Šmilauer, T. Cosmological themes in conteporary art. [Master thesis] Prague 2012. 83 pages Charles univerzity in Prague, Faculty of education, department of art education. This work examines the relationship between man and the cosmos, and deals with topics cosmos and cosmology in terms of philosophical and scientific, but also seeks connection with religion and mythology. The aim is to interpret and define the concepts of the cosmos and cosmology, and find these contents in visual culture and fine art. This thesis is also finding ways to use cosmological issues in educational practice. Keywords: cosmos, cosmology, nature, man, visual perception and imaging, microcosm, macrocosm, art

The objective of this study was to evaluate the antimicrobial and anti-caries effects of two plant extracts. The first chapter dealt with a review of the literature whose objective was to discuss the antimicrobial potential of Brazilian natural agents on the biofilm related to dental caries and gingivitis/periodontal disease. The research of the articles was carried out using PubMed. We found a total of 23 papers. Most of the studies were performed using planktonic microorganisms or under clinical trials. Nineteen articles were focused on cariogenic bacteria. From these nineteen articles, eleven were also about periodontopathogenic bacteria. Four studies addressed only periodontopathogenic bacteria. The most tested Brazilian natural agents were green propolis, essential oils of Lippia sidoides and Copaifera sp. Most of the tested agents showed similar results when compared to positive control (essential oils and extracts) or better effect than negative control (green propolis). More studies involving protocols closer to the clinical condition and the use of response variables that allows understanding the mechanism of action of natural agents are necessary before the incorporation of these natural agents into dental products. The second chapter aimed to test the effect of the hydroalcoholic extracts of Myracrodruon urundeuva All. and Qualea grandiflora Mart. leaves on the viability of the microcosm biofilm and on the prevention of enamel demineralization. The microcosm biofilm was produced on bovine enamel, using human saliva pool mixed with McBain saliva (0.2% sucrose) for 14 days. The biofilm was treated daily with the extracts for 1 min. M. urundeuva at 100, 10 and 0.1 g/ml and Q. grandiflora at 100 and 0.1 g/ml reduced cell viability similarly to the positive control and significantly more than negative control. M. urundeuva at 1000, 100 and 0.1 g/ml were able to reduce the counting formation unit-CFU counting of lactobacilli sp. and Streptococcus mutans, while Q. grandiflora at 1000 and 1.0 g/ml significantly reduced the S. mutans CFU counting. On the other hand, the natural extracts did not reduce the production of extracellular polyssacharides, lactic acid and the development of enamel caries lesions. The third chapter aimed to evaluate the effect of hydroalcoholic extracts of M. urundeuva and Q. grandiflora (alone or combined) on the viability of S. mutans biofilm and the prevention of enamel demineralization. S. mutans strain (ATCC 21175) was reactivated in BHI broth. Minimum inhibitory concentration, minimum bactericidal concentration, minimum biofilm inhibitory concentration and minimum biofilm eradication concentration were determined to choose the concentrations to be tested under the biofilm model. S. mutans biofilm (5x105 CFU/ml) was produced on bovine enamel using McBain saliva with 0.2% sucrose for 3 days. The biofilm was treated daily with the extracts for 1 min. M. urundeuva (isolated or combined) at concentrations equal or higher than 0.625 mg/ml was able to reduce the bacteria viability, whereas Q. grandiflora extract alone showed antimicrobial effect at 5 mg/ml only (p<0.05). On the other hand, none of the extracts was able to reduce the development of enamel caries lesions. Despite the tested natural extracts have antimicrobial effect; they are unable to prevent caries in enamel. / O objetivo foi avaliar os efeitos antimicrobiano e anti-cárie de dois extratos de plantas. O primeiro capítulo se referiu a uma revisão da literatura cujo objetivo foi discutir o potencial antimicrobiano dos agentes naturais brasileiros sobre o biofilme relacionado à cárie dentária e à gengivite/doença periodontal. A pesquisa dos artigos foi realizada usando o PubMed. Foram encontrados 23 trabalhos. A maioria dos estudos foi realizada utilizando microorganismos na fase planctônica ou ensaios clínicos. Dezenove artigos foram focados em bactérias cariogênicas. Dos dezenove artigos, onze também eram sobre bactérias periodontopatogênicas. Quatro estudos abordaram apenas bactérias periodontopatogênicas. Os agentes naturais brasileiros mais testados foram própolis verde, óleos essenciais de Lippia sidoides e Copaifera sp. Os agentes testados apresentaram resultados similares quando comparados ao controle positivo (óleos essenciais e extratos) ou melhor efeito que o controle negativo (própolis verde). Mais estudos próximos da condição clínica e o uso de variáveis de resposta que permitam entender o mecanismo de ação são necessários, para permitir a incorporação desses agentes naturais em produtos odontológicos. O segundo capítulo teve como objetivo testar o efeito dos extratos hidroalcoólicos de Myracrodruon urundeuva All. e Qualea grandiflora Mart. sobre a viabilidade do biofilme microcosmo e na prevenção da desmineralização do esmalte. O biofilme microcosmo foi produzido em esmalte bovino, utilizando pool de saliva humana misturada à saliva de McBain (0,2% de sacarose) durante 14 dias. O biofilme foi tratado diariamente com os extratos durante 1 min. M. urundeuva a 100, 10 e 0,1 g/ml e Q. grandiflora a 100 e 0,1 g/ml reduziram a viabilidade dos microrganismos de forma semelhante ao controle positivo e significativamente maior do que o controle negativo. M. urundeuva a 1000, 100 e 0,1 g/ml foi capaz de reduzir a contagem de Unidade formadora de colônia-UFC para Lactobacilos totais e Streptococcus mutans, enquanto a Q. grandiflora a 1000 e 1,0 g/ml reduziu significativamente a contagem de UFC para S. mutans. Os extratos naturais não conseguiram reduzir a produção de polissacarídeos extracelulares-PEC, ácido lático e o desenvolvimento da lesão cariosa em esmalte. O terceiro capítulo teve como objetivo avaliar o efeito dos extratos hidroalcoólicos de M. urundeuva. e Q. grandiflora (sozinhos ou combinados) sobre a viabilidade do biofilme de S. mutans e na prevenção da desmineralização do esmalte. Cepa de S. mutans (ATCC 21175) foi reativada em caldo BHI. Concentração inibitória mínima, concentração bactericida mínima, concentração inibitória mínima de biofilme e concentração de erradicação mínima de biofilme foram determinadas para escolher as concentrações a serem testadas sob o modelo de biofilme. O biofilme de S. mutans (5x105 CFU/ml) foi produzido em esmalte bovino, utilizando saliva de McBain com 0,2% de sacarose durante 3 dias. O biofilme foi tratado diariamente com os extratos durante 1 min. M. urundeuva (isolada ou combinada) nas concentrações iguais ou superiores a 0,625 mg/ml foi capaz de reduzir a viabilidade das bactérias, enquanto que o extrato da Q. grandflora apresentou efeito antimicrobiano somente a 5 mg/ml (p<0,05). Nenhum dos extratos reduziu o desenvolvimento da lesão da cárie. Apesar dos extratos naturais terem efeito antimicrobiano, são incapazes de prevenir o desenvolvimento da lesão cariosa em esmalte.

The amount of organic carbon (OC) present in Siberian Arctic permafrost soils is estimated at twice the amount of carbon currently in the atmosphere. The shelf seas of the Arctic Ocean receive large amounts of this terrestrial OC from Eurasian Arctic rivers and from coastal erosion. Degradation of this land-derived material in the sea would result in the production of dissolved carbon dioxide and may then add to the atmospheric carbon dioxide reservoir. Observations from the Siberian Arctic suggest that transfer of carbon from land to the marine environment is accelerating. However, it is not clear how much of the transported OC is degraded and oxidized, nor how much is removed from the active carbon cycle by burial in marine sediment. Using bulk geochemical parameters, total OC, d13C and D14C isotope composition, and specific molecular markers of plant wax lipids and lignin phenols, the abundance and composition of OC was determined in both dissolved and particulate carrier phases: the colloidal OC (COC; part of the dissolved OC), particulate OC (POC), and sedimentary OC (SOC). Statistical modelling was used to quantify the relative contribution of OC sources to these phases. Terrestrial OC is derived from the seasonally thawing top layer of permafrost soil (topsoil OC) and frozen OC derived from beneath the active layer eroded at the coast, commonly identified as yedoma ice complex deposit OC (yedoma ICD-OC). These carbon pools are transported differently in the aquatic conduits. Topsoil OC was found in young DOC and POC, in the river water, and the shelf water column, suggesting long-distance transport of this fraction. The yedoma ICD-OC was found as old particulate OC that settles out rapidly to the underlying sediment and is laterally transported across the shelf, likely dispersed by bottom nepheloid layer transport or via ice rafting. These two modes of OC transport resulted in different degradation states of topsoil OC and yedoma ICD-OC. Terrestrial CuO oxidation derived biomarkers indicated a highly degraded component in the COC. In contrast, the terrestrial component of the SOC was much less degraded. In line with earlier suggestions the mineral component in yedoma ICD functions as weight and surface protection of the associated OC, which led to burial in the sediment, and limited OC degradation. The degradability of the terrestrial OC in shelf sediment was also addressed in direct incubation studies. Molecular markers indicate marine OC (from primary production) was more readily degraded than terrestrial OC. Degradation was also faster in sediment from the East Siberian Sea, where the marine contribution was higher compared to the Laptev Sea. Although terrestrial carbon in the sediment was degraded slower, the terrestrial component also contributed to carbon dioxide formation in the incubations of marine sediment. These results contribute to our understanding of the marine fate of land-derived OC from the Siberian Arctic. The mobilization of topsoil OC is expected to grow in magnitude with climate warming and associated active layer deepening. This translocated topsoil OC component was found to be highly degraded, which suggests degradation during transport and a possible contribution to atmospheric carbon dioxide. Similarly, the yedoma ICD-OC (and or old mineral soil carbon) may become a stronger source with accelerated warming, but slow degradation may limit its impact on active carbon cycling in the Siberian Shelf Seas. / <p>At the time of the doctoral defense, the following papers were unpublished and had a status as follows: Paper 3: Manuscript. Paper 4: Manuscript.</p>

L'évaluation du risque lié aux contaminants est généralement basée sur des données collectées au cours d'essais monospécifiques (à une seule espèce). Par conséquent, les interactions entre espèces, bien qu'elles structurent les écosystèmes, ne sont pas prises en compte. Pour explorer les effets des contaminants sur la dynamique des espèces en interaction, cette thèse vise à modéliser le fonctionnement d'un microcosme de laboratoire de deux litres incluant trois espèces, la daphnie Daphnia magna, la lentille d'eau Lemna minor et la microalgue Pseudokirchneriella subcapitata, exposées à une contamination par le cadmium. La dynamique des trois espèces ainsi que leurs interactions et les effets du cadmium ont été décrits par un modèle mécaniste basé sur des équations différentielles ordinaires couplées. Les principaux processus intervenant dans ce microcosme de trois espèces ont donc été formalisés, notamment la croissance et la survie des daphnies, la croissance et la sédimentation des algues, la croissance des lentilles, le broutage des algues par les daphnies, la compétition interspécifique entre algues et lentilles et les effets du cadmium sur ces différents processus. Les paramètres du modèle ont été estimés par inférence bayésienne, en utilisant simultanément toutes les données issues de différentes expérimentations en laboratoire, réalisées au cours de la thèse spécialement pour cette étude / Contaminant risk assessment is generally based on data collected during single species bioassays (including only one species). As a consequence, interactions between species that occur in ecosystems are not taken into account. To investigate the effects of contaminants on interacting species dynamics, this thesis aims at modelling the functioning of a 2-L laboratory microcosm with three species, the daphnid Daphnia magna, the duckweed Lemna minor and the microalgae Pseudokirchneriella subcapitata, exposed to cadmium contamination. We modelled the dynamics of the three species, their interactions and the effects of cadmium using a mechanistic model based on coupled ordinary differential equations. The main processes occurring in this three-species microcosm were thus formalized, including growth and survival of daphnids, growth and settling of algae, growth of duckweeds, grazing of algae by daphnids, interspecific competition between the algae and duckweeds, and the effects of cadmium on these processes. We estimated model parameters by Bayesian inference, using simultaneously all the data issued from multiple laboratory experiments specifically conducted for this study during the thesis

The objective of this study was to evaluate the antimicrobial and anti-caries effects of two plant extracts. The first chapter dealt with a review of the literature whose objective was to discuss the antimicrobial potential of Brazilian natural agents on the biofilm related to dental caries and gingivitis/periodontal disease. The research of the articles was carried out using PubMed. We found a total of 23 papers. Most of the studies were performed using planktonic microorganisms or under clinical trials. Nineteen articles were focused on cariogenic bacteria. From these nineteen articles, eleven were also about periodontopathogenic bacteria. Four studies addressed only periodontopathogenic bacteria. The most tested Brazilian natural agents were green propolis, essential oils of Lippia sidoides and Copaifera sp. Most of the tested agents showed similar results when compared to positive control (essential oils and extracts) or better effect than negative control (green propolis). More studies involving protocols closer to the clinical condition and the use of response variables that allows understanding the mechanism of action of natural agents are necessary before the incorporation of these natural agents into dental products. The second chapter aimed to test the effect of the hydroalcoholic extracts of Myracrodruon urundeuva All. and Qualea grandiflora Mart. leaves on the viability of the microcosm biofilm and on the prevention of enamel demineralization. The microcosm biofilm was produced on bovine enamel, using human saliva pool mixed with McBain saliva (0.2% sucrose) for 14 days. The biofilm was treated daily with the extracts for 1 min. M. urundeuva at 100, 10 and 0.1 g/ml and Q. grandiflora at 100 and 0.1 g/ml reduced cell viability similarly to the positive control and significantly more than negative control. M. urundeuva at 1000, 100 and 0.1 g/ml were able to reduce the counting formation unit-CFU counting of lactobacilli sp. and Streptococcus mutans, while Q. grandiflora at 1000 and 1.0 g/ml significantly reduced the S. mutans CFU counting. On the other hand, the natural extracts did not reduce the production of extracellular polyssacharides, lactic acid and the development of enamel caries lesions. The third chapter aimed to evaluate the effect of hydroalcoholic extracts of M. urundeuva and Q. grandiflora (alone or combined) on the viability of S. mutans biofilm and the prevention of enamel demineralization. S. mutans strain (ATCC 21175) was reactivated in BHI broth. Minimum inhibitory concentration, minimum bactericidal concentration, minimum biofilm inhibitory concentration and minimum biofilm eradication concentration were determined to choose the concentrations to be tested under the biofilm model. S. mutans biofilm (5x105 CFU/ml) was produced on bovine enamel using McBain saliva with 0.2% sucrose for 3 days. The biofilm was treated daily with the extracts for 1 min. M. urundeuva (isolated or combined) at concentrations equal or higher than 0.625 mg/ml was able to reduce the bacteria viability, whereas Q. grandiflora extract alone showed antimicrobial effect at 5 mg/ml only (p<0.05). On the other hand, none of the extracts was able to reduce the development of enamel caries lesions. Despite the tested natural extracts have antimicrobial effect; they are unable to prevent caries in enamel. / O objetivo foi avaliar os efeitos antimicrobiano e anti-cárie de dois extratos de plantas. O primeiro capítulo se referiu a uma revisão da literatura cujo objetivo foi discutir o potencial antimicrobiano dos agentes naturais brasileiros sobre o biofilme relacionado à cárie dentária e à gengivite/doença periodontal. A pesquisa dos artigos foi realizada usando o PubMed. Foram encontrados 23 trabalhos. A maioria dos estudos foi realizada utilizando microorganismos na fase planctônica ou ensaios clínicos. Dezenove artigos foram focados em bactérias cariogênicas. Dos dezenove artigos, onze também eram sobre bactérias periodontopatogênicas. Quatro estudos abordaram apenas bactérias periodontopatogênicas. Os agentes naturais brasileiros mais testados foram própolis verde, óleos essenciais de Lippia sidoides e Copaifera sp. Os agentes testados apresentaram resultados similares quando comparados ao controle positivo (óleos essenciais e extratos) ou melhor efeito que o controle negativo (própolis verde). Mais estudos próximos da condição clínica e o uso de variáveis de resposta que permitam entender o mecanismo de ação são necessários, para permitir a incorporação desses agentes naturais em produtos odontológicos. O segundo capítulo teve como objetivo testar o efeito dos extratos hidroalcoólicos de Myracrodruon urundeuva All. e Qualea grandiflora Mart. sobre a viabilidade do biofilme microcosmo e na prevenção da desmineralização do esmalte. O biofilme microcosmo foi produzido em esmalte bovino, utilizando pool de saliva humana misturada à saliva de McBain (0,2% de sacarose) durante 14 dias. O biofilme foi tratado diariamente com os extratos durante 1 min. M. urundeuva a 100, 10 e 0,1 g/ml e Q. grandiflora a 100 e 0,1 g/ml reduziram a viabilidade dos microrganismos de forma semelhante ao controle positivo e significativamente maior do que o controle negativo. M. urundeuva a 1000, 100 e 0,1 g/ml foi capaz de reduzir a contagem de Unidade formadora de colônia-UFC para Lactobacilos totais e Streptococcus mutans, enquanto a Q. grandiflora a 1000 e 1,0 g/ml reduziu significativamente a contagem de UFC para S. mutans. Os extratos naturais não conseguiram reduzir a produção de polissacarídeos extracelulares-PEC, ácido lático e o desenvolvimento da lesão cariosa em esmalte. O terceiro capítulo teve como objetivo avaliar o efeito dos extratos hidroalcoólicos de M. urundeuva. e Q. grandiflora (sozinhos ou combinados) sobre a viabilidade do biofilme de S. mutans e na prevenção da desmineralização do esmalte. Cepa de S. mutans (ATCC 21175) foi reativada em caldo BHI. Concentração inibitória mínima, concentração bactericida mínima, concentração inibitória mínima de biofilme e concentração de erradicação mínima de biofilme foram determinadas para escolher as concentrações a serem testadas sob o modelo de biofilme. O biofilme de S. mutans (5x105 CFU/ml) foi produzido em esmalte bovino, utilizando saliva de McBain com 0,2% de sacarose durante 3 dias. O biofilme foi tratado diariamente com os extratos durante 1 min. M. urundeuva (isolada ou combinada) nas concentrações iguais ou superiores a 0,625 mg/ml foi capaz de reduzir a viabilidade das bactérias, enquanto que o extrato da Q. grandflora apresentou efeito antimicrobiano somente a 5 mg/ml (p<0,05). Nenhum dos extratos reduziu o desenvolvimento da lesão da cárie. Apesar dos extratos naturais terem efeito antimicrobiano, são incapazes de prevenir o desenvolvimento da lesão cariosa em esmalte.

Les approches physico-chimiques étant insuffisantes pour évaluer l'impact de la pollution sur les écosystèmes , de nombreux bioessais, variant de par le niveau d'organisation représenté, ont été développés. Parmi ces essais on trouve les essais en microcosme aquatique de laboratoire qui sont un compromis entre les essais monospécifiques standards de laboratoire, méthodes couramment employées mais très simplifiées et peu représentatives sur le plan écologique et les essais en mésocosme extérieurs, plus représentatifs mais coûteux, lourds à mettre en œuvre, moins réplicables et plus difficiles à interpréter. Dans ce travail, nous nous sommes plus particulièrement intéressés à l'essai initialement développé par Clément et Cadier (1998). Cet outil permet d'évaluer l'effet de substances ou de matrices potentiellement contaminées sur un écosystème artificiel composé d'eau et de sédiment, dans lesquels sont introduites simultanément 5 espèces aquatiques d'eau douce usuellement employées dans des essais de toxicité mono-spécifiques : l'algue Pseudokirchneriella subcapitata, la lentille d'eau Lemna minor, la daphnie Daphnia magna, l'amphipode Hyalella azteca et l'insecte Chironomus riparius. Cet essai en microcosme a été utilisé dans de nombreux projets depuis sa conception mais sa variabilité demeurait la principale limite malgré les améliorations successives. Le principal objectif de ce travail était donc d'optimiser l'essai. La principale amélioration testée a été le renouvellement continu de l'eau du système, qui a permis de stabiliser les paramètres physico-chimiques de la colonne d'eau des microcosmes et la densité algale, et ainsi d'améliorer le développement des organismes et la réplicabilité de l'essai. Le cadmium a été utilisé comme contaminant modèle afin d'évaluer les développements méthodologiques proposés. La diminution de la variabilité en présence de renouvellement d'eau augmente la capacité à détecter des effets sublétaux sur les organismes pélagiques avec les tests statistiques classiques. Le développement d'un cadre de modélisation dynamique a permis de comparer la sensibilité des daphnies au cadmium dans des expériences aux profils d'exposition différents. / The physico-chemical approaches are insufficient to assess the impact of pollution on ecosystems. Thus many bioassays, varying in the level of organization represented, have been developed, as laboratory aquatic microcosm tests. These tests are a compromise between single-species tests, which are standard laboratory methods commonly used but highly simplified and not very ecologically representative, and outdoor mesocosm tests, which are more representative but more expensive, heavy to implement, less replicable and more difficult to interpret. In this work, we focused on the bioassay originally developed by Clément and Cadier (1998). This tool allows to evaluate the effect of substances or potentially contaminated matrices on an artificial ecosystem consisting of water and sediment in which are introduced simultaneously five freshwater aquatic species commonly used in monospecific toxicity testing : the algea Pseudokirchneriella subcapitata, the duckweed Lemna minor, the daphnia Daphnia magna, the amphipod Hyalella azteca and the insect Chironomus riparius. This test was used in many projects since its conception but its variability remains the main limitation despite successive improvements. The main objective of this study was to optimize the test. The main improvement was continuous renewal of the water system, which helped to stabilize the physico-chemical parameters of the water column and algal density, and thus improve the development of organisms and replicability of the test. Cadmium was used as a model contaminant to evaluate the proposed methodological developments. The decrease in variability in flowthrough microcosms increases the ability to detect sublethal effects on pelagic organisms with conventional statistical tests. The development of a dynamic modeling framework was used to compare the sensitivity of Daphnia to cadmium in experiments with different exposure pattern.

The aim of the dissertation thesis is to study the non-mathematical content of textbooks of mathematics. Textbooks of mathematics are not only a pedagogical document but also a cultural artefact that is produces in a particular society with its own cultural norms. While working with a textbook of mathematics, pupils come across many images of everyday life. Yet, since the main goal of a mathematics textbook is to help pupils gain knowledge and skills in mathematics, not much attention is paid to textual (non-mathematical, cultural) content. This means that pupils almost on everyday basis visit a world that tries to awaken the illusion of being "real", of being model of reality but in fact is a model for what is perceived as normal. The question asked in the presented research is what images of everyday life pupils come across while working with Czech textbooks of mathematics and whether there are differences among textbooks by different authors in this respect. Within the frame of this research, five sets of textbooks for 6th grade of lower secondary schools and four textbooks for 9th grade (only the chapter on financial mathematics, an area closely connected to everyday life) were analysed with respect to their non-mathematical, cultural content. The method used in the research comes out of the...

Sammanfattning: Wood decay fungi are the main decomposer of lignocellulose material stored in wood. Thus, all factors that affect them could affect their ecological function. This in return, may affect ecosystem functioning in terms of altered carbon emissions from dead wood. Increased temperature is one of the main factors influencing fungal decay. The aim of the current study is to explore the effects of temperature and assembly history (order of species arrival), two important regulators of fungal communities, on wood decomposition. I conducted a microcosm experiment with two temperature treatments and eight assembly histories where each species was allowed to colonize the wood two weeks ahead of the rest of the species. The temperature treatments were set to mimic the effect of climate induced warming. Therefore, I had one treatment with relatively high temperature, representing the expected temperatures year 2100 given the current emission trends of the northern inland of Sweden, and another treatment representing the current normal temperature (1961-1990). The temperature treatments had an average difference of 5°C. In order to see how climate induced warming and fungal assembly history influenced decomposition, I measured and analyzed initial fungal growth, fungal respiration and wood weight loss. Both temperature and assembly history had a significant influence on fungal growth, fungal respiration and wood decomposition. There was also strong interaction between the two factors. The average increase in mass loss under elevated temperature was 19% compared to 14% under normal temperature. The highest mass loss (25%) was when Phlebia centrifuga was the initial species under elevated temperature and the lowest (12%) was when Climacocystis borealis was initial species under normal temperature. All assembly histories had higher mass loss under elevated temperature, but the magnitude varied. For example, when C. borealis was the initial species, mass loss increased by 60% compared to only 7% when Antrodia sinuosa was the initial species. Six out of eight assembly histories had higher CO2 under elevated temperature, with the highest increase (88%) in P. centrifuga histories and the lowest (7%) in C. borealis histories. Even if the results need to be confirmed by field studies, my data illustrates that climate induced warming probably results in higher fungal respiration and deadwood decomposition and that the magnitude of this effect depends on fungal assembly history.

Stand carrying capacity is the maximum size of population for a species under given environmental conditions. Site resources limit the maximum volume or biomass that can be sustained in forest stands. This study was aimed at estimating and determining the carrying capacity in loblolly pine. Maximum stand basal area (BA) that can be sustained over a long period of time can be regarded as a measure of carrying capacity. To quantify and project stand BA carrying capacity, one approach is to use the estimate from a fitted cumulative BA-age equation; another approach is to obtain BA estimates implied by maximum size-density relationships (MSDRs), denoted implied maximum stand BA. The efficacy of three diameter-based MSDR measures: Reineke's self-thinning rule, competition-density rule and Nilson's sparsity index, were evaluated. Estimates from three MSDR measures were compared with estimates from the Chapman-Richards (C-R) equation fitted to the maximum stand BA observed on plots from spacing trials. The spacing trials, established in the two physiographic regions (Piedmont and Coastal Plain), and at two different scales (operational and miniature) were examined and compared, which provides a sound empirical basis for evaluating potential carrying capacity. Results showed that the stands with high initial planting density approached the stand BA carrying capacity sooner than the stands with lower initial planting density. The maximum stand BA associated with planting density developed similarly at the two scales. The potential carrying capacity in the two physiographic regions was significantly different. The value of implied maximum stand BA converted from three diameter-based MSDR measures was similar to the maximum stand BA curve obtained from the C-R equation. Nilson's sparsity index was the most stable and reliable estimate of stand BA carrying capacity. The flexibility of Nilson's sparsity index can illustrate the effect of physiographic regions on stand BA carrying capacity. Because some uncontrollable factors on long-term operational experiments can make estimates of stand BA carrying capacity unreliable for loblolly pine, it is suggested that the stand BA carrying capacity could be estimated from high initial planting density stands in a relatively short period of time so that the risk of damages and the costs of experiments could be reduced. For estimating carrying capacity, another attractive option is to choose a miniature scale trial (microcosm) because it shortens the experiment time and reduces costs greatly. / Master of Science

Grâce au développement des technologies de métagénomique au cours des dix dernières années, il a été constaté que les micro-organismes représentent la plus grande ressource de diversité métabolique et génétique sur Terre. En effet, un gramme de sol contient 109 cellules bactériennes et 103-104 différentes espèces bactériennes. Certaines sont en mesure de réaliser des réactions enzymatiques conduisant à la dégradation complète de certains polluants toxiques pour l’environnement comme les composés organiques tels que la quinoléine. Cependant, l'immense réservoir de molécules et enzymes microbiennes n'a pas encore été exploité, car plus de 99% d'entre elles ne sont, pour l’instant, pas cultivables in vitro. Mon travail s’inscrit dans le cadre d’une collaboration entre l’Université SJTU (Shanghai Jiao Tong Université en Chine) et le groupe de G. M.E (Génomique Microbienne Environmentale) du laboratoire Ampère à l’Ecole Centrale de Lyon. Nos partenaires à l’Université SJTU ont construit un réacteur de dénitrification à l'échelle du laboratoire capable de dégrader la quinoléine en retirant la demande chimique en oxygène. Un nouvel outil appelé "Genefish" a été developpé dans notre laboratoire comme une méthode alternative de la métagénomique pour aider à la découverte de nouveaux gènes d’intérêt industriel ou environnemental. A la suite des premiers travaux réalisés dans notre laboratoire, ma thèse présentée ici comporte deux parties.Dans la première partie de ce travail, nous avons étudié le potentiel de dégradation de la quinoléine présente dans les bactéries d’un sol de référence largement étudié au laboratoire. Pour cela nous avons mis en place des expériences de microcosme qui visent à révéler la diversité potentielle des bactéries responsables de la dégradation de la quinoléine. Des analyses comparatives des profils RISA (Ribosomal Intergenic Spacer analysis) nous ont permis de mettre en évidence des changements dans la structure de la communauté des bactéries du sol incubé en conditions aérobie et anaérobie en présence de quinoléine. La dégradation de la quinoléine a été confirmée par technique de GC/MS (Gas Chromatography-Mass Spectrometry). Les travaux futurs seront de vérifier la communauté de bactéries responsables de la dégradation de quinoléine en utilisant la technique de NGS (Next Generation Sequencing).Le deuxième objectif de ma thèse a été d'utiliser Genefish dont la finalité est de capturer des gènes ciblés (le gène bcr qui serait responsable de la degradation de quinoléine dans le réacteur de nos partenaires) dans l'ADN métagénomique extrait du sol. Genefish consiste à élaborer une souche d’E.coli incluant un plasmide de capture permettant de pêcher les gènes recherchés dans un échantillon d’ADN metagénomique par recombinaison homologue. Le plasmide de capture comprend une cassette de deux gènes toxiques pour la souche qui activés par induction chimique vont permettre la sélection positive directe des clones recombinants, et deux sites multiples de clonage dans lesquels sont insérées les zones de recombinaison qui vont jouer le rôle d’hameçons. Nous avons testé la capacité de Genefish à capturer des produits PCR du gène bcr, l'efficacité de recombinaison reste faible à cause de la persistance de plusieurs copies du plasmide suicide dans la cellule après l’ évenement de recombinaison. Par conséquent, trois stratégies ont été essayées pour améliorer l’efficacité: la co-électroporation, la ségrégation de plasmide et la construction de plasmide suicide en mono-copie. Finalement, la stratégie de la ségrégation plasmidique fonctionne mais l'efficacité de recombinaison est encore trop faible peut-être due à l’incertitude des modèles de recombinaison homologue. Les travaux futurs se concentreront sur l'amélioration des fréquences de recombinaison par transfert de fragments du plasmide de capture dans le chromosome de la souche Genefish. / As the development of metagenomic technologies in the past ten years, it is unquestionned that microorganisms encompass the largest resource of metabolic and genetic diversity in the world. Actually, one gramme of soil contains more than 109 bacteria and 103-104 species. Some of their members are able to carry out enzymatic reactions leading to the complete degradation of pollutants (such as quinoline). So, the biodegradation of some highly toxic or organic compounds by microorganisms will be a general trend for pollutant treatment. However, the huge reservoir of molecules and enzymes from microorganisms still need to be explored because more than 99% of microorganisms cannot be cultivated in vitro.My work was based on collaboration between the University SJTU and Ecole Centrale de Lyon. Our partners at the University SJTU have built a laboratory scale denitrification reactor which was capable of degrading quinoline by removing the chemical oxygen demand. A new tool called "Genefish" has been developed in our laboratory as an alternative method for metagenomics which aims to discover novel industrial or environmental genes of interest. Following the early work in our laboratory, my thesis is presented here in two parts.In the first part, we set up a quinoline microcosm experiment both under aerobic and anaerobic condition using reference soil extensively studied in the laboratory at Ecole Centrale de LYON. This work aimed to reveal the potential bacterial diversity and even genes responsible for quinoline degradation. We used RISA(Ribosomal intergenic Spacer analysis) to analyze the bacteria community structure changes and GC/MS (Gas Chromatography-Mass Spectrometry) was also used to detect the quinoline degradation and reveal potential quinoline metabolic pathways under aerobic and anaerobic condition. Results showed great bacteria community structure changes and high quinoline degradation activity after the quinoline addition under aerobic condition. The future work is to investigate the bacteria community which may be responsible for quinoline degradation using the technique of NGS (Next Generation Sequencing).The second object of my thesis was to use the Genefish tool to capture targeted genes (the bcr gene responsible for the quinoline degradation in the wastewater treatment bioreactor) from the soil metagenome. The aim was to construct an E.coli strain containing a capture plasmid and Red system for capturing targeted genes from metagenomic DNA by homologous recombination. The capture plasmid includes a toxic cassette consisting of two suicide genes which can be activated by chemical induction, finally support the positive recombinants selection. It also contains two multiply cloning sites in which highly conserved sequences were inserted and works as the bait during recombination. We have tested the capacity of Genefish to capture the PCR products of bcr gene; the efficiency was low because of the persistence of several copies of the capture plasmid into the Genefish strain after recombination events. So, three strategies were tried to improve the recombination efficiency: co-electroporation, plasmid segregation and mono-copy capture plasmid construction. Finally, the strategy of plasmid segregation works but the recombination efficiency was still low maybe caused by the uncertain model of homologous recombination. The further research will focus on the transfer of the toxic cassette and homologous arms into the host strain chromosome, this new strategy will exclude the bad effect of low copy number capture plasmid, uncertain model of λ Red induced homologous recombination and the homologous arms site in the capture plasmid which are the most important factors influencing the homologous recombination efficiency in Genefish.