of synthetic inhibitors or compounds to probe the substrate specificity and biological interactions of the PRLs, are nonetheless now providing critical insight into potential biological substrates and roles of the PRL phosphatases. The recent identification of PTEN as a substrate for PRL2 provided the foundation for studies to further define the role of PRL2 in oncogenesis and, by analogy, the normal physiological function of PRL2. In the studies described herein, a novel PRL2 conditional knock-out animal was generated and used to validate the PRL2/PTEN interaction in a leukemic phenotype, and further demonstrated that PRL2 inhibition can restore dysregulated PTEN/AKT pathways to significantly attenuate disease progression. Inhibition of PRL2 therefore represents a novel potential therapeutic strategy in the management and treatment of AML. This thesis project also sought to further examine the role of the PRLs in oncogenesis through their regulation and interaction of targets within the TME. Functional analyses revealed that PRL3 was the only PRL to have a prominent role in host response to TME development, and that previously proposed roles for PRL3 in angiogenesis and immune cell recruitment is dependent upon PRL3 expression and activity in cells external to the TME. The study also revealed a previously unrecognized synergism between VEGF and PRL3 in the host in promoting TME angiogenesis. The studies of PRL3 in the TME suggest the potential physiological role of PRL3 in wound healing.</p>