Manguezais são ecossistemas que se distribuem ao redor do globo e desempenham funções ecológicas que são fundamentais para os ambientes costeiros adjacentes. Além de fornecerem uma ampla variedade de organismos para o subsídio humano, são áreas de produção e exportação de matéria orgânica, e também fornecem abrigo, alimentação e local para a reprodução de diversos animais marinhos. Apesar de sua enorme importância, esse ambiente encontra-se fortemente ameaçado e sob risco de desaparecer. As árvores de mangue são o seu componente mais básico e visível, sendo consideradas bastante produtivas, com grande parte do carbono orgânico encontrado nesse ambiente sendo proveniente da liteira e raízes das plantas. Micro-organismos são extremamente diversos, dinâmicos e estão distribuídos por todo o planeta, desempenhando importantes funções ecológicas, e dentro dos manguezais, eles são responsáveis pela maioria das transformações de nutrientes. Diversos estudos apontam a importância da comunidade bacteriana para uma equilibrada manutenção dos processos que ocorrem nesse ambiente, sendo um destes a decomposição de serapilheira. Dessa forma, este trabalho teve como objetivo estudar a dinâmica da comunidade bacteriana durante o processo de degradação de material vegetal em sedimentos de manguezais do Estado de São Paulo. Para isso, foi realizado o sequenciamento em larga escala do gene rRNA 16S do domínio Bacteria presente sobre a superfície do material vegetal. Paralelamente a isto, foi feita a quantificação da emissão CO2, N2O e CH4, durante os diferentes estágios de degradação foliar e também a análise da dinâmica e estrutura das comunidades. Os resultados obtidos por meio de sequenciamento em larga escala do gene rRNA 16S apontam o filo Proteobacteria como o grupo dominante nos três manguezais estudados, independente da espécie de planta. A classe Gammaproteobacteria apresentou uma maior abundância nos estágios iniciais de decomposição do material vegetal (7 e 15 dias), sofrendo um decaimento bem acentuado nas fases mais avançadas (60 dias). A alfa diversidade sofreu um aumento ao longo do tempo, com todas as amostras exibindo valores maiores nos estágios finais do processo de decomposição foliar. Em relação à emissão de gases de efeito estufa (GGE) em tratamentos em microcosmo, para N2O e CO2 tempo e local foram significativamente importantes. Já para CH4 somente o local foi relevante nas taxas de emissão. Foi possível identificar grupos de bactérias predominantes nas fases de decomposição foliar ao longo do período estudado. Gammaproteobacteria foi uma classe que se apresentou em maior quantidade nos estágios iniciais (7 e 15 dias), enquanto Alphaproteobacteria foi um grupo mais expressivo nas fases mais avançados de degradação (30 e 60 dias). / Mangroves are ecosystems that are distributed around the globe and perform ecological functions that are critical to the adjacent coastal environments. In addition to providing a wide variety of organisms for human activities, they have high productivity and are known as areas of production and export of organic matter, and also provide shelter, food and location for reproduction of various marine animals. Despite its enormous importance, this environment is at risk of disappearing. Mangrove trees are its most basic and visible component, being considered quite productive, with most of the organic carbon found in this environment being from the litter and plant roots. Micro-organisms are extremely diverse, dynamic and are spread across the globe, contributing with important environmental roles, and within the mangroves, they are responsible for most of nutrient transformations. Several studies point to the importance of the bacterial community for the balanced maintenance of the processes that are occurring in this environment. One of the most crucial of them is the decomposition of leaf-litter. Thus, this study aimed to evaluate the dynamics of bacterial communities during the degradation of plant material on sediments of São Paulo State mangroves by high throughput sequencing of 16S rRNA gene of Bacteria present on the surface of the plant material. In parallel, we quantified the emissions of CO2, N2O and CH4 during the different stages of leaf degradation and also the analysis of the dynamics and structure of communities. The results obtained by the sequencing of the 16S rRNA gene indicate the phylum Proteobacteria as the dominant group in the three mangroves, regardless of plant species. The Gammaproteobacteria class showed a greater abundance in the early stages of decomposition of the plant material (7 and 15 days), suffering a very sharp decay in the later stages (60 days). Alpha diversity has increased over time, with all the samples showing higher values in the final stages of the leaf decomposition process. It was possible to identify groups of bacteria predominant in the stages of decomposition of plant material throughout the study period. Regarding greenhouse gas emissions (GHG) in treatments in microcosm, time and location were significantly important factors to N2O and CO2 emissions. As for CH4 only the site was relevant in emission rates. It was possible to identify groups of bacteria predominant in the stages of leaf decomposition during the studied period. Gammaproteobacteria was a class that contains the main amount in the early stages (7 and 15 days), while Alphaproteobacteria was a more significant group in the most advanced stages of degradation (30 and 60 days).

The C₄ biochemical pathway is the most efficient form of photosynthesis in warm environments and introducing this system into globally significant, but less efficient, C₃ photosynthetic crops could bring major yield increases. The most photosynthetically efficient C₄ grass species have a specialised leaf anatomy characterised by high vein density with two distinct cell types radially arranged around the vascular bundles (Kranz anatomy). Although this anatomy was first described in 1882, the genetic regulators controlling Kranz development are still not known. In recent years, transcriptomic analysis has allowed researchers to identify candidate Kranz regulator genes, and a model for Kranz development has been proposed, however, this model has not been experimentally validated. This study used in situ hybridisation to visualise expression patterns for a set of candidate Kranz regulator genes in maize and the orthologous genes in rice. Further, morphological analysis of rice lines with constitutive expression of the candidate Kranz regulator genes AINTEGUMENTA 1 and DAG-LIKE 1 and 2 were used to characterise protein function during C₃ monocot leaf development. The function of maize AINTEGUMENTA in the C₃ eudicot arabidopsis was also investigated. The results of the in situ hybridisation experiments led to the refinement of the Kranz model and identified potential roles for the candidate regulators during leaf development. The constitutive expression experiments highlighted the regulatory differences between eudicot and monocot leaf development and implicated the regulation of auxin-cytokinin homeostatis as a key factor in Kranz development. Ultimately, this work can be used to guide research into Kranz development and has direct implications for engineering C₄ photosynthesis into rice.

The number one highest growth-limiting factor in Swedish forests is nitrogen, because of that fertilization often gives a significant growth increase, wherever you are in Sweden. Specific leaf area (SLA) can be used as a standard measurement of how much resources a tre has to use to build up light absorbing leaf area of needles/leaves. Since there is a strong linear relationship between tree growth and leaf area, there should also be a clear correlation between each leaf area of single trees and its diameter, basal area and volume growth (Xiao, 2005).The datamaterial for the study was collected at the forest estate, Toftaholm, near Ljungby in Kronoberg County (57 ° 0´N; 14 ° 3`E). Data were collected from birches growing in both in fertilized and unfertilized young stands of Birch during the growing season of 2018. The biomass sampling occured in May, July and August. At each occasion, samples were taken from 40 birches (a total of 120 samples were collected).The average value of SLA for all samples on the fertilized treatment was 17.33 m² / kg and 16.41 m² / kg for the non-fertilized treatment (Figure 4). The significance analysis obtained a p-value of 0.019 (Table 2), which confirms that there is a significant difference between the fertilized and the unfertilized treatment.In the significance analysis, it could be concluded that with a 95% probability, there is a significant difference between the comparison of all samples from the fertilized (G) and non-fertilized (OG) treatment.

Transpiration is the loss of water in vapor form from a plant. This is essentially the same process as evaporation except that it is modified by plant structure. Large quantities of water are removed from the soil, transferred through the conducting tissues of the plant, and dissipated into the air each day. As soon as the water is lost to the atmosphere, it becomes unavailable for human use. Few people are aware of the actual magnitude of this process. Over 95 percent of the water absorbed by the plant is lost through transpiration, the other 5 percent being used in photosynthesis and as a plant constituent. Herbaceous plants may transpire several times their own volume of water in a single day. Many forests lose over 20 inches of water in a year. Such large quantities, when dissipated in vapor form, are sufficient to modify the climate in the surrounding area.

Three perennial tropical Panicum species were grown under ambient and elevated (900 ppm) carbon dioxide concentrations in especially designed microclimate chambers. The study aimed to investigate the influence of high carbon dioxide concentrations on morphology/anatomy with physiological change among three closely related species possessing distinctly different photosynthetic pathways. The anatomy of the leaf was investigated using light microscopy (LM), transmission electron microscopy (TEM), and graphics image analysis. A suitable schedule for fixation, dehydration and embedding of leaf specimens for both forms of microscopy was developed. The anatomy of the species investigated did not change qualitatively, but there were detectable changes in leaf thickness and tissue proportions of the epidermis, mesophyll and thickened tissues (sclerenchyma, bundle sheath, vascular elements) that differed with species. This study is also relevant to the investigation of the evolution of C4, although species, and the progression involved in plants with characteristics intermediate between those of C3 and C4 species. These intermediate species have been mainly characterized by CO2 exchange and biochemical analysis, but they also display anatomical characteristics in between those of C3 and C4 plants. The evolutionary progression of the C3 to C4 species remains unsolved, although current studies indicate that the evolutionary step was from the C3 plant to the C4. Thus the intermediate C3/C4 plants may not be intermediate in an evolutionary sense and they could be seen as a simple hybridization between a C3 plant and C4 plant. In most of the parameters measured the C3/C4 P. decipiens resembled either the C3 P. tricanthum or the C4 P. antidotale. It may therefore be likened to a physiological chimera rather than to a true intermediate form / Doctor of Philosophy (PhD)

Thesis (M.S.)--Oregon State University, 2007. / Printout. Includes bibliographical references (leaves 41-47). Also available on the World Wide Web.

Mikromatriser handlar numera inte bara om att alstra genuttrycksdata i snabb takt, utan det är minst lika viktigt att effektivt ta hand om informationen efteråt. I den här avhandlingen presenteras ett arbetsflöde för att mäta, lagra och analysera genuttrycksdata i asp och poppel (Populus spp.). En Populus} mikromatrisdatabas - UPSC--BASE - tillgänglig för alla intresserade, utvecklades i syfte att samla in och lagra genuttrycksdata. Flertalet analysverktyg gjordes samtidigt tillgängliga, för att möjliggöra ett smidigt arbetsflöde från rådata till biologiska slutsatser. En av de stora utmaningarna i analys av mikromatriser är att kunna särskilja bruset från värdefull biologisk information. Att studera träd som växer utomhus är komplext eftersom de interagerar med omgivningen i mycket större utsträckning än vad som är fallet i växthusets kontrollerade miljö. Det här arbetet visar att det är möjligt, med hjälp av avancerad statistik och god försöksplanering, att följa och jämföra genuttrycket i blad från aspar utomhus under flera år för att dra värdefulla slutsatser om geners reglering. Den lagrade biologiska informationen i UPSC-BASE är avsedd att vara en värdefull tillgång för växtfältet i stort. I databasen finns nästan hundra olika experiment som innefattar alltifrån unga blad till ved, insektsangrepp, kyla och torka samt studier av genmodifierade växter. Informationen kan användas både för jämförande studier inom olika aspförsök, men också för att jämföra med andra växter. För att illustrera möjligheterna, studerades och grupperades gener i blad baserat på hur de uppträder över alla dessa experiment. Dessa grupperingar användes sedan för att definiera gener som är viktiga i bladutvecklingen. Sammanfattningsvis ger arbetet som presenteras i denna avhandling tillgång till verktyg och kunskap för storskaliga studier av genuttryck och den lagrade informationen har bevisats vara en värdefull tillgång för mer ingående studier av geners reglering. / DNA microarray analysis today is not just generation of high-throughput data, much more attention is paid to the subsequent efficient handling of the generated information. In this thesis, a pipeline to generate, store and analyse Populus transcriptional data is presented A public Populus microarray database - UPSC--BASE - was developed to gather and store transcriptomic data. In addition, several tools were provided to facilitate microarray analysis without requirements for expert-level knowledge. The aim has been to streamline the workflow from raw data through to biological interpretation. Differentiating noise from valuable biological information is one of the challenges in DNA microarray analysis. Studying gene regulation in free-growing aspen trees represents a complex analysis scenario as the trees are exposed to, and interacting with, the environment to a much higher extent than under highly controlled conditions in the greenhouse. This work shows that, by using multivariate statistics and experimental planning, it is possible to follow and compare gene expression in leaves from multiple growing seasons, and draw valuable conclusions about gene expression from field-grown samples. The biological information in UPSC-BASE is intended to be a valuable transcriptomic resource also for the wider plant community. The database provides information from almost a hundred different experiments, spanning different developmental stages, tissue types, abiotic and biotic stresses and mutants. The information can potentially be used for both cross-experiment analysis and for comparisons against other plants, such as Arabidopsis or rice. As a demonstration of this, microarray experiments performed on Populus leaves were merged and genes preferentially expressed in leaves were organised in to regulons of co-regulated genes. Those regulons were used to define genes of importance in leaf development in Populus. Taken together, the work presented in this thesis provides tools and knowledge for large-scale transcriptional studies and the stored gene expression information has been proven to be a valuable information resource for in-depth studies about gene regulation.

How patterns arise from an apparently uniform group of cells is one of the classical problems in developmental biology. The mechanism is complicated by the fact that patterning occurs on a growing medium. Therefore, changes in an organism’s size and shape affect the patterning processes. In turn, patterning itself may affect growth. This interaction between growth and patterning leads to the generation of complex shapes and structures from simpler ones. Studying such interactions requires the possibility to monitor both processes in vivo. To this end, we developed a new technique to monitor and quantify vein patterning in a growing leaf over time using the leaves of Arabidopsis thaliana as a model system. We used a transgenic line with fluorescent markers associated with the venation. Individual leaves are followed in many samples in vivo through time-lapse imaging. Custom-made software allowed us to extract the leaf surface and vein pattern from images of each leaf at each time point. Then average spatial maps from multiple samples that were generated revealed spatio-temporal gradients. Our quantitative description of wild type vein patterns during leaf development revealed that there is no constant size at which a part of tissue enclosed by vasculature will become irrigated by a new vein. Instead, it seemed that vein formation depends on the growth rate of the tissue. This is the first time that vein patterning in growing leaves was quantified. The techniques developed will later be used to explore the interaction between growth and patterning through a variety of approaches, including mutant analysis, pharmacological treatments and variation of environmental conditions.

Fiber optic sensors are designed to measure various parameters. The distributed fiber optics sensor has been a very promising candidate for the structural health monitoring. In this thesis, we characterized LEAF (Large Effective Area Fiber) fiber’s Brillouin scattering spectrum and investigated its potentiality for the distributed Brillouin temperature and strain sensor. Optical fibers with complex refractive index profiles are applied to improve the Brillouin threshold by varying the Brillouin linewidth. As LEAF fiber has a modified refractive index profile, we investigated its Brillouin linewidth’s dependence on the square of the pump light’s frequency. We verified the Brillouin frequency’s variation with input SOP experimentally for LEAF fiber in the spontaneous regime. This sets a limitation for the frequency resolution of distributed Brillouin sensors. We also realized a simultaneous temperature and strain sensor with LEAF fiber applying the Brillouin optical time domain analysis. Based on the direct detection of LEAF beat frequencies, a simultaneous strain and temperature sensor was demonstrated.

The fungus <i>Colletotrichum truncatum</i> (Schw.) Andrus and Moore causes lentil anthracnose, which is a major challenge to lentil production in Western Canada. The pathogen infects leaves and stems, resulting in defoliation, stem girdling, plant wilting, and possibly plant death. Two races, Ct0 and Ct1, have been identified in the pathogen population in Canada. However, the differences in the infection process between the two races have not been described in detail. Currently, several lentil cultivars, such as CDC Redberry, CDC Robin, CDC Rosetown, CDC Rouleau, and CDC Viceroy, have resistance against race Ct1, whereas there are no cultivars showing resistance to race Ct0. The objective of this study was to investigate differences in the infection process between race Ct0 and race Ct1 using the fully susceptible cultivar Eston and the race Ct1-resistant cultivar CDC Robin. Experiments on glass well slides showed that race Ct0 had no inherently different conidium germination rate compared to race Ct1, and that differences in conidium germination between the two races on lentil plants were the result of specific interactions between the two races and lentil resistance. Investigations of the infection process of the two races on detached and attached leaves of both lentil cultivars were conducted starting 12 h postinoculation (hpi) until 72 hpi, including conidium germination, appressorium formation, and leaf penetration. Results indicated that differences in virulence of the two races may be related to the ability of conidia to germinate and form appressoria, as well as the ability of primary infection hyphae to grow in response to cues from the lentil cultivars. Furthermore, resistance of lentil to isolates of race Ct1 appeared to involve an inhibition in and/or delay of the spread of primary infection hyphae inside the plant tissue. Results of infection studies of one isolate from each race on attached leaves did not completely agree with results of the same isolates on detached leaves. Based on this study, race Ct0 and race Ct1 do not appear to be classical physiological races, but may represent aggressive races or some intermediate forms.