The main title of the doctoral thesis - ART/CRIME - CRIME/ART - point to a general investigation of these two phenomenons. This investigation makes up the background of the main theme of the thesis, which is an actual event of the mysterious death of the painter and shepherd K.. At work I spend time with alternative investigations of this death and the goal is an attempt to reconstruct the events and effort of discovering the answers what happened that night and whether or not a killer really existed or not.

Duckweed species L. turionifera and W. borealis grow on Wellsville Municipal Sewage Lagoons in northern Utah and, when harvested, contribute to the removal of phosphorus and pharmaceuticals from wastewater. Microcosm studies showed that duckweed contains an average of 1% phosphorus (dry weight) and removes 113 mg-P/m2day under 200 μmol/m2sec light. Duckweed in laboratory experiments reduced influent phosphorus ranging from 3.88 to 5.2 mg-TP/L to effluent concentrations of 0.88 mg-P/L in 3 days to 0.16 mg-P/L (0.32 mg-TP/L) with continual harvesting and a liquid retention time of 46 days. Duckweed removal of pharmaceuticals was comparable to removal by membrane bio-reactors. Duckweed removed 99% acetaminophen mainly by plant uptake; 98% progesterone primarily by absorption to plant tissue; 90% fluoxetine by adsorption with some biological removal attributed to plants; and sulfamethoxazole removal varied between 25 to 90% depending on polarity. Carbamazepine did not react with duckweed. Typical influent wastewater concentrations of the five pharmaceuticals in this study were not toxic to duckweed with an EC50 value of 614 μg/L per compound. HPLC/MS detection of pharmaceuticals in liquid samples using solid phase extraction at a neutral pH and silanized glassware produced 92-102% recoveries. Analysis of extracted solids produced lower recoveries. Solid extraction efficiencies ranged from 56-70% for samples stored for 24 hours and decreased with increasing storage time. Field growth studies showed higher than expected duckweed growth rates in the spring compared to three models due to turion germination after the ice melts. The growth rates decreased in the fall due to turion formation in preparation for winter. Harvesting duckweed from the Wellsville Municipal Sewage Lagoons should begin after full surface coverage around June 17th and end when temperatures fall below 15 °C around September 15th. Bi-weekly harvests with a starting plant density of 75 g-dry duckweed/m2 for the lagoons operating at 0.547 MGD and 5 mg-TP/L are required to physically remove enough phosphorus in order to meet the city’s 432 kg-P/yr discharge permit. A duckweed phosphorus harvesting system in Wellsville was estimated to produce enough biomass to meet the P-discharge limit until the flow increases above 0.656 MGD around the Year 2017.

Indiana University-Purdue University Indianapolis (IUPUI) / Dental biofilm is a main contributing factor in the initiation and progression of dental caries. The maturation of dental biofilms is expected to alter the anti-caries efficacy of fluoride compounds. In the first aim, we conducted a series of modeldevelopment experiments to test different variables to standardize a reproducible in-vitro microbial caries model. We evaluated: surface conditioning using saliva; sucrose concentrations and caries lesion severity; growth media conditions and mineral saturation; dental substrate types; pH cycling protocol characteristics. In the second aim, we used the developed model to evaluate the changes in the anti-caries efficacy of three fluoride compounds (Sodium fluoride (NaF); Stannous fluoride (SnF2); Amine fluoride (AmF); and deionized water (DIW- negative control)) at increasing maturation of a microcosm biofilm. We continued the pH cycling protocol for 4 days, 8 days, and 12 days. We tested biofilm cariogenicity and carious lesion severity at each maturation stage. In the third aim, we used the developed model to test the effect of different exposure periods (early vs. late exposure) of the biofilm to three fluoride compounds (NaF, SnF2, AmF, DIW) in comparison to DIW. We also evaluated the recovery of biofilm cariogenicity with each exposure period. We evaluated, for each exposure period and recovery stage, biofilm cariogenicity and carious lesion severity. We analyzed the relationships between different variables (biofilm age, fluoride compound type, exposure period) using ANOVA models. In conclusion: 1. The present model allows testing the effect of biofilm maturation on the anti-caries efficacy of fluoride compounds. 2. Biofilm maturation plays an important role in increasing biofilm tolerance against fluoride treatment; it could also influence the selection of fluoride compounds to achieve optimum cariostatic effect. 3. Exposure period, and type of fluoride compound, both influence the biofilm tolerance to fluoride anti-caries effect; they may also result in a sustainable release of fluoride over time. / 2021-08-21

京都大学 / 新制・課程博士 / 博士(農学) / 甲第24677号 / 農博第2560号 / 新制||農||1100(附属図書館) / 学位論文||R5||N5458(農学部図書室) / 京都大学大学院農学研究科応用生物科学専攻 / (主査)教授 吉田 天士, 教授 澤山 茂樹, 准教授 神川 龍馬 / 学位規則第4条第1項該当 / Doctor of Agricultural Science / Kyoto University / DGAM

No description available.

Environmental use of genetically-engineered microorganisms (GEMs) has raised concerns over potential ecological impact. Development of microcosm systems useful in preliminary testing for risk assessment will provide useful information for predicting potential structural, functional, and genetic effects of GEM release. This study was executed to develop techniques that may be useful in risk assessment and microbial ecology, to ascertain which parameters are useful in determining risk and to predict risk from releasing an engineered strain of Erwinia carotovora. A terrestrial microcosm system for use in GEM risk assessment studies was developed for use in assessing alterations of microbial structure and function that may be caused by introducing the engineered strain of E. carotovora. This strain is being developed for use as a biological control agent for plant soft rot. Parameters that were monitored included survival and intraspecific competition of E. carotovora, structural effects upon both total bacterial populations and numbers of selected bacterial genera, effects upon activities of dehydrogenase and alkaline phosphatase, effects upon soil nutrients, and potential for gene transfer into or out of the engineered strain. No significant difference was found in survival of the engineered strain as compared to its wildtype parent. Both strains survived for over two months in microcosms. The effects of both strains upon populations of total bacteria and selected bacterial genera were determined; while some effects upon community structure were observed, they were not significant. The engineered strain was not found to be a superior competitor compared to its parent; three different doses of engineered and wildtype strains were used. ln addition, neither strain affected activities of dehydrogenase or alkaline phosphatase in soil. Likewise, no effects were observed upon the nutrients monitored. However, transfer of the kanamycin resistance gene that had been inserted into the engineered E. carotovora strain may have occurred. Five species of indigenous bacteria displayed kanamycin resistance 15 days after being exposed to the engineered Erwinia. DNA from these strains was isolated, purified, and hybridization experiments executed to determine if any homology existed between these DNAs and the kanamycin resistance gene that had been inserted into E. carotovora. Using biotin-Iabeled probes and Iow-stringency washing conditions, homology was observed. However, before gene transfer can be proven, additional studies, including amplification and sequencing, may be required. Although a simple microcosm design was employed, it yielded sufficient information to conclude that release of the engineered Erwinia carotovora will not affect any of the microbial measures of integrity that were studied in a manner different from that of the wildtype. Effects upon plant material and other higher taxa will be the focus of future studies. / Ph. D.

Sistemas de testes biológicos com espécies representativas têm sido utilizados para avaliar os efeitos causados por substâncias tóxicas no meio aquático. Os bioensaios contam com protocolos definidos, porém os organismos estão isolados de seu meio. O objetivo deste trabalho é desenvolver um sistema de testes capaz de avaliar os efeitos adversos, não apenas sobre uma única espécie, mas sobre um ecossistema. Para esta finalidade foi construído em laboratório um ecossistema aquático microbiano experimental capaz de gerar uma comunidade microbiológica e reproduzir em escala reduzida os componentes de um ecossistema natural, formando uma estrutura ecológica. Dois grupos morfológicos foram observados em sequência ecológica na medida em que as condições do meio eram alteradas. Curvas de dinâmicas de crescimento indicaram comportamento típico para o grupo de protozoários ciliados e apresentaram crescimento logarítmico em torno do quarto dia de aeração. Inibição no crescimento fora observada quando concentrações de 12,28 mg/l de cobre (3,12 ppm) e 2,5 ml/l de inseticida DDVP 20 são introduzidos nos sistemas. Não foi observada dinâmica típica para o grupo de bactérias filamentosas. Para análise dos resultados foi aplicado teste estatístico de análise de variância. O método não permitiu o estudo de relações ecológicas que se estabelecem, mas fornece informações sobre aspectos teóricos da ecologia referentes ao funcionamento dos ecossistemas e seus atributos como a capacidade de auto-organização e o processo de sucessão ecológica. Para maior precisão do método, sugere-se estudo da composição da comunidade incluindo métodos de biologia molecular, alongamento do período do experimento e aplicação de modelos populacionais. / Biological testing systems with representative species have been used to assess the effects caused by toxic substances in the aquatic environment. Bioassays rely on defined protocols, but organisms are isolated from their environment. The objective of this work is to develop a test system capable of evaluating adverse effects, not only on a single species, but on an ecosystem. For this purpose an experimental microbial aquatic ecosystem was built in the laboratory capable of generating a microbiological community and reproducing the components of a natural ecosystem in a reduced scale, forming an ecological structure. Two morphological groups were observed in ecological sequence as the conditions of the environment were altered. Growth dynamics curves indicated typical behavior for the group of ciliate protozoa and presented logarithmic growth around the fourth day of aeration. Growth inhibition was observed when concentrations of 12.28 mg / l copper (3.12 ppm) and 2.5 ml / l DDVP 20 insecticide are introduced into the systems. No typical dynamics were observed for the group of filamentous bacteria. Statistical analysis of variance was applied to analyze the results. The method did not allow the study of established ecological relations, but provides information on the theoretical aspects of ecology related to the functioning of ecosystems and their attributes such as the capacity of self-organization and ecological succession process. For better precision of the method, we suggest a study of community composition including methods of molecular biology, elongation of the experiment period and application of population models.

L’établissement correspond à la formation d’une population pérenne dans l’aire d’introduction. Les populations introduites ayant des effectifs faibles, elles sont sujettes à plusieurs mécanismes augmentant leurs risques d’extinction. La structure spatiale de l’aire d’introduction, une mosaïque hétérogène de patchs d’habitat appelée « paysage », peut affecter la persistance de la population introduite. L’objectif de cette thèse est d’étudier l’interaction entre cette structure spatiale et ces mécanismes, ainsi que leur impact sur l’établissement. Les recherches entreprises ont été conduites en utilisant des modèles stochastiques afin de simuler des invasions et faire émerger des prédictions, et en testant expérimentalement ces prédictions grâce à des introductions artificielles de Trichogramma chilonis en microcosmes. Ces travaux ont permis d’identifier un effet fort de la connectivité du site d’introduction, qui peut diminuer les chances d’établissement au niveau local en favorisant l’émigration depuis le site d’introduction, et augmenter les chances d’établissement à un niveau plus large en permettant la colonisation d’autres patchs dans l’aire d’introduction. Au niveau du paysage, nous avons identifié l’impact des hubs, des patchs concentrant les flux de dispersion, qui accroissent fortement la vitesse de colonisation mais diminuent le taux d’établissement. L’établissement était également favorisé par l’agrégation de la ressource et la colonisation par sa dissémination à travers le paysage. La nature stochastique des dynamiques de colonisation est telle qu’il est nécessaire de les prendre en compte pour étudier l’établissement. / Establishment is an important stage of biological invasions, which corresponds to the formation of a persistent population in the introduction area. It is not trivial, as introduced populations are often small, and subject to various specific mechanisms, which increase extinction risks. The spatial structure of the introduction area, which is usually a heterogeneous mosaic of habitat patches called a “landscape”, can interact with those mechanisms and impact the introduced population persistence. This thesis objective is to study the interaction between this spatial structure and those mechanisms, as well as their impact on establishment. On the one hand, we used stochastic models to simulate invasions and formulate predictions. On the other hand, we tested these predictions by performing artificial introductions of Trichogramma chilonis in laboratory microcosms. We were able to identify the impact of the introduction site connectivity, which could decrease establishment probabilities at a local level by increasing the emigration rate from the introduction site, and increase establishment at the landscape level by increasing the colonisation rate of other patches in the introduction area. At the landscape level, we identified the impact of hubs, i.e. patches concentrating dispersal fluxes. They strongly increased colonisation speed, but also decreased establishment. The clustering of resources increased establishment, while its scattering increased colonization. Our results show that introduced population dynamics are highly sensitive to their size. The stochastic nature of colonization dynamics is also necessary to study establishment.

abstract: This dissertation explores the use of bench-scale batch microcosms in remedial design of contaminated aquifers, presents an alternative methodology for conducting such treatability studies, and - from technical, economical, and social perspectives - examines real-world application of this new technology. In situ bioremediation (ISB) is an effective remedial approach for many contaminated groundwater sites. However, site-specific variability necessitates the performance of small-scale treatability studies prior to full-scale implementation. The most common methodology is the batch microcosm, whose potential limitations and suitable technical alternatives are explored in this thesis. In a critical literature review, I discuss how continuous-flow conditions stimulate microbial attachment and biofilm formation, and identify unique microbiological phenomena largely absent in batch bottles, yet potentially relevant to contaminant fate. Following up on this theoretical evaluation, I experimentally produce pyrosequencing data and perform beta diversity analysis to demonstrate that batch and continuous-flow (column) microcosms foster distinctly different microbial communities. Next, I introduce the In Situ Microcosm Array (ISMA), which took approximately two years to design, develop, build and iteratively improve. The ISMA can be deployed down-hole in groundwater monitoring wells of contaminated aquifers for the purpose of autonomously conducting multiple parallel continuous-flow treatability experiments. The ISMA stores all sample generated in the course of each experiment, thereby preventing the release of chemicals into the environment. Detailed results are presented from an ISMA demonstration evaluating ISB for the treatment of hexavalent chromium and trichloroethene. In a technical and economical comparison to batch microcosms, I demonstrate the ISMA is both effective in informing remedial design decisions and cost-competitive. Finally, I report on a participatory technology assessment (pTA) workshop attended by diverse stakeholders of the Phoenix 52nd Street Superfund Site evaluating the ISMA's ability for addressing a real-world problem. In addition to receiving valuable feedback on perceived ISMA limitations, I conclude from the workshop that pTA can facilitate mutual learning even among entrenched stakeholders. In summary, my doctoral research (i) pinpointed limitations of current remedial design approaches, (ii) produced a novel alternative approach, and (iii) demonstrated the technical, economical and social value of this novel remedial design tool, i.e., the In Situ Microcosm Array technology. / Dissertation/Thesis / Ph.D. Biological Design 2013

Ecosystems in the modern world face a vast array of disturbances, from globally shifting abiotic conditions, to increasingly variable extreme natural events, to high intensity discrete human-caused disturbances. Well-developed, applicable theoretical frameworks on how ecosystems can respond to and withstand these disturbances are needed for adequate management of valued ecological systems. To date, the most promising theoretical development for understanding ecological response to complex sets of disturbances is resilience. Ecological resilience acknowledges non-linear ecosystem behavior, incorporates the role of slowly changing environmental parameters in ecological dynamics, and offers one of the few potential methods to predict, and avoid, impending ecological collapse. However, as ecological resilience has evolved conceptually to include social, political, and economic fields, it has become increasingly difficult to clearly define in, and apply to, managed ecosystems. This dissertation pairs ecological resilience with other, well-established attributes of ecological response to disturbance, namely resistance, persistence, and recovery. By doing so, we can clearly define and quantify each attribute in a range of ecosystem types and over a variety of ecological scales. In Chapter 1, we use microcosm communities to test the relationship between one potential mechanism, landscape connectivity, and multiple attributes of ecological response to disturbance including resistance, resilience, and recovery. We find that each attribute responds uniquely to connectivity, and that generalizing the role of connectivity over all three may give an inaccurate prediction of how ecosystems may respond to individual disturbances. In Chapter 2, we experimentally investigate the presence of early warning indicators of approaching critical thresholds. Using water table drawdown treatments in bog, we test for critical slowing and increased autocorrelation as the bog approaches a transition to forest. We find that critical slowing is clear in composition and moss cover, but that autocorrelation is not apparent. The decoupling of critical slowing and increased autocorrelation could be due to a number of complex ecosystem dynamics, all of which are common in ecosystem management globally. Thus, early warning indicators likely need further development if they are to become applicable. In Chapter 3, we observationally study how conservation management actions may increase or decrease ecological resilience. In particular, we explore how invasive species management intensity correlates with changes in functional redundancy, response diversity, and spatial occurrence of regime shifts in Garry oak meadows. We find that more intense management correlates with less area lost to woody encroachment and increases in functional redundancy through time. However, the relationship was strongly mediated by individual landscape settings. Finally, in Chapter 4, we scale up to a provincial study, investigating persistence of ecosystems and large mammal species in the face of the continuous pressures of land use change. In the results from all four chapters, it is clear that individual attributes of ecological response to disturbance, i.e. resistance, persistence, resilience, or recovery, all play unique roles in ecosystem dynamics. Additionally, the metric chosen to quantify each attribute can play a pivotal role in how we interpret observed dynamics. The work in this dissertation highlights that we cannot understand or predict ecological response to disturbance without clear, measurable concepts. Around a single state of interest, resilience is only one among a suite of attributes that are important to understand. Its additional strength, of potentially predicting the occurrence of ecological thresholds, is still being developed as we explore methods of quantification and application in individual ecosystems. / Graduate