This thesis presents consolidated research results of a low-cost, high efficiency, high throughput detection system for fluorescence-based bio-assays. Such high throughput screening process is an invaluable tool for the multifaceted field of Systems Biology, where it is widely used in genomics and proteomics for drug and gene discovery applications. The thesis is divided into three parts: addressing the feasibility of using hydrogenated amorphous silicon photodiodes as the sensor, the development of an associated compact model suitable for circuit-level simulations, and integration of the sensors and switches to realize the array. Requirements of fluorescent bio-assays demand low sensor dark current densities in the order of 10¯¹¹A/cm² at room temperature. Fabrication of high quality segmented a–Si:H n–i–p photodiodes with such specification is achieved by tailoring defects at photodiode junction sidewalls, where both the dry etching and passivation conditions play important roles. Measurements of the fabricated photodiodes at different temperatures allowed the extraction of reverse current components, which are necessary in modeling such sensors in Verilog-A. Two prototype array designs are fabricated with pixel dimensions matching ANSI standard microwell plates. The functionalities of the small arrays are demonstrated with green LEDs to simulate fluorescent dyes that are commonly used in the high throughput bio-assay processes.

This thesis presents consolidated research results of a low-cost, high efficiency, high throughput detection system for fluorescence-based bio-assays. Such high throughput screening process is an invaluable tool for the multifaceted field of Systems Biology, where it is widely used in genomics and proteomics for drug and gene discovery applications. The thesis is divided into three parts: addressing the feasibility of using hydrogenated amorphous silicon photodiodes as the sensor, the development of an associated compact model suitable for circuit-level simulations, and integration of the sensors and switches to realize the array. Requirements of fluorescent bio-assays demand low sensor dark current densities in the order of 10¯¹¹A/cm² at room temperature. Fabrication of high quality segmented a–Si:H n–i–p photodiodes with such specification is achieved by tailoring defects at photodiode junction sidewalls, where both the dry etching and passivation conditions play important roles. Measurements of the fabricated photodiodes at different temperatures allowed the extraction of reverse current components, which are necessary in modeling such sensors in Verilog-A. Two prototype array designs are fabricated with pixel dimensions matching ANSI standard microwell plates. The functionalities of the small arrays are demonstrated with green LEDs to simulate fluorescent dyes that are commonly used in the high throughput bio-assay processes.

Dans le milieu marin, toute surface immergée est rapidement colonisée par des bactéries, puis par d’autres micro-organismes, conduisant à la formation de structures tridimensionnelles complexes appelées biofilms. Cette étape est généralement suivie par l’installation de macro-colonisateurs. Néanmoins, un certain nombre d’organismes marins, tels que les macro-algues, présentent des surfaces peu épiphytées à l’échelle macroscopique. Des algues méditerranéennes (Taonia atomaria et Dictyota spp.) ont été sélectionnées dans le cadre de ces travaux de thèse pour leur capacité à conserver leur surface peu colonisée. Cependant, des observations de leurs surfaces par microscopie ont montré l’existence de biofilms diversifiés à la surface de leurs thalles. Le but de cette thèse est de mieux comprendre les mécanismes de médiation chimique entre ces algues et les bactéries associées à leur surface. La première partie de ce travail a été consacrée à l’étude du rôle de molécules d’origine algale vis-à-vis de l’adhésion de bactéries marines. Pour cela, la composition chimique totale des algues sélectionnées a été analysée conduisant à l’isolement et à la caractérisation structurale de 12 molécules, dont trois se sont révélées être originales. L’activité anti-adhésion de la majorité de ces composés a ensuite été évaluée : le 1-O-octadecenoylglycérol s’est avéré être le produit le plus actif (20 µM < CE50 <55 µM). La deuxième partie a été dédiée plus particulièrement à l’étude du métabolome de surface de T. atomaria dans le but d’évaluer son implication dans les interactions écologiques entre l’algue et les bactéries associées à sa surface. Un protocole d’obtention et d’analyse spécifique des extraits surfaciques a tout d’abord été développé. Ce protocole est basé sur le trempage des thalles dans des solvants organiques et un contrôle de l’intégrité des cellules membranaires des algues y est associé. L’échantillonnage a été effectué mensuellement à Carqueiranne (Nord-ouest de la Méditerranée, France) durant la période allant de février à juillet 2013. Les résultats obtenus montrent qu’un sesquiterpène est exprimé majoritairement à la surface de l’algue. Il a été démontré que ce composé inhibe l’adhésion de souches bactériennes de référence tout en restant inactif vis-à-vis de celles isolées à la surface de l’algue. Une telle spécificité n’a pas été observée ni dans le cas de biocides commerciaux, ni pour les autres métabolites produits par T. atomaria. Dans un second temps, un suivi saisonnier des extraits de surface ainsi que des communautés bactériennes associées a été effectué par métabolomique (LC-MS) et DGGE, respectivement. Des fluctuations saisonnières de ces deux paramètres ont été reportées sans mettre en évidence de corrélation évidente entre eux. La présence de la molécule majeure de surface durant tout le suivi saisonnier a été notée ainsi que sa capacité à diffuser dans l’eau de mer. Enfin, l’étude de l’implication potentielle des bactéries associées à T. atomaria dans le contrôle du biofilm a été entreprise en évaluant l’activité de leurs extraits vis-à-vis de l’adhésion de souches de référence. En conclusion, nous émettons l'hypothèse que T. atomaria pourraient contrôler partiellement le biofilm associé à sa surface en faisant intervenir des métabolites spécifiques. / In the marine environment, all submerged surfaces are rapidly colonized by bacteria and other microorganisms, resulting in the formation of complex three-dimensional structures called biofilms. This step could be followed by the attachment of macro-colonizers. Nevertheless, a number of marine organisms, such as macro-algae, appeared to be relatively free of epibionts at a macroscopic scale. In this study, several Mediterranean algae (Taonia atomaria and Dictyota spp.) were selected for their ability to keep their surface free of biofouling. However, microscopic techniques allowed the observation of a diversified biofilm on the surface of their thalli. The purpose of this work was to understand how this alga could interact with its associated bacteria using a chemical ecological approach. The first part of this work deals with studying the anti-adhesion properties of algal molecules against a range of marine bacteria. For this, the whole chemical composition of the two algae was analyzed leading to the isolation and structural characterization of 12 molecules from which three were found to be new. The anti-adhesion activity of some of these compounds was then evaluated: 1-O-octadecenoylglycerol proved to be the most active product (20 µM < EC50 <55 µM). The second part of this study was dedicated to the study of the surface metabolome of T. atomaria in order to assess its involvement in the ecological interactions between the alga and its associated bacteria. A specific extraction protocol was optimized for the surface compounds using a dipping technique in organic solvents associated with the integrity control of algal cell membrane. Sampling was carried out monthly at Carqueiranne (N W Mediterranean Sea, France) between February and July 2013. The results showed the presence of a major molecule in accordance with a sesquiterpenic structure. Anti-adhesion capacity against reference bacterial strains was noticed for this compound, while it remained inactive against strains isolated from the algal surface. This specificity was not observed for commercial biocides and the other molecules purified from crude algal extracts of T. atomaria. Then, changes in surface extracts and associated bacterial surface communities were monitored using metabolomics (LC-MS) and DGGE, respectively. Seasonal fluctuations for the two parameters could be reported without any evident correlation between them. The occurrence of the major molecule throughout the seasonal monitoring was also noticed and its capacity to diffuse in the marine environment was shown. Finally, the study of the potential involvement of the associated bacteria in the biofilm control was conducted by evaluating the anti-adhesion activity of their crude extracts against reference strains. In conclusion, we hypothesize that T. atomaria could control at least partially the biofilm at its surface using specific metabolites.

Thesis (Ph.D. (Zoology))--North-West University, Potchefstroom Campus, 2008.

POPs are a group of chemicals that have been extensively studied over the last few years. The main reason that these chemicals have received so much scientific attention is the myriad of negative effects they have on the environment and human health. The properties that cause the deleterious effects include a high molecular stability, rendering them highly persistent. Added to this is the lipophilic and hydrophobic nature of the compounds. POPs will thus tend to bio-accumulate and bio-magnify in the environment, causing a direct threat to humans and wildlife. To address this threat, the Stockholm Convention on Persistent Organic Pollutants, under the supervision of United Nations Environment programme (UNEP), was initiated and became legally binding on 17 May 2004. All countries, including South Africa, which ratified this agreement, will be expected to monitor and regulate the formation of POPs. Polychlorinated dibenzo-p-dioxins (PCDDs), polychlorinated dibenzofurans (PCDFs) and polychlorinated biphenyls (PCBs) are all members of the dioxin-like family of POPs. This family of chemicals pose serious health threats such as carcinogenic effects and negative effects on reproduction. These substances, with the exception of PCBs, are formed unintentionally as by-products of industrial and thermal processes. One of the main sources of dioxin-like chemicals is medical waste incinerators. In this project the area surrounding a medical waste incinerator was monitored using a bio-assay technique. The determination of dioxin concentrations is usually preformed by chemical analysis, however, bio-assays have proven themselves to be a cheaper and time-saving screening method. The Toxic Equivalency Quotient (TEQs) determined through bio-assays can support chemical analysis in determining biologically-relevant risk assessments since bio-assay data has ecotoxicological relevance. These assays represent an integrated biological response to chemical pollutants, where biological effects are accounted for which is not possible in chemical analyses. One of the bio-assays used in the determination of the dioxin-like chemical TEQ is the H411 E reporter gene bio-assay. This assay is based on the Ah-receptor mediated toxicity of dioxin-like chemicals. Using this technique the TEQs for areas surrounding an active incinerator were determined, to indicate the distribution of these substances. The TEQs for the soil samples collected ranged between nondetectable and 154 ngTEQ/kg. There was no clear distributional pattern and the total organic carbon content in the soil did not seem to play a crucial role in the distribution of dioxin-like chemicals. Although a decrease in soil tillage showed a corresponding increase in TEQ. The predominant wind direction was taken into account but no correlation could be seen. However, meteorological parameters such as the ambient temperature and low precipitation in the area may have contributed to lower TEQ values. Cytotoxicity excluded data points and the phenomenon has to be addressed. High TEQ values in a residential area where free-range chickens are raised pose a serious concern to the level of dietary dioxin-like chemical intake. Eggs in the area could theoretically contain between 2.75 and 28.75 pgTEQ/g egg fat. Further studies are needed to determine how much dioxin-like chemicals are being transferred to humans through the consumption of free-range eggs / Thesis (M. Environmental Science)--North-West University, Potchefstroom Campus, 2006.

Natural products have been a source of many pharmaceutical drugs and a number of drugs that are currently used in the treatment of cancer are derivatives of compounds originally isolated from natural products. There is evidence that extracts of Tulbaghia violacea can be used to treat cancer. The activation of apoptosis in cancer cells is a target for the development of novel anti-cancer drugs since one of the characteristics of cancer cells is resistance to apoptosis due to the deregulation of biochemical pathways leading to apoptosis. In fact, many current anti-cancer drugs exert their effects through the activation of apoptosis. Previous studies showed that extracts of T.violacea induce apoptosis in cancer cells and one study reported on the isolation of a compound (methyl-ԃ-D-glucopyranoside), which is responsible for the pro-apoptotic activity of the T.violacea extract. Therefore the aim of this study was to investigate the anti-cancer activity of methyl-ԃ-Dglucopyranoside and extracts prepared from T.violacea. In this study the pro-apoptotic activity of methyl-ԃ-D-glucopyranoside and extracts prepared from T.violacea were investigated on a panel of human cancer cell lines, which included HepG2, MCF7, H157, HT29 and the non-cancerous cell line, KMST6. The induction of apoptosis was evaluated by flow cytometry using several bioassays which measures biochemical events (caspase activation, phosphatidylserine externalisation and reactive oxygen species (ROS) production that is associated with the induction of apoptosis. The results demonstrated that the effects of methyl--D-glucopyranoside on cultured cells are transient and that the cells recover from the effects of methyl--D-glucopyranoside. This suggested thatmethyl-ԃ-D-glucopyranoside is not the compound responsible for the pro-apoptotic bioactivity in the T.violacea extract. This study also showed that cytotoxic and pro-apoptotic bioactivity of the leaf-extract was significantly higher in comparison to the tuber-extract. The bioactivity of the organic solvent extracts (dichloromethane, hexane, methanol and 50% methanol/water) of T.violacea leaves was also significantly higher than water extracts of T.violacea leaves. A comparison of the different organic extracts prepared from the T.violacea leaves showed that the highest activity was observed for the dichloromethane and hexane extracts. In an effort to identify the bioactive compound(s) the dichloromethane extract was subjected to Versaflash® column chromatography. However, due to problems experienced with the solubility of the dichloromethane sub-fractions, these compounds could not be tested for their bioactivity. Palmitone (16-hentriacontanone) was identified as one of the major compounds present in the dichloromethane sub-fractions. This compound was previously shown to have anticonvulsant bioactivity but there is no evidence in the literature that it has anti-cancer or pro-apoptotic activities. Fingerprinting of the methanol extract showed the presence of long chain fatty acid derivatives, flavonoids and allicin derivatives in the methanol extract. Although, this study failed to isolate the pro-apoptotic bioactive compound(s) present in the extracts of T.violacea, it confirmed that extracts of this plant induce apoptosis in cultured human cancer cell lines.

Natural products have been a source of many pharmaceutical drugs and a number of drugs that are currently used in the treatment of cancer are derivatives of compounds originally isolated from natural products. There is evidence that extracts of Tulbaghia violacea can be used to treat cancer. The activation of apoptosis in cancer cells is a target for the development of novel anti-cancer drugs since one of the characteristics of cancer cells is resistance to apoptosis due to the deregulation of biochemical pathways leading to apoptosis. In fact, many current anti-cancer drugs exert their effects through the activation of apoptosis. Previous studies showed that extracts of T.violacea induce apoptosis in cancer cells and one study reported on the isolation of a compound (methyl-ԃ-D-glucopyranoside), which is responsible for the pro-apoptotic activity of the T.violacea extract. Therefore the aim of this study was to investigate the anti-cancer activity of methyl-ԃ-Dglucopyranoside and extracts prepared from T.violacea. In this study the pro-apoptotic activity of methyl-ԃ-D-glucopyranoside and extracts prepared from T.violacea were investigated on a panel of human cancer cell lines, which included HepG2, MCF7, H157, HT29 and the non-cancerous cell line, KMST6. The induction of apoptosis was evaluated by flow cytometry using several bioassays which measures biochemical events (caspase activation, phosphatidylserine externalisation and reactive oxygen species (ROS) production that is associated with the induction of apoptosis. The results demonstrated that the effects of methyl--D-glucopyranoside on cultured cells are transient and that the cells recover from the effects of methyl--D-glucopyranoside. This suggested thatmethyl-ԃ-D-glucopyranoside is not the compound responsible for the pro-apoptotic bioactivity in the T.violacea extract. This study also showed that cytotoxic and pro-apoptotic bioactivity of the leaf-extract was significantly higher in comparison to the tuber-extract. The bioactivity of the organic solvent extracts (dichloromethane, hexane, methanol and 50% methanol/water) of T.violacea leaves was also significantly higher than water extracts of T.violacea leaves. A comparison of the different organic extracts prepared from the T.violacea leaves showed that the highest activity was observed for the dichloromethane and hexane extracts. In an effort to identify the bioactive compound(s) the dichloromethane extract was subjected to Versaflash® column chromatography. However, due to problems experienced with the solubility of the dichloromethane sub-fractions, these compounds could not be tested for their bioactivity. Palmitone (16-hentriacontanone) was identified as one of the major compounds present in the dichloromethane sub-fractions. This compound was previously shown to have anticonvulsant bioactivity but there is no evidence in the literature that it has anti-cancer or pro-apoptotic activities. Fingerprinting of the methanol extract showed the presence of long chain fatty acid derivatives, flavonoids and allicin derivatives in the methanol extract. Although, this study failed to isolate the pro-apoptotic bioactive compound(s) present in the extracts of T.violacea, it confirmed that extracts of this plant induce apoptosis in cultured human cancer cell lines.

Persistent organic pollutants (POPs) are a threat to the environment and human health because they are ubiquitous, resistant to degradation, can bio-accumulate in organisms and bio-magnify in food chains. They have a detrimental effect on the reproductive, nervous and immunity systems of vertebrates. An international treaty, the Stockholm Convention on POPs, came into force in 2004 and aims to limit and eventually prohibit any use and unintentional production of POPs. South Africa ratified the Convention in 2002. Those compounds currently listed by the Stockholm Convention as POPs include chlorinated pesticides such as dichlorodiphenyltrichlorethane (DDT), chlordane and dieldrin, and industry-related compounds such as polychlorinated biphenyls (PCBs) and hexachlorobenzene. Polychlorinated dibenzo-p-dioxins (PCDDs) and polychlorinated dibenzofurans (PCDFs) are also regarded as POPs but - together with some PCBs - they are the unintentional result of anthropogenic activity. This study focussed on the PCDDs, PCDFs and dioxin-like PCBs in the aquatic environment of South Africa particularly because the water resources in this country are under pressure. Despite the fact that South Africa has the sources of these compounds, little is known about the levels of these three groups of compounds. The concentration of twelve dioxin-like PCBs, seven PCDDs and ten PCDFs were determined for 22 sites selected on the grounds of their proximity to possible pollution sources. Analytical determinations included gas chromatography/mass spectrometry and a cell-based bio-assay, the H4IIE-/17C reporter gene assay. Possible sources of the observed pollution were inferred using the following statistical investigative methods: principal component and hierarchical cluster analysis. Seven of the sites had levels higher than the threshold effect concentration of Canada's sediment quality guidelines of 0.85 ngTEQ kg'1 (Toxic Equivalency Quotient). The other sites had lower levels. The highest concentration, 17.8 ng TEQ kg"1, was measured at a site in the southern Gauteng Province. Most of the PCDD/F pollution seemed to have come from combustion sources related to human activity, rather than industrial combustion. Most of the dioxin-like PCB pollution seemed to have been from commercial PCB preparations. Future research would require better characterisation of the sources in order to reduce the formation of these compounds, but also to better understand the exposure and risk scenarios, if humans are to be in close contact with these sources. / Thesis (Ph.D. (Zoology))--North-West University, Potchefstroom Campus, 2008.

POPs are a group of chemicals that have been extensively studied over the last few years. The main reason that these chemicals have received so much scientific attention is the myriad of negative effects they have on the environment and human health. The properties that cause the deleterious effects include a high molecular stability, rendering them highly persistent. Added to this is the lipophilic and hydrophobic nature of the compounds. POPs will thus tend to bio-accumulate and bio-magnify in the environment, causing a direct threat to humans and wildlife. To address this threat, the Stockholm Convention on Persistent Organic Pollutants, under the supervision of United Nations Environment programme (UNEP), was initiated and became legally binding on 17 May 2004. All countries, including South Africa, which ratified this agreement, will be expected to monitor and regulate the formation of POPs. Polychlorinated dibenzo-p-dioxins (PCDDs), polychlorinated dibenzofurans (PCDFs) and polychlorinated biphenyls (PCBs) are all members of the dioxin-like family of POPs. This family of chemicals pose serious health threats such as carcinogenic effects and negative effects on reproduction. These substances, with the exception of PCBs, are formed unintentionally as by-products of industrial and thermal processes. One of the main sources of dioxin-like chemicals is medical waste incinerators. In this project the area surrounding a medical waste incinerator was monitored using a bio-assay technique. The determination of dioxin concentrations is usually preformed by chemical analysis, however, bio-assays have proven themselves to be a cheaper and time-saving screening method. The Toxic Equivalency Quotient (TEQs) determined through bio-assays can support chemical analysis in determining biologically-relevant risk assessments since bio-assay data has ecotoxicological relevance. These assays represent an integrated biological response to chemical pollutants, where biological effects are accounted for which is not possible in chemical analyses. One of the bio-assays used in the determination of the dioxin-like chemical TEQ is the H411 E reporter gene bio-assay. This assay is based on the Ah-receptor mediated toxicity of dioxin-like chemicals. Using this technique the TEQs for areas surrounding an active incinerator were determined, to indicate the distribution of these substances. The TEQs for the soil samples collected ranged between nondetectable and 154 ngTEQ/kg. There was no clear distributional pattern and the total organic carbon content in the soil did not seem to play a crucial role in the distribution of dioxin-like chemicals. Although a decrease in soil tillage showed a corresponding increase in TEQ. The predominant wind direction was taken into account but no correlation could be seen. However, meteorological parameters such as the ambient temperature and low precipitation in the area may have contributed to lower TEQ values. Cytotoxicity excluded data points and the phenomenon has to be addressed. High TEQ values in a residential area where free-range chickens are raised pose a serious concern to the level of dietary dioxin-like chemical intake. Eggs in the area could theoretically contain between 2.75 and 28.75 pgTEQ/g egg fat. Further studies are needed to determine how much dioxin-like chemicals are being transferred to humans through the consumption of free-range eggs / Thesis (M. Environmental Science)--North-West University, Potchefstroom Campus, 2006.

Water resources in South Africa are scarce, and should therefore be protected against pollutants, also from persistent organic pollutants (POPs). POPs are a global concern due to their ubiquitous presence, persistence and toxicity. This is emphasised by the Stockholm Convention on POPs, which aims at reducing and ultimately eliminating them. South Africa signed and ratified the treaty, and it became international law on 17 May 2004, but there is still a lack of information regarding POPs in South Africa. This study focussed on establishing the levels of POPs and other organic pollutants, which included various organochlorine pesticides (OCPs), polycyclic aromatic hydrocarbons (PAHs), dioxin-like compounds (DLCs), non-dioxin-like polychlorinated biphenyls (PCBs) and polybrominated diphenyl ether (PBDE). Sampling regions included the industrial cities – Cape Town, Richards Bay, Durban and Bloemfontein, and low-income, high density residential areas surrounding a wetland in Soweto/Lenasia and Botshabelo. Additionally, rivers flowing into neighbouring countries, rivers in the vicinity of paper and pulp producers and high altitude rivers were included. Sediment samples were firstly screened for the presence of DLCs by the H4IIE-luc bio-assay, whereafter sites eliciting quantifiable responses were selected for further chemical analysis by high resolution gas chromatography-high resolution mass spectrometry (HRGC/HRMS). Of the 96 sites, only 23 had quantifiable levels of DLCs. These sites were mainly of industrial, semi-industrial or low-income residential nature. PAHs were the predominant class of compounds at most of the sites, while OCPs and PCBs were present in moderate concentrations and PBDEs in minor concentrations. The concentration of pollutants measured in South African soils and sediments were intermediate when compared to the levels measured in some European, Asian and Scandinavian countries, with the exception of a few sites where exceptionally high levels of compounds were measured. The carbon content normalized concentrations of certain compounds at some of the sites exceeded the Canadian sediment quality guidelines. The estimated cancer risk associated with dermal absorption of OCPs measured in this study was negligible when compared to the background cancer risk expected for South Africans due to life style factors. However, it was estimated that dermal exposure to PCBs, DLCs and PAHs may lead to severe increases in cancer cases, and may seriously impact on human health. / Thesis (Ph.D. (Environmental Science))--North-West University, Potchefstroom Campus, 2011.