Manufacturing companies today face increasingly uncertain and volatile market demands. Product designs and the required quantities change rapidly to meet the needs of customers. To maintain competitiveness in this uncertain environment, manufacturing companies need to possess agility to dynamically and effectively adapt to the changing environment. Agility at the machine level can be thought of as the ability to reconfigure manufacturing machines in response to changing needs and opportunities. This thesis is concerned with a design method for machine level agility for reconfigurable manufacturing machines. This thesis is divided into two portions: a design approach for reconfigurable manufacturing machines and the embodiment of this approach in a computational synthesis example. In developing this design method, various approaches and reconfigurable systems are presented to develop an overview of the applications and current related research to reconfigurable manufacturing machines. From this related research, a research gap is identified pertaining to the identification of the evolving architecture of reconfigurable manufacturing machines. The key contribution is the design approach based on co-evolution. This design approach involves the implementation of agent based co-evolutionary algorithms. In this implementation, each agent synthesizes the configuration of a machine for a product in the range of products it is to manufacture and co-evolves with other agents which are synthesizing machines for other products to reduce the reconfiguration cost. Finally, an in-depth case study of the design approach is presented in which the approach is tested relative to various product changes; thus, showing the advantages of employing an evolving reconfigurable machine architecture. These product changes include batch size variations, geometry changes, and material changes. Hence, the core objective is to identify the necessary reconfigurable manufacturing machine architecture for the range of configurations required for machining various products.

The Capsalidae is a diverse family of ectoparasites of marine fish (Platyhelminthes: Monogenea). It is a large family with approximately 180 described species and many more yet to be discovered. Capsalids have a global distribution and parasitise a diversity of hosts from the Chondrichthyes to bony fishes. A morphological classification exists for the family based on a few key characters such as testes number, their arrangement and morphology of the posterior attachment organ (haptor). Phylogenetic relationships within the family and its position within the Monogenea are largely unexplored. I have used various molecular phylogenetic techniques to resolve relationships and explore the evolution and radiation of this family. Specimens from the Capsalidae and other monogenean families (outgroups) were obtained through fresh collections and generous donations by other parasitologists. Specimens were stored in 95% undenatured ethanol. Three unlinked nuclear genes (28S ribosomal RNA, Histone 3 and Elongation Factor 1 α) and two mitochondrial genes (Cytochrome Oxidase 3 and Cytochrome B) were amplified for 78 capsalid taxa in 28 genera representing all nine subfamilies and 30 outgroup taxa (eight Polyopisthocotylea and 22 Monopisthocotylea). Analyses showed the Capsalidae is monophyletic, with the sister group remaining unresolved. Some analyses supported Gyrodactylidae and Udonellidae as the sister group but in other analyses, it was unresolved with the Monocotylidae and Microbothriidae also possible sister groups. The Capsalinae, Encotyllabinae and Nitzschiinae are monophyletic, but analyses did not support monophyly for the Benedeniinae, Entobdellinae and Trochopodinae. Monophyly was supported for Capsala, Capsaloides, Encotyllabe, Entobdella, Listrocephalos, Neobenedenia, Nitzschia and Tristoma, but Metabenedeniella is paraphyletic and Benedenia and Neoentobdella are polyphyletic. Comparisons of the distribution of character states for the small number of morphological characters on a molecular phylogeny show a high frequency of apparent homoplasy. Consequently the current morphological classification for the Capsalidae shows little correspondence with the phylogenetic hypotheses I present. I also sequenced the first complete mitochondrial (mt) genome for a capsalid species, Benedenia seriolae. The mt genome of B. seriolae shows some tRNA rearrangements in comparison to three Gyrodactylus spp. (Gyrodactylidae), the only other complete monopisthocotylean mt genomes sequenced. It also lacks the duplicated, conserved non-coding regions present in Gyrodactylus spp. making the genome smaller in size. I combined this genome with other available platyhelminth mt genomes to investigate the monophyly of Monogenea and the evolution of diet across the Neodermata. Results confirm paraphyly for the Monogenea and also suggest paraphyly for the epidermal feeding Monopisthocotylea. I hypothesise that the Monopisthocotylea represent the first shift to parasitism in the Neodermata from a free living ancestor and following this, there was a dietary shift to blood feeding (Polyopisthocotylea). The Digenea and Cestoda independently evolved dietary specialisations to suit their diverse microhabitats and broad range of vertebrate final hosts. Using Elongation Factor 1 α I have estimated molecular divergence dates for the Neodermata, Monogenea and Capsalidae. Molecular clock analyses estimate the Neodermata diverged from the free living platyhelminths 513 million years ago (mya) (95% HPD [highest posterior density]: 473–605) before the appearance of vertebrates in the fossil record. The Monogenea diverged from the other neodermatan classes 441 mya (95% HPD: 420–547) coinciding with the appearance of fish in the fossil record. The most recent common ancestor of the Capsalidae arose approximately 235 million years ago (95% HPD: 200–274) following the Permian/Triassic extinction event and coinciding with the diversification of bony fishes in the marine environment. I compared the capsalid phylogeny to a phylogeny of fishes that I generated using eight nuclear and three mt genes to explore the evolution and the radiation of the Capsalidae across fishes. There is no significant global signal of coevolution with only five parasite-host associations that may be a result of coevolution. Estimated molecular divergence dates are also compared and do not reveal temporal congruence. Radiation of the family may have been driven by host switching constrained by shared host ecology, biology, behaviour and plasticity in morphological adaptations by the parasites. This study advances our understanding of the evolution of this monogenean family and provides insights into the evolution of the Neodermata and the complicated realities of reconstructing the evolutionary history of parasitic groups. / http://proxy.library.adelaide.edu.au/login?url= http://library.adelaide.edu.au/cgi-bin/Pwebrecon.cgi?BBID=1522353 / Thesis (Ph.D.) -- University of Adelaide, School of Earth and Environmental Sciences, 2010

Thesis (M.S.)--Missouri University of Science and Technology, 2008. / Vita. The entire thesis text is included in file. Title from title screen of thesis/dissertation PDF file (viewed April 26, 2008) Includes bibliographical references (p. 65-68).

Thesis (Ph. D.)--University of Wyoming, 2007. / Title from PDF title page (viewed Feb. 9, 2009). Includes bibliographical references.

Thesis (Ph. D.)--Ludwig-Maximilians-Universität München, 2003. / Title from PDF title page (viewed on May 13, 2006). Vita. Includes bibliographical references (p. 136-146).

As pressões seletivas impostas por interações ecológicas são uma das forças que moldam a adaptação por seleção natural em populações. Entre os resultados possíveis das pressões seletivas impostas por interações está a coevolução, isto é, mudanças evolutivas recíprocas que ocorrem nas populações das espécies que interagem. Um dos principais desafios para a ecologia evolutiva é entender se e como o processo coevolutivo ocorre quando espécies interagem com muitas outras espécies formando redes de interações. Nesta tese desenvolvi, com a ajuda de colaboradores, modelos que descrevem a coevolução entre espécies que interagem de forma antagonista. Interações antagonistas são interações ecológicas interespecíficas que resultam em consequências negativas para a aptidão de indivíduos de uma das espécies envolvidas e positivas para indivíduos da outra espécie. Busquei uma melhor compreensão sobre os mecanismos ecológicos e evolutivos responsáveis pela formação, manutenção e evolução das redes de interação antagonista. Em primeiro lugar, encontrei que a assimetria da seleção influenciou a dinâmica evolutiva em antagonismos. A dinâmica coevolutiva gerou corridas armamentistas quando a intensidade da seleção foi maior sobre as vítimas do que sobre os exploradores. Por outro lado, os valores dos fenótipos flutuaram quando a intensidade da seleção foi maior sobre os exploradores do que sobre as vítimas. No entanto, a dinâmica coevolutiva dependeu da estrutura das redes formadas por antagonistas. Redes aninhadas favoreceram a evolução de resistência em vítimas atacadas por exploradores generalistas. A dinâmica evolutiva também reorganizou as redes de interação e, especialmente em cenários nos quais a seleção favoreceu forte acoplamento fenotípico, formou módulos de espécies interagentes. Em segundo lugar, encontrei que regras de interação baseadas no acoplamento fenotípico ou em barreiras fenotípicas reproduziram a estrutura de redes antagonistas empíricas, mas as duas relações funcionais entre fenótipos e aptidão tenderam a subestimar o aninhamento e superestimar a modularidade das redes empíricas. No entanto, a evolução das características foi diferentemente moldada por essas relações funcionais, sendo mais flutuante no modelo de acoplamento fenotípico e mais direcional no modelo de barreiras fenotípicas. Portanto, a coevolução mediada por diferentes relações funcionais resultou em diferentes dinâmicas coevolutivas mas não teve impacto sobre a organização das redes de interação antagonistas. Em terceiro lugar, estudei como variações nas abundâncias e nos fenótipos estão relacionadas e encontrei que a coevolução rápida mediada por forte pressões seletivas impostas por interações ecológicas pode resultar em uma baixa variabilidade nas abundâncias das populações e alta variabilidade fenotípica. Em contraste, em cenários nos quais a seleção imposta por interações é fraca, encontrei uma alta variabilidade nos tamanhos populacionais e baixa variabilidade fenotípica. Portanto, a rápida resposta evolutiva reduziu as flutuações nos tamanhos populacionais, reduzindo extinções devido a flutuações demográficas. Porém, este resultado foi influenciado pela estrutura da rede: a modularidade aumentou a estabilidade das interações enquanto que o aninhamento esteve associado a maior flutuação demográfica. Por fim, estudei espalhamento de um parasita que infecta diferentes espécies de hospedeiros e que pode ser transmitido por meio da predação de um hospedeiro infectado ou por meio de vetores biológicos. Combinei as diferentes redes antagonistas formadas a partir das interações mediadas por cada mecanismo de transmissão em uma rede de interação múltipla espacialmente explícita. Por meio de um modelo matemático, obtive que a transmissão do parasita é maximizada quando ambos os mecanismos de transmissão são considerados ao mesmo tempo e quando os processos ocorrem com probabilidade semelhante. A análise da cartografia da rede múltipla aliada a simulações de imunização de diferentes tipos de hospedeiros mostraram que a estrutura da rede múltipla pode indicar o papel que cada espécie de hospedeiro desempenha na transmissão do parasita em um determinado ecossistema / Mutualisms are interactions in which organisms of different species exploit each other with net benefits for both interacting individuals. Multispecific mutualistic system can be depicted as interaction networks, such as those formed by plant-pollinator interactions, dispersal systems, species interacting in cleaning stations in reef environments, protective ants in plants, müllerian mimicry, and nitrogen fixing bacteria on the roots of plants. Mutualistic interaction is subject to cheating by individuals who, by means of a diversity of behavioral strategies, achieve the benefit provided by the partner offering nothing or few in return. However, the mutualistic interactions persist despite the existence of cheaters. In this work I show that the parasites of mutualistic interactions increase the resilience of mutualistic networks to disturbances in nested networks, typically found in species-rich mutualisms. Therefore the joint effect of cheating, structure and dynamics of mutualistic networks have implications for how biodiversity is maintained. I subsequently study the conditions under which tubular flowers, which suffer stronger damages when interacting with nectar robbers, can coexist with planar flowers, pollinators, and robbers through indirect effects of cheating on their reproductive success. The theft of nectar may increase the success of a plant if its interactions with robbers generate higher degrees of cross-pollination, thus increasing the reproductive success of plants that interact with both floral visitors. This study suggests a new source of continued cooperation and diversity strategies through non-linear effects of the interactions between different strategies. Finally, I study how local interactions can promote the prevalence of mimic (the cheaters) in a given population in the absence of their models. I found that prey interacting locally may favor the predominance of mimic preys and avoid predators that, after a few generations and under a non-random distribution of individuals in space, can further strengthen this unexpected effect allopatry of the mimic and its model

The intestinal tract microbiota – microbial community of the gut – is an important field in microbiology not only because of its critical role in the host development, but also increasingly large number of diseases are associated with certain state of the gut microbiota. The community structure and function of the gut microbiota is relatively well studied in humans and related higher vertebrates, but is severely understudied in fish. This is especially true for the coral reef fishes, who constitute the most diverse assemblage of vertebrates spread over a very local scale, and are essential for the resilience of the reefs. In order to bridge this gap in knowledge, this dissertation studied the community structure, interactions and functions of the gut microbial community from the surgeonfishes in the Red Sea – with special focus on the surgeonfish enteric symbiont Epulopiscium spp. Initially, I studied the composition of the gut microbiota of nine surgeonfish and three nonsurgeonfish species from the Red Sea using 454 pyrosequencing. Upon discovering the high abundance of Epulopiscium spp. in herbivorous surgeonfishes, I then proceeded to identify their phylogenetic diversity, distribution, as well as deducing their coevolutionary relationship with the host. Because Epulopiscium spp. undergo substantial changes in the cell size (grow up to ~600μm) and the DNA concentration (from 85 to over 250pg per cell) throughout their diel lifecycle, I also studied the temporal changes in their expression pattern using RNA-seq. Overall, this dissertation shed light on the complex structure, interaction and function of an important family of coral reef fish from the Red Sea through range of molecular techniques.

Dans une première partie, je présente le travail que j’ai accompli sur la coévolution moléculaire. Je présente le contexte biologique et les différentes mesures qui permettent de détecter la conservation et la coévolution à l’échelle des acides aminés. Ensuite, je montre une application de ces mesures à la détection des résidus critiques dans la protéine P53 liée au cancer. Dans ce but, j’ai créé une évaluation des différentes méthodes de prédiction. J’utilise ensuite la même méthodologie sur une base de données de mutations liées à des maladies génétiques. Je montre également comment la coévolution au niveau des résidus permet de découvrir des interactions protéine-protéine sur le virus de l’hépatite C. Enfin, je présente l’algorithme PruneTree, qui permet de filtrer des ensembles de séquences utilisés comme entrée par les programmes de détection de coévolution.Dans une deuxième partie, je m’intéresse à l’étude de l’évolution à l’échelle du génome, en particulier aux mécanismes de recombinaison méiotique. Pour cela j’ai considéré le taux de recombinaison le long du génome et sa cause, les cassures double-brin de l’ADN. Je présente alors un modèle de la distribution de ces cassures et de la liaison des différentes protéines liées à la recombinaison. Je présente également une méthode de détection de périodicité le long du génome basée sur les transformées de Fourier.Enfin, dans la dernière partie, je présente un nouvel algorithme pour simuler l’évolution des génomes de façon à évaluer les outils de reconstruction, et le paquet R-CLAG permettant d’utiliser l’algorithme de classification CLAG depuis R. / In a first part, I show the work I have done on molecular evolution. I present the general biological background and the measures that allow us to detect both conservation and coevolution at the amino-acid level. Then, I present an application of these measures to the detection of critical residues in the cancer protein P53. To this end, I have made a benchmark of different prediction methods. I then use the same methodology on a large scale database of pathogenic mutations linked to genetic diseases. After that, I show how residue-level coevolution can help us discover protein-protein interactions in the hepatitis C virus. Finally, I present the PruneTree algorithm, which allows filtering sequence sets used as input for molecular coevolution detection methods. In a second part, I have studied evolution at the genome level, in particular the recombination mechanisms that occur during meiosis. I have looked at the recombination rates along the genomes and its primary cause, the double-strand breaks, but also at the density of other proteins involved in recombination. I also present a method based on Fourier transforms to analyze these genomic signals, and a model for the distribution along the genome of double-strand breaks and recombination proteins. Finally, I present the other tools I have developed. I describe a novel algorithm that can simulate the evolution of genomes in order to benchmark the phylogenetic reconstruction algorithm PhyChro. Finally, I present the R-CLAG package that allows for easy use of the clustering algorithm CLAG.

京都大学 / 0048 / 新制・課程博士 / 博士(理学) / 甲第18497号 / 理博第4012号 / 新制||理||1578(附属図書館) / 31383 / 京都大学大学院理学研究科生物科学専攻 / (主査)教授 山内 淳, 教授 工藤 洋, 教授 田村 実 / 学位規則第4条第1項該当 / Doctor of Science / Kyoto University / DFAM

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