BODIPY dyes for application in the photo-oxidation of pollutants, photodynamic antimicrobial chemotherapy, and nonlinear optics
- Authors: Kelechi, Lebechi Augustus
- Date: 2020
- Subjects: Dyes and dyeing -- Chemistry , Fluorescent probes , Fluorescence spectroscopy
- Language: English
- Type: text , Thesis , Masters , MSc
- Identifier: http://hdl.handle.net/10962/140298 , vital:37859
- Description: The synthesis and structural characterization of a series of BODIPY dyes to analyze both the effects of halogenations at the 2,6-positions and the introduction of styryl groups at the 3,5-positions. The photophysical properties of these dyes were investigated to determine their suitability as singlet oxygen-generating photosensitiser dyes for application in photocatalytic degradation of azo dyes and in photodynamic antimicrobial chemotherapy (PACT). Upon halogenation, the dyes showed high to moderate singlet oxygen quantum yields. The potential utility of electrospun polystyrene (PS) nanofibres embedded with halogenated BODIPY dyes for the photocatalytic degradation of Orange G and Methyl Orange from textile industry effluents were investigated. A comparison of the singlet oxygen quantum yield of the BODIPY dyes in solution and when embedded in the PS nanofibres support demonstrates that its photosensitiser properties are maintained in the nanofibre mats. The photocatalytic degradation properties of the PS nanofibres for Orange G and Methyl Orange were determined by using a 530 nm and 660 nm light-emitting diodes. The rate of photodegradation increases with both the Orange G and Methyl Orange concentrations and follows pseudo-first-order kinetics. The PACT activities of brominated BODIPYs on Escherichia coli and Staphylococcus aureus were investigated. Log reduction values of over 9 were obtained during the photoinactivation of Staphylococcus aureus. To be able to red-shift the main spectral band of the BODIPY dyes into the therapeutic window, styryl groups were introduced at the 3,5-positions through a modified Knoevenagel condensation reaction. Because the red-shifted spectral band lies above 532 nm, the second harmonic of the Nd:YAG laser, there is very minute absorption at this wavelength. One of the novel brominated BODIPY dyes was investigated for its potential utility as optical limiting materials in nonlinear optics (NLO), and the dyes demonstrated typical nonlinear absorption behaviour characterised by reverse saturable absorption (RSA) in Z-scan measurements. Excellent optical limiting parameters were obtained for third-order susceptibility and hyperpolarisability.
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- Date Issued: 2020
Developing social indicators for the evaluation of natural resource management programmes using a capability approach in the Eastern Cape, South Africa
- Authors: Human, Johanna Susanna
- Date: 2020
- Subjects: Environmental education -- South Africa -- Eastern Cape , Natural resources -- Management -- Study and teaching (Continuing education) -- South Africa -- Eastern Cape , Sustainable development -- Study and teaching (Continuing education) -- South Africa -- Eastern Cape , Environmental economics -- Study and teaching (Continuing education) -- South Africa -- Eastern Cape , Subsistence farming -- South Africa -- Eastern Cape , Watersheds -- South Africa -- Eastern Cape , Capabilities approach (Social sciences) , Tsitsa River Catchment (Eastern Cape, South Africa)
- Language: English
- Type: Thesis , Masters , MEd
- Identifier: http://hdl.handle.net/10962/147348 , vital:38628
- Description: The dissertation investigates how the capability approach can be used to develop social indicators for a natural resource management (NRM) programme. The study aimed to develop an understanding of what the beneficiaries of the programme value being and doing to guide the development of social indicators that will take into consideration their personal development aspirations. These valued beings and doings were then overlaid with the programme goals and objectives to identify and select the final indicators. The study was situated in the Tsitsa catchment in the Eastern Cape, South Africa and was part of a natural resource management programme, focused on land restoration and avoided degradation. Methods used to collect data for this study and develop an understanding of what the residents’ valued beings and doings were, included semi-structured interviews, workshops and document analysis. The research population was non-homogenous. I tried to include voices representing different prominent groups of land users in the study. This included established commercial farmers, emerging commercial farmers, commercial forestry, residents residing in communal areas and engaged with subsistence farming and residents from these communal areas who are now residing elsewhere but continue to have connections to the catchment. Understanding the voices of these different groups who reside in the catchment was important to develop an inclusive understanding of what residents of the catchment valued beings and doings were. The research process was supported by participatory approaches. This process, and the lessons learnt during the research process, were valuable for the further development and implementation of the planned participatory monitoring evaluation reflection and learning (PMERL) framework. The research process involved learning from the research participants about their valued beings and doings and what was important for the programme implementers. Some of the research participants from the Rhodes University implementation team (RUIT) were also involved in selecting the indicators they thought the programme should monitor. Overall, using the capability approach helped me to gain insight and understanding with regard to what the valued beings and doings are for the residents of the catchment and what they would like development programmes, such as the Tsitsa Project, to address. It was surprising to find many areas of overlap between the valued beings and doings of the different residents in the catchment, as well as the similarities between these and the goals and objectives of the Tsitsa Project. In conclusion, using the capability approach was useful to learn what was important for the residents of the catchment to help develop the social indicators but also to learn how to guide and steer participatory monitoring and evaluation processes in the future.
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- Date Issued: 2020
Technology in conservation: towards a system for in-field drone detection of invasive vegetation
- Authors: James, Katherine Margaret Frances
- Date: 2020
- Subjects: Drone aircraft in remote sensing , Neural networks (Computer science) , Drone aircraft in remote sensing -- Case studies , Machine learning , Computer vision , Environmental monitoring -- Remote sensing , Invasive plants -- Monitoring
- Language: English
- Type: text , Thesis , Masters , MSc
- Identifier: http://hdl.handle.net/10962/143408 , vital:38244
- Description: Remote sensing can assist in monitoring the spread of invasive vegetation. The adoption of camera-carrying unmanned aerial vehicles, commonly referred to as drones, as remote sensing tools has yielded images of higher spatial resolution than traditional techniques. Drones also have the potential to interact with the environment through the delivery of bio-control or herbicide, as seen with their adoption in precision agriculture. Unlike in agricultural applications, however, invasive plants do not have a predictable position relative to each other within the environment. To facilitate the adoption of drones as an environmental monitoring and management tool, drones need to be able to intelligently distinguish between invasive and non-invasive vegetation on the fly. In this thesis, we present the augmentation of a commercially available drone with a deep machine learning model to investigate the viability of differentiating between an invasive shrub and other vegetation. As a case study, this was applied to the shrub genus Hakea, originating in Australia and invasive in several countries including South Africa. However, for this research, the methodology is important, rather than the chosen target plant. A dataset was collected using the available drone and manually annotated to facilitate the supervised training of the model. Two approaches were explored, namely, classification and semantic segmentation. For each of these, several models were trained and evaluated to find the optimal one. The chosen model was then interfaced with the drone via an Android application on a mobile device and its performance was preliminarily evaluated in the field. Based on these findings, refinements were made and thereafter a thorough field evaluation was performed to determine the best conditions for model operation. Results from the classification task show that deep learning models are capable of distinguishing between target and other shrubs in ideal candidate windows. However, classification in this manner is restricted by the proposal of such candidate windows. End-to-end image segmentation using deep learning overcomes this problem, classifying the image in a pixel-wise manner. Furthermore, the use of appropriate loss functions was found to improve model performance. Field tests show that illumination and shadow pose challenges to the model, but that good recall can be achieved when the conditions are ideal. False positive detection remains an issue that could be improved. This approach shows the potential for drones as an environmental monitoring and management tool when coupled with deep machine learning techniques and outlines potential problems that may be encountered.
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- Date Issued: 2020
Thermoluminescence and phototransferred phermoluminescence of synthetic quartz
- Authors: Dawam, Robert Rangmou
- Date: 2020
- Subjects: Thermoluminescence , Quartz
- Language: English
- Type: text , Thesis , Doctoral , PhD
- Identifier: http://hdl.handle.net/10962/145849 , vital:38472
- Description: The main aim of this investigation is on thermoluminescence and phototransferred thermoluminescence of synthetic quartz. Thermoluminescence was one of the tools used in characterising the electron traps parameters. The samples of quartz annealed at various temperatures up to 900̊C and the unannealed were used. The thermoluminescence glow curve was measured at 1̊C s~ 1 following beta irradiation to 40 Gy from the samples annealed at 500̊C and the unannealed consist of main peak at 70̊C and secondary peaks at 110, 180 and 310̊C. In comparison, the thermoluminescence glow curve for the sample annealed at 900̊C have main peak at 86̊C and the secondary ones at 170 and 310̊C. The kinetic analysis was carried out only on the main peak in each case. The activation energy was found to be decreasing with increase in annealing temperatures. The samples annealed at 500̊C and the unannealed were found to be affected by thermal quenching while sample annealed at 900̊C shows an inverse quenching for irradiation dose of 40 Gy. However, when the dose was reduce to 3 Gy the effects of thermal quenching was manifested. The activation energy of thermal quenching was also found to decrease with increase in annealing temperature. Thermally assisted optically stimulated luminescence measurement was carried out using continuous wave optical stimulated luminescence (CW-OSL). The samples studied were those annealed at 500̊C for 10 minutes, 900̊C for 10, 30, 60 minutes and 1000̊C for 10 minutes prior to use. The CW-OSL is stimulated using 470 nm blue LEDs at sample temperatures between 30 and 200̊C. It is measured after preheating to either 300 and 500̊C. When the integrated OSL intensity is plotted as a function of measurement temperature, the intensity goes through a peak. The increase in OSL intensity as a function of temperature is associated to thermal assistance and the decrease to thermal quenching. The kinetic parameters were evaluated by fitting the experimental data. The values of activation energies of thermal quenching are the same within experimental uncertainties for all the experimental conditions. This shows that annealing temperature, duration of annealing and irradiation dose have a negligible influence on the recombination site of luminescence using OSL. Phototransferred thermoluminescence (PTTL) induced from annealed samples using 470 nm blue light was also investigated. The quartz were annealed at 500 _C for 10 minutes, 900̊C for 10, 30, 60 minutes and 1000̊C for 10 minutes prior to use. The glow curves of conventional TL measured at 1 _C s1 following irradiation to 200 Gy shows six peaks in each case labelled I-VI for ease of reference whereas peaks observed under PTTL are referred to as A1 onwards. Only the first three peaks were reproduced under phototransfer for the sample annealed at 900̊C for 60 minutes and 1000̊C C for 10 minutes. Interestingly, for the intermediate duration of annealing of 30 minutes, the only peak that appears under phototransfer is the A1. For quartz annealed at 900̊C for 10 minutes, the PTTL appears as long as the preheating temperature does not exceed 560̊C. All other annealing temperatures, PTTL only appears for preheating to 450 and below. This shows that the occupancy of deep electron traps at temperatures beyond 450̊C or 560̊C is low. The activation energy for peaks A1, A2 and A3 were calculated. The PTTL peaks were studied for thermal quenching and peaks A1 and A3 were found to be affected. The activation energies for thermal quenching were determined as 0.62 ± 0.04 eV and 0.65 ± 0.02 eV for peaks A1 and A3 respectively. The experimental dependence of PTTL intensity on illumination time is modelled using sets of coupled linear differential equations based on systems of donors and acceptors whose number is determined by preheating temperature.
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- Date Issued: 2020
Understanding of the underlying resistance mechanism of the Kat-G protein against isoniazid in Mycobacterium tuberculosis using bioinformatics approaches
- Authors: Barozi, Victor
- Date: 2020
- Subjects: Mycobacterium tuberculosis , Isoniazid , Drug resistance in microorganisms , Proteins -- Microbiology
- Language: English
- Type: text , Thesis , Masters , MSc
- Identifier: http://hdl.handle.net/10962/146592 , vital:38540
- Description: Tuberculosis (TB) is a multi-organ infection caused by rod-shaped acid-fast Mycobacterium tuberculosis. The World Health Organization (WHO) ranks TB among the top 10 fatal infections and the leading the cause of death from a single infection. In 2017, TB was responsible for an estimated 1.3 million deaths among both the HIV negative and positive populations worldwide (WHO, 2018). Approximately 23% (roughly 1.7 billion) of the world’s population is estimated to have latent TB with a high risk of reverting to active TB infection. In 2017, an estimated 558,000 people developed drug resistant TB worldwide with 82% of the cases being multi-drug resistant TB (WHO, 2018). South Africa is ranked among the 30 high TB burdened countries with a TB incidence of 322,000 cases in 2017 accounting for 3% of the world’s TB cases. TB is curable and is clinically managed through a combination of intensive and continuation phases of first-line drugs (isoniazid, rifampicin, ethambutol, and pyrazinamide). Second-line drugs which include fluoroquinolones, injectable aminoglycoside and injectable polypeptides are used in cases of first line drug resistance. The third-line drugs include amoxicillin, clofazimine, linezolid and imipenem. These have variable but unproven efficacy to TB and are the last resort in cases of total drug resistance (Jilani et al., 2019). TB drug resistance to first-line drugs especially isoniazid in M. tuberculosis has been attributed to single nucleotide polymorphisms (SNPs) in the catalase peroxidase enzyme (katG), a protein important in the activation of the pro-drug isoniazid. The SNPs especially at position 315 of the katG enzyme are believed to reduce the sensitivity of the M. tuberculosis to isoniazid while still maintaining the enzyme’s catalytic activity - a mechanism not completely understood. KatG protein is important for protecting the bacteria from hydro peroxides and hydroxyl radicals present in an aerobic environment. This study focused on understanding the mechanism of isoniazid drug resistance in M. tuberculosis as a result of high confidence mutations in the katG through modelling the enzyme with its respective variants, performing MD simulations to explore the protein behaviour, calculating the dynamic residue network analysis (DRN) of the variants in respect to the wild type katG and finally performing alanine scanning. From the MD simulations, it was observed that the high confidence mutations i.e. S140R, S140N, G279D, G285D, S315T, S315I, S315R, S315N, G316D, S457I and G593D were not only reducing the backbone flexibility of the protein but also reducing the protein’s conformational variation and space. All the variant protein structures were observed to be more compact compared to the wild type. Residue fluctuation results indicated reduced residue flexibility across all variants in the loop region (position 26-110) responsible for katG dimerization. In addition, mutation S315T is believed to reduce the size of the active site access channel in the protein. From the DRN data, residues in the interface region between the N and C-terminal domains were observed to gain importance in the variants irrespective of the mutation location indicating an allosteric effect of the mutations on the interface region. Alanine scanning results established that residue Leucine at position 48 was not only important in the protein communication but also a destabilizing residue across all the variants. The study not only demonstrated change in the protein behaviour but also showed allosteric effect of the mutations in the katG protein.
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- Date Issued: 2020