Oyster reef habitats have declined from historic levels due to a variety of reasons, including overharvest, disease, and degraded water quality. The harvesting of oysters has led to a loss of reef habitat for both oysters and reef-associated fauna. When oysters spawn, the larval oysters, or spat, depend on hard substrate for settlement and growth. Oyster shell is the preferred substrate for use in restoration because it most closely matches natural reef habitat, but it is often expensive and in limited supply. This study incorporated field and laboratory experiments to assess the relative habitat value of alternative substrates (crushed concrete, porcelain, crushed limestone, and river rock, as well as oyster shell) for larval oyster recruitment as well as reef resident fishes and macro-invertebrates. Replicate trays of each substrate type were deployed in St. Charles Bay, TX for four months during spring and summer 2012 and assessed for oyster recruitment and faunal diversity and density. Concrete, river rock, limestone and porcelain had similar spat recruitment densities compared to oyster shell (1300-2300 spat). Spat shell heights were also larger on these substrates (13-16 mm), while spat on porcelain substrates were slightly smaller (10-13 mm). All substrates except bare sediment had similar fauna species densities (200-500 individuals m-2). Limestone had lower fauna diversity (H’; 0-1) than concrete and shell (1-2). Laboratory experiments compared the effectiveness of these substrates in providing prey refuge from pinfish and blue crab predators. All substrates performed similarly resulting in very low (<20 %) prey mortality rates for either predator. Results may enable future restoration plans to be implemented at a lower cost while providing similar habitat functions.

No description available.

No description available.

The fundamental motivation for this dissertation is to address the widening interconnect gap between integrated circuit (IC) demands and package substrates specifically for high frequency digital-RF systems applications. Moore's law for CMOS ICs predicts that transistor density on ICs will double approximately every 18 months. The current state-of-the-art in IC package substrates is at 20µm lines/spaces and 50-60µm microvia diameter using epoxy dielectrics with loss tangent above 0.01. The research targets are to overcome the barriers of current technologies and demonstrate a set of advanced materials and process technologies capable of 5-10µm lines and spaces, and 10-30µm diameter microvias in a multilayer 3-D wiring substrate using 10-25µm thin film dielectrics with loss tangent in the <0.005. The research elements are organized as follows with a clear focus on understanding and characterization of fundamental materials structure-processing-property relationships and interfaces to achieve the next generation targets. (a) Low CTE Core Substrate, (b) Low Loss Dielectrics with 25µm and smaller microvias, (c) Sub-10µm Width Cu Conductors, and (d) Integration of the various dielectric and conductor processes.

<p>Every living cell faces a multitude of DNA threats in its lifetime because damage to DNA is intrinsic to life itself. A double-strand break (DSB) is the most cytotoxic type of DNA damage and is a potent inducer of chromosomal aberrations. Defects in DSB repair are a major driver of tumorigenesis and are associated with numerous developmental, neurological and immunological disorders. To counteract the deleterious effects of DSBs, organisms have evolved a homologous repair (HR) mechanism that is highly precise. The key to its error-free nature lies in its use of a homologous template in restoring the DSB and its preferential occurrence during late S and G2 phase of the cell cycle when identical sister chromatids are available as templates for repair. However, HR can also engage homologous chromosomes and ectopic substrates that share homology, resulting in mitotic loss-of-heterozygosity (LOH) and unwanted chromosomal aberrations. In this case, understanding of the underlying mechanisms and molecular factors that influence accurate sequence transfer and exchange between two homologous substrates becomes crucial. </p><p>The focus of this dissertation is examination of the genetic factors and molecular processes occurring at early intermediate steps (DNA end resection and DNA synthesis) of mitotic recombination in Saccharomyces cerevisiae. To model DSB repair, we established a unique plasmid-based assay with a small 8-base pair (bp) gap in the middle of an 800-bp plasmid substrate. To delineate the molecular structures of strand exchange intermediates during HR, we used a 2% diverged plasmid substrate relative to a chromosomal repair template to generate mismatch-containing heteroduplex DNA (hetDNA) intermediates. The assay was performed in a mismatch repair (MMR)-defective background allowing hetDNA to persist and to segregate into daughter cells at the next round of replication. Unexpectedly, even when MMR was inactivated, sequence analysis of the recombinants revealed patches of gene conversion and restoration reflecting mismatch correction within hetDNA tracts. We showed that, in this system, MMR and nucleotide excision repair (NER) correct mismatches via two different mechanisms. While mispairing of nucleotides triggers MMR, NER is recruited by the subtle 6-methyladenine mark on the plasmid substrate, leading to coincident correction of mismatches. The methylation marks on the plasmid were acquired from the bacterial host’s native restriction-modification system during plasmid propagation. </p><p>Formation of hetDNA occurs when a plasmid substrate engages the chromosomal template for repair, forming a D-loop intermediate. D-loop extension requires DNA synthesis by DNA polymerase/s. Translesion synthesis (TLS) polymerases have been implicated in HR in both chicken DT40 cells and fruit fly, but not in yeast. This class of polymerases is known for its low fidelity due to a lack of exonuclease domain and is commonly used for lesion bypass and in extending ends with mismatches. We reported for the first time a requirement of Polζ-Rev1 and Polη (TLS polymerases in S. cerevisiae) for completing gap repair. Moreover, gap-repair efficiency suggested that these two polymerases function independently. We concluded that TLS polymerases are involved in either extending the invading 3’ end and/or in the gap-filling process that completes recombination. </p><p>DNA resection of a DSB serves as a primary step to generate a 3’ single-stranded DNA (ssDNA) for subsequent homologous template invasion, but this process has mostly been studied in the absence of a repair template or when downstream HR steps are disabled. To analyze the individual contributions of identified nucleases to DSB resection in the context of repair, we established a chromosomal assay; the substrate size was increased to 4 kilobases (kb) and 85 SNPs were present at ~50 bp intervals. In this chromosomal assay, resection and DNA synthesis influence the length of hetDNA tracts in the final recombinants, allowing these two steps to be analyzed. We specifically focused on synthesis-dependent strand annealing (SDSA) events, where hetDNA reflects DNA synthesis and extent of resection. Our main conclusions are as follows. DNA end resection on the annealing end of NCO products generated by SDSA is not as extensive as one might expect from resection measured in single-strand annealing (SSA) assays. In addition, although the two long-range resection pathways (Sgs1-Dna2 and Exo1) can support recombination in a redundant manner, hetDNA was significantly reduced upon loss of either. End processing of DSBs is predominantly 5’ to 3’, but we also observed loss of sequences (greater than 8 nt but less than 40 nt) at the 3’ termini. We have tested and ruled out the involvement of Mre11 and Polε proofreading activity. Lastly, Pol32 functions as a subunit of Polδ to promote extensive repair synthesis during SDSA. hetDNA tract lengths were significantly shorter in the absence of the Pol32 subunit of Polδ, providing direct evidence that Polδ extends the invading end during HR. Together, this work advances our understanding of how resection nucleases and DNA polymerase/s function to regulate mitotic recombination outcome and influence the molecular patterns of NCOs.</p> / Dissertation

La Division mitotique est une phase essentielle du cycle cellulaire qui assure la répartition correcte du contenu génétique. La mitose implique une réorganisation cellulaire profonde qui est principalement induite par une phosphorylation massive de protéines. Cette phosphorylation a lieu grâce à un équilibre fin entre kinases et phosphatases. À l'entrée mitotique, la phosphorylation protéique est induite par l'activation de la kinase cycline B/CDK1 et par l'inhibition de la phosphatase PP2A-B55. Résultats de notre et d'autres laboratoires ont récemment découvert une nouvelle voie essentielle pour moduler la phosphatase PP2A-B55 pendant la transition G2-M. Cette voie inclut la kinase Greatwall (GW) et ses substrats Arpp19 et ENSA. À l'entrée mitotique GW est activé et phosphoryle Arpp19 et ENSA les convertissant en inhibiteurs puissants de PP2A-B55. Étonnamment, aucun autre substrat de GW n'a été identifié jusqu'ici. Cependant, plusieurs éléments suggèrent fortement de nouveaux rôles de GW indépendamment de Arpp19 et de ENSA. L'objectif principal de ce travail était l'identification de nouveaux substrats de GW. À cette fin, j'ai utilisé plusieurs approches, y compris: (1) fractionnement biochimique des lysats de cellules ou des extraits d'oeufs de Xenopus combiné suivi d’une phosphorylation in vitro avec une kinase GW recombinante, (2) SILAC/phosphoproteomique des lysats de cellules exprimant différents niveau de GW, (3) Co-Immunoprecipitation, (4) BioID, et (5) une approche dirigée candidat. Les résultats de la phosphorylation in vitro ont révélé la présence de deux bandes de phosphorylation intéressantes qui sont actuellement analysées. Les deux approches SILAC/phosphoprotéinique et interactome ont révélé l'enrichissement des protéines impliquées dans la régulation post-transcriptionnelle de l'expression génique et des processus liés à l'ARN, une fonction physiologique déjà décrite pour cette voie chez la levure. Enfin, nous avons directement étudié la phosphorylation présumée par GW de trois candidats connus pour être impliqués dans le contrôle du cycle cellulaire. Bien que phosphorylées in vitro par GW, nous n’avons pu identifier le site de phosphorylation que dans l'une de ces trois protéines. Cette protéine, qui correspond à un inhibiteur de phosphatase, semble contrôler la sortie mitotique par la modulation de la déphosphorylation protéique. Un mutant non phosphorylable de cet inhibiteur induit une sortie mitotique perturbée avec une déphosphorylation ralentie des substrats mitotiques et une altération de la dégradation de la cycline B. J’ai pu attribuer ce défaut à une association perturbée de l'inhibiteur avec la phosphatase et, par conséquent, à un timing aberrant de l'inhibition de la phosphatase. Enfin, j'ai identifié le site de phosphorylation par GW comme le facteur clé contrôlant cette association. En résumé, j'ai identifié dans cette étude un nouveau substrat de GW contrôlant l'activité de la phosphatase essentielle pour une division mitotique correcte. / Mitotic division is an essential phase of the cell cycle that ensures the correct repartition of the genetic content. Mitosis involves profound cellular reorganization that is mostly induced by massive protein phosphorylation. This phosphorylation is achieved thanks to the fine-tuning of the balance between kinases and phosphatases. At mitotic entry, protein phosphorylation is induced by the activation of the master kinase Cdk1-cyclin B and the inhibition of the phosphatase PP2A B55. Previous results from our and other laboratories recently discovered a new pathway essential to modulate PP2A-B55 during G2-M transition. This pathway includes the kinase Greatwall (GW) and its substrates Arpp19 and Ensa. At mitotic entry GW is activated and promotes the phosphorylation of Arpp19/Ensa converting them into potent inhibitors of PP2A B55. Surprisingly, no other substrates of GW have been identified so far. However, several pieces of data strongly suggest new roles of GW independently of Arpp19 and Ensa. The main aim of this work was the identification of new substrates of GW. To this end, I used several approaches including: (1) Biochemical fractionation of cell lysates or Xenopus egg extracts combined with in vitro phosphorylation with recombinant GW kinase, (2) SILAC/phosphoproteomics from cell lysates expressing different GW amounts, (3) Co-Immunoprecipitation, (4) BioID and (5) a candidate directed approach. Results from in vitro phosphorylation revealed the presence of two interesting phosphorylated bands that are currently being analysed. Both SILAC/phosphoproteomic and interactome approaches yielded the enrichment of proteins involved post-transcriptional regulation of gene expression and RNA related processes, a physiological function already described for this pathway in yeast. Finally, we directly investigated the putative phosphorylation by GW of three candidates known to be involved in the control of cell cycle. Although phosphorylated in vitro by GW, we could only identify the phosphorylation site in one of these three proteins. This protein, corresponding to a phosphatase inhibitor, appears to control mitotic exit through the modulation of mitotic protein dephosphorylation. A non-phosporylable mutant of this inhibitor promotes a perturbed mitotic exit with delayed dephosphorylation of mitotic substrates and impaired cyclin B degradation. I could attribute this defect to a perturbed association of the inhibitor with the phosphatase and consequently to an aberrant timing of phosphatase inhibition. Finally, I identified the GW phosphorylation site as a key factor controlling this association. In summary, I identified in this study a new substrate of GW controlling phosphatase activity essential for correct mitotic division.

Transparent electrodes (TEs) require materials that have both transparency and electrical conductivity, a combination not usually found in nature. They are in increasing demand for use in solar cells, touch screens, displays, transparent heating films and several other devices. Most TEs used today are made of indium tin oxide (ITO). However, it has several disadvantages, such as high fabrication cost, rigidity and brittleness. Many ITO alternatives are being pursued, among which metallic nanowire (NW) networks on transparent substrates such as glass or polymer, have received much attention. This thesis demonstrates ordered silver NW networks on polyimide, fabricated by the field-directed chaining technique. We achieved a sheet resistance of 27 Ω/sq and 95.4% transparency at 550nm, with a Figure of Merit (FOM) 0.023Ω-1, which is higher than the FOM of commercial ITO, 0.005Ω-1. We have demonstrated that ordered NW networks, directed by alternative current (AC) electric fields, are easy to fabricate over a large area and at low cost, on rigid and flexible substrates. The AC electric field changes with different experiment setup. In this work, the effect of polymer thickness, electric field frequency, and gap size between electrodes are explored by COMSOL simulation and validated experimentally. By choosing the appropriate frequency and gap size, ordered NW networks are successfully created on a 23μm polyethylene terephthalate (PET) sheet. Fluid motion is one of the disruptors during NW chaining. We demonstrate control of this disruptor by the use of sandwiched channels for the NW suspension. Post-fabrication treatments are important and necessary for improving the connectivity and conductivity of Ag NW networks. In this work, we explore Joule heating and show its potential to improve the conductivity over other post-treatment approaches. However, Joule heating can also cause failures of NW networks. Ordered NW networks present better optical-electrical properties than random NW networks. Post-fabrication treatment can improve the properties, but there is a limit. In this work, a mathematical model is built for optical-electrical properties of perfectly ordered NW networks, which sets the upper bound of performance for transparent electrodes made of NW networks. A linear relationship is found between the transmittance and inverse sheet resistance. The model is then modified with factors to account for departure from the ideal. / Graduate / 2019-12-12

Ce travail concerne l'étude du phénomène de décharges partielles dans les matériaux isolants utilisés en électronique de puissance. En utilisant des méthodes de détection électrique et optique, le mécanisme de décharge partielle sur des substrats d'AlN dans l'huile silicone a été étudié sur un grand nombre d'échantillons. La variation de la nature du substrat (AlN, Al2O3 et composite verre/époxy) et du matériau d'encapsulation (huile silicone, huile de colza, huile minérale de transformateur, liquide d'imprégnant du condensateur Jarylec et Ugilec) met en évidence l'origine des décharges partielles de l'ensemble substrat – encapsulant. Les décharges partielles sur les substrats céramiques frittés ne dépendent pas du passivant, et se produisent dans le volume du substrat. L'évolution temporelle de la lumière émise dans les liquides en configuration pointe – plan et sur le substrat dans différents liquides montre que l'émission de lumière est un phénomène très complexe influencé par de nombreux paramètres : électroluminescence du solide, de l'encapsulant, décharges partielles, absorption des matériaux. Le phénomène d'électroluminescence du liquide est activé par une illumination extérieure. Les mesures de spectroscopie diélectrique haute tension n'apportent pas d'information supplémentaire sur le phénomène de décharges partielles, car les pertes correspondantes sont très faibles. / This work concerns the study of partial discharge phenomena on insulating materials used in power electronics. Using electrical and optical detection methods, the mechanism of partial discharges on AlN substrates in silicon oil is studied with a large number of samples. Changing the nature of substrates (AlN, and Al2O3 composite glass/epoxy) and of encapsulating materials (silicone oil, rapeseed oil, mineral transformer oil, capacitor impregnating liquids Jarylec and Ugilec) provides a number of conclusions about the origin of partial discharges on embedded substrates. Partial discharges on sintered ceramic substrates do not depend on the encapsulating material nature, but on the nature of the substrates themselves. The temporal evolution of light emitted by the liquid in a point - plane configuration, and on embedded substrates shows that the light during emission is a very complex phenomenon influenced by many parameters: electroluminescence of the solid, of the encapsulating material, partial discharges, and light absorption of materials. The electroluminescence of the liquid is activated by external light. Measurements of high voltage dielectric spectroscopy are also performed, but no additional information on partial discharges is obtained since corresponding losses are very low.

Ultrathin films of Cobalt, Iron and Manganese have been thennally evaporated onto an fcc Copper (111) single crystal substrate and investigated using a variety of surface structural teclmiques. The small lattice mismatch between these metals and the Cu (111) substrate make them an ideal candidate for the study of the phenomena of pseudomorphic film growth. This is important for the understanding of the close relationship between film structure and magnetic properties. Growing films with the structure of their substrate rather than their bulk phase may provide an opportunity to grow materials with novel physical and magnetic properties, and hence new technological applications. Both Cobalt and Iron have been found to initially maintain a registry with the fee Cu (111) surface in a manner consistent with pseudomorphic growth. This growth is complicated by island rather than layer-by-layer growth in the initials stages of the film. In both cases a change in the structure of the film seems to occur at a point where the coalescence of islands in the film may be expected to occur. When the film does change structure they do not form a perfect over-layer with the structure of their bulk counterpart. The films do contain a number of features representative of the bulk phase but also contain considerable disorder and possibly remnants of fcc (111) structure. The order present in these films can be greatly improved by annealing. Manganese appears to grow with an fee Mn (111) lattice spacing and there is no sign of a change in structure in films of up to 4.61 ML thick. The gradual deposition and annealing of a film to 300°C, with a total deposition time the same as that for a 1 ML thick film, causes a surface reconstruction to occur that is apparent in a R30° (√3×√3) LEED pattern. This is attributed to the formation of a surface alloy, which is also supported by the local expansion of the Cu lattice in the (111) direction.

Um dos fatores críticos nos processos de fotocatálise, que inviabiliza sua utilização em larga escala, é a necessidade de operações unitárias para a separação entre fotocatalisador e efluente. Uma solução para este problema é o uso do catalisador imobilizado em suportes. Assim, neste trabalho, o dióxido de titânio foi fixado em tecido de algodão, pelo uso de ácidos policarboxílicos (ácido succínico, cítrico e maleico) como ligantes, através do método deposição-enxugamento-cura. Foram usados planejamentos de experimentos para estabelecer as condições mais adequadas de concentração do ligante, tempo e temperatura de cura. Além disso, foram avaliados a massa de catalisador depositada, pelo método gravimétrico e a morfologia resultante nos materiais formados, pela Microscopia Eletrônica de Varredura. A melhor condição de tratamento, para cada um dos ligantes, foi utilizada para preparação de amostras que foram expostas ao UV, à vazão de água e ao borbulhamento de ar por 24 h, comparando-se a atividade e a estabilidade dos materiais obtidos. Os testes fotocatalíticos foram realizados adaptando-se uma metodologia existente na literatura para imobilização em vidro. Nesta, a partir da formulação de uma tinta indicadora de atividade e dispositivos de coleta e avaliação de imagem, é possível acompanhar o andamento da reação fotocatalítica. Os resultados mostraram que a atividade fotocatalítica e a massa depositada aumentam, dentro dos limites do planejamento, com a elevação da temperatura de cura, variável significativa estatisticamente para todos os ligantes testados. Contudo, o aumento na massa de fotocatalisador depositada não é sempre acompanhado pelo aumento na atividade fotocatalítica, indicando que a distribuição das partículas de fotocatalisador na matriz têxtil também é de grande importância para a eficiência fotocatalítica. Os resultados para o comportamento das variáveis na atividade fotocatalítica obtidos para o ligante ácido maleico diferenciam-se dos resultados obtidos para os outros ligantes, o que possivelmente pode ser explicado pela interação do mesmo com o catalisador NaH2PO2 e pelas diferenças na reação de reticulação da celulose. Além disso, imagens de MEV evidenciaram a deposição do catalisador de forma heterogênea, característica de superfícies irregulares como as dos têxteis. A avaliação dos resultados e de fatores econômicos e ambientais sugere que o ácido cítrico seja o agente mais promissor no processo de imobilização de dióxido de titânio em tecidos de algodão. / A critical factor in photocatalytic processes, which prevents its large scale usage, is the need for unit operations in order to remove the photocatalyst from the effluent. One possible solution to this problem is the use of photocatalyst immobilized on supports. In this work, titanium dioxide was immobilized into cotton textile by polycarboxylic acids binders (succinic, citric and maleic acid), through deposition-pad-cure method. Experimental design tests were performed to establish the most appropriate conditions of each binder concentration, curing time and temperature. In addition, the photocatalyst deposited mass was evaluated by gravimetric method and the resulting material morphology by Scanning Electron Microscopy (SEM). The optimum conditions of treatment for each binder was used to prepare samples that were exposed to UV, water flow and aeration for 24 h, in pursuance of comparing the materials activity and stability. The photocatalytic tests were performed by adapting an existing literature method for glass substrates. From a photoactivity indicator ink formulation and image capture and evaluation devices, it is possible to follow the photocatalytic reaction progress. The results showed an increase on the photocatalytic activity and deposited mass, within the experimental design limits, by raising curing temperature, variable statistically significant for all tested binders. However, the increase in photocatalyst mass deposition is not always followed by an increase in photocatalytic activity, indicating that photocatalyst particles distribution in the textile matrix is also of great importance for the photocatalytic efficiency. The results of variables behavior on photocatalytic activity for maleic acid binder are different from results obtained for other binders, which can possibly be explained by its interaction with the catalyst NaH2PO2 and differences in the cellulose crosslinking reaction. Moreover, SEM images showed heterogeneous photocatalyst deposition, characteristic of uneven surfaces such as textiles. The evaluation of these results and the economic and environmental factors suggests that citric acid is the most promising binder for titanium dioxide immobilization process into cotton fabrics.