Many multicellular cyanobacteria produce specialized nitrogen-fixing heterocysts. During diazotrophic growth of the model organism Anabaena (Nostoc) sp. strain PCC 7120, a regulated developmental pattern of single heterocysts separated by about 10 to 20 photosynthetic vegetative cells is maintained along filaments. Heterocyst structure and metabolic activity function to accommodate the oxygen-sensitive process of nitrogen fixation. This dissertation focuses on my research on heterocyst development, including morphogenesis, transport of molecules between cells in a filament, differential gene expression, and pattern formation. We using microarray experiments we found that conR (all0187) gene is necessary for normal septum-formation of vegetative cells, diazotrophic grow, and heterocyst morphogenesis. In our studies we characterized the expression of sigma factors genes in Anabaena PCC 7120 during heterocyst differentiation, and we found that the expression of sigC, sigG and sigE is localized primarily in heterocysts. Expression studies using sigE mutant showed that nifH is under the control of this specific sigma factor.

Thesis (Ph. D.)--University of Missouri-Columbia, 2003. / Typescript. Vita. Includes bibliographical references (leaves 135-143). Also available on the Internet.

Thesis (Ph. D.)--University of Oregon, 2003. / Typescript. Includes vita and abstract. Includes bibliographical references (leaves 95-102). Also available for download via the World Wide Web; free to University of Oregon users.

Thesis (Ph. D.)--University of Missouri-Columbia, 2003. / Typescript. Vita. Includes bibliographical references (leaves 135-143). Also available on the Internet.

<p>Diverse mechanisms have been proposed to explain natural pattern formation processes, such as slime mold aggregation, feather branching, and tissue stratification. Regardless of the specific molecular interactions, the vast majority of these mechanisms invoke morphogen gradients, which are either predefined or generated as part of the patterning processes. However, using E. coli programmed by a simple synthetic gene circuit, I demonstrate here the generation of robust, self-organized ring patterns of gene expression in the absence of an apparent morphogen gradient. Interestingly, modeling and experimental tests show that the temporal dynamics of the global morphogen concentration serve as a timing mechanism to trigger formation and maintenance of these ring patterns, which are readily tunable by experimentally controllable environmental factors. This mechanism represents a novel mode of pattern formation that has implications for understanding natural developmental processes. In addition, the system can be coupled with inkjet printing technology and metabolic engineering approaches to develop future complex patterned biomaterials.</p> / Dissertation

Μελετάμε την ροή κοκκώδους σε κεκλιμένη πειραματική διάταξη δυο διαστάσεων, αποτελούμενη από Κ το πλήθος γραμμές και Μ το πλήθος στήλες δοχείων, τα οποία αναταράσσονται κάθετα. Η ροή του υλικού από δοχείο σε δοχείο περιγράφεται από ένα μοντέλο ροής [Eggers, 1999; Van der Weele, 2008]. Υποκινούμενοι από δυσλειτουργίες που παρουσιάζονται στις σύγχρονες βιομηχανικές μονάδες μεταφοράς (όπως είναι ο σχηματισμός συσσωματωμάτων), εισάγουμε σταθερή ποσότητα υλικού στην πρώτη γραμμή των δοχείων, και καθορίζουμε τις συνθήκες κάτω από τις οποίες η ροή παραμένει ομαλή και συνεχής μέχρι την τελευταία γραμμή. Ενώ στην περίπτωση μιας και μόνο σειράς δοχείων (Μ=1) η εκροή μηδενίζεται με την εμφάνιση ενός και μόνο συσσωματώματος [Κανελλόπουλος, 2008], για Μ>1 απαιτούνται περισσότερα συσσωματώματα για τον μηδενισμό της. Μελετάμε τον τρόπο με τον οποίο αυτά τα συσσωματώματα διατάσσονται στα δοχεία, ο οποίος πολλές φορές όπως βλέπουμε μπορεί να είναι ιδιαίτερα πολύπλοκος, αποτελώντας έτσι ένα εξαίρετο παράδειγμα μορφογένεσης σε δυναμικά συστήματα [Cross and Hohenberg, 1993]. Εντοπίζουμε τα βασικά χαρακτηριστικά αυτής της μορφογένεσης και εξηγούμε πως αυτά σχετίζονται με το μοντέλο ροής. Για την περαιτέρω μαθηματική και φυσική τους ερμηνεία προτείνουμε το συνεχές όριο του μοντέλου ροής, το οποίο θα αποτελέσει την απαρχή για μελλοντικές έρευνες [Van der Weele et al, 2008]. Αναφορές: •J. Eggers, Sand as Maxwell’s demon, Phys. Rev. Lett. 83, 5322 (1999). •K. van der Weele, Granular gas dynamics: How Maxwell’s demon rules in a nonequilibrium system, Contemporary Phys. 49, 157-175 (2008). •Γ. Κανελλόπουλος, Οριακή ροή κοκκώδους υλικού σε διάδρομο μεταφοράς, Διπλωματική Εργασία, Τμήμα Μαθηματικών, Πανεπιστήμιο Πατρών (2008). •M.C. Cross and P.C. Hohenberg, Pattern formation outside of equilibrium, Rev.Mod.Phys. 65, 851 (1993). •K. van der Weele, G. Kanellopoulos, C. Tsiavos, and D. van der Meer, Transient granular shock waves and upstream motion on a staircase (submitted, 2009). / We study the dynamics of granular material in a 2-dimensional tilted setup, consisting of K rows and M columns of equal sized compartments, which is brought into motion by vertical shaking. Particles are inserted into the system along the upper row of compartments, then flow downwards, and eventually exit the system from the bottom row. Similar setups are encountered frequently in industrial transport machinery and are notorious for the tendency of the particles to form dense clusters, which obstruct the flow. We model the particle flow from box to box by a flux function and determine the maximal value of the inflow rate for which the flow remains steady. If the inflow rate exceeds this value, clusters are formed. The way in which these clusters are distributed over the KxM compartments is a fine example of spontaneous pattern formation. We analyze the main characteristics of this cluster formation, its dependence on the various parameters of the system, and its sensitivity to experimental fluctuations.

This thesis describes the comparison of time-lapse field observations of suncups on alpine snow with numerical simulations. The simulations consist of solutions to a nonlinear partial differential equation which exhibits spontaneous pattern formation from a low amplitude, random initial surface. Both the field observations and the numerical solutions are found to saturate at a characteristic height and fluctuate chaotically with time. The timescale of these fluctuations is found to be instrumental in determining the full set of parameters for the numerical model such that it mimics the nonlinear dynamics of suncups. These parameters in turn are related to the change in albedo of the snow surface caused by the presence of suncups. This suggests the more general importance of dynamical behaviour in gaining an understanding of pattern formation phenomena.

Die vorliegende Arbeit beschäftigt sich mit der Oberflächenglättung und selbstorganisierten Musterbildung auf Si(100) und Ge(100) durch Beschuss mit niederenergetischen Edelgasionen (Ne, Ar, Kr, Xe). Die Untersuchungen wurden für Ionenenergien zwischen 400 eV und 2000 eV für Ioneneinfallswinkel von 0° bis 85° durchgeführt. Zudem wurde die zeitliche Entwicklung spezifischer Erosionsformen durch die Variation der Fluenz über zwei Größenordnungen analysiert. In den Experimenten finden sich deutliche Anzeichen einer Facettierung sowie einer Vergröberung der Strukturen mit zunehmender Erosionszeit. Diese Beobachtungen deuten darauf hin, dass von Beginn an gradientenabhängiges Zerstäuben und die Reflexion von Primärionen einen wesentlichen Einfluss auf die Strukturentwicklung haben. Die Ergebnisse werden im Kontext bestehender Musterbildungsmodelle diskutiert.

<p>Sorted bedforms are spatial extensive (100 m-km) features present on many inner continental shelves with subtle bathymetric relief (cm-m) and localized, abrupt variations in grain size (fine sand to coarse sand/gravel). Sorted bedforms provide nursery habitat for fish, are a control on benthic biodiversity, function as sediment reservoirs, and influence nearshore waves and currents. Research suggests these bedforms are a consequence of a sediment sorting feedback as opposed to the more common flow-bathymetry interaction. This dissertation addresses three topics related to sorted bedforms: 1) Modeling the long-term evolution of bedform patterns, 2) Refinement of morphological and sediment transport relations used in the sorted bedform model with `machine learning'; 3) Development of a new sorted bedform model using these new `data-driven' components.</p><p> Chapter 1 focuses on modeling the long term evolution of sorted bedforms. A range of sorted bedform model behaviors is possible in the long term, from pattern persistence to spatial-temporal intermittency. Vertical sorting (a result of pattern maturation processes) causes the burial of coarse material until a critical state of seabed coarseness is reached. This critical state causes a local cessation of the sorting feedback, leading to a self-organized spatially intermittent pattern, a hallmark of observed sorted bedforms. Various patterns emerge when numerical experiments include erosion, deposition, and storm events. </p><p> Modeling of sorted bedforms relies on the parameterization of processes that lack deterministic descriptions. When large datasets exist, machine learning (optimization tools from computer science) can be used to develop parameterizations directly from data. Using genetic programming (a machine learning technique) and large multisetting datasets I develop smooth, physically meaningful predictors for ripple morphology (wavelength, height, and steepness; Chapter 2) and near bed suspended sediment reference concentration under unbroken waves (Chapter 3). The new predictors perform better than existing empirical formulations. </p><p> In Chapter 3, the new components derived from machine learning are integrated into the sorted bedform model to create a `hybrid' model: a novel way to incorporate observational data into a numerical model. Results suggest that the new hybrid model is able to capture dynamics absent from previous models, specifically, the two observed end-member pattern modes of sorted bedforms (i.e., coarse material on updrift bedform flanks or coarse material in bedform troughs). However, caveats exist when data driven components do not have parity with traditional theoretical components of morphodynamic models, and I address the challenges of integrating these disparate pieces and the future of this type of `hybrid' modeling.</p> / Dissertation

<p>During embryogenesis, a single zygote gives rise to a multicellular embryo with distinct spatial territories marked by differential gene expression. How is this patterning process organized? How robust is this function to perturbations? Experiments that examine normal and regulative development will provide direct evidence for reasoning out the answers to these fundamental questions. Recent advances in technology have led to experimental determinations of increasingly complex gene regulatory networks (GRNs) underlying embryonic development. These GRNs offer a window into systems level properties of the developmental process, but at the same time present the challenge of characterizing their behavior. A suitable modeling framework for developmental systems is needed to help gain insights into embryonic development. Such models should contain enough detail to capture features of interest to developmental biologists, while staying simple enough to be computationally tractable and amenable to conceptual analysis. Combining experiments with the complementary modeling framework, we can grasp a systems level understanding of the regulatory program not readily visible by focusing on individual genes or pathways. </p><p>This dissertation addresses both modeling and experimental challenges. First, we present the autonomous Boolean network modeling framework and show that it is a suitable approach for developmental regulatory systems. We show that important timing information associated with the regulatory interactions can be faithfully represented in autonomous Boolean models in which binary variables representing expression levels are updated in continuous time, and that such models can provide direct insight into features that are difficult to extract from ordinary differential equation (ODE) models. As an application, we model the experimentally well-studied network controlling fly body segmentation. The Boolean model successfully generates the patterns formed in normal and genetically perturbed fly embryos, permits the derivation of constraints on the time delay parameters, clarifies the logic associated with different ODE parameter sets, and provides a platform for studying connectivity and robustness in parameter space. By elucidating the role of regulatory time delays in pattern formation, the results suggest new types of experimental measurements in early embryonic development. We then use this framework to model the much more complicated sea urchin endomesoderm specification system and describe our recent progress on this long term effort. </p><p>Second, we present experimental results on developmental plasticity of the sea urchin embryo. The sea urchin embryo has the remarkable ability to replace surgically removed tissues by reprogramming the presumptive fate of remaining tissues, a process known as transfating, which in turn is a form of regulative development. We show that regulative development requires cellular competence, and that competence is lost early on but can be regained after further differentiation. We demonstrate that regulative replacement of missing tissues can induce distal germ layers to participate in reprogramming, leading to a complete re-patterning in the remainder of the embryo. To understand the molecular mechanism of cell fate reprogramming, we examined micromere depletion induced non-skeletogenic mesoderm (NSM) transfating. We found that the skeletogenic program was greatly temporally compressed in this case, and that akin to another NSM transfating case, the transfating cells went through a hybrid regulatory state where NSM and skeletogenic marker genes were co-expressed.</p> / Dissertation