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Understanding cage aquaculture adoption decisions and factors affecting adoption is necessary to ensure that fish production from cage aquaculture in Ghana is both significant and sustainable. The goal of this study was to provide a framework for understanding cage aquaculture adoption decisions and to identify factors affecting adoption, to inform decision makers as they formulate policies aimed at promoting cage aquaculture adoption in Ghana. I surveyed 122 respondents comprising current cage fish farmers, farmers who have abandoned cage aquaculture, and potential adopters of cage aquaculture such as, fish traders, fishermen and land-based fish farmers. Respondents answered questions related to knowledge, interest, constraints in cage aquaculture, and demographics. I used non-metric multidimensional scaling and discriminant function analysis to identify unique groups within the respondents, classify respondents according to their position in the innovation-decision continuum, and identify factors affecting cage aquaculture adoption. Based on their differences in knowledge and interests, I placed respondents into one of three stages of the cage aquaculture innovation-decision process model I developed: (1) Unawareness, (2) Knowledge, Persuasion, and Decision (KPD), and (3) Implementation (Confirmation and Abandonment). Respondents in the KPD and Implementation stages had knowledge, were more interested in cage aquaculture, and were aware of constraints in cage aquaculture, whereas respondents in the Unawareness stage lacked knowledge and interest in cage aquaculture, and did not clearly understand the constraints. Respondents who were males, belonged to the tribes Ewe and Akan, and who had fishing experience tended to be more interested in cage aquaculture. The lack of capital, high input costs, inability to adequately market fish, theft, lack of information sources, conflict over water use, and cage destruction by storms, were identified as the main constraints to cage aquaculture adoption in Ghana. The results of the study suggest that programs aimed at encouraging new entrants into cage aquaculture should focus on demographic characteristics such as gender, and tribe. However, demographic characteristics may affect adoption decisions and it may be important to consider them as such. Some recommendation to address the major constraints in cage aquaculture include: the Fisheries Directorate should (1) develop an efficient extension program that farmers can access regularly, especially, for farmers with no other information sources, (2) provide feed subsidy to enable farmers produce fish at competitive prices, (3) facilitate the formation of fish farmers' cooperative groups that would purchase large quantities of feed, (4) encourage local production of high quality fish feed, and (5) develop credit facilities that can be accessed by individuals interested in cage aquaculture to assist potential farmers who would, otherwise, not be able to adopt cage aquaculture . In addition, fish farmers should (6) be proactive in marketing their fish by identifying potential niche markets prior to production, and (7) join cooperative groups to ease the burden of accessing loans to increase production. / Master of Science

Thesis (MSc)--Stellenbosch University, 2013. / ENGLISH ABSTRACT: Plant defensin peptides have become promising and attractive candidates to be used as antifungal agents in agricultural biotechnology. These peptides have a broad spectrum antifungal activity and play a vital role in the innate immune system of plants. Plant diseases caused by fungi are a major contributor to the decrease in the quality and safety of agricultural products. Due to the dangerous effects and negative environmental impact of pesticides, an effective, safe, natural and durable method to control crop pathogens has therefore become one of the major concerns in modern agriculture. Although these peptides are promising and attractive candidates, their precise mechanism of action is to date still unknown. Several common observations have been made. These include the antagonistic effect of cations on the activity of plant defensins. It is of vital importance to understand the underlying mechanism of the cation-antagonistic effect on the antifungal potency of defensin peptides in order to evaluate the possible contribution to defence reactions against microorganisms in planta. To this end we set out to characterize the effect of cations in the form of biological salts, NaCl, KCl, MgCl2 and CaCl2 on the structural stability and activity in terms of growth inhibition, morphological effects and permeabilization. In order to perform these characterization experiments, a production method resulting in a greater yield and involving simple and rapid purification methods was required. Heliophila coronopifolia peptides have previously been produced in a bacterial system, however the purification methods were tedious resulting in poor yields. Pichia pastoris was selected as production system as several other plant defensins have been successfully produced in this eukaryotic system. Hc-AFP1 and Hc-AFP3 was successfully produced using the Pichia production system and rendered active peptides. Hc-AFP2 and Hc- AFP4 was, however, not produced correctly, due to a post-translational modification event leading to the cyclization of the N-terminal glutamine to generate pyroglutamic acid. This modification negatively influenced the activity of these peptides. An active Hc-AFP2 could be produced by replacing the production buffer with a reduced ionic buffer. The effect of divalent and monovalent cations on the secondary structure of Hc-AFP1 was evaluated by circular dichroism spectroscopy. These cations induced a conformational change in the secondary structure of Hc-AFP1, with NaCl and MgCl2 inducing a more defined secondary structure and KCl and CaCl2 inducing a less defined secondary structure. Monovalent cations caused a slight reduction in the growth inhibition activity of Hc-AFP1 on Botrytis cinerea, however, characteristic hyperbranching and other morphogentic effects were still visible. Divalent cations had a greater antagonistic effect on the activity of Hc-AFP1, completely abolishing the growth inhibitory activity of the peptide, but the induced morphological effects on hyphae remained present. The activity of Hc-AFP1 to permeabilize B. cinerea hyphae was not influenced by the addition of cations, however it was in fact increased to up to 10-fold. However, since the growth inhibition activity of Hc-AFP1 was reduced in the presence of the biological salts indicates that permeabilization is not the sole activity responsible for growth inhibition caused by Hc-AFP1. This peptide probably has an alternative/primary target and more complex MOA. This is the first known report of the investigation of the influence of cations on the structure of plant defensin peptides. It is clear that cations induce a secondary structural conformational change in Hc-AFP1. This may be linked to the antagonism on the activity of this peptide. This study provides significant progress towards the structure-function analysis of plant defensins. / AFRIKAANSE OPSOMMING: Plantdefensinpeptiede word beskou as belowende en aantreklike kandidate vir gebruik as swammiddles in agribiotegnologie. Hierdie peptiede beskik oor breë spektrum antifungiese aktiwiteit en speel ‘n essensiële rol in die ingebore immuunsisteem van plante. Plant siektes wat deur swamme veroorsaak word dra betekenisvol by tot die afname in die kwaliteit en veiligheid van landbouprodukte. As gevolg van die skadelike effekte en negatiewe omgewingsimpak van plaagdoders, het effektiewe, veilige, natuurlike en duursame metodes om gewaspatogene te beheer, van die belangrikste vraagstukke van moderne landbou geword. Alhoewel hierdie peptiede belowende en aantreklike kandidate is vir die toepassing, is hulle presiese meganisme van aksie tot vandag toe steeds onbekend. Verskeie algemene waarnemings is egter al gemaak. Dit sluit die antagonistiese effek van katione op die aktiwiteit van plantdefensinpeptiede in. Dit is kernbelangrik om die onderliggende meganisme van die katioon-antagonistiese effek op die antifungiese effektiwiteit te verstaan om die moontlike bydrae van die peptiede tot die verdedigingsreaksies teen mikro-organismes in planta te evalueer. Met die doel voor oë het ons gemik om die effek van katione, spesifiek in die vorm van die biologiese soute NaCl, KCl, MgCl2 en CaCl2, op die strukturele stabiliteit en aktiwiteit in terme van groei inhibisie, morfologiese effekte en permeabilisasie te karakteriseer. Om uiteindelik hierdie karakterisasie eksperimente uit te voer was dit nodig om ‘n metode met ‘n groter opbrengs en wat vinnige suiwering van die peptied ondersteun, te optimiseer. Heliophila coronopifolia peptiede was voorheen in ‘n bakteriese sisteem geproduseer, maar die suiweringsmetodes was tydsaam en het gelei tot ‘n swak opbrengs. Pichia pastoris is dus geselekteer as die produksie sisteem aangesien verskeie ander plantdefensinpeptiede al suksesvol geproduseer is in hierdie eukariotiese sisteem. Hc-AFP1 and Hc-AFP3 is suksesvol vervaardig in die Pichia sisteem en het aktiewiteit getoon. Hc-AFP2 and Hc-AFP4 kon egter nie korrek vervaardig word nie as gevolg van ‘n na-vertalingsverandering wat gelei het tot die siklisering van die N-terminale glutamien, om piroglutamiensuur te lewer. Hierdie verandering het die aktiwiteit van die peptied negatief beinvloed. ‘n Aktiewe Hc-AFP2 kon wel vervaardig word deur die produksiebuffer te vervang met ‘n lae-ionise buffer. Die effek van divalente en monovalente katione op die sekondêre struktuur van Hc-AFP1 is ge-evalueer deur van sirkulêre dikroisme spektroskopie gebruik te maak. Hierdie katione het ‘n vouingsverandering in die sekondêre struktuur van Hc-AFP1 geïnduseer, NaCl and MgCl2 het ‘n meer gedefinieërde sekondêre struktuur induseer, terwyl KCl and CaCl2 ‘n minder gedefinieërde sekondêre struktuur geinduseer het. Monovalente katione het ‘n effense vermindering in die groei-inhibisie aktiwiteit van Hc-AFP1 op Botrytis cinerea veroorsaak, alhoewel kenmerkende hife-oorvertakking en ander morfologiese effekte nogsteeds sigbaar was. Divalente katione het ‘n sterker antagonistiese effek gehad op die aktiwiteit van Hc-AFP1, waar dit totaal en al die groei-inhibisie aktiwiteit van die peptied vernietig het, alhoewel die geïnduseerde morfologiese effekte op die hiffes steeds sigbaar was . Die aktiwiteit van Hc-AFP1 om B. cinerea hyphae te permeabiliseer is nie negatief beinvloed deur die byvoeging van katione nie, tewens dit het die aktiwiteit tot 10-voudig verhoog. Aangesien die groei-inhibisie aktiwiteit van Hc-AFP1 nie verminder is in die teenwoordigheid van die biologiese soute nie, dui dit aan dat permeabilisasie nie die enigste aktiwiteit is wat die groei inhibisie veroorsaak het nie. Die peptied het dus moontlik ‘n alternatiewe of primêre teiken en ‘n meer komplekse meganisme van aksie. Dit is die eerste verslag wat die invloed van katione op die struktuur van plantdefensinpeptiede ondersoek het. Dit is duidelik dat katione ‘n sekondêre strukturele vouingsverandering in Hc-AFP1 induseer. Hierdie verandering mag dalk bydra tot die antagonistiese uitwerking op die aktiwiteit van hierdie peptied. Hierdie studie het betekensisvolle vordering gemaak met die analise van die struktuur-funksie interaksie van plantdefensinpeptiede. / The National Research Foundation (NRF), Institute of Wine Biotechnology (IWBT), THRIP and Winetech for financial assistance.

Right Ventricular (RV) dysfunction is a common cause of heart failure in patients with congenital heart defects and often leads to impaired functional capacity and premature death. 3D cardiac magnetic resonance imaging (CMR)-based RV/LV combination models with fluid-structure interactions have been introduced to perform mechanical analysis and optimize RV remodeling surgery. Obtaining accurate RV/LV morphology is a very important step in the model-constructing process. A semi-automatic segmentation process was introduced in this project to obtain RV/LV/Valve geometry from patient-specific 3D CMR images. A total of 420 contour results were obtained from one patient CMRI data using QMASS software package at Department of Cardiology of Children¡¯s hospital. The digital contour data were automatically acquired using a self-developed program written in MATLAB. 3D visualizations of the RV/LV combination model at different phases throughout the cardiac cycle were presented and RV/LV volume curves were given showing the volume variation based on digital contour data under MATLAB environment. For the patient considered, the RV stoke volume (SV) is 190.8 ml (normal value is 60-136 ml) and ejection fraction is 43.5% (normal value is 47%-63%). In future work, the surgical, CMR imaging and computational modeling will be integrated together to optimize patch design and RV volume reduction surgery procedures to maximize recovery of RV cardiac function.

Iron oxide nanoparticles (NPs) are promising materials for use in many applications, including new cancer treatments and in cleaning water, because they exhibit size-dependent magnetic and absorptive properties. NP properties are caused by structural attributes of the NPs, like surface disorder and cation vacancies. However, NP synthetic methods also impact structure, therefore properties, of NPs. Furthermore, the synthetic method is often changed in order to change the core diameter of NPs. Determining if properties are caused by the dimensions of the NP is impossible if there are also structural features present in the NP caused by the synthetic method, like grain boundaries or polycrystalline shells. In Chapter II of this dissertation, we show a new continuous growth synthesis of spinel iron oxide where the diameter of NPs is changed by the amount of precursor added to the reaction, meaning the only structural feature changing between the NPs is size. Continuous growth, therefore, can be used to probe the impact that size has on NP structure and properties. We report that saturation magnetization of NPs produced from continuous growth is size-dependent and higher in magnitude than NPs of the same core diameter made by other syntheses. In chapter III of this dissertation we determine nanoscale structure by Pair Distribution Function (PDF) analysis of Total X-ray Scattering data of NPs isolated from the reaction with core diameters between 3-10 nm. In Chapter IV of this dissertation we monitored the growth of NPs in situ with Total X-ray Scattering to gain insight on the structures of NPs while forming. In situ measurements of Total X-ray Scattering data gave insights into how precursor oxidation state influences the structures formed during formation of NPs, with more oxidized precursor giving a more oxidized product and a reduced precursor yielding a more reduced product even though the NPs formed by either method are indistinguishable by ex situ analysis. This dissertation includes previously published and unpublished co-authored material. / 2021-04-30

京都大学 / 新制・課程博士 / 博士(人間・環境学) / 甲第23287号 / 人博第1002号 / 新制||人||236(附属図書館) / 2020||人博||1002(吉田南総合図書館) / 京都大学大学院人間・環境学研究科相関環境学専攻 / (主査)教授 内本 喜晴, 教授 田部 勢津久, 准教授 戸﨑 充男 / 学位規則第4条第1項該当 / Doctor of Human and Environmental Studies / Kyoto University / DFAM

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Alpacas kept in Central Europe are often deficient in vitamin D3, which is supplemented orally or by injection by the owners or veterinarians. Vitamin D3 can be specified in two different units (IU and µg), which differ by a factor of 40. By mixing up these units, an overdosage can be induced. In this study, three alpaca crias were examined after vitamin D3 intoxication, with particular reference to kidney function. All three animals developed non-specific clinical alterations 1–2 weeks after a vitamin D3 overdose of approximately 40 times. Plasma of the animals revealed several alterations. The main findings were severe azotemia, hypercalcemia and hyperphosphatemia, 15 days after treatment. Kidney function analysis (endogenous creatinine clearance) in two of the crias revealed severe glomerular damage. All crias died despite intensive treatment within 23 days after vitamin D3 treatment. Necropsy revealed calcification in different organs, mainly the kidneys, lungs and liver. Since nine other crias in the same group were treated with comparable doses of vitamin D3 and no clinical signs were observed in these animals, it is concluded that individual animals show different levels of sensitivity to vitamin D3.

Estuaries are vital environmental and economic resources, providing habitat for thousands of species, absorbing runoff, and supporting recreation and commerce. Yet, despite their importance, estuaries are threatened by human activities. Empirical Orthogonal Function (EOF) analysis and Cross Spectral techniques were used in the analysis and prediction of estuarine morphology. The estuaries selected for study were Suisun Bay, CA and Mobile Bay, AL. It was found that EOF is an effective and efficient technique to analyze morphology, a coupling with cross spectral methods such as Fourier Transformation (FFT) resulted in determination of forcing functions responsible for imparting variance to the bathymetry. In both the estuaries it was found that the first two eigenvalues represented almost 80% of the morphological/bathymetric dataset. The second eigenfunction was found to be closely dependent on the freshwater inflows to the estuaries. EOF analysis on Suisun Bay revealed that the bay is depositional particularly in the shallow bays of Honker and Grizzly, whereas the main channels as well as Carquinez Straits maintained their depths throughout the period studied. Utilizing a Cross spectral technique, Amplitude Response Function (ARF), temporal eigenfunctions for the bay were determined for year 2100. The temporal eigenfunctions were predicted for cases where river inflows to the bay were varied by 1 standard deviation unit. These predicted eigenfunction values combined with the eigenvalues resulted in the recovery of predicted depths for year 2100. It was found that Suisun Bay remains depositional through the year 2100 and maintains depths in the main channels as well as Carquinez Straits. This depositional behavior results in the decrease of bay volume to almost 40% of the volume in 1989. EOF analysis on Mobile Bay revealed that the bay is predominantly depositional except in the navigation channel and the shoreline of the Bay. The navigation channel maintaining it depth is attributed to the regular dredging carried to facilitate shipping. The second temporal eigenfunction showed a close correlation with river inflows as in the case of Suisun Bay. However, a cross correlation performed on the second temporal eigenfunction and inflows revealed that the response of the eigenfunction is perturbed by almost 9 years, as opposed to 6 to 9 years for Suisun Bay. An ARF on the temporal eigenfunctions combined with a reverse EOF resulted in the formation of bathymetric datasets for the year 2100 for inflows variation of 1 standard deviation. It was revealed that increasing the flows results in an increase of bay volume by approximately 30% and a decrease in flows results in a loss of volume by approximately 20%.

Activated sludge treatment systems rely on a microbial consortium structurally organized in bioflocs to treat pollutants present in wastewater. The treatment process efficiency in these systems can be severely affected by toxic chemicals present in the influent wastewater. The effects of chemical toxins at the treatment process level are determined by the mechanisms that occur at the biofloc and cellular levels, which can be physical, chemical and physiological in nature. We believe that the overall process effects of chemical toxins on activated sludge systems likely result from a combination of all three types of mechanisms and that they are interdependent, in the sense that specific bacterial stress response mechanisms (physiological mechanisms that protect the cell from toxic conditions) may lead to physical/chemical alterations at the floc level, and vice-versa. Ultimately, understanding the mechanisms that occur at the floc and metabolic scales will help to design more robust and efficient treatment systems, and to develop tools to prevent and mitigate the effects of toxic chemicals on activated sludge systems. In this research, we set out to establish the link between the effects of chemical toxins on activated sludge cultures at the process, floc and metabolic scales. First, the effects of shock loads of different toxic sources (1-chloro-2,4-dinitrobenzene (CDNB), cadmium, 1-octanol, 2,4-dinitrophenol (DNP), weakly complexed cyanide, pH 5, 9 and 11, and high ammonia levels) on activated sludge process parameters (biomass growth, respiration rate, flocculation, chemical oxygen demand (COD) removal, dewaterability and settleability) were studied. For all chemical shocks except ammonia and pH, concentrations that caused 15, 25 and 50% respiration inhibition were used to provide a single pulse chemical shock to sequencing batch reactor (SBR) systems containing a nitrifying (10 day solids retention time – SRT) and a non-nitrifying (2 day SRT) biomass. We found that cadmium and pH 11 shocks were the conditions that most detrimentally affected all the processes, followed by CDNB. DNP and cyanide primarily led to effects on respiration, while pH 5, 9, octanol and various ammonia concentrations did not impact the treatment process to a significant extent. Additionally, there was a clear correlation between biomass deflocculation and increases in the effluent soluble COD of the shocked reactors for different chemical sources. With this study, we were able to establish a source-effect matrix linking classes of chemical toxins to their potential inhibitory effects on activated sludge processes, thereby contributing to a better understanding of the potential effects of toxic industrial discharges into biological treatment systems. The findings of the first phase of the research, specifically the correlation between chemical-induced deflocculation and increases in soluble COD, served as a motivation to explore the role of floc structure in the response of activated sludge cultures to toxic compounds, and to conduct a more in-depth analysis of the supernatant (soluble phase) of toxin-exposed activated sludge. In one study, we evaluated the respiration inhibition induced by octanol, cadmium, N-ethylmaleimide (NEM), cyanide and DNP on activated sludge biomasses with different floc structures but similar physiological characteristics, with the objective of assessing the role of the extracellular polymeric substances (EPS) in flocs as a protection barrier against chemical toxins. Mechanical shearing was applied to fresh mixed liquor to produce biomasses with different floc structure properties and specific oxygen uptake rate assays were conducted on the sheared and unsheared mixed liquors. The results showed that the respiration inhibition by octanol and cadmium was more intense in sheared mixed liquor (which had less EPS material available in the flocs and smaller floc sizes) than in the unsheared biomass. Conversely, the respiration inhibition induced by NEM and cyanide was similar for the different mixed liquors tested. These results allowed us to conclude that the EPS matrix functions as a protective barrier for the bacteria inside activated sludge flocs to chemicals that it has the potential to interact with, such as hydrophobic (octanol) and positively-charged (cadmium) compounds, but that the toxicity response for soluble, hydrophilic toxins (NEM and cyanide) is not significantly influenced by the presence of the polymer matrix. In the final study that was conducted, we used the metabolomics-based technique metabolic footprinting to assess if the soluble phase of mixed liquor exposed to different chemical toxins exhibited a toxin-specific biochemical composition. We hypothesized that toxin-specific effects could be distinguished through footprint patterns of those soluble samples. The impact of cadmium, DNP and NEM shock loads on the composition of the soluble fraction of activated sludge mixed liquor was analyzed by liquid chromatography-mass spectrometry (LC-MS). The results from this study indicated that there was a significant release of biomolecules (proteins, carbohydrates and humic acids) from the floc structure into the bulk liquid due to chemical stress. More importantly, using a multivariate statistical method called discriminant function analysis with genetic algorithm variable selection (GA-DFA), we were able to show that the soluble phase samples from the different reactors could be differentiated, thereby indicating that the footprints generated by LC-MS were different for the four conditions tested and, therefore, toxin-specific. These footprints, thus, contain information about specific biomolecular differences between the samples, and we found that only a limited number of m/z (mass to charge) ratios from the mass spectra data was needed to differentiate between the control and each chemical toxin-derived samples. In addition, since the experiments were conducted with mixed liquor from four distinct wastewater treatment plants, the discriminating m/z ratios may potentially be used as universal stress biomarkers. These results are promising and indicate that LC-MS may be used for the discovery of activated sludge stress biomarkers, to allow the development of new toxin detection technologies for prevention of upset events in activated sludge systems. / Ph. D.