9 pp. / When we go to the grocery store it is a fairly easy task to select and purchase nutritious meals. A readily available, predictable food supply is conveniently organized and displayed in the aisles. The nutritional composition of most foods is clearly labeled so you can immediately know what nutrients (and perhaps, toxins) you will be consuming. In contrast, rangeland animals live in a world where nutrients and toxins are constantly changing across space and time. For example, there may be 10s to 100s of plant species growing on a single acre, and each plant can differ widely in the kinds and amounts of nutrients and toxins it offers to free-ranging herbivores. Even at the level of the individual plant, plant parts vary in their concentration of nutrients and toxins; leaves, stems, and flowers, all differ in the kinds and amounts of nutrients and toxins they contain. Nutrient and toxin content of the same plant species can also vary depending on where it grows (in the sun vs. shade, on a wet vs. dry site, on a fertile vs. infertile site, etc.). Mother Nature can also drastically alter foraging environments as a result of natural disasters like floods, fires, or droughts. Wild animals may find themselves in unfamiliar environments during their natural migration patterns. Range and wildlife management practices can also place wild and domestic herbivores in unfamiliar environments via relocation and reintroduction programs or via grazing management practices. Despite all these challenges, rangeland herbivores are remarkably adept at selecting plants that meet their nutritional needs while largely avoiding plants that do not. The fact that animals preferentially select plant species that are more nutritious than what is available, on average, is strong evidence that animals are able to somehow detect nutrient and toxin levels in plants as they change across space and time. In this paper, we examine recent important discoveries that underscore the importance of learning as a critical mechanism which allows rangeland herbivores to survive in a world where the only constant is change (Provenza, 2003; www.behave.net).

abstract: Yersinia enterocolitica is a major foodborne pathogen found worldwide that causes approximately 87,000 human cases and approximately 1,100 hospitalizations per year in the United States. Y. enterocolitica is a very unique pathogen with the domesticated pig acting as the main animal reservoir for pathogenic bio/serotypes, and as the primary source of human infection. Similar to other gastrointestinal infections, Yersinia enterocolitica is known to trigger autoimmune responses in humans. The most frequent complication associated with Y. enterocolitica is reactive arthritis - an aseptic, asymmetrical inflammation in the peripheral and axial joints, most frequently occurring as an autoimmune response in patients with the HLA-B27 histocompatability antigen. As a foodborne illness it may prove to be a reasonable explanation for some of the cases of arthritis observed in past populations that are considered to be of unknown etiology. The goal of this dissertation project was to study the relationship between the foodborne illness -Y. enterocolitica, and the incidence of arthritis in individuals with and without contact with the domesticated pig. / Dissertation/Thesis / Doctoral Dissertation Anthropology 2015

Philosophiae Doctor - PhD / The domesticated apple (Malus x domestica Borkh.) has been distributed into diverse climatic conditions worldwide for commercial production of fruit. Apple trees need exposure to cold temperatures, referred to as chill unit (CU) accumulation during winter, in order for budbreak to occur promptly and uniformly after winter. In warmer production areas the application of dormancy breaking chemicals has enabled successful production of high chilling requiring apple cultivars in suboptimal environmental conditions. In the Western Cape region of South Africa it is common orchard practice to apply dormancy breaking chemicals after winter in order to stimulate vegetative growth. If this is not done prolonged dormancy symptoms (PDS) are experienced which include extended rest, less synchronised breaking of buds and reduced branching. An increasing awareness of both global warming and the negative effects associated with the use of chemical sprays (for both pest and disease resistance and growth regulation) has resulted in the need to breed cultivars better adapted to current and future environmental conditions. The breeding of new cultivars using conventional breeding methods is a time consuming process, especially in perennial tree species with a long juvenile phase such as apple. The implementation of marker-assistedbreeding (MAB) and selection (MAS) will enable the selection of favourable genotypes at a very early seedling stage. Although markers linked to genes involved in disease resistance for a variety of known apple pathogens have been identified and are already in use in breeding programs, the genetic determinants of dormancy related characteristics residing within the bud itself (endodormancy) are poorly understood. This hampers the genetic improvement of such characters. Although this study focused on time of initial vegetative budbreak IVB, there are various other characteristics that can be associated with dormancy, such as position and number of budbreak and budbreak duration. The unravelling of the genetic basis of complex traits such as dormancy, can be done through the construction of a genetic linkage map followed by the identification of genomic regions, known as quantitative trait loci (QTL), that can be ssociated with the trait of interest. This study involved the construction of genetic linkage maps for two mapping pedigrees where the low chilling requiring cultivar ‘Anna’ was used as common male parent in crosses with the higher chilling requiring ‘Golden Delicious’ and ‘Sharpe’s Early’. A third mapping pedigree, with ‘Golden Delicious’ as female parent and ‘Prima’ as male parent, was also included. Maps consisted of transferable SSR markers only, facilitating the alignment with the proposed apple reference map (Silfverberg-Dilworth et al., 2006) and adherence to the common LG numbering system now being used for apple genetic linkage maps (Maliepaard et al., 1998). A number of newly developed EST-SSR markers are reported, some of which are candidates for filling large gaps between adjacent SSR markers on the apple reference map. An interactive database was developed to successfully manage the large amount of data generated during this investigation. A selective mapping, or bin mapping strategy (Vision et al., 2000) was developed for two of the three mapping populations in order to facilitate the incorporation and positioning of newly developed markers onto existing genetic linkage maps. This involves the screening of new markers on a small subset of the population, drastically reducing the cost and time involved. Genetic linkage maps constructed allowed for the detection of 18 putative QTLs affecting the time of IVB. Four of these QTLs co-localize with previously identified QTLs. A QTL identified on LG 8 confirms a previously identified QTL (Segura et al., 2007), while one of the QTLs identified on LG 9 might coincide with a QTL identified on the corresponding LG 3 of the genetic linkage map constructed by Conner et al. (1998). Two QTLs identified on LG 10 might coincide with markers found to co-segregate with time of budbreak in an earlier study conducted by Lawson et al. (1995). An additional 14 QTLs involved in time of IVB have been identified. We proposed the testing of four markers in a validation study conducted on a second mapping pedigree derived from a cross between ‘Anna’ and ‘Golden Delicious’. These markers are CH04a12, CH04c06y, CH01h01 and A267. Not only do these markers show significant levels of association with the time of IVB, but segregation of parental alleles from the cultivar ‘Anna’ for two of these markers, CH04c06y and CH01h01, were found to be associated with the time of IVB in different genetic backgrounds. The identification of markers closely associated with time of IVB will facilitate the implementation of MAS in breeding programs in order to breed cultivars that are better adapted to local climatic conditions.

Os elementos de transposicão (TEs) são sequências genéticas móveis. Sua capacidade mutagênica faz deles uma importante fonte de variabilidade nos genomas. Outro importante papel dos TEs na evolução dos genomas é o de doadores de domínios protéicos na formação de novos genes. 276 clones de cDNA homólogos a TEs foram previamente identificados no banco de dados do SUCEST (projeto de sequenciamento de etiquetas expressas de cana-de-acúcar). Neste trabalho nós realizamos o sequenciamento completo de 156 destes clones e a classificação e caracterização de suas sequências comparando-as com bancos de dados. Foram identificadas 9 diferentes famílias de transposons e 11 diferentes famílias de retrotransposons. As famílias mais representadas entre os transposons foram MuDr e hAT (que engloba os elementos do tipo Ac e Tam3), para os quais foram identificados 43 e 32 clones de cDNA, respectivamente. Entre os retrotransposons, a família mais representada foi Hopscotch, apresentando 25 clones de cDNA. Após esta análise global, o foco das investigações voltou-se para os cDNAs do tipo hAT. Uma análise comparativa destes cDNAs revelou que as sequências homólogas a hAT estão distribuídas em dois grupos. O grupo I, é composto por sequências com alta conservação no nível de nucleotídeos, está presente no genoma de todas as gramíneas analisadas (híbridos e parentais da cana-de-acúcar, milho e arroz) com um baixo número de cópias, teve a sua expressão detectada em folhas, raízes e mais intensamente em calos cana. Além disso, apresenta alta similaridade de sequências com transposases domesticadas descritas na literatura. O grupo II, por sua vez, é composto por sequências mais heterogêneas, que apresentam similaridade com os transposons originais que constituem a superfamília hAT: hobo (de Drosophila melanogaster), Ac (de Zea mays) e Tam3 (de Antirrhinum majus). Sua distribuição é restrita ao genoma de Saccharum, com um número de cópias maior que o grupo I. Um ensaio de PCR-Inversa identificou terminações inversas repetidas (TIRs) para o cDNA TE221 do grupo II. A partir de iniciadores desenhados sobre estas TIRs foi possível recuperar dois elementos, de 3,5kb e 4,2kb, respectivamente, e um MITE de 250 pb, todos homólogos a hAT. Este resultado demonstrou que a estratégia utilizada para recuperar elementos do genoma da cana-de-açúcar a partir do cDNA TE221 mostrou-se eficiente. Homólogos aos grupos I e II de cana-de-acúcar foram identificados em bancos de dados de milho, arroz e arabidopsis. Estes dados sugerem que a separação dos dois grupos ocorreu antes da divergência entre as classes Monocotiledonea e Eudicotiledonea. Com base nos resultados aqui apresentados sugerimos que um transposon ancestral do tipo hAT, presente nas angiospermas anteriormente à separação de Monocotiledonea e Eudicotiledonea, teve sua transposase capturada na formação de um gene com função celular. A partir do evento da domesticação, estas transposases seguiram dois caminhos evolutivos distintos, um como gene funcional e outro como um transposon tradicional. Estas duas formas de transposase do tipo hAT podem ser encontradas no genoma da cana-de-acúcar, representadas pelos elementos dos grupos I e II, respectivamente. / Transposable elements (TEs) are mobile genetic sequences. Their mutagenic capacity makes them important sources of variation in the genomes. These elements have another important evolutionary role as donors of functional protein domains in the formation of new genes. 276 cDNA clones homologous to TEs were previously identified in the Brazilian Sugarcane Expressed Sequence Tag Project (SUCEST) databases. In this work, we have obtained the full sequences of 156 for these clones. These sequences were compared with Genbank database. We have identified 9 families of transposons and 11 families of retrotransposons. The most representative families found amongst the transposons were MuDr and hAT (wich encompass Ac and Tam3), with 43 and 32 cDNAs, respectively. Amongst the retrotransposons, the most representative family was Hopscotch, with 25 cDNAs. After this global analysis, we have focused our investigation in the hAT-like cDNAs. A comparative analysis of these cDNAs has revealed a profile of two distinct groups. Group I is composed of sequences with high conservation at nucleotide level, it is present in the genome of all grasses analysed (hybrids and parentals of sugarcane, maize and rice) with low copy number, it is expressed in leaves and roots of sugarcane, and more intensely in callus. In addition, group I sequences have clustered with domesticated transposases. The group II is composed of more heterogeneous sequences similar with the original elements that constitute the hAT superfamily: hobo (from Drosophilla melanogaster), Ac (from Zea mays) and Tam3 (from Antirrhinum majus). This group was shown to be restricted to the genome of Saccharum, with higher copy number than group one. Inverse-PCR assays has identified terminal inverted repeats (TIRs) to the cDNA TE221 from group II. Primers based on the sequences of the TIRs allowed us to recover three elements hAT-like from sugarcane’s genomic DNA: one of 3,5kb and another of 4,2kb, and a MITE of 250 bp. These results corroborate the strategy applied in order to recover elements from the sugarcane´s genome. Sequences homologous to both sugarcane group I and group II were found also in maize and rice, as well as in arabidopsis databases. These data suggest that the divergence of the two groups occured before the separation between the classes Monocotiledonea and Eudicotiledonea. Based on our results, we suggest the existence of an ancestral transposon hAT-like, present in angiosperms before the separation between Monocotiledonea and Eudicotiledonea, of which the transposase was captured to compose a new gene with some cellular function. Since the domestication event, these transposases followed distinct evolutive pathways, one as a regular gene and another as a bona fide transposon. These two forms of hAT-like transposases could be found in the sugarcane’s genome, represented by the elements from groups I and II, respectively.

Os elementos de transposicão (TEs) são sequências genéticas móveis. Sua capacidade mutagênica faz deles uma importante fonte de variabilidade nos genomas. Outro importante papel dos TEs na evolução dos genomas é o de doadores de domínios protéicos na formação de novos genes. 276 clones de cDNA homólogos a TEs foram previamente identificados no banco de dados do SUCEST (projeto de sequenciamento de etiquetas expressas de cana-de-acúcar). Neste trabalho nós realizamos o sequenciamento completo de 156 destes clones e a classificação e caracterização de suas sequências comparando-as com bancos de dados. Foram identificadas 9 diferentes famílias de transposons e 11 diferentes famílias de retrotransposons. As famílias mais representadas entre os transposons foram MuDr e hAT (que engloba os elementos do tipo Ac e Tam3), para os quais foram identificados 43 e 32 clones de cDNA, respectivamente. Entre os retrotransposons, a família mais representada foi Hopscotch, apresentando 25 clones de cDNA. Após esta análise global, o foco das investigações voltou-se para os cDNAs do tipo hAT. Uma análise comparativa destes cDNAs revelou que as sequências homólogas a hAT estão distribuídas em dois grupos. O grupo I, é composto por sequências com alta conservação no nível de nucleotídeos, está presente no genoma de todas as gramíneas analisadas (híbridos e parentais da cana-de-acúcar, milho e arroz) com um baixo número de cópias, teve a sua expressão detectada em folhas, raízes e mais intensamente em calos cana. Além disso, apresenta alta similaridade de sequências com transposases domesticadas descritas na literatura. O grupo II, por sua vez, é composto por sequências mais heterogêneas, que apresentam similaridade com os transposons originais que constituem a superfamília hAT: hobo (de Drosophila melanogaster), Ac (de Zea mays) e Tam3 (de Antirrhinum majus). Sua distribuição é restrita ao genoma de Saccharum, com um número de cópias maior que o grupo I. Um ensaio de PCR-Inversa identificou terminações inversas repetidas (TIRs) para o cDNA TE221 do grupo II. A partir de iniciadores desenhados sobre estas TIRs foi possível recuperar dois elementos, de 3,5kb e 4,2kb, respectivamente, e um MITE de 250 pb, todos homólogos a hAT. Este resultado demonstrou que a estratégia utilizada para recuperar elementos do genoma da cana-de-açúcar a partir do cDNA TE221 mostrou-se eficiente. Homólogos aos grupos I e II de cana-de-acúcar foram identificados em bancos de dados de milho, arroz e arabidopsis. Estes dados sugerem que a separação dos dois grupos ocorreu antes da divergência entre as classes Monocotiledonea e Eudicotiledonea. Com base nos resultados aqui apresentados sugerimos que um transposon ancestral do tipo hAT, presente nas angiospermas anteriormente à separação de Monocotiledonea e Eudicotiledonea, teve sua transposase capturada na formação de um gene com função celular. A partir do evento da domesticação, estas transposases seguiram dois caminhos evolutivos distintos, um como gene funcional e outro como um transposon tradicional. Estas duas formas de transposase do tipo hAT podem ser encontradas no genoma da cana-de-acúcar, representadas pelos elementos dos grupos I e II, respectivamente. / Transposable elements (TEs) are mobile genetic sequences. Their mutagenic capacity makes them important sources of variation in the genomes. These elements have another important evolutionary role as donors of functional protein domains in the formation of new genes. 276 cDNA clones homologous to TEs were previously identified in the Brazilian Sugarcane Expressed Sequence Tag Project (SUCEST) databases. In this work, we have obtained the full sequences of 156 for these clones. These sequences were compared with Genbank database. We have identified 9 families of transposons and 11 families of retrotransposons. The most representative families found amongst the transposons were MuDr and hAT (wich encompass Ac and Tam3), with 43 and 32 cDNAs, respectively. Amongst the retrotransposons, the most representative family was Hopscotch, with 25 cDNAs. After this global analysis, we have focused our investigation in the hAT-like cDNAs. A comparative analysis of these cDNAs has revealed a profile of two distinct groups. Group I is composed of sequences with high conservation at nucleotide level, it is present in the genome of all grasses analysed (hybrids and parentals of sugarcane, maize and rice) with low copy number, it is expressed in leaves and roots of sugarcane, and more intensely in callus. In addition, group I sequences have clustered with domesticated transposases. The group II is composed of more heterogeneous sequences similar with the original elements that constitute the hAT superfamily: hobo (from Drosophilla melanogaster), Ac (from Zea mays) and Tam3 (from Antirrhinum majus). This group was shown to be restricted to the genome of Saccharum, with higher copy number than group one. Inverse-PCR assays has identified terminal inverted repeats (TIRs) to the cDNA TE221 from group II. Primers based on the sequences of the TIRs allowed us to recover three elements hAT-like from sugarcane’s genomic DNA: one of 3,5kb and another of 4,2kb, and a MITE of 250 bp. These results corroborate the strategy applied in order to recover elements from the sugarcane´s genome. Sequences homologous to both sugarcane group I and group II were found also in maize and rice, as well as in arabidopsis databases. These data suggest that the divergence of the two groups occured before the separation between the classes Monocotiledonea and Eudicotiledonea. Based on our results, we suggest the existence of an ancestral transposon hAT-like, present in angiosperms before the separation between Monocotiledonea and Eudicotiledonea, of which the transposase was captured to compose a new gene with some cellular function. Since the domestication event, these transposases followed distinct evolutive pathways, one as a regular gene and another as a bona fide transposon. These two forms of hAT-like transposases could be found in the sugarcane’s genome, represented by the elements from groups I and II, respectively.

Chicken is a major protein source and intensively selected for economically important traits by humans. As such, this generated a huge range of phenotypes that representing a diverse spectrum of genetic variation. Understanding the functional basis of the genetic variants that underlie these traits, however, remains a formidable endeavour particularly for complex traits. Nonetheless, molecular phenotyping of an organism from sequenced data is doable with the advances in bioinformatics analysis and unparalleled surveys of genome wide genetic variants. This provides the opportunity to gain insights into the genome architecture and assists in identifying chromosomal regions underlying selection through a “sequences to consequences” approach. Combining a whole genome re-sequencing (WGS) approach with the knowledge of selection history, this thesis aimed to study the chromosomal regions and genetic variants underlying traits of interest in various selected chicken populations. To achieve this, genetic (quantitative and population genetics), genomic and bioinformatics approaches were employed and integrated to investigate the genome wide selection signatures in a number of different lines of chicken selected for different complex traits. This includes analysing: (i) divergently selected broilers for fatness traits (Chapter 2), (ii) a closed population of layer chickens (Chapter 3), (iii) selection signatures unique to broiler or layer chickens (Chapter 4) and (iv) selection signatures in colony stimulating factor 1 (CSF1) associated with gene expression differences in broiler and layer populations (Chapter 5). Candidate genes and nucleotides underlying potential selection regions were identified, and attempts were made to further elucidate the potential interplay between genes and the biological pathways involved in regulating traits in these selected chicken lines. Incorporating integrative approaches, variants within selection signatures were annotated to provide further evidence of their functional consequences. Overall, non-coding regions were enriched in selection signatures implied that causative variants may have regulatory roles. Capitalising on the millions of genetic variants discovered from WGS, chromosomal regions subject to selection were detected using a number of population genetics statistics. In broiler chicken lines divergently selected for very low-density plasma lipoprotein (VLDL) (Chapter 2), incorporating signatures of selection helped to improve the resolution of previously mapped quantitative traits loci (QTL) intervals. This research demonstrated that the integration of the analysis of selection signatures with functional annotation of genetic variants enabled refinement and characterisation of the QTL for fatness traits. In a closed population of brown leghorn layers (Chapter 3), evidence of selection signatures was found through Tajima’s D analysis. The analysis unravelled selection signatures encoding genes involved in numerous pathways and genes having key roles such as in behaviour, including feather pecking. Combining population differentiation statistic (FST) and Tajima’s D, a number of regions subject to divergent selection between broilers and white egg layers were identified (Chapter 4). Selection signatures were found to harbour mutations involved in cellular and tissue development, including genes having important roles in growth, fatness, egg shell strength and muscle development. These regions and the overlapping genes thereby may be potentially contributing to the different phenotypic variations observed between broilers and layers. In Chapter 5, a revised gene model for colony stimulating factor 1 (CSF1) showing complex pattern of alternate transcripts was predicted from transcriptome analysis of RNA isolated from 21 different tissues. In parallel, selection signatures analysis with the FST statistic, identified selection signatures that differentiate broilers to white egg layers (3 regions) or brown egg layers to white egg layers (4 regions). All these selection signatures were located within non-coding regions, indicating potential divergent selection of CSF1 within regulatory regions. Overall, the results presented in this thesis using the “sequences to consequences” approach, link several genomic regions and genes to phenotypic variation in domesticated chicken lines. The work reported here serves as a foundation for further study to decipher the relationship between “genotype and phenotype” and its functional consequences due to selection.

This study investigates the symbolic role of the domestic dog in Iron Age and Roman Britain through contextual analysis of their faunal remains and interpretation of their representations in iconography. Previous studies have highlighted linkages between the species and ideas about death, healing and regeneration (Jenkins 1957, Ross 1967, Toynbee 1973, Henig 1984, Green 1992). Although these connections clearly did exist in the cosmologies of Britain and the Western provinces of Rome, this detailed examination of the evidence seeks to identify reasons why this might have been so. The enquiry was also designed to highlight any previously unnoticed patterns in the dataset that might add a further dimension to our understanding of how the domestic dog was perceived at a symbolic level. It has been established for some time that dogs appear in statistically significant numbers, compared to other species, in the special animal deposits that are a feature of certain Iron Age pits (Grant 1984, Wait 1985, Hill 1995). Dramatic evidence for ritual practice involving animals found at a Romano-British temple complex in Springhead, Kent, and comparable finds from both sacred and secular sites, suggest that domestic dogs were also a favoured sacrifice during this period. As well as analysing such archaeological evidence, this study draws on anthropological, psychological and historical writings about human relationships with the domestic dog in an attempt to forward our understanding of religious expression during antiquity.

Abstract Although the present day management of semi-domesticated reindeer (Rangifer t. tarandus L.) and its operational environment have changed from the past, knowledge of the ecological mechanisms typical of traditional herding is still important. The main objective of this study was to examine factors related to stock productivity and carrying capacity of pastures in the Finnish semi-domesticated reindeer management area during 1960-1990's in order to clarify the basis of the present management strategies in Finland. In the Oraniemi district, before 1987, calf production was more affected by the snow conditions of the previous winter, than the weather conditions of the previous summer. Slaughtering mass of calves was more affected by the weather and precipitation in spring and summer than the snow conditions of the previous winter. Thick snow cover and unfrozen soil in early winter also probably affect the quality of natural winter food of reindeer by favouring the growth of certain micro fungi on pastures. Before the mid-1990's in the northern part of the management area, calf production decreased and its variability increased between the districts when reindeer densities on forest and heath land increased, amount of lichen (Cladonia spp.) pastures per reindeer decreased and condition of these pastures deteriorated. Variability in calf production increased especially when the amount of arboreal lichen (Alectoria, Bryoria spp.) pastures per reindeer decreased. The slaughtering mass of reindeer decreased when reindeer densities on all pastures increased. Intensive calf slaughtering increased reindeer stock productivity although it was density dependent. Because of intensified feeding, reindeer densities on winter pastures did not affect stock productivity in the whole management area between 1993 and 1999. Stock productivity could be increased markedly by feeding. Still, slaughtering mass and meat production per reindeer decreased when reindeer densities on summer pastures increased. In the Finnish grazing system, reindeer densities should have remained well below 10 reindeer/km2 lichen range for maintaining lichen ranges in a good condition. The average lichen biomass of lichen ranges in the management area in the mid-1990's was 13% of the lichen biomass at the maximum production. Lichen ranges should have been ungrazed for an average 18 years to recover to the maximum production. The time needed for the lichen ranges to recover to a good condition, would have been 7 years. This study showed that the amount and condition of pastures had a fundamental part in the productivity of Finnish reindeer stock. Calf slaughtering and feeding were effective ways to increase and stabilize stock productivity in the situation where the economic carrying capacity of winter ranges has obvuously been exceeded due to overgrazing and the effects caused by the other land use. This has made reindeer management more and more dependent on feeding. Improvements of the state and condition of winter ranges would only be possible during a long period by regulating reindeer stock size, developing pasture rotation and protecting reindeer pastures from the other land use.

Made available in DSpace on 2016-04-28T20:15:34Z (GMT). No. of bitstreams: 1 2008 - Wyslaine Costa da Cruz.pdf: 1345930 bytes, checksum: 9a654e122d8b4c1490d3af518d57d643 (MD5) Previous issue date: 2008-02-27 / Coordena??o de Aperfei?oamento de Pessoal de N?vel Superior / Blastocystis hominis is one of the most prevalent parasites of the human gastrointestinal tract, but its pathogenic role still remains uncertain. Some organisms similar to B. hominis have been described in a range of non-human hosts and are denominated Blastocystis sp., but their zoonotic potential still needs clarification. The objective of this work was to investigate the occurrence of natural infection by Blastocystis sp. in three species of domesticated birds sold at cooperative markets (with individual vendor stalls) in two districts of the city of Rio de Janeiro and to characterize the morphology of these organisms found in bird droppings, to enable a precise diagnosis. A total of 214 birds were purchased: 35 ducks (Anas platyrhynchos) from market A and 38 from market B, 35 quails (Coturnix japonica) from market A and 36 from market B and 35 chicks (Gallus gallus) from market A and 35 from market B. Of the birds studied from market A, 8 chicks (22.9%), 15 quails (42.9%) and 13 ducks (37.1%) presented biological forms of Blastocystys sp. in their droppings, while at the market B, the respective figures were 15 chicks (42.9%), 2 quails (5.56%) and 21 ducks (55.3%). There was no statistically significant difference in relation to the occurrence of infection in ducks and chicks between the two markets studied, but there was between the quails at the two markets. Considering the number of infected birds at the two markets irrespective of species, the difference was statistically significant. From the observations of the stained fecal smears of the animals that were positive for Blastocystis sp., it was possible to characterize six forms of organisms, namely vacuolar, granular, ameboid, cystic, avacuolar and multivacuolar. It was also possible to characterize the reproductive forms of Blastocystis sp. as binary division, endodyogeny, budding, plamotomy and schizogeny. Even though there are no studies confirming the zoonotic and pathogenic potential of Blastocystis sp., either to human or animal hosts, we suggest that environmental contamination can be occurring at these markets, due to the poor hygienic and sanitary conditions, thus posing a risk to both the animals and the people who circulate there. The knowledge of evaluative forms that were found and characterized in this work is important to gives a precise and faithful diagnosis of Blastocystis sp. in dropping. / Blastocystis hominis ? um dos parasitos de maior preval?ncia no trato gastrintestinal de humanos, por?m seu papel patog?nico ainda permanece incerto. Alguns organismos semelhantes ? B. hominis t?m sido descritos em uma variedade de hospedeiros n?o-humanos sendo denominado Blastocystis sp., mas seu potencial zoon?tico n?o est? esclarecido. O objetivo desse trabalho foi verificar a ocorr?ncia de infec??o natural de Blastocystis sp. em tr?s esp?cies de aves dom?sticas comercializadas em dois mercados municipais do Rio de Janeiro, caracterizando morfologicamente esses organismos encontrados em material fecal para a emiss?o de um diagn?stico preciso. Foram adquiridas 214 aves, sendo 35 patos (Anas platyrhynchos) do mercado A e 38 do mercado B, 35 codornas (Coturnix japonica) do mercado A e 36 do mercado B, e 35 pintos (Gallus gallus)do mercado A e 35 do mercado B. Das aves pesquisadas no mercado A, 8 (22,9%) pintos, 15 (42,9%) codornas e 13 (37,1%) patos apresentaram formas biol?gicas de Blastocystis sp. nas fezes, enquanto que no mercado B, 15 (42,9%) pintos, 2 (5,56%) codornas e 21 (55,3%) patos apresentaram tais formas nas fezes. N?o houve uma diferen?a estatisticamente significativa em rela??o ? ocorr?ncia de infec??o em patos e pintos dos dois mercados municipais pesquisados, ocorrendo essa diferen?a somente entre as codornas dos dois mercados. Ao considerarmos o n?mero de aves infectadas nos dois mercados, independentemente da esp?cie, observou-se que n?o houve uma diferen?a estatisticamente significativa entre os dois mercados. Das observa??es de esfrega?o de fezes coradas com Giemsa daqueles animais que apresentaram positividade para Blastocystis sp., foi poss?vel caracterizar seis formas do organismo, sendo estas: vacuolar, granular, ameb?ide, c?sticas, avacuolar e multivacuolar. Tamb?m foi poss?vel caracterizar as formas reprodutivas de Blastocystis sp. como: divis?o bin?ria, endodiogenia, brotamento, plamatomia e esquizogonia. Mesmo n?o tendo estudos que confirmem o potencial zoon?tico e patog?nico de Blastocystis sp., tanto para hospedeiros humanos quanto para animais, sugere-se que nesses mercados de comercializa??o pode ocorrer a contamina??o ambiental, devido ?s condi??es higi?nicas e sanit?rias serem de p?ssima qualidade, sendo um risco para os animais, assim como para a popula??o humana que comumente freq?entam esses ambientes. O conhecimento das formas evolutivas que foram encontradas e caracterizadas no presente trabalho ? de grande import?ncia para que se tenha um diagn?stico preciso e confi?vel de Blastocystis sp. em material fecal.

>Magister Scientiae - MSc / The Rosaceae family contains major temperate crops such as the domesticated apple(Malus x domestica Borkh.), peach (Prunus persica L. Batsch) and European pear (Pyrus communis L.). However, despite its evident economic importance, it is generally poorly studied in genomic terms, relative to the other major crop groups. Microsatellite and Diversity Array Technology (DArT) genetic markers have been exploited in this work and are essential tools in genetic map construction and marker-assisted selection (MAS) of high quality apples and other rosaceous crops. Microsatellites are advantageous in that they are co-dominant, highly polymorphic, abundant, transferable and reliably reproducible; hence their use in this study. In order for budbreak to take place in a timely and homogenous fashion, apple trees need a period of exposure to low temperatures.Within orchards the application of chemicals that induce budbreak in unsuitable environments is required to produce apples from cultivars that require high chilling levels. However, this and other practices using chemicals in orchards tend to pollute the environment. One of the solutions to this problem is to breed low chill apples such as ‘Anna’ cultivar, which was used as one of the parents in this study.This work was aimed at understanding the underlying genetic factors that determine chilling requirements for the time of initial vegetative budbreak trait in the apple cross ‘Anna’ x ‘Austin’. This was achieved through linkage map construction using SSR and DArT molecular markers followed by QTL analysis. This thesis has therefore exploited the large number of Expressed Sequence Tags (ESTs) and genome sequence data for the apple, using Tandem Repeats Finder, to design a total of 98 new SSR primers pairs. The other 369 SSR markers used in this work were from published work. JoinMap! 4.1 software was used to create an integrated genetic map with 17 linkage groups, for the domesticated apple cultivar, ‘Austin’ x ‘Anna’ mapping population with 80 individuals.The result of this process was a genetic map 1 212cM in length, and a total of 429 markers (314 DArT and 115 SSR), at an average density of a marker every 4 cM. This map was used identify the Quantitative Trait Loci (QTLs) determining chilling requirements for time of vegetative budbreak (IVB). In this process, putative IVB QTLs were identified in the ‘Anna’ x ‘Austin’ mapping population using the rMQM analysis function of MapQTL! 6.0, for both adult and seedling data collected over 3 growing seasons from 1996 to 1998. These QTLs were detected on linkage groups 2, 9 and 14,and explained 0.3 to 12.8 % of the observed phenotypic variation for the adult population,and 5.3 - 21 % for the seedling population. Seedling (LG 14) and adult (LGs 5, 7, 10) specific QTLs were also detected for the ‘Anna’ x ‘Austin’ cross. These QTLs will provide the basis for marker validation on related mapping populations in the apple breeding programme, and for the future identification of candidate genes controlling the process of budbreak.