Browsing by Author "Reynolds, Chevonne"

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Synthesis of potentially biologically active aromatic and hetero-aromatic compounds
(2011-03-29) Reynolds, Chevonne
The first part of this dissertation deals with employing the use of multi-component coupling reactions (MCC) for the synthesis of large diverse compound libraries. A review of selected literature identified the growing need for more potent and selective HIV/AIDS drugs due to the extremely high mutation rate of the HI virus. We thus chose to test our synthesised compound library against the HIV enzyme, reverse transcriptase (RT) in the hopes of identifying a potential novel non-nucleoside reverse transcriptase inhibitor (NNRTI). Two different MCC approaches were used in order to give two different classes of compounds; firstly the Groebke-Blackburn reaction for the synthesis of imidazo[1,2-a]pyridines and secondly a reaction developed by Poigny and co-workers for the synthesis of 3-amino-1-cyano-indolizines. We were successful in utilizing the Groebke-Blackburn to synthesise a variety of imidazo[1,2-a]pyridines in varying yields. However, all of the compounds showed poor inhibition of the RT enzyme in the biological assay. We thus turned our attention to the synthesis of the 3-amino-1-cyano-indolizines, which proved to be very difficult. It was discovered that this reaction did not proceed to completion and the product generally isolated from this MCC reaction was the more stable aldol condensation intermediate. In some of the experiments we were able to isolate mostly small quantities of indolizine compound, but when tested against the RT enzyme the results once again were very poor. A short review in the second section of this dissertation showed the lack of methodology available for the synthesis of the dihydrobenzo[b]phenanthridine motif which constitutes the backbone of a secondary metabolite known as Jadomycin B. The major aim of this segment of the project was thus to develop methodology to synthesise this biologically important scaffold. However, our methodology failed to yield the desired product as it was not possible to reduce the nitrile intermediate to the required amine. In an attempt to determine whether similar methodology could be used for the synthesis of pyranonaphthoquinone containing compounds an unexpected and novel reaction was discovered. It was found that treatment of [2-(1,4-dimethoxynaphthalen-2-yl)phenyl]methanol with brominating agent NBS results in the synthesis of a naphthopyranone ring system known as 12-methoxy-6H-dibenzo[c,h]chromen-6-one. Following this discovery it was attempted to elucidate the mechanism by which NBS performs this novel reaction. Unfortunately we were unable to determine the exact mechanism responsible for this transformation conclusively. The most likely mechanism shows NBS oxidising the benzylic alcohol to an aldehyde, which is then converted to an acid bromide facilitating ring closure. Finally we wished to determine if this strategy could be applied in the synthesis of related naphthopyranone ring systems, which was shown to be possible with the synthesis of 3-bromo-2-methoxy-6H-benzo[c]chromen-6-one.
The application of machine learning methods to satellite data for the management of invasive water hyacinth
(University of the Witwatersrand, Johannesburg, 2023-06) Singh, Geethe; Reynolds, Chevonne; Byrne, Marcus; Rosman, Benjamin
Biological invasions are responsible for some of the most devastating impacts on the world’s ecosystems, with freshwater ecosystems among the worst affected. Invasions threaten not only freshwater biodiversity, but also the provision of ecosystem services. Tackling the impact of invasive aquatic alien plant (IAAP) species in freshwater systems is an ongoing challenge. In the case of water hyacinth (Pontederia crassipes, previously Eichhorniae crassipes), the worst IAAP presents a long-standing management challenge that requires detailed and frequently updated information on its distribution, the context that influences its occurrence, and a systematic way to identify effective biocontrol release events. This is particularly urgent in South Africa, where freshwater resources are scarce and under increasing pressure. This research employs recent advances in machine learning (ML), remote sensing, and cloud computing to improve the chances of successful water hyacinth management. This is achieved by (i) mapping the occurrence of water hyacinth across a large extent, (ii) identifying the factors that are likely driving the occurrence of the weed at multiple scales, from a waterbody level to a national extent, and (iii) finally identifying periods for effective biocontrol release. Consequently, the capacity of these tools demonstrates their potential to facilitate wide-scale, consistent, automated, pre-emptive, data-driven, and evidence-based decision making for managing water hyacinth. The first chapter is a general introduction to the research problem and research questions. In the second chapter, the research combines a novel image thresholding method for water detection with an unsupervised method for aquatic vegetation detection and a supervised random forest model in a hierarchical way to localise and discriminate water hyacinth from other IAAP’s at a national extent. The value of this work is marked by the comparison of the user (87%) and producer accuracy (93%) of the introduced method with previous small-scale studies. As part of this chapter, the results also show the sensor-agnostic and temporally consistent capability of the introduced hierarchical approach to monitor water and aquatic vegetation using Sentinel-2 and Landsat-8 for long periods (from 2013 - present). Lastly, this work demonstrates encouraging results when using a Deep Neural Network (DNN) to directly detect aquatic vegetation and circumvents the need for accurate water extent data. The two chapters that follow (Chapter 3 and 4 described below) introduce an application each that build off the South African water hyacinth distribution and aquatic vegetation time series (derived in Chapter 2). The third chapter uses a species distribution model (SDM) that links climatic, socio-economic, ecological, and hydrological conditions to the presence/absence of water hyacinth throughout South Africa at a waterbody level. Thereafter, explainable AI (xAI) methods (specifically SHapley Additive exPlanations or SHAP) are applied to better understand the factors that are likely driving the occurrence of water hyacinth. The analyses of 82 variables (of 140 considered) show that the most common group of drivers primarily associated with the occurrence of water hyacinth in South Africa are climatically related (41.4%). This is followed by natural land cover categories (32.9%) and socio-economic variables (10.7%), which include artificial land-cover. The two least influential groups are hydrological variables (10.4%) including water seasonality, runoff, and flood risk, and ecological variables (4.7%) including riparian soil conditions and interspecies competition. These results suggest the importance of considering landscape context when prioritising the type (mechanical, biological, chemical, or integrated) of weed management to use. To enable the prioritisation of suitable biocontrol release dates, the fourth chapter forecasts 70-day open water proportion post-release as a reward for effective biocontrol. This enabled the simulation of the effect of synthetic biocontrol release events under a multiarmed bandit framework for the identification of two effective biocontrol release periods (late spring/early summer (mid-November) and late summer (late February to mid-March)). The latter release period was estimated to result in an 8-27% higher average open-water cover post-release compared to actual biocontrol release events during the study period (May 2018 - July 2020). Hartbeespoort Dam, South Africa, is considered as a case study for improving the pre-existing management strategy used during the biocontrol of water hyacinth. The novel frameworks introduced in this work go a long way in advancing IAAP species management in the age of both ongoing drives towards the adoption of artificial intelligence and sustainability for a better future. It goes beyond (i) traditional small-scale and infrequent mapping, (ii) standard SDMs, to now include the benefits of spatially explicit model explainability, and (iii) introduces a semi-automated and widely applicable method to explore potential biocontrol release events. The direct benefit of this work, or indirect benefits from derivative work outweighs both the low production costs or equivalent field and lab work. To improve the adoption of modern ML and Earth Observation (EO) tools for invasive species management, some of the developed tools are publicly accessible. In addition, a human-AI symbiosis that combines strengths and compensates for weaknesses is strongly recommended. For each application, directions are provided for future research based on the drawbacks and limitations of the introduced systems. These future efforts will likely increase the adoption of EO-derived products by water managers and improve the reliability of these products.
Woody plant encroachment drives population declines in 20 of common open ecosystem bird species
(Wiley) White, Joseph; Stevens, Nicola; Fisher, Jolene; Reynolds, Chevonne