We study kinetics of phase segregation in multicomponent mixtures via Monte Carlo simulations of the q-state Potts model, in two spatial dimensions, for 2 ≤ q ≤ 20. The associated growth of domains in finite boxes, irrespective of q and temperature, can be described by a single universal finite-size scaling function, with only the introduction of a nonuniversal metric factor in the scaling variable. Our results show that although the scaling function is independent of the type of transition, the q-dependence of the metric factor hints to a crossover at q = 5 where the type of transition in the model changes from second to first order.

In my dissertation I investigate two genera of geckos (Cyrtodactylus and Cnemaspis) that are distributed across Southeast Asia with an emphasis on Cnemaspis. In Chapter 1 I use a multilocus dataset, ancestral area analyses, and molecular clock dating to generate a species level time calibrated phylogeny to test the monophyly of Cyrtodactylus and to identify major biogeographical patterns. I identified that Cyrtodactylus is monophyletic only if the the Sri Lankan genus often recognized as Geckoella is included. The results of the Biogeographical analyses reveal a west to east pattern of diversification. Chapter 2 I use a traditional morphological dataset to describe a new species of Cnemaspis from Peninsular Malaysia. In Chapter 3 my colleagues and I use a multilocus dataset and morphological characters to revise the taxonomy of all Cnemaspis species and put this in a phylogenetic context. This resulted in the description of eight new species and allowed us to generate hypotheses relating to parallel evolution, diversity, and biogeography. In Chapter 4 I use additional taxon sampling of Cnemaspis from Thailand to generate a more complete phylogeny and use an integrative taxonomic approach to describe three new species. In Chapter 5 I used high throughput sequencing of sequence capture and Ultra Conserved Elements to test for a rapid radiation in Cnemaspis and to investigate biogeographic hypotheses relating to the diversification and evolution of Cnemaspis. I determined that there was a temporal rapid radiation of Cnemaspis that coincides with the temporal diversification of other terrestrial vertebrates across Sundaland. The results of these studies indicate that the species diversity of Cnemaspis is underestimated and that both genera have experienced similar temporal and spatial diversification coinciding with major vicariant events during the Eocene and the Oligocene-Miocene transition.

In my dissertation I investigate two genera of geckos (Cyrtodactylus and Cnemaspis) that are distributed across Southeast Asia with an emphasis on Cnemaspis. In Chapter 1 I use a multilocus dataset, ancestral area analyses, and molecular clock dating to generate a species level time calibrated phylogeny to test the monophyly of Cyrtodactylus and to identify major biogeographical patterns. I identified that Cyrtodactylus is monophyletic only if the the Sri Lankan genus often recognized as Geckoella is included. The results of the Biogeographical analyses reveal a west to east pattern of diversification. Chapter 2 I use a traditional morphological dataset to describe a new species of Cnemaspis from Peninsular Malaysia. In Chapter 3 my colleagues and I use a multilocus dataset and morphological characters to revise the taxonomy of all Cnemaspis species and put this in a phylogenetic context. This resulted in the description of eight new species and allowed us to generate hypotheses relating to parallel evolution, diversity, and biogeography. In Chapter 4 I use additional taxon sampling of Cnemaspis from Thailand to generate a more complete phylogeny and use an integrative taxonomic approach to describe three new species. In Chapter 5 I used high throughput sequencing of sequence capture and Ultra Conserved Elements to test for a rapid radiation in Cnemaspis and to investigate biogeographic hypotheses relating to the diversification and evolution of Cnemaspis. I determined that there was a temporal rapid radiation of Cnemaspis that coincides with the temporal diversification of other terrestrial vertebrates across Sundaland. The results of these studies indicate that the species diversity of Cnemaspis is underestimated and that both genera have experienced similar temporal and spatial diversification coinciding with major vicariant events during the Eocene and the Oligocene-Miocene transition.

Given the ongoing biodiversity decline during a time of Indigenous resurgence, Indigenous Protected and Conserved Areas (IPCAs) are garnering interest from the academic community, Indigenous and state governments, and protected area practitioners. Though Indigenous forms of land and sea protection have existed for millennia, these actors are exploring how IPCA development and support can meet needs to protect biodiversity and respect Indigenous rights and roles in conservation. My main research objective was to advance academic and practical applications of IPCAs by drawing from global IPCA research while assisting the Kitasoo/Xai’xais Nation’s IPCA planning process. I investigated two research questions: 1. What are the key successes, challenges, and lessons from IPCA research globally? 2. What can we learn from the Kitasoo/Xai’xais Nation’s rationale and process for developing an IPCA? To answer my first question, I reviewed 58 papers, describing 86 specific IPCA initiatives involving at least 68 Indigenous Peoples across 25 countries. Indigenous Peoples established IPCAs independently and through local- and broad-scale partnerships. Where state IPCA support existed, it was through formal legislation, agreements, and policies, and informally through local relationships and shared values. IPCAs created socio-cultural, political, and ecological benefits. Challenges limited benefits while demanding additional resources for mitigation. I recommend that states and other external actors create/improve IPCA policies, legislations, and resources as defined by Indigenous Peoples; facilitate Indigenous leadership to shape external IPCA establishment and development mechanisms; and create internal Indigenous engagement/partnerships mechanisms. I suggest that Indigenous Peoples would benefit from building partnerships to support and manage their IPCAs. Finally, I recommend that IPCA managers commit more resources, particularly in monitoring and management that integrates management priorities with local and larger scale social-environmental issues. To answer my second question, in collaboration with the Kitasoo/Xai’xais Nation, we used participatory action research to assist efforts to plan a land-and-sea IPCA in Kitasoo/Xai’xais Territory. Together, we used mixed methods to summarize the Nation’s rationale and process. IPCA development is an iteration of ongoing efforts to address limitations of state protected areas to better reflect Kitasoo/Xai’xais rights and responsibilities while preserving culture, biodiversity, and economic opportunity. The Kitasoo/Xai’xais process is rooted in long-term Territory planning and contemporary stewardship capacity building, has benefitted from global IPCA research, and has ongoing multi-generational engagement. The Nation faces challenges similar to other protected areas and is additionally burdened by ongoing colonization impacts. To address these challenges, the Nation is seeking state legislative IPCA recognition, applying Indigenous and complementary western stewardship approaches, and pursuing responsibility-based partnerships. This research makes both practical and academic contributions. It assisted the Kitasoo/Xai’xais IPCA process by contributing to planning and documentation, to be used and modified by the Nation to implement current and future IPCAs. Other Indigenous organizations can adapt the lessons and processes described for their IPCA interests. Additionally, this work provides recommendations for states and other actors at various scales to improve IPCA support and recognition. This work also contributes to literature which highlight Indigenous-led conservation initiatives, including IPCAs, as potential pathways towards supporting biodiversity conservation and Indigenous resurgence. / Graduate

A group of small GTPases consist of over twenty protein families in the super class P-loop. It has a very diverse cell functions. Small GTPases regulate the formation of vesicular follicles, cytoskeleton and nuclear transport. They participate also on cell proliferation and signaling. The aim of my work is to find important amino acids that define family and distinguish each other. I focus on families Arf, Rab, Ran, Ras and Rho. At the Rho family I am also devoted to classes Rho, Rac and Cdc42. Amino acids are identified using bioinformatic programs selected Consurf and Sca5. The objective is also to test P2RANK specialized tool developed at the Charles University in Prague that predict ligand binding sites from protein structure in different families. Founding amino acids can have a big role in the functional divergence of individual families and classes of small GTPases and can be the basis for future study example for the proliferation of cancerous cells. 1.1 Keywords Powered by TCPDF (www.tcpdf.org)

Uma generalização dos modelos de Toda bidimensionais pela inclusão de campos de Dirac é estudada através de métodos algébricos que possibilitam a construção de cargas e soluções para o modelo. Após desenvolver o formalismo matemático necessário, as cargas conservadas do modelo em questão são determinadas para soluções sóliton, a partir da órbita do vácuo. Uma comparação direta com o modelo de sine-Gordon revela que o mesmo processo de interação entre os sólitons ocorre em ambas as teorias, indicando a possibilidade deste modelo ser utilizado para analisar a equivalência entre esse modelo e os de sine-Gordon e Thirring. / A generalization of two dimensional Toda models by the inclusion of Dirac fields is studied through algebraic methods that allow the construction of charges and solutions. After developing the necessary mathematical formalism, the conserved charges of such model are determined forsoliton solutions belonging to the orbits of the vacuum. A direct comparison between Toda model coupled to matter fields and sine-Gordon model shows that the same interaction process among solitons occurs in both theories, indicating the possibility of this model to be used to analyze the equivalence between sine-Gordon and Thirring models.

Os modelos de Toda admitem uma representação de suas equações de movimento em termos da curvatura nula, isto é, existem potenciais que são funcionais dos campos da teoria e pertencem a uma álgebra de Kac-Moody tal que a condição de curvatura nula seja equivalente às equações de movimento. Para a construção das soluções solitônicas e cargas conservadas são necessários a gradação inteira da álgebra de Kac-Moody e a existência de soluções de vácuo, de forma que os potenciais assumam valores em uma subálgebra abeliana quando calculados nestas soluções de vácuo. A gradação da álgebra é de extrema importância pois garante que o potencial transformado tenha a mesma estrutura que o potencial de vácuo. As cargas conservadas são então construídas partindo de soluções da órbita do vácuo por meio de transformações de dressing, que consistem na aplicação da decomposição de Gauss para a produção de um potencial transformado a partir de duas transformações de Gauge. Nesta dissertação calculamos as infinitas cargas conservadas dos modelos de Toda sl(3) e também sl(N), avaliadas nas soluções pertencentes à órbita do vácuo sob transformações de dressing. As soluções de interesse físico, como sólitons e breathers pertencem a esta órbita, e as cargas conservadas para tais soluções são escritas como uma soma sobre os sólitons. Mostramos que a energia e o momento proveem de termos de superfície. / The Toda models admit a zero curvature representation of their equations of motion, i.e. there exist potentials, (A), wich are functionals of the fields of the theory and which belong to a Kac-Moody algebra G such that the zero curvature condition is equivalent to the equations of motion. For the construction of the solitons solutions and conserved charges is required an integer gradation of the Kac-Moody algebra and a ``vacuum solution\'\', such that the potentials evaluated on it belong to an abelian subalgebra. The gradation of the algebra is of extreme importance since it guarantees that the transformed potential have the same structure as the vacuum potential. The conserved charges are then constructed using the dressing method, that through the Gauss decomposition, leads to the transformed potentials by two gauge transformations. In this dissertation we calculate the infinite conserved charges of models Toda sl (3) and also sl (N) evaluated on the solutions belonging to the orbit of the vacuum under dressing transformations. The solutions of physical interest, like solitons and breathers belong to this orbit and the conserved charges for such solutions are written as a sum over the number the solitons. We show that the energy and momentum are boundary terms.

Submitted by Sandro Camargo (sandro.camargo@unipampa.edu.br) on 2015-05-07T22:43:52Z No. of bitstreams: 1 126110038.pdf: 2182930 bytes, checksum: 1d0e56324e775d985abbaf5cea8f4038 (MD5) / Made available in DSpace on 2015-05-07T22:43:52Z (GMT). No. of bitstreams: 1 126110038.pdf: 2182930 bytes, checksum: 1d0e56324e775d985abbaf5cea8f4038 (MD5) Previous issue date: 2014-03-21 / As abelhas apresentam uma combinação de características individuais e ainda de cooperação animal não encontrada no restante do reino animal. São insetos sociais e participam da polinização de diversas plantas que fornecem alimento para o homem. No Brasil com a africanização das abelhas, essas tornaram-se altamente produtoras e enxameadoras, o que vem tornando o país uma potência na produção de mel e outros produtos originados da atividade apícola. Muitas doenças podem afetar as abelhas, dentre elas muitas causadas por vírus. Controlar as infecções virais é essencial para a manutenção ecológica das abelhas e da produção apícola. Ao mesmo tempo, existe a possibilidade de relacionar vírus que infectam humanos com os vírus que infectam as abelhas, visto que os tratamentos utilizados para os seres humanos poderiam ser utilizados em colméias e, ao mesmo tempo, utilizar as abelhas como modelo de estudo para o desenvolvimento de novos antivirais. Na busca por um ponto em comum analisamos filogeneticamente a protease 3C, que ocorre nos vírus da super-família Picorna-like, onde encontram-se os vírus que parasitam as abelhas. Essa protease tem a capacidade de clivar a poliproteína viral nas proteínas maduras do vírus e ainda causar a degradação proteolítica das proteínas do hospedeiro. Até hoje não foi encontrada uma forma de utilizar a protease 3C em estudos filogenéticos pois existe muita divergência das suas sequências entre os vírus. O objetivo dessa pesquisa foi identificar uma forma de analisar filogeneticamente a protease 3C. As sequências da protease 3C e da RdRp de 55 vírus foram coletadas do NCBI ( National Center of Biotechnology Information) e submetidas ao MEME ( Multiple Em for Motif Elicitation), onde foram obtidos quatro sítios conservados. Após foi realizada a análise filogenética dos sítios conservados por Máxima Verossimilhança e análise da distância entre os sítios por parcimônia e ainda foi construída uma árvore com base na RdRp. As árvores dos sítios 1 e 2 apresentaram uma melhor robustez estatística e agrupamento dos vírus. Essas regiões conservadas da protease 3C-Pro podem ser o início para estabelecermos uma relação entre as proteases dos picornavírus e vírus picorna-like na busca da compreensão do seu mecanismo de infecção viral e também uma alternativa de estudo para outras sequências com alta variabilidade. O uso dos domínios 1 e 2 proporcionou a árvore com maior robustez apresentada até o dia de hoje para esta proteína viral. / The bees have a combination of individual features and animal cooperation is not yet found in the rest of the animal kingdom . They are social insects and participate in the pollination of many plants that provide food for man . In Brazil with the africanization of bees , these have become highly producing and swarm , which is making the country a power in the production of honey and other products derived from beekeeping . Many diseases can affect bees , among them many caused by viruses . Control viral infections is essential for ecological maintenance of bees and beekeeping . At the same time , it is possible to relate viruses that infect humans and viruses that infect the bees , whereas the treatments for humans could be used in beehives and at the same time using the bees as a model for development of new antiviral agents. In the search for a common point analyzed phylogenetically 3C protease , which occurs in the superfamily Picorna -like, which are viruses that parasitize bees virus. This protease is capable of cleaving the polyprotein, the mature viral proteins and viruses also cause the proteolytic degradation of host proteins . Until today there a way to use the 3C protease was found in phylogenetic studies because there is much divergence of their sequences between virus.The objective of this research was to identify a way to analyze phylogenetically 3C protease . The 3C protease and RdRp sequences of 55 viruses were collected from the National Center for Biotechnology Information , submitted to MEME , where four conserved sites were obtained . Upon phylogenetic analysis of the conserved sites and by maximum likelihood analysis of the distance between sites by parsimony was performed and was still a tree constructed based on the RdRp . Trees of sites 1 and 2 had a better statistical robustness and clustering of virus. These conserved regions of the 3C protease - Pro may be the start to establish a relationship between the proteases of the picornavirus and Picorna-like viruses in the quest to understand the mechanism of viral infection and also an alternative study for other sequences with high variability . The use of domains 1 and 2 provided the tree with greater robustness displayed until today for this viral protein.

<p>Paralogs arise by duplications and belong to families. Ten paralogs (insulin; <i>IGF-1</i> and <i>-2</i>; <i>INSL3-6</i> and 3-relaxins) constitute the human insulin-relaxin family. The aim of this study was to outline the duplications that gave rise to the vertebrate insulin-relaxin genes and the chromosomal regions in which they reside. Neurotrophin and Trk-receptor families with more than 300, otherwise unrelated, families had paralogs in the regions hosting insulin/relaxin genes, defining two quadruplicate paralogy-regions, namely: insulin/IGF and INSL/relaxin paralogons. Thereby, the localization of insulin/relaxins in human shows that these regions were formed during two genome duplications at the stem of the vertebrates.</p><p>We characterized insulin-like genes (<i>INS-L1</i>, <i>-L2</i> and <i>-L3</i>) in the <i>Ciona intestinalis</i> genome, a species that split from the chordate lineage before the genome duplications. Conserved synteny between the Ciona region hosting the <i>INS-Ls</i> and two human paralogons as well as linkage of the actual paralogons, suggest that a segmental duplication gave rise to the entire region prior to the genome duplications. Synteny together with gene and protein structures demonstrate that <i>INS-L1</i> is orthologous to the vertebrate <i>INSLs</i>/relaxins, <i>INS-L2</i> to insulins and <i>INS-L3</i> to <i>IGFs</i>. This indicates that pro-orthologs of the insulin-relaxin family were formed before Ciona. Our analysis also implies that the INSL/relaxin ancestor switched receptor from tyrosine kinase- to GPCR-type. This probably occurred after the Ciona-stage, but before the genome duplications.</p><p>Using genes residing within the analyzed human paralogons that were present in a chromosomal region in the Ciona-human ancestor, we identified 37 segments with conserved synteny between the <i>Drosophila melanogaster</i> and human genomes. Orthologs residing in Ciona-, sea urchin- and the fly syntenic segments imply that such segments approximate an ancestral region from which the human paralogons originated.</p><p>To conclude, the human paralogons are remnants of genome duplications that in addition to segmental- and single duplications, shaped the extant vertebrate genomes. Using the quadruplicate paralogy-regions we were able to deduce duplication events of the insulin-relaxin genes and their chromosomal regions.</p>

Paralogs arise by duplications and belong to families. Ten paralogs (insulin; IGF-1 and -2; INSL3-6 and 3-relaxins) constitute the human insulin-relaxin family. The aim of this study was to outline the duplications that gave rise to the vertebrate insulin-relaxin genes and the chromosomal regions in which they reside. Neurotrophin and Trk-receptor families with more than 300, otherwise unrelated, families had paralogs in the regions hosting insulin/relaxin genes, defining two quadruplicate paralogy-regions, namely: insulin/IGF and INSL/relaxin paralogons. Thereby, the localization of insulin/relaxins in human shows that these regions were formed during two genome duplications at the stem of the vertebrates. We characterized insulin-like genes (INS-L1, -L2 and -L3) in the Ciona intestinalis genome, a species that split from the chordate lineage before the genome duplications. Conserved synteny between the Ciona region hosting the INS-Ls and two human paralogons as well as linkage of the actual paralogons, suggest that a segmental duplication gave rise to the entire region prior to the genome duplications. Synteny together with gene and protein structures demonstrate that INS-L1 is orthologous to the vertebrate INSLs/relaxins, INS-L2 to insulins and INS-L3 to IGFs. This indicates that pro-orthologs of the insulin-relaxin family were formed before Ciona. Our analysis also implies that the INSL/relaxin ancestor switched receptor from tyrosine kinase- to GPCR-type. This probably occurred after the Ciona-stage, but before the genome duplications. Using genes residing within the analyzed human paralogons that were present in a chromosomal region in the Ciona-human ancestor, we identified 37 segments with conserved synteny between the Drosophila melanogaster and human genomes. Orthologs residing in Ciona-, sea urchin- and the fly syntenic segments imply that such segments approximate an ancestral region from which the human paralogons originated. To conclude, the human paralogons are remnants of genome duplications that in addition to segmental- and single duplications, shaped the extant vertebrate genomes. Using the quadruplicate paralogy-regions we were able to deduce duplication events of the insulin-relaxin genes and their chromosomal regions.