<p> A noninvasive method using fluorescence quenching (FQ) to determine the conditional stability constants (logK') for aluminum with naturally occurring organic ligands has been developed. The method utilizes the Stern-Volmer equation to interpret data from ligand fluorescence suppression by aluminum. The total ligand concentration can also be determined using the measured stability constant and the Ryan-Weber equation. The method has been validated with the model ligand salicylic acid; logK' was found to be 3.5 ± 0.01 vs. 4.0 from the literature. The method was applied to the reference ligand Armadale fulvic acid and chemically realistic values were obtained. In addition, the expected trend of increasing stability constant with decreasing pH was observed. The method was further validated by determining the stability constant for Armadale fulvic acid using an independent technique, PCV colourimetry; the results agreed very well logK' = 4.7 vs. 4.65 for FQ analysis. Application of the method to whole filtered beaver pond water showed an increasing trend in the stability constant as the dissolved organic carbon (DOC) decreased. The Log of the stability constants were 3.15 ± 0.03, 3.26 ± 0.03, and 3.63 ± 0.02 for DOC concentrations 23, 14, and 10 ppm respectively. The method was also applied to size fractionated waters form lake Skjervatjern in Norway and the expected trend of increasing stability constant with increasing molecular weight was observed.</p> / Thesis / Bachelor of Science (BSc)

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The critical heat flux (CHF) point for a reactor core system is one of the most important factors to discuss in regards to reactor safety. If this point is reached, standard coolant systems are not enough to handle the temperature increase in the cladding, and the likelihood of meltdown greatly increases. While the nucleate boiling and film boiling regimes have been well-investigated, the transition boiling regime between the point of departure from nucleate boiling (DNB) and the minimum film boiling temperature (T_min) remains difficult to study. This is due to both the complexity of the phenomena, as well as limitations in measurement, where experiments typically utilize thermocouples for temperature data acquisition. As a result of technological advancement in the field of fiber optics, it is possible to measure the quenching temperature to a much higher degree of precision. Optical fiber sensors are capable of taking many more measurements along a fuel simulator length than thermocouples, which are restricted to discrete points. In this way, optical fibers can act as an almost continuous sensor, calculating data at a resolution of less than one millimeter where a thermocouple would only be able to measure at one point. In this thesis, the results of a series of quenching experiments performed on stainless steel, Monel k500, and Inconel 600 rods at atmospheric pressure, with different subcooling levels and surface roughnesses, will be discussed. The rewetting temperature measurement is performed to compare results between thermocouples and optical fiber sensors in a 30 cm rod. These results are further discussed with regard to future application in two-phase flow experiments. / Master of Science / There are multiple types of boiling that can occur depending on the heat transfer capabilities of the system and the power applied to the coolant. The most common is nucleate boiling, where vapor produced at the surface forms bubbles and move away from the surface due to buoyancy. At a high enough power, the bubbles can coalesce into a film and lead to a point at which the liquid coolant can no longer contact the surface. Since vapor is not as effective at transferring heat from the surface, the temperature will increase drastically. In nuclear reactors, this situation (known as departure from nucleate boiling), can quickly lead to a meltdown of the fuel rods. Another important safety parameter in nuclear reactors is the minimum temperature at which this vapor film can be maintained, T_min. This parameter is a source of significant concern with regard to accident scenarios such as LOCA (loss of coolant accident), where reintroducing coolant to the rods efficiently is of top priority. While much research has been done on nucleate and film boiling, it has been difficult to study the transition period between the two regimes due to both its transient nature and the lack of continuous measurement capabilities. Typically, temperature is measured using thermocouples, which are point-source sensors that do not allow for high spatial resolution over a large area. This thesis deals with the utilization of optical fibers for temperature measurement, which are capable of calculating data at every millimeter, potentially a much more precise measurement system than with the thermocouples. The experiments performed in this paper are quenching experiments, where a rod embedded with thermocouples and an optical fiber is heated to well above T_min and quickly plunged into a volume of water, in order to view the transition from film to nucleate boiling.

Metallic nanoparticles (NPs) are exploited for their ability to interact with organic compounds and to increase significantly the fluorescence intensity and the photostability of many fluorescent dye molecules. Metal enhanced fluorescence (MEF) is therefore widely investigated for biosensing applications. When used in immunoassays, silver island films (SIFs) could augment the fluorescence intensity of fluorescein by a factor of seventeen; SIFs were also able to double or triple the emission intensity of cyanine dyes which are commonly used in (deoxyribonucleic acid) DNA microarrays. The emission intensity of indocyanine green — widely used as a contrast agent in medical imaging — was about twenty times higher in the proximity of SIFs. This enhancement phenomenon — due to the surface plasmon polaritons associated with the metallic NPs — can be explained by energy transfer from the metal NPs to the fluorescent dye molecules or by a modified local electromagnetic field experienced by the fluorophores in the vicinity of metal surfaces. Our research focused on the optical characterization of colloidal gold-silver alloy NPs containing different ratios of gold and silver (Au_1.00-Ag_0.00, Au_0.75-Ag_0.25, Au_0.50-Ag_0.50, and Au_0.25-Ag_0.75), as well as their interaction with three fluorophores: rose bengal, rhodamine B, and fluorescein sodium. Depending upon the dye quantum yield and its concentration in solution, enhancement or quenching of fluorescence was obtained. Thus, a three to five times increase in fluorescence intensity was observed in a 2.0 mM solution of rose bengal with all nanoalloys, a slight enhancement of fluorescence (1.2 – 1.6 times) was noticed in a 0.13 mM solution of rhodamine B with all four types of NPs, and fluorescence quenching occurred in all the fluorescein-NP solutions regardless of the dye concentration. / Master of Science

Swimming bacteria are ubiquitous in aqueous environments ranging from oceans to fluidic environments within a living host. Furthermore, engineered bacteria are being increasingly utilized for a host of applications including environmental bioremediation, biosensing, and for the treatment of diseases. Often driven by chemotaxis (i.e. biased migration in response to gradients of chemical effectors) and quorum sensing (i.e. number density dependent regulation of gene expression), bacterial population dynamics and emergent behavior play a key role in regulating their own life and their impact on their immediate environment. Computational models that accurately and robustly describe bacterial population behavior and response to environmental stimuli are crucial to both understanding the dynamics of microbial communities and efficiently utilizing engineered microbes in practice. Many existing computational frameworks are finely-detailed at the cellular level, leading to extended computational time requirements, or are strictly population scale models, which do not permit population heterogeneities or spatiotemporal variability in the environment. To bridge this gap, we have created and experimentally validated a scalable, computationally-efficient, agent-based model of bacterial chemotaxis and quorum sensing (QS) which robustly simulates the stochastic behavior of each cell across a wide range of bacterial populations, ranging from a few to several hundred cells. We quantitatively and accurately capture emergent behavior in both isogenic QS populations and the altered QS response in a mixed QS and quorum quenching (QQ) microbial community. Finally, we show that the model can be used to predictively design synthetic genetic components towards programmed microbial behavior. / Master of Science / Bacteria are an integral part of life and possess a host of characteristics that make them a powerful tool with which to confront many modern day problems. Using genetic engineering and the burgeoning field of synthetic biology, these single-celled organisms can be manipulated to perform many useful tasks such as detecting oil spills or other environmental pollutants, producing pharmaceuticals such as insulin, and even invading and killing cancer cells. Accurate computational simulations of microbial behavior will aid in the efficient design of such synthetic bacteria-based systems and reduce dependency on the current time-intensive “guess and check” paradigm. Towards this goal, we have built a comprehensive computer simulation of bacterial swimming behavior, response to chemo-effector concentration gradients called chemotaxis, a form of microbial communication called quorum sensing (QS), and a form of communication disruption called quorum quenching (QQ). Not only do we demonstrate an unprecedented level of accuracy in predicting experimental results, but we also couple the simulation with synthetic biology to precisely tune bacteria QS behavior, neither of which have previously been reported in literature. The overarching outcome of this thesis is a tool that could be used to improve the design process of useful bacteria-based systems in diverse areas of biotechnology.

Most galaxies are either actively forming stars or quenched, but there is a small number of galaxies in transition from one population to the other. These galaxies are "quenching" if they are in the process of becoming quenched or "rejuvenating" if they are returning to the star-forming main sequence after a period of being quenched. Quenching occurs when a galaxy’s limited cold gas supply is heated or removed, halting star formation, while rejuvenation refers to any process that reintroduces cold gas to quenched galaxies, reigniting star formation. Rejuvenating galaxies, which are significantly rarer and less well-studied than quenching galaxies, can offer valuable insights into galaxy evolution processes. This thesis investigates the properties of transitional galaxies, with a focus on their gas content, to explore the mechanisms driving quenching and rejuvenation. We employ a recent classification method using GALEX NUV and Sloan Digital Sky Survey H-alpha measurements to identify transitional galaxies and analyze the derived gas properties of those in the xGASS and xCOLD GASS surveys. We find that rejuvenating and quenching galaxies have intermediate gas fractions compared to actively star-forming and quenched galaxies, and that rejuvenating and quenching galaxies have similar depletion times to star-forming and quenched galaxies, respectively. We also find that the rejuvenating population, particularly at lower stellar mass, is efficient at converting its atomic gas supply to molecular hydrogen, which could be attributed to their high gas-phase metallicities at low stellar mass. / Thesis / Master of Science (MSc)

With the increase of agricultural production, there is an improvement in the use of mineral fertilizers, which may cause different environmental problems, besides the soil salinization. A possible alternative for reducing the application of these products is the use of plant growth-promoting bacteria (PGPB), that can be used alone or in co-inoculation, resulting in an alternative environmentally and economically feasible. Better results can be obtained if the interaction among bacteria-bacteria and bacteria-plant be elucidated, and strategy developed to optimize these interactions. Thus, the plant growth-promoting Bacillus sp. RZ2MS9, previous described as a potential PGPB in maize and soybean, was GFP-tagged and monitored alone and co-inoculated with Azospirillum brasilense (Ab-v5::pWM1013) during maize colonization. The interaction of tagged strains in maize were monitored by fluorescent microscopy (FM) and quantitative PCR (qPCR), demonstrating an endophytic behavior of Bacillus sp. RZ2MS9. Although the non-detection of Ab-v5::pWM1013, the co-inoculation resulted in the best increase in root and shoot dried weight, root volume and in root diameter, showing that inoculation with more than one strain can be a good choice to development of bio-fertilizers. One important system to bacterial interaction is the quorum sensing (QS). The QS is an important cell-cell communication system that allows bacterial cells to recognize their own population and modulate their gene expression. This, system is also involved in the interspecific communication, including other bacterial species and plants. In the other hand, enzymes able to detect and degrade these molecules evolved, the called quorum quenching (QQ) system, that has been evolved in some bacteria as competitive advantage for niches colonization. The aiiA gene, was one of the first gene related with the QQ in Bacillus. The aiiA was found in Bacillus sp. RZ2MS9 genome. Through construction of a new QQ biosensor, Agrobacterium tumefaciens At11006, and validated by A. tumefaciens NTL4, the ability of RZ2MS9 to degrade QS molecules was confirmed. The knockout of aiiA gene was performed using the CRISPR-Cas9 system, confirming this gene function. By these results, the influence of QQ system of Bacillus sp. RZ2MS9 during maize colonization and RZ2MS9 - A. brasilense - maize can be better investigated, opens the possibility to better understand the role of QQ system in the interaction among PGPB and plants. / Concomitantemente ao aumento da produção agrícola, há o aumento do uso de fertilizantes minerais, que pode acarretar no desenvolvimento de diferentes problemas ambientais, além de causar a salinização dos solos. Uma possível alternativa para tentar reduzir a aplicação desses produtos é o uso de bactérias promotoras de crescimento de plantas (BPCPs), que podem ser usadas isoladamente ou em co-inoculação com outras bactérias, tornando-as uma alternativa ambientalmente e economicamente viável. Melhores resultados podem ser obtidos se a interação bactéria-bactéria e bactéria-planta for elucidada, permitindo que estratégias sejam desenvolvidas para otimizar essas interações. Em vista disso, a bactéria Bacillus sp. RZ2MS9, previamente descrita como uma potencial BPCP em milho e soja, foi marcada com GFP e monitorada durante a colonização de milho inoculada sozinha, bem como em co-inoculação com Azospirillum brasilense (Ab-v5::pWM1013). A interação dessas linhagens marcadas em milho, foi monitorada por microscopia de fluorescência (FM) e PCR quantitativo (qPCR), revelando um comportamento endofítico de Bacillus sp. RZ2MS9. Em plantas co-inoculadas, apesar da linhagem Ab-v5::pWM1013 não ter sido detectada por qPCR, a co-inoculação resultou no aumento do peso seco das raízes e da parte aérea, no volume e no diâmetro do sistema radicular, demonstrando que a inoculação com mais de uma linhagem bacteriana pode ser uma boa alternativa para o desenvolvimento de bio-fertilizantes. O quorum sensing (QS) é um importante sistema de comunicação célula-célula que permite que as bactérias reconheçam sua própria população e modulem sua expressão gênica. Este sistema também está envolvido na comunicação interespecífica, incluindo outras espécies bacterianas e plantas. Co-evolutivamente, enzimas capazes de detectar e degradar essas moléculas evoluíram, dando origem ao chamado quorum quenching (QQ), sistema que evoluiu em algumas bactérias como uma vantagem competitiva para a colonização de nichos. O gene aiiA, foi um dos primeiros genes relacionados ao sistema QQ descrito no gênero Bacillus, gene este que foi anotado no genoma de RZ2MS9. Através da construção de uma nova linhagem biossensora de QQ, Agrobacterium tumefaciens At11006, e validada através da linhagem A. tumefaciens NTL4, a capacidade de RZ2MS9 de degradar moléculas de QS foi confirmada. O knockout do gene aiiA foi realizado utilizando o sistema CRISPR-Cas9, confirmando a função desse gene. Através dos resultados obtidos neste trabalho, a influência do sistema QQ de Bacillus sp. RZ2MS9 durante a colonização do milho, bem como a interação RZ2MS9 - A. brasilense - milho pode ser melhor investigada, abrindo a possibilidade de uma melhor compreensão do papel do sistema QQ na interação entre bactérias promotoras de crescimento e plantas.