The pathogen C. jejuni is now recognised as the leading cause of bacterial foodborne enteritis in the industrial world. The yearly estimate for Campylobacter infections in the United States alone is 2.4 million people or 1% of the population. Illness caused by C. jejuni is self-limiting, however, some individuals develop complications resulting in autoimmune responses. Despite being a major health burden, the pathogenic process is not fully understood. One aspect of importance is the ability of C. jejuni to adhere to glycosaminoglycans (GAGs), such as heparin. GAGs, sulphated carbohydrates expressed on or in host cells, can serve as receptors for bacterial proteins. In the first study, five heparin-binding proteins of C. jejuni NCTC 11168H were identified. For PEB3 (Cj0289c), this work showed that native wild-type PEB3 and purified recombinant PEB3 produced in E. coli bind heparin. The location of two PEB3 heparin-binding clusters: 62KAKKD65 and 122NKKVRI127, was investigated via site-directed mutagenesis, resulting in impaired heparin-binding. These data suggest GAG-protein-binding may play a role in the pathogenesis of C. jejuni. As well as GAG-binding PEB3 binds 3-PG. Though its exact in vivo role remains unclear, it may act to deliver 3-PG. Scrutiny of the C. jejuni NCTC 11168H genome revealed an uncharacterised gene next to peb3 encoding glpT, or a putative 3-PG transporter. The location of glpT adjacent to peb3 may suggest a related function for the corresponding proteins with PEB3 as the periplasmic binding partner for the transport of 3-PG via GlpT. In this thesis, the roles of peb3 and glpT for two independent phenotypes, 3-PG dependent growth and fosfomycin sensitivity was studied in vitro. The findings indicate glpT has an effect on both, but not peb3. Furthermore, the NCTC 11168H glpT pseudogene, despite containing two frameshift mutations, has the capacity to encode a functional protein. Lastly, the NCTC 11168H peb3/glpT locus was compared with other C. jejuni strains and closely related species C. coli, C. lari and C. upsaliensis genome sequences. The majority of strains peb3/glpT locus followed the gene arrangement lpxB, peb3, glpT, surE. However, the findings indicate the gene loci between lpxB/surE in remaining strains to be hypervariable. Further analysis shows peb3 to be relatively conserved, whereas, the majority of glpT genes display genetic diversity due to interruptions such as indels and deletion. Lastly, I display the organisation of the peb3/glpT locus and glpT structure in their evolutionary context through MLST. In summary, the findings provide for further characterisation of the PEB3 protein and explores the importance of the uncharacterised GlpT of C. jejuni.

Submitted by Jorge Silva (jorgelmsilva@ufrrj.br) on 2016-10-20T19:09:28Z No. of bitstreams: 1 2016 - Carlos Magno Moreira de Oliveira.pdf: 3071191 bytes, checksum: 379c33cebd9108d71d2092ecebb6104d (MD5) / Made available in DSpace on 2016-10-20T19:09:28Z (GMT). No. of bitstreams: 1 2016 - Carlos Magno Moreira de Oliveira.pdf: 3071191 bytes, checksum: 379c33cebd9108d71d2092ecebb6104d (MD5) Previous issue date: 2016-02-26 / CAPES / Commercial plantations of Eucalyptus has increased in Brazil, mainly in the state of Minas Gerais. The assessment of the effects of soil and climatic variables on the growth of trees becomes important tool to optimize management activities. In this perspective, this study aims to adjust and parameterize the 3-PG model for the North of Minas Gerais, using data from permanent plots of forest inventory, climate data from weather stations and data from remote sensing. This study was conducted in Eucalyptus of commercial plantations in the city of Bocaiuva (Minas Gerais). To parameterize the constant parameters of the relationship between DAP and height (H) relationship of power between DAP and height (NHB), constant relationship between volume and DAP (aV) and relationship of power between volume and DAP (NVB) were used in 2031 comments. The PG-3 model was run with parameters suggested in literature for the region and then executed with changes in the parameters mentioned above. To evaluate the effect of climate variability on planting were assessed estimates of 3-PG model fed with climatological normal and monthly averages and then analyzed the effects of environmental modulators fans and fDPV on the growth of planting. The database of climatological normals were obtained from INMET and global solar radiation was obtained from the GL 1.2 model for South America. The database with monthly average was acquired by INMET, and the precipitation was obtained from tropical TRMM satellite and solar radiation was estimated by the model proposed by FAO 56. Subsequently, we evaluated the efficiency of the 3-PG model in estimating the growth and production of settlement regarding estimates of empirical models, considering the FR parameter (Fertility Rating) as a site quality indicator. Through significant improvement was observed statistical analysis of procedural modeling with the modification of the suggested parameters, indicating that the values of this parameter can be used for other municipalities that region. Statistical analyzes showed that there was a reduction of variation of the data through the standard error of estimate (Syx%) and model efficiency (EF) greater than 0.80 for DBH, height and volume, indicating significant improvement in the model estimates . Comparing the estimates of dendrometric variables with climatological normal and monthly averages, it is observed, the graphics, the estimates were similar, with the monthly averages showed higher estimates. Statistical analysis demonstrated that the monthly averages were closer to those observed data, Syx 28% and EF 0.82 to volume while normal climatic Syx% showed almost 60% and EF 0.22. fAS modulator showed greater restriction on the development of trees, especially in the months of July, August and September. The procedural modeling showed average yield estimates in respect of empirical modeling, and the site estimated by 3-PG showed values close to the average estimated by site traditional model. The FR parameter on soil fertility, showed good relationship with the classification of production sites, and further studies to improve the accuracy in the classification of sites indexes. The 3-PG model can make accurate estimates of dendrometric variables, showing an important tool for evaluating areas with fitness for forest production, considering the effect of environmental and climate variables in the growth of trees. The procedural modeling can be used together with empirical tools to assess the growth and production of forest plantations on different management activities and in the future producing areas. / Plantios comerciais de Eucalyptus tem aumentado no Brasil, principalmente no estado de Minas Gerais. A avalia??o dos efeitos das vari?veis ed?ficas e clim?ticas sobre o crescimento das ?rvores torna-se ferramenta importante para otimizar as atividades de manejo. Nessa perspectiva, esse trabalho tem por objetivo ajustar e parametrizar o modelo 3-PG para regi?o Norte de Minas Gerais, utilizando dados de parcelas permanentes de invent?rio florestal, dados clim?ticos de esta??es climatol?gicas e dados oriundos de sensoriamento remoto. Esse estudo foi realizado em plantios comerciais do g?nero Eucalyptus no munic?pio de Bocai?va (MG). Para parametrizar os par?metros constante de rela??o entre DAP e altura (aH), pot?ncia de relacionamento entre DAP e altura (nHB), constante de relacionamento entre volume e DAP (aV) e pot?ncia de relacionamento entre volume e DAP (nVB) foram utilizados 2031 observa??es. O modelo 3-PG foi executado com par?metros sugeridos na bibliografia para regi?o e posteriormente executada com modifica??es nos par?metros mencionados anteriormente. Para avaliar o efeito da variabilidade clim?tica sobre o plantio, foram avaliadas as estimativas do modelo 3-PG alimentado com normais climatol?gicas e m?dias mensais e posteriormente analisado os efeitos dos moduladores ambientais fAS e fDPV sobre o crescimento do plantio. O banco de dados das normais climatol?gicas foram obtidas do INMET e a radia??o solar global foi obtido do modelo GL 1.2 para am?rica do sul. O banco de dados com m?dias mensais foi adquirido pelo INMET, sendo que a precipita??o foi obtida do sat?lite tropical TRMM e a radia??o solar global foi estimado pelo modelo proposto pela FAO 56. Posteriormente, foi avaliado a efici?ncia do modelo 3-PG em estimar o crescimento e produ??o do povoamento em rela??o as estimativas dos modelos emp?ricos, considerando o par?metro FR (Fertility Rating) como indicador da qualidade de s?tio. Por meio de an?lises estat?sticas foi observado melhora significativa da modelagem processual com a modifica??o dos par?metros sugeridos, indicando que os valores dessa parametriza??o podem ser utilizados para outros munic?pios dessa regi?o. As an?lises estat?sticas demonstram que houve redu??o da varia??o dos dados por meio do erro padr?o da estimativa (Syx%) e efici?ncia do modelo (EF) maior que 0,80 para as vari?veis DAP, Altura e Volume, indicando melhoria significativa nas estimativas do modelo. Comparando-se as estimavas das vari?veis dendrom?tricas com normais climatol?gicas e medias mensais, observa-se, pelos gr?ficos, que as estimativas foram semelhantes, sendo que as medias mensais apresentaram estimativas superiores. A an?lise estat?stica demonstra que as medias mensais foram mais pr?ximas aos dados observados, com Syx% 28 e EF de 0,82 para volume, enquanto que as normais climatol?gicas apresentaram Syx% de quase 60% e EF de 0,22. O modulador fAS apresentou maior restri??o no desenvolvimento das ?rvores, principalmente nos meses de julho, agosto e setembro. A modelagem processual apresentou estimativas de produ??o m?dia em rela??o a modelagem emp?rica, sendo que o s?tio estimado pelo 3-PG apresentou valores pr?ximos ao s?tio m?dio estimado pela modelam tradicional. O par?metro FR, relativo a fertilidade do solo, apresentou boa rela??o com a classifica??o de s?tios de produ??o, sendo necess?rios outros estudos para melhorar a acur?cia na classifica??o dos ?ndices de s?tios. O modelo 3-PG pode realizar estimativas precisas de vari?veis dendrom?tricas, mostrando-se ferramenta importante para avalia??o de ?reas com aptid?o para produ??o florestal, por considerar o efeito de vari?veis ambientais e clim?ticas no crescimento das ?rvores. A modelagem processual pode ser utilizada juntamente com ferramentas emp?ricas para avaliar o crescimento e produ??o de plantios florestais sobre diferentes atividades de manejo e tamb?m em ?reas futuramente produtoras.

Made available in DSpace on 2015-03-26T13:53:06Z (GMT). No. of bitstreams: 1 texto completo.pdf: 631158 bytes, checksum: 02116694fb47515646edb72c63edbe00 (MD5) Previous issue date: 2009-02-16 / Coordenação de Aperfeiçoamento de Pessoal de Nível Superior / An alternative to quantify and predict the forest potential productivity is the use of process-based models (PBMs). Among the various existent models in the forest area, the 3- PG (Physiological Principles in Prediction Growth) has been used more recently, which, in essence, is a model of water and solar radiation use efficiency and of carbon partitioning. In Brazil, the results obtained with this model have been good, but these results also show the need of parameterisation and calibration of the model through the adjustment of the values of the parameters and relationships, for the conditions of forest sites. There are not works of this type for the cerrado of Minas Gerais (MG). In this study, we made a parameterisation, calibration and validation of the 3- PG model for fast-growing eucalypt plantations at the cerrado of Minas Gerais. The study was conducted with data from the regions of Curvelo and Itacambira MG and two genetic materials (hybrid clones of E. grandis x E. urophylla) were evaluated during a cycle of production (0,25, 1, 2, 3, 5 and 7 years). At the stage of parameterisation, plots constituted of 40 plants were established. The diameter of the plants was measured at 1,30 m high (dbh), and four plants with dbh of around the average per plot were sampled destructively. The diameter (dbh), the total (H) and commercial (Hc) height, the stand volume excluding branch & bark (V) and the aboveground and root biomass were measured in these trees. It was also determined the specific leaf area (σf), the wood density (ρ) and the fraction of stem biomass as branch and bark (pBB). The litterfall rate has been monitored through collectors of 0.5 x 0.5 m distributed in six random points in each plot. Through non-linear models allometric relationships were adjusted, that describe the relationship among the total height, the stem biomass including branches and bark, and the stand volume as a function of dbh, and also equations that describe the behavior of the σf, ρ and pBB as a function of the age. During the stage of calibration, the estimates for dbh, H, V, dry matter of stem and basal area, obtained through the parameterised model, were compared to data measured in the field in each situation and the eventual deviations were minimized by adjusting the values of some variables of the model that were not measured. At the stage of validation, estimates for dbh, V and H, obtained through the parameterized and calibrated model, were compared to independent data (continuum and pre-cut forest inventory) to evaluate the reliability and capacity of extrapolation of the model. In relation to the dendrometric data, the material 3334 has a much more superior productivity than the material 3336 in the region of Curvelo, but in Itacambira the behavior of both materials in terms of productivity is similar. As concerning the performance of the model, it was satisfactory when simulating the growth of eucalypt forests for the clones 3334 and 3336 in Itacambira, and for the clone 3336 in the region of Curvelo. The estimates obtained through the general model developed for the region of cerrado also present significant correlation with the observed data, either at the stage of calibration or at the stage of validation. For the material 3334 in Curvelo, even after alterations in important variables of the model it was not possible to obtain a satisfactory adjustment of the 3-PG, however, the performance of the adjusted model for this condition was superior to the other available parameterisations. In conclusion, the 3-PG model adjusted for the cerrado of Minas Gerais was efficient in simulate the growth of eucalypt forests in the region, and the performance of the model was superior to other parameterisations of available models. / Uma alternativa para a quantificação e prognose do potencial produtivo de florestas plantadas é o emprego de modelos baseados em processos. Dentre os vários modelos existentes na área florestal, mais recentemente tem-se utilizado o 3-PG (Physiological Principles in Prediction Growth), que, em essência, é um modelo de eficiência de uso de radiação solar e água, e de partição de carbono. Os resultados obtidos com este modelo no Brasil tem sido bons, mas mostram a necessidade de parametrização e calibração do mesmo, por meio de ajustes dos valores dos parâmetros e relacionamentos, para as condições do sitio florestal, não havendo trabalhos desse tipo para o cerrado de Minas Gerais (MG). Neste trabalho, realizou-se a parametrização, calibração e validação do modelo 3-PG para plantios de eucalipto na região do cerrado de MG. Para tanto, o trabalho foi conduzido com dados das regiões de Curvelo e Itacambira MG, para dois materiais genéticos (híbridos clonais de E. grandis x E. urophylla), avaliados ao longo de um ciclo produtivo (0,25, 1, 2, 3, 5 e 7 anos). Na etapa de parametrização foram estabelecidas parcelas constituídas por 40 plantas, nas quais foi medido o diâmetro a 1,30 m de altura (dap), sendo abatidas quatro plantas com dap em torno da média por parcela. O diâmetro (dap), a altura total (H) e comercial (Hc), o volume de lenho (V) e a biomassa da parte aérea e raiz foram mensuradas nestas árvores. Foram determinadas também a área foliar específica (σf), a densidade da madeira (ρ) e a fração de galho e casca em relação à biomassa da parte aérea (pBB) excluindo as folhas. A taxa de queda de litter tem sido monitorada por meio de coletores de 0,5 x 0,5 m espalhados em 6 pontos aleatórios em cada parcela. Por meio de modelos não-lineares foram ajustadas equações alométricas que descrevem o relacionamento entre a altura total, a biomassa de stem (lenho + casca + galhos) e o volume de lenho em função do dap, e também equações que descrevem o comportamento da σf, ρ e pBB em função da idade. Durante a etapa de calibração, as estimativas para dap, H, V, matéria seca de stem e área basal, obtidas pelo modelo parametrizado, foram comparadas com dados medidos no campo em cada situação e os eventuais desvios foram minimizados por meio de ajustes ( tuning ) nos valores de algumas variáveis do modelo que não foram medidas. Na etapa de validação, estimativas para dap, V e H, obtidas pelo modelo parametrizado e calibrado, foram comparadas com dados independentes (inventário florestal contínuo e précorte) para avaliar a confiabilidade e a capacidade de extrapolação do modelo. Com relação aos dados dendrométricos, o material 3334 tem produtividade muito superior ao 3336 na região de Curvelo, mas em Itacambira o comportamento dos dois materiais em termos produtivos é semelhante. Já quanto ao desempenho do modelo, o mesmo foi satisfatório, ao simular o crescimento de florestas de eucalipto para os clones 3334 e 3336 em Itacambira e para o clone 3336 na região de Curvelo. As estimativas obtidas pelo modelo geral desenvolvido para a região do cerrado também apresentaram correlação significativa, com os dados observados, tanto na etapa de calibração, quanto na de validação. Para o material 3334 em Curvelo, mesmo após alterações em variáveis importantes do modelo, não foi possível obter ajuste do 3-PG que fosse satisfatório, sendo, no entanto, o desempenho do modelo ajustado para essa condição, superior ao de outras parametrizações disponíveis. Dessa forma, conclui-se que o modelo 3-PG ajustado para o Cerrado de Minas Gerais foi eficiente em simular o crescimento de florestas de eucalipto na região, sendo o desempenho do mesmo, superior ao de outras parametrizações do modelo disponíveis.

During this study two models were developed to predict growth of Pinus radiata D.Don plantations in Canterbury, New Zealand. The first, CanSPBL(1.2), is a model for whole rotations of stands owned by Selwyn Plantation Limited in Canterbury. The second model, CanSPBL(water) is a hybrid growth model for the Selwyn estate in Canterbury that incorporates an index of root zone water balance over the simulation period. An existing stand growth and yield model CanSPBL was examined using a validation dataset of PSP measurements that were not used in model fitting. Projection bias was shown for mean top height, basal area per hectare, and residual stand stocking particularly for stands at elevations exceeding 450 metres. The new model, CanSPBL(1.2) showed an increase in precision of 4 - 46% over CanSPBL(1.0) at a stand level. The components of the stand model include mean top height, basal area per hectare, stems per hectare, and diameter distribution. The mortality model was made in conjunction with managers at CanSPBL to exclude catastrophic mortality events from model projections. Data used for model fitting was filtered using a mortality index based on the -3/2 power law. An examination of this model with an independent dataset showed little apparent bias. The new model, CanSPBL(water) was developed to include an index of water balance over the simulation period. Water balance estimates were made using a sub model for root zone water balance included in the hybrid physiological model 3-PG (Landsberg and Waring, 1997). The new model showed an increase in precision of 1 - 4% over CanSPBL(1.2) at a stand level (with the exception of the model for maximum diameter which showed a decrease in precision of 0.78%) using climatic inputs that included yearly variation. However the model showed increases of precision from 0.5 to 8% (with the exception of maximum diameter again, showing a decrease in precision of 0.13%) using long term monthly average climatic inputs. The components of the stand model also include mean top height, basal area per hectare, stems per hectare, and diameter distribution. The mortality model was also fitted with a data set filtered using a mortality severity index based on the -3/2 power law to exclude catastrophic mortality events. An examination of this model with an independent dataset showed little apparent bias. Two models to predict a one sided canopy leaf area index (LAI) of radiata pine stands in the Canterbury Plains of New Zealand were also developed. The models were fitted using non-linear least squares regression of LAI estimates against stem measurements and stand characteristics. LAI estimates were derived from digital analysis of fisheye lens photography. The models were kept simple to avoid computational circularity for physiological modelling applications. This study included an objective comparison and validation of a range of model types. The models CANTY (Goulding, 1995), CanSPBL(1.2) (Pinjuv, 2005), CanSPBL-water (Pinjuv, 2005), and 3-PG (Landsberg and Waring, 1997) were compared and validated with the main criteria for comparison being each model s ability to match actual historical measurements of forest growth in an independent data set. Overall, the models CanSPBL(water), and CanSPBL(1.2) performed the best in terms of basal area and mean top height prediction. Both models CanSPBL(water), and CanSPBL(1.2) showed a slightly worse fit in predictions of stocking than did the model CANTY. The hybrid model 3PG showed a better fit for the prediction of basal area than the statistically based model CANTY, but showed a worse fit for the prediction of final stocking than all other models. In terms of distribution of residuals, CanSPBL(1.2) had overall the lowest skewness, kurtosis, and all model parameters tested significant for normality. 3PG performed the worst on average, in terms of the distribution of residuals, and all models tested positively for the normality of residual distribution.