The Distal-less homeobox (Dlx) genes encode homeodomain transcription factors that play important roles in the development of limbs, sensory organs, branchial arches and the forebrain. In the forebrain, Dlx1 and Dlx2 are expressed in neuronal progenitor cells and play essential roles in GABAergic neuron differentiation and migration. In order to understand the fate of neuronal progenitor cells that express dlx1a/2a genes in the brain, we produced lines of Tg(dlx1a/2a:CreERT2) transgenic fish expressing the CreERT2 recombinase driven by regulatory elements from the dlx1a/2a locus. CreERT2 expression in these fish faithfully recapitulates that of dlx1a/2a genes in the forebrain. These fish were mated with Tg(ubi:Switch) reporter fish that express a loxP-flanked GFP gene followed by mCherry, driven by the ubiquitin promoter. Upon tamoxifen treatment, the double transgenic fish express mCherry in dlx1a/2a-expressing cells. Live imaging data showed that mCherry-expressing cells were observed first in the telencephalon and prethalamus, regions from which they migrated and populated the telencephalon, prethalamus and hypothalamus by 10dpf. Fate mapping of mCherry-expressing cells in double transgenic fish demonstrated that a majority of dlx1a/2a-expressing cells give rise to GABAergic neurons. Furthermore, as zebrafish produce new neurons throughout life, the role of dlx1a/2a during adult neurogenesis was examined. Our preliminary data showed that dlx1a/2a-expressing progenitor cells populate various domains of the forebrain during adult neurogenesis. Our lineage tracing system provides a powerful tool to investigate the origin of GABAergic neuron progenitors and the mechanisms by which they populate or repopulate the adult brain.

Dire wolves are considered to be one of the most common and widespread large carnivores in Pleistocene America1, yet relatively little is known about their evolution or extinction. Here, to reconstruct the evolutionary history of dire wolves, we sequenced five genomes from sub-fossil remains dating from 13,000 to more than 50,000 years ago. Our results indicate that although they were similar morphologically to the extant grey wolf, dire wolves were a highly divergent lineage that split from living canids around 5.7 million years ago. In contrast to numerous examples of hybridization across Canidae2,3, there is no evidence for gene flow between dire wolves and either North American grey wolves or coyotes. This suggests that dire wolves evolved in isolation from the Pleistocene ancestors of these species. Our results also support an early New World origin of dire wolves, while the ancestors of grey wolves, coyotes and dholes evolved in Eurasia and colonized North America only relatively recently.

The Manta platform is a unified commercial product for data flow analysis and vi- sualization. Manta platform supports many technologies. One category of technologies is intermediate languages. These include, for example, Java or C#. There is a scanner for each of these technologies. This thesis focuses on extending the C# Scanner with support for database and ORM related plugins. First, we provide a brief description of how the Manta platform works. Then we quickly introduce the C# Scanner, some of its important parts, and explain some of the concepts and algorithms that are used to analyze C# code. This is followed by an analysis of the context of ORM frameworks and Entity Framework Core from the perspective of data flow analysis. After explaining the context, we describe the C# Scanner extensions, solutions and troubleshooting. Towards the end of the thesis we describe support for one specific ORM framework - Entity Framework Core. Again, we discuss problem solving and solution description. At the end of the thesis it is possible to find limitations of the solution and possible extensions. 1

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O presente trabalho teve como objetivo avaliar novilhos resultantes da seleção genética de diferentes linhagens da raça Canchim (5/8 Charolês, 3/8 Zebu), recriados a pasto e terminados em confinamento, em relação ao consumo alimentar, desempenho, emissão de metano entérico, características de carcaça e cortes cárneos. O experimento foi desenvolvido na Empresa Brasileira de Pesquisa Agropecuária, unidade Pecuária Sudeste, São Carlos/SP. Foram utilizados 46 novilhos da raça Canchim (15 meses, 291 kg de peso vivo), 13 pertencentes a linhagem antiga, 20 a linhagem nova e 13 provenientes do acasalamento entre estas linhagens. A linhagem antiga é mantida como rebanho fechado desde 1953 e foi formada com base em 53 touros Charoleses importados da França, já a linhagem nova teve origem a partir de 1990 com a utilização de touros Charoleses de diferentes origens (Argentina, Brasil, Estados Unidos, França, Inglaterra), e a partir de 1998, com o acasalamento entre as duas linhagens formou-se a linhagem cruzada. Durante a recria a pasto (165 dias), os animais foram alojados em uma área de pastagem (Panicum maximum cv. Tanzânia), onde o manejo adotado foi o de pastejo rotacionado com lotação variável, para as medidas de desempenho foram executadas pesagens a cada 33 dias, e a mensuração da emissão de metano entérico através da técnica do gás traçador hexafluoreto de enxofre realizada em 12 animais da linhagem antiga e 12 da nova. No período de terminação em confinamento, os animais foram dispostos em 4 baias e receberam alimentação ad libitum durante 105 dias, o ganho de peso foi medido a cada 28 dias e para a mensuração de emissão de metano os mesmos animais avaliados a pasto, tiveram acesso ao sistema automatizado GreenFeed®. No momento do abate, foram coletadas informações sobre o peso de carcaça quente, e após 24 horas de resfriamento em câmara fria, o peso da carcaça fria, do traseiro especial, dianteiro e ponta de agulha e na desossa os pesos individuais dos cortes cárneos comerciais. A linhagem nova mostrou-se superior a antiga no período de recria nas variáveis de ganho médio diário, conversão e eficiência alimentar, não se diferenciando dos cruzados. Durante a terminação em confinamento, foi observado o mesmo em relação ao ganho médio diário, já em relação ao consumo, a linhagem nova e os cruzados apresentaram maiores ingestões de alimento comparados à linhagem antiga, enquanto a conversão alimentar dos animais cruzados apresentou maior valor comparados às das linhagens. Na recria a pasto, para se obter maiores ganhos de peso, melhor conversão alimentar e eficiência alimentar, devem ser utilizados animais resultantes de processos de seleção genética. A seleção genética para características de desempenho produtivo não garante animais com menores emissões de metano em condições de pastejo. Nos animais em fase de terminação em confinamento, o maior ganho de peso, melhor conversão alimentar e melhor acabamento de carcaça são obtidos através da utilização de animais resultantes de processos de seleção genética. O mesmo tipo de seleção para características de desempenho produtivo em confinamento leva a maiores consumos diários de alimento e consequentemente a maiores emissões de metano diárias. / The objective of this study was to evaluate steers resulting from the genetic selection of different Canchim (5/8 Charolais, 3/8 Zebu) lineages, rearing to pasture and finished in feedlot, in relation to feed intake, performance, enteric methane emission, carcass traits and retail cuts. The experiment was carried out at the Brazilian Agricultural Research Corporation (Embrapa), Southeast Livestock, São Carlos / SP. A total of 46 Canchim steers (15 months, 291 kg live weight) were used, 13 from the ancient lineage, 20 from the new lineage and 13 from the mating between these lineages. The ancient lineage is kept as a closed herd since 1953 and was formed by 53 Charolais bulls imported from France. The new lineage originated from 1990 with the use of Charolais bulls from different origins (Argentina, Brazil, the United States, France, England), and from 1998 the crossed lineage was formed with the mating between the two lineages. During grazing (165 days), the animals were housed in an pasture area (Panicum maximum cv. Tanzania), where the management used was rotational grazing with variable stocking, for the performance measures were performed weighing every 33 days, and the measurement of the enteric methane emission through the sulfur hexafluoride tracer gas technique was performed in 12 animals of the ancient and 12 of the new lineage. In feedlot the animals were housed in 4 pens and fed ad libitum for 105 days. The weight gain was measured every 28 days and as for the measurement of methane emission the same animals evaluated on pasture had access to the GreenFeed® automated system. Information on the hot carcass weight was collected at the time of slaughter and after 24 hours of cooling in the cold chamber, the weights of the cold carcass, of the special hind, fore and spare ribs, and the individual weights of the retail cuts in boning. The new lineage was superior to the ancient one in the rearing period in the variables of average daily gain, conversion and feed efficiency, not differing from the animals crossed. During feedlot, it was observed the same in relation to the average daily gain, already in relation to intake, the new lineage and the crossbreeds presented higher feed intakes compared to the ancient lineage while the feed conversion of the crossed animals presented higher value compared with the new and ancient lineages. In pasture recreating, in order to obtain greater weight gains, better feed conversion and feed efficiency, animals resulting from genetic selection processes must be used. Genetic selection for performance traits does not guarantee animals with lower methane emissions under grazing conditions. For feedlot animals, the highest weight gain, better feed conversion and better carcass finishing are obtained through the use of animals resulting from genetic selection processes. The same type of selection for traits of performance in feedlot leads to higher daily feed intake and consequently to higher daily methane emissions.

Stem cells have yet to contribute to their full potential in the field of regenerative medicine and further understanding of the underlying kinetics of cell differentiation could be the step forward. Various methods have been used to characterise stem cell lineage commitment. However, most of these techniques are end-point assays and provide very little information about the changes occurring in the early stages of the differentiation process. This project aims to explore if the structural and geometrical specificity of the cytoskeletal components (actin in particular) encode information regarding cell lineage. Adipogenic and osteogenic differentiation lineages were selected, as they have been extensively studied over the past few decades. We have developed a novel approach to describe cells by defining their cytoskeletal and nuclear morphology in terms of 19 geometric measurements. This set of parameters has a range of complexity, extending from one dimensional (e.g. fibre length, fibre thickness) to compound geometrical readings (e.g. chirality and fibre alignment), while some estimate morphological and mechanical properties of the nucleus i.e. Poisson ratio and chromatin condensation. A proprietary image analysis algorithm is used to analyse fluorescent images of cells biochemically and mechanically stimulated to differentiate for a period of up to 10 days. Our analysis pipeline is currently optimised for images acquired at x20 magnification using epi-fluorescence but can be further adapted for high throughput live cell imaging. Factorial analysis of the measured features showed that some parameters change markedly in the early stages of differentiation. More interestingly we observed these changes to be non-linear and non-monotonic. This analysis, in light with previously published literature on the subject has allowed us to more intricately hypothesise probable mechanisms involved with mechanotransduction which direct the lineage commitments. As our technique quantifies the morphology of individual cells, we used our extracted feature data to characterise each cell using a multivariate predictive model (LDA).

Pluripotent stem cells have the capacity to develop into different cell lineages and can be manipulated into certain cell types through the use of small molecule inducers. Retinoic acid (RA) signaling through retinoic acid receptors (RAR) and retinoid X receptors (RXR) has the ability to direct lineage determination but has yielded disappointing results in promoting skeletal myogenesis in embryonic stem (ES) cells. RXR is crucial in embryonic development although it is generally considered to act as a silent partner for other nuclear receptors such as RAR. Our findings demonstrate that rexinoid specific signaling enhances skeletal myogenesis and requires β-catenin but not RAR. Moreover, RXR signalling in mouse ES cells can efficiently enhance skeletal myogenesis and closely recapitulates sequential events observed in vivo. Since ES cells closely represent the properties of the developing embryo, efficiently generating skeletal muscle provides a means to further scrutinize signaling pathways in myogenic development in view of developing therapies for muscle related diseases.

The data delivery architectures in most enterprises are complex and under documented. Conceptual business models and business analytics applications are created to provide a simplified, and easy to navigate view of enterprise data for analysts. But the construction of such interfaces is tedious, manually intensive to build, requiring specialized technical expertise, and it is especially difficult to map exactly where data came from in the organization. In this paper we investigate how two aspects (lineage and requests for data i.e. semantics and new reports) can be addressed by tying metadata documentation to a systematic data delivery architecture in order to support business analytics applications. We propose a tool framework that includes a metadata repository for each step in the data delivery architecture, a web based interface to access and manage that repository and mapping tools that capture data lineage to support step by step automation of data delivery.

Pluripotent stem cells have the capacity to develop into different cell lineages and can be manipulated into certain cell types through the use of small molecule inducers. Retinoic acid (RA) signaling through retinoic acid receptors (RAR) and retinoid X receptors (RXR) has the ability to direct lineage determination but has yielded disappointing results in promoting skeletal myogenesis in embryonic stem (ES) cells. RXR is crucial in embryonic development although it is generally considered to act as a silent partner for other nuclear receptors such as RAR. Our findings demonstrate that rexinoid specific signaling enhances skeletal myogenesis and requires β-catenin but not RAR. Moreover, RXR signalling in mouse ES cells can efficiently enhance skeletal myogenesis and closely recapitulates sequential events observed in vivo. Since ES cells closely represent the properties of the developing embryo, efficiently generating skeletal muscle provides a means to further scrutinize signaling pathways in myogenic development in view of developing therapies for muscle related diseases.

The data delivery architectures in most enterprises are complex and under documented. Conceptual business models and business analytics applications are created to provide a simplified, and easy to navigate view of enterprise data for analysts. But the construction of such interfaces is tedious, manually intensive to build, requiring specialized technical expertise, and it is especially difficult to map exactly where data came from in the organization. In this paper we investigate how two aspects (lineage and requests for data i.e. semantics and new reports) can be addressed by tying metadata documentation to a systematic data delivery architecture in order to support business analytics applications. We propose a tool framework that includes a metadata repository for each step in the data delivery architecture, a web based interface to access and manage that repository and mapping tools that capture data lineage to support step by step automation of data delivery.