The genetic manipulation of perennial woody tree species presents a range of additional challenges compared to that of annual weedy crop species. These include long generation times and reproductive cycle, the heterogeneity of plants under investigation and, when investigating xylogenesis, a number of physical and biochemical limitations to microscopic and molecular experimentation. Efforts have been made to understand molecular aspects of xylogenesis and have involved functional gene testing using transgenic approaches. These methods involve the production of plantlets from a variety of plant tissues using in vitro full plant regeneration techniques. Although these systems are effective, the time taken from transformation event, to plant establishment and growth, then finally to secondary wood production can take up to several years and requires high labor and technical inputs. (For complete abstract open document)

Coordenação de Aperfeiçoamento de Pessoal de Nível Superior - CAPES / In this work, we investigate the pattern formation of a reaction-diffusion generalist predator-prey system with constant alternative food source and a Holling type III functional response. The local model can exhibit up to six equilibria, bistability, limit cyles and several bifurcations. We analyse diffusive instability conditions and verify the spatial distribution of preys and predators in a two-dimensional habitat with reflective zero-flux boundary conditions. We investigate the spatial behavior for three parameters combinations: Case 1: single coexistence equilibrium; Case 2: bistability; and Case 3: bistability and limit cycle. This work is divided as follows: nn Chapter 1, we present the stability analysis of the local model; in Chapter 2, we consider the movement by diffusion and find diffusive instability conditions; lastly, in Chapter 3 we perform extensive numerical simulations in order to investigate the spatial distribution of preys and predators. / Neste trabalho, investigamos a formação de padrões em um modelo de reação-difusão presa-predador generalista com fonte de alimento alternativa constante e resposta funcional Holling tipo III. O modelo local pode apresentar até seis equilíbrios, biestabilidade, ciclos limite e diversas bifurcações. Analisamos as condições de instabilidade difusiva e verificamos a distribuição espacial de presas e predadores em um habitat bidimensional com fronteira reflexiva. Investigamos o comportamento espacial para três combinações de parâmetros: Caso 1: equilíbrio de coexistência único; Caso 2: biestabilidade; e Caso 3: biestabilidade e ciclo limite. O trabalho está dividido da seguinte forma: no Capítulo 1, apresentamos a análise de estabilidade do modelo local; no Capítulo 2, inserimos a difusão no modelo e encontramos as condições de instabilidade difusiva; por fim, no Capítulo 3, realizamos diversas simulações numéricas a fim de investigar a distribuição espacial de presas e predadores.

Made available in DSpace on 2015-03-26T13:35:25Z (GMT). No. of bitstreams: 1 texto completo.pdf: 4745443 bytes, checksum: e9df978dd48087897127e59c83f364af (MD5) Previous issue date: 2006-03-29 / Coordenação de Aperfeiçoamento de Pessoal de Nível Superior / In this work we study the pattern formation in the interface between two types of granular materials in a Hele-Shaw cell. Different types of patterns, ranging from almost circular to fingered ones were observed, varying the ratio between the size of the grains and the cell spacing. The transition from patterns with fingers to rounded patterns seems to be continuous. The Fourier transform was obtained for the patterns with and without fingers. Patterns that present fingers showed mode selection, contrary to what happens for the rounded patterns. The dependence of the gyration radius and the number of particles at the border of the pattern was studied as a function of the number of particles inside the pattern. We observed that the gyration radius as well as the number of particles at the border of the pattern follow power laws. Analyses of the pattern border roughness showed that the Hurst exponent decreases as the patterns become more rounded. The roughness does not obey a power law with time. For the patterns with fingers the roughness increases with time and as the patterns become more regular it seem to tend to a saturation value. Finger formation is explained in terms of force transmission through the grains. / Em nosso trabalho, estudamos a formação de padrões na interface entre dois tipos de materiais granulares em uma célula de Hele-Shaw. Diferentes tipos de padrões, variando de desde quase-circulares a até padrões com dedos, formaram- se variando a razão entre o tamanho dos grãos e o espaçamento da célula. A transição de padrões com dedos para padrões arredondados parece ser contínua. Foi obtida a transformada de Fourier para os padrões com e sem dedos, sendo que padrões com dedos apresentam seleção de modos, ao contrário do que ocorre para os padrões sem dedos. A dependência do raio de giração e do número de partículas na borda do padrão foi estudada em função do número de partículas dentro do padrão. Observamos que tanto o raio de giração quanto o número de partículas na borda do padrão obedecem a leis de potência. A análise da rugosidade da borda dos padrões mostrou que o expoente de Hurst decresce à medida que os padrões se tornam mais arredondados. A rugosidade não obedece a uma lei de potência com o tempo. Para padrões com dedos a rugosidade aumenta com o tempo e à medida que os padrões se tornam mais regulares ela parece tender a um valor de saturação. A formação dos dedos é explicada em termos da transmissão de forças através dos grãos.

Onde há luz suficiente ,os estômatos, pequenos poros localizados na superfície das folhas, com abertura regulável, tendem a abrir . Isto permite a absorção de C02 (e, portanto, a fotossíntese) , e a evaporação de água, que não pode, porém, ser excessiva. As plantas conseguem ajustar a sua abertura dos estômatos, otimizando a absorção de C02 e adequando-se, ao mesmo tempo, à disponibilidade de água no ambiente. Recentemente, inúmeras experiências mostraram que, ao contrário do que se supunha, a abertura de um estômato parece depender da interação deste com seus estômatos vizinhos. Sob estresse hídrico, o movimento de abrir e fechar, dos estômatos de uma região da folha, freqüentemente se sincroniza, formando padrões espaço-temporais persistentes. Este trabalho teve como objetivo o estudo da dinâmica desses padrões. Reproduzimos, num primeiro momento deste estudo, um modelo proposto por Haefner e colaboradores, para entender melhor o problema. Este modelo , no entanto, demonstrou ser ineficiente sob vários aspectos, ao contrário do que observam os autores. Novos modelos foram então propostos, com resultaados mais próximos aos observados nos experimentosque apresentam melhor concordância com os experimentos. Em particular, destacamos o Modelo de Veias Aleatórias com Histerese, que utiliza a hipótese da existência de um retardo e uma histerese no mecanismo de abertura e fechamento dos estômatos, com resultados que reproduzem a diversidade de comportamento da dinâmica estomática observada experimentalmente. / When there is enough light, stomata - variable aperture pores distributed on plant´s leaves - tend to open. This mechanism allows the absorption of C02 (and so the reaction of photosynthesis) as well as the evaporation of water. The plant can adjust its stomatal aperture over time, in order to maximize C02 uptake with an water loss compatible with environmental conditions. Recently, many experiments have shown that the aperture of a single stomata depends on its interaction with the neighbors in an emergent complex behavior. Under water stress the opening and closing of stomata aperture often becomes synchronized in spatially extended patches, with a rich dynamical behavior. In this work we have studied this phenomena. We first reproduce a model proposed by Haefner and collaborators, in an attempt to better understand this phenomena. The model, however, has been unable to generate patches or an oscillatory behavior in the steady state, as claimed by th authors. We proposed then new models, that show better agreement with experiments. In a particular, the model called by us Randon Vein Model with Hysteresis was able to reproduce most of the behaviors observed in real leaves, including the formation of patches and an non-regular oscillations in the steady state.

Beim Stoffübergang einer grenzflächenaktiven Substanz in einem flüssigen Zweiphasensystem kann solutale Marangoni-Instabilität einsetzen. Die weitere nichtlineare Entwicklung der Marangoni-Instabilität geht mit einer enormen Vielfalt von Strömungsmustern einher. In der Literatur wird dieser Aspekt häufig unter dem unscharfen Ausdruck „Grenzflächenturbulenz“ zusammengefasst. Diese Arbeit stellt heraus, dass drei grundlegende Strukturformen existieren: Rollzellen, Relaxationsoszillationen und Relaxationsoszillationswellen. Ein großer Teil der Komplexität der Strömungsmuster ist dadurch begründet, dass die Grundstrukturen unterschiedliche Hierarchieebenen aufweisen. Es werden die zugrunde liegenden Bedingungen für das Auftreten der jeweiligen Strukturtypen, ihre transiente Natur und die Bildung der hierarchischen Strömungsmuster untersucht. Des Weiteren betrachtet diese Arbeit die Wechselwirkungen mit Dichteeffekten, die sowohl die Charakteristik der Strukturen als auch ihre zeitliche Entwicklung beeinflussen.

Several mechanisms have been proposed to explain the process of vein pattern formation in plant tissues. The most widely accepted amongst biologists is the canalization hypothesis, derived from pea root and stem experiments. According to this hypothesis, a signal, thought to be the phytohormone auxin, is transported polarly from cell to cell from the shoot to the root and is canalized progressively into narrow channels of high auxin fluxes that later differentiate to become vascular tissue. In this project, we set out to test whether auxin canalization drives vein pattern formation, using Arabidopsis thaliana mutants with increased auxin transport (max4-1, max3-9, max2-1 and max1-1). We predicted that the mutants would have distinct vein patterns and especially different angles between the primary and secondary veins, compared to the wild type. First rosette leaves of 15 plants per genotype were harvested for analysis each day from 7 to 17 days after sowing, giving a total of eight hundred twenty-five leaf samples to analyze. Venation patterns were extracted and analyzed using custom-made software written with Matlab. Overall, compared with the wild type, mutants with the highest auxin transport (max4-1 and max3-9) had different vein patterns at early developmental stages, confirming a role for auxin transport in vein patterning. However, veins of mutants and wild type connected at similar angles, which is not consistent with the auxin canalization hypothesis, as originally formulated.

No description available.

A highly structured tissue is formed from an unstructured accumulation of cells during morphogenesis. The pioneering works by Thompson, Turing and Meinhardt introduced physical principles allowing the breaking of symmetry, i.e. the emergence of patterns. This started an ongoing effort to understand the physics behind morphogenesis. In this thesis I will analyze spatial and temporal aspects of morphogenesis for different biological systems in separate parts. The planarian is an ideal model animal to understand mechanisms of spatial body axis formation. This is due to the possibility to measure its body orientation field which utilizes the orientation of the cilia of the planarian’s ventral tissue. Moreover, their astonishing regeneration capabilities allow extensive perturbation experiments. I propose a minimal model which demonstrates the emergence of the wild type body orientation as well as the development of dual-head body orientation due to beta-Catenin RNAi treatment. The topological defects of the body orientation field are calculated on a lattice for simulations and lattice-free for experimental data. These topological defects are a robust way to analyze and compare experiments with simulations. My minimal model reveals sufficient components and mechanisms for robust body axis regeneration. The second important aspect of morphogenesis is the growth regulation of tissues which is often driven by cell proliferation. The regulation of growth is not only important during growth, but also to maintain homeostasis. As fast renewing tissues are very dynamic they may have more pathways of morphogenesis active than non-renewing tissues which points to mechanisms of morphogenesis. The in vivo measurement of this proliferation rate is a challenging task. In this thesis the analysis of DNA labelling assays and the carbon 14 dating method are extended. The carbon 14 dating method can be used to determine cell renewal rates on time scales as long as the lifetime of organism last. Moreover, this method can be applied for tissues in any terrestrial organism because it utilizes the change of carbon 14 in the atmosphere due to atmospheric nuclear bomb tests in the 1960s. The method is extended to gain a better understanding of the tissue dynamics of liver, muscles and amygdala. On the other hand, the DNA labelling assays are used to estimate cell cycle parameters for fast cycling cells. The measurements are fatal to the samples and involve plenty of labor resulting in few sampled data for a time series. The deterministic Nowakowski model is extended to a stochastic model accounting for cell-to-cell and sample-to-sample variability to fully exploit the information contained even in the fluctuations of the data points. A comprehensive parameter recovery study with synthetic ground truth data is performed to evaluate the models. The new stochastic model shows no bias, a good accuracy and scales well with the number of measurements in contrast to the deterministic text-book method. I conclude with proposed applications of my new models and methods that can advance our understanding of growth and pattern formation during morphogenesis. All python software developed in this thesis is shared as open source and a website makes the stochastic analysis of DNA labelling assays available to experimentalists in a user-friendly way.

Cette thèse porte sur la mise en place et le développement d’une approche expérimentale pour l’étude de la dynamique spatio-temporelle de réseaux de réactions à base d’ADN. Nos résultats démontrent la capacité des réseaux d’ADN à se spatialiser sous la forme d’ondes progressives. Nous avons également pu obtenir des motifs stationnaires à base d’ADN et d’assemblages de billes. Ce travail contribue donc à la conception de motifs spatio-temporels de réactions chimiques et de matériaux par le biais de réseaux réactionnels biochimiques programmables. Nous apportons également de nouvelles données sur l’émergence d’ordre spatio-temporel à partir de processus de réaction-diffusion. De ce fait, cette étude contribue à une meilleure compréhension des principes fondamentaux qui régissent l’apparition d’une auto-organisation moléculaire dans un système chimique hors-équilibre. De plus, la combinaison de réseaux synthétiques d’ADN, du contrôle du coefficient de diffusion de plusieurs espèces d’ADN et de la micro-fluidique peut donner lieu à des motifs spatiaux stables, comme par exemple, les fameuses structures de Turing, ce qui tend à confirmer le rôle de celles-ci dans la morphogénèse. / This PhD work is devoted to developing an experimental framework to investigate chemical spatiotemporal organization through mechanisms that could be at play during pattern formation in development. We introduce new tools to increase the versatility of DNA-based networks as pattern-forming systems. The emergence of organization in living systems is a longstanding fundamental question in biology. The two most influential ideas in developmental biology used to explain chemical pattern formation are Wolpert's positional information and Turing's reaction-diffusion self-organization. In the case of positional information, the pattern emerges from a pre-existing morphogen gradient across space that provides positional values as in a coordinate system. Whereas, the Turing mechanism relies on self-organization by driving a system of an initially homogeneous distribution of chemicals into an inhomogeneous pattern of concentration by a process that involves solely reaction and diffusion. Although numerical simulations and mathematical analysis corroborate the incredible potential of reaction-diffusion mechanisms to generate patterns, their experimental implementation is not trivial. And despite of the exceptional achievements in pattern formation with Belousov–Zhabotinsky systems, these are difficult to engineer, thus limiting their experimental implementation to few available mechanisms. In order to engineer reaction-diffusion systems that display spatiotemporal dynamics the following three key elements must be controlled: (i) the topology of the network (how reactions are linked to each other, i.e. in a positive or negative feedback manner), (ii) the reaction rates and (iii) the diffusion coefficients. Recently, using nucleic acids as a substrate to make programmable dynamic chemical systems together with the lessons from synthetic biology and DNA nanotechnology has appeared as an attractive approach due to the simplicity to control reaction rates and network topology by the sequence. Our experimental framework is based on the PEN-DNA toolbox, which involves DNA hybridization and enzymatic reactions that can be maintained out of equilibrium in a closed system for long periods of time. The programmability and biocompatibility of the PEN-DNA toolbox open new perspectives for the engineering of the reaction-diffusion chemical synthesis, in particular in two directions. Firstly, to study biologically-inspired pattern-forming mechanisms in simplified, yet relevant, experimental conditions. Secondly to build new materials that would self-build by a process inspired from embryo morphogenesis. We worked towards the goal of meeting the two requirements of Turing patterning, transferring chemical spatiotemporal behavior into material patterns, and imposing boundary conditions to spatiotemporal patterns. Therefore, the structure of this document is divided into four specific objectives resulting in four chapters. In chapter 1 we worked on testing a DNA-based reaction network with an inhibitor-activator topology. In chapter 2 we focused on developing a strategy to tune the diffusion coefficient of activator DNA strands. In chapter 3 we explored how chemical patterns determine the shape of a material. Finally, in chapter 4 we addressed the issue of controlling the geometry over a DNA-based reaction-diffusion system. Overall, we have expanded the number of available tools to study chemical and material pattern formation and advance towards Turing patterns with DNA.

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.