A mechanistic and trait-based approach to investigating macroinvertebrates distribution and exposure to microplastics in riverine systems
- Authors: Owowenu, Enahoro Kennedy
- Date: 2024-10-11
- Subjects: Microplastics Environmental aspects , Water quality biological assessment , Hydrodynamics , Hydrogeomorphology , Biotope , Flow type
- Language: English
- Type: Academic theses , Doctoral theses , text
- Identifier: http://hdl.handle.net/10962/466666 , vital:76765 , DOI https://doi.org/10.21504/10962/466666
- Description: Microplastics in rivers pose an ecological risk. Hydraulic biotopes form distinct flow patches that vary longitudinally along the river, potentially influencing the transport dynamics of microplastics. Macroinvertebrates exhibit adaptations to different hydraulic biotopes through their unique traits. These traits can mediate their exposure to microplastics, thereby imposing selective pressures on these organisms. Different taxa often demonstrate preferences for specific hydraulic biotopes characterized by distinct flow regimes. Understanding the transport dynamics of microplastics mediated by hydraulic biotopes and the potential exposure of macroinvertebrates at the hydraulic biotope scale is important for determining the fate of riverine microplastics and detecting species at risk. Both empirical and theoretical studies have highlighted the interconnectedness of hydrology, geomorphology, and microplastic transport in rivers, yet, there remains a gap in understanding how a hydro-geomorphological approach could enhance the understanding of the microplastic transport process. Little is known about the role of traits in driving macroinvertebrate exposure to microplastics at a scale relevant to ecological dynamics. This study addressed these gaps by applying a hydro-geomorphological approach to investigate the distribution of microplastics at the hydraulic biotope scale and assessed the potential exposure of macroinvertebrates using a trait-based approach. This study also explored the relationship between microplastic abundance and selected water physicochemical properties, as well as the influence of adjacent land use types. By integrating these aspects the research provided a comprehensive understanding of microplastics dynamics in river systems, shedding light on both environmental factors shaping their distribution and the potential impacts on aquatic organisms. The study was conducted over the wet and dry seasons (October 2021 – July 2022) at 10 sites located in the upper, middle, and lower reaches of the Swartkops and Buffalo River systems in the Eastern Cape Province of South Africa. The hydraulic biotopes (i.e., pools, runs, riffles) were grouped into two conceptualised forms, namely, sink and flush hydraulic zones and were characterized by hydraulic indices such as the Froude number and the Reynolds number. The flush hydraulic zone represents hydraulic biotopes where microplastics can potentially be remobilized quickly into suspension, and the sink represents biotopes where microplastics can potentially accumulate and remobilisation is far slower. Fast-to-moderate flowing hydraulic biotopes were conceptualised as microplastics flush zones while slow-flowing to still biotopes as microplastic sink zones. Samples were collected at different depths in each hydraulic zone to quantify suspended and settled forms of microplastics. Microplastics targeted in this study ranged in size from 0.063 mm to less than 5 mm. Classification was achieved through microscopic observation, and confirmation via Fourier Transform Infrared Spectroscopy (FTIR-ATR) was conducted for samples ranging from 0.5 mm to less than 5 mm. At the site level, settled microplastics showed statistically significant spatial and temporal variations between the sites, and between the seasons (P < 0.05). The suspended microplastic varied only spatially. Fibres and fragments were the dominant microplastic shape, while polyethylene and polypropylene were the dominant microplastic polymers. Suspended microplastics showed statistically significant variation between urban land cover and other land cover categories (industrial, agricultural, rural, and natural land cover). Microplastics abundance was associated with high levels of turbidity, total suspended solids, total inorganic nitrogen, higher temperatures and increasing electrical conductivity. At the hydraulic biotope scale, the mean occurrence of suspended microplastics (1.76 ± 1.44 items/L; mean + SD) in the flush hydraulic zone was higher than that in the sink zone (1.54 ± 1.46 items/L), while settled microplastics were more abundant in the sink hydraulic zone (1.82 ± 1.98 items/L) than the flush hydraulic zone (1.32 ± 1.49 items/L). This observation was in line with the prediction in this study. The mean suspended and settled microplastics concentrations were higher during the wet season across the flush and sink hydraulic zones than in the dry season. Global multivariate analysis of variance (MANOVA) and two-way analysis of variance (ANOVA) revealed significant spatial and temporal variations in settled microplastics abundances between the flush and sink hydraulic zones. The results indicated that geomorphologically defined units such as riffles and moderate to fast runs (flush) generally contained lower amounts of settled microplastics compared to pools and backwaters (sink). However, this distinction between the flush and sink microplastic zones was observed only for settled microplastics and not for suspended microplastics. Suspended and settled microplastics showed a statistically significant relationship with the Froude number index. The generalised additive model indicated that settled microplastics abundance distribution decreased significantly with increasing Froude number value in the flush zone. Suspended microplastics decreased at low Froude number values and showed an increasing trend at higher Froude number values of about 0.75. The results indicate the usefulness of the hydraulic biotope scale microplastic monitoring approach in detecting microplastic hotspots and explaining variations in microplastics abundances driven by instream hydraulics. Four traits and ecological preferences of macroinvertebrates including body size, gill type, feeding habit, and velocity preferences were selected and resolved into 17 trait attributes. The sink hydraulic zones such as pools were indicated to favour exposure to and ingestion of microplastics compared to the flush zones such as riffles and fast runs. Large body size macroinvertebrates were associated with the sink zone. Taxa with a very small body size had a higher likelihood for microplastics ingestion than taxa with other body sizes. Collectorgathering macroinvertebrates taxa that have operculate gills with small body sizes were more prone to exposure to microplastics in hydraulic biotopes with slow to very slow velocities. Fibres were the most abundant plastic ingested by macroinvertebrates preferring the flush zone while fibres and fragments were mostly ingested by those preferring the sink zones. The binomial logistic model revealed a highly significant result for the likelihood of operculate gill shape to clog in the sink hydraulic zone. The result of the binomial logistic regression indicates the usefulness of the trait-based approach for predicting exposure to microplastics. Overall, the study reveals the influences of hydro-geomorphological features on the transport dynamics of microplastics and the usefulness of the trait-based approach in the ecological study of microplastics in riverine systems. , Thesis (PhD) -- Faculty of Science, Institute for Water Research, 2024
- Full Text:
- Authors: Owowenu, Enahoro Kennedy
- Date: 2024-10-11
- Subjects: Microplastics Environmental aspects , Water quality biological assessment , Hydrodynamics , Hydrogeomorphology , Biotope , Flow type
- Language: English
- Type: Academic theses , Doctoral theses , text
- Identifier: http://hdl.handle.net/10962/466666 , vital:76765 , DOI https://doi.org/10.21504/10962/466666
- Description: Microplastics in rivers pose an ecological risk. Hydraulic biotopes form distinct flow patches that vary longitudinally along the river, potentially influencing the transport dynamics of microplastics. Macroinvertebrates exhibit adaptations to different hydraulic biotopes through their unique traits. These traits can mediate their exposure to microplastics, thereby imposing selective pressures on these organisms. Different taxa often demonstrate preferences for specific hydraulic biotopes characterized by distinct flow regimes. Understanding the transport dynamics of microplastics mediated by hydraulic biotopes and the potential exposure of macroinvertebrates at the hydraulic biotope scale is important for determining the fate of riverine microplastics and detecting species at risk. Both empirical and theoretical studies have highlighted the interconnectedness of hydrology, geomorphology, and microplastic transport in rivers, yet, there remains a gap in understanding how a hydro-geomorphological approach could enhance the understanding of the microplastic transport process. Little is known about the role of traits in driving macroinvertebrate exposure to microplastics at a scale relevant to ecological dynamics. This study addressed these gaps by applying a hydro-geomorphological approach to investigate the distribution of microplastics at the hydraulic biotope scale and assessed the potential exposure of macroinvertebrates using a trait-based approach. This study also explored the relationship between microplastic abundance and selected water physicochemical properties, as well as the influence of adjacent land use types. By integrating these aspects the research provided a comprehensive understanding of microplastics dynamics in river systems, shedding light on both environmental factors shaping their distribution and the potential impacts on aquatic organisms. The study was conducted over the wet and dry seasons (October 2021 – July 2022) at 10 sites located in the upper, middle, and lower reaches of the Swartkops and Buffalo River systems in the Eastern Cape Province of South Africa. The hydraulic biotopes (i.e., pools, runs, riffles) were grouped into two conceptualised forms, namely, sink and flush hydraulic zones and were characterized by hydraulic indices such as the Froude number and the Reynolds number. The flush hydraulic zone represents hydraulic biotopes where microplastics can potentially be remobilized quickly into suspension, and the sink represents biotopes where microplastics can potentially accumulate and remobilisation is far slower. Fast-to-moderate flowing hydraulic biotopes were conceptualised as microplastics flush zones while slow-flowing to still biotopes as microplastic sink zones. Samples were collected at different depths in each hydraulic zone to quantify suspended and settled forms of microplastics. Microplastics targeted in this study ranged in size from 0.063 mm to less than 5 mm. Classification was achieved through microscopic observation, and confirmation via Fourier Transform Infrared Spectroscopy (FTIR-ATR) was conducted for samples ranging from 0.5 mm to less than 5 mm. At the site level, settled microplastics showed statistically significant spatial and temporal variations between the sites, and between the seasons (P < 0.05). The suspended microplastic varied only spatially. Fibres and fragments were the dominant microplastic shape, while polyethylene and polypropylene were the dominant microplastic polymers. Suspended microplastics showed statistically significant variation between urban land cover and other land cover categories (industrial, agricultural, rural, and natural land cover). Microplastics abundance was associated with high levels of turbidity, total suspended solids, total inorganic nitrogen, higher temperatures and increasing electrical conductivity. At the hydraulic biotope scale, the mean occurrence of suspended microplastics (1.76 ± 1.44 items/L; mean + SD) in the flush hydraulic zone was higher than that in the sink zone (1.54 ± 1.46 items/L), while settled microplastics were more abundant in the sink hydraulic zone (1.82 ± 1.98 items/L) than the flush hydraulic zone (1.32 ± 1.49 items/L). This observation was in line with the prediction in this study. The mean suspended and settled microplastics concentrations were higher during the wet season across the flush and sink hydraulic zones than in the dry season. Global multivariate analysis of variance (MANOVA) and two-way analysis of variance (ANOVA) revealed significant spatial and temporal variations in settled microplastics abundances between the flush and sink hydraulic zones. The results indicated that geomorphologically defined units such as riffles and moderate to fast runs (flush) generally contained lower amounts of settled microplastics compared to pools and backwaters (sink). However, this distinction between the flush and sink microplastic zones was observed only for settled microplastics and not for suspended microplastics. Suspended and settled microplastics showed a statistically significant relationship with the Froude number index. The generalised additive model indicated that settled microplastics abundance distribution decreased significantly with increasing Froude number value in the flush zone. Suspended microplastics decreased at low Froude number values and showed an increasing trend at higher Froude number values of about 0.75. The results indicate the usefulness of the hydraulic biotope scale microplastic monitoring approach in detecting microplastic hotspots and explaining variations in microplastics abundances driven by instream hydraulics. Four traits and ecological preferences of macroinvertebrates including body size, gill type, feeding habit, and velocity preferences were selected and resolved into 17 trait attributes. The sink hydraulic zones such as pools were indicated to favour exposure to and ingestion of microplastics compared to the flush zones such as riffles and fast runs. Large body size macroinvertebrates were associated with the sink zone. Taxa with a very small body size had a higher likelihood for microplastics ingestion than taxa with other body sizes. Collectorgathering macroinvertebrates taxa that have operculate gills with small body sizes were more prone to exposure to microplastics in hydraulic biotopes with slow to very slow velocities. Fibres were the most abundant plastic ingested by macroinvertebrates preferring the flush zone while fibres and fragments were mostly ingested by those preferring the sink zones. The binomial logistic model revealed a highly significant result for the likelihood of operculate gill shape to clog in the sink hydraulic zone. The result of the binomial logistic regression indicates the usefulness of the trait-based approach for predicting exposure to microplastics. Overall, the study reveals the influences of hydro-geomorphological features on the transport dynamics of microplastics and the usefulness of the trait-based approach in the ecological study of microplastics in riverine systems. , Thesis (PhD) -- Faculty of Science, Institute for Water Research, 2024
- Full Text:
Selected medicinal plants leaves identification: a computer vision approach
- Authors: Deyi, Avuya
- Date: 2023-10-13
- Subjects: Deep learning (Machine learning) , Machine learning , Convolutional neural network , Computer vision in medicine , Medicinal plants
- Language: English
- Type: Academic theses , Master's theses , text
- Identifier: http://hdl.handle.net/10962/424552 , vital:72163
- Description: Identifying and classifying medicinal plants are valuable and essential skills during drug manufacturing because several active pharmaceutical ingredients (API) are sourced from medicinal plants. For many years, identifying and classifying medicinal plants have been exclusively done by experts in the domain, such as botanists, and herbarium curators. Recently, powerful computer vision technologies, using machine learning and deep convolutional neural networks, have been developed for classifying or identifying objects on images. A convolutional neural network is a deep learning architecture that outperforms previous advanced approaches in image classification and object detection based on its efficient features extraction on images. In this thesis, we investigate different convolutional neural networks and machine learning algorithms for identifying and classifying leaves of three species of the genus Brachylaena. The three species considered are Brachylaena discolor, Brachylaena ilicifolia and Brachylaena elliptica. All three species are used medicinally by people in South Africa to treat diseases like diabetes. From 1259 labelled images of those plants species (at least 400 for each species) split into training, evaluation and test sets, we trained and evaluated different deep convolutional neural networks and machine learning models. The VGG model achieved the best results with 98.26% accuracy from cross-validation. , Thesis (MSc) -- Faculty of Science, Mathematics, 2023
- Full Text:
- Authors: Deyi, Avuya
- Date: 2023-10-13
- Subjects: Deep learning (Machine learning) , Machine learning , Convolutional neural network , Computer vision in medicine , Medicinal plants
- Language: English
- Type: Academic theses , Master's theses , text
- Identifier: http://hdl.handle.net/10962/424552 , vital:72163
- Description: Identifying and classifying medicinal plants are valuable and essential skills during drug manufacturing because several active pharmaceutical ingredients (API) are sourced from medicinal plants. For many years, identifying and classifying medicinal plants have been exclusively done by experts in the domain, such as botanists, and herbarium curators. Recently, powerful computer vision technologies, using machine learning and deep convolutional neural networks, have been developed for classifying or identifying objects on images. A convolutional neural network is a deep learning architecture that outperforms previous advanced approaches in image classification and object detection based on its efficient features extraction on images. In this thesis, we investigate different convolutional neural networks and machine learning algorithms for identifying and classifying leaves of three species of the genus Brachylaena. The three species considered are Brachylaena discolor, Brachylaena ilicifolia and Brachylaena elliptica. All three species are used medicinally by people in South Africa to treat diseases like diabetes. From 1259 labelled images of those plants species (at least 400 for each species) split into training, evaluation and test sets, we trained and evaluated different deep convolutional neural networks and machine learning models. The VGG model achieved the best results with 98.26% accuracy from cross-validation. , Thesis (MSc) -- Faculty of Science, Mathematics, 2023
- Full Text:
Pharmaco-chemical investigation of Erythrina caffra: extracts, isolated compounds and their biological activities
- Authors: Nogqala, Simnikiwe
- Date: 2023-03-29
- Subjects: Coast coral tree , Traditional medicine South Africa , Antibacterial agents , Antineoplastic agents , Organic compounds
- Language: English
- Type: Academic theses , Master's theses , text
- Identifier: http://hdl.handle.net/10962/422459 , vital:71944
- Description: In this study, secondary metabolites isolated from Erythrina caffra, a medicinal plant indigenous to South Africa, were investigated. E. caffra is well-known for its healing properties and it is traditionally used for treating bacterial infections like tuberculosis (TB), abscesses, tooth aches and ear infections. Its extracts have also been used to treat cancer. Though many studies have been done on this plant, most of them tended to focus solely on the isolated compounds. In the present study however, extracts, fractions and isolated compounds from E. caffra were evaluated for their anticancer, anti-oxidant, anti-enzymatic, antibacterial and cytotoxicity. The methanol crude extract (B1) from the stem bark of E. caffra was used to extract alkaloidic fractions (B2 and B3) using ethyl acetate and n-butanol respectively, a third fraction (B4) was also extracted using ethyl acetate this fraction was called a neutral fraction. The neutral fraction (B4) was fractionated and through a sequence of column chromatography three active secondary metabolites were isolated. The isolated compounds included Lupeol (1), stigmasterol (2) and 5,7-Dihydroxy-4'-methoxy-3',5'-diprenylflavanone (3). These isolated compounds were characterized and identified using spectroscopic techniques including IR, NMR and high-resolution Mass Spectrometry. Using the cell line HCC-70, isolated from a primary ductal carcinoma, in vitro anticancer assays were carried out on the crude extract from the bark, fractions, isolated compounds and an unseparated mixture of two compounds. These samples were also evaluated for their anti-oxidant, anti-enzymatic, antibacterial and cytotoxicity activities. The crude extract inhibited the cell viability by over 30% and had no effect on the HeLa cells at concentrations of 20μM. Abyssinone V’ 4-methyl-ether (3) and the mixture of stigmasterol (2) and an unidentified compound exhibited potent anticancer activity against the HCC-70 cell line with IC50 of 18.05μM and 9.04μM respectively. Antibacterial assays were also carried out on the crude extracts, fractions and concoctions made from the fractions with the best activity combined with the ones that performed poorly. The concoctions were prepared as two separate series (S and N series). The crude extract inhibited more than 80% of the Staphylococcus aureus cells at a concentration of 20μM with only minimal damage to the HeLa cells. In the concoctions however, the N series managed to inhibit over 96% of the S. aureus while exhibiting no cytotoxicity towards HeLa cells. The extract and its fractions also showed good anti-oxidant activities. Molecular docking of these compounds was done on the Human estrogen receptor (PDB ID:3ERT) and Abyssinone V’ 4-methyl-ether (3) showed the best docking score of -6.6 Kcal/mol, for the simulation against Epidermal growth factor receptor (PDB ID: 1M17) Stigmasterol (2) showed the best docking score of -3.8 Kcal/mol. In silico docking on 3ERT and 1M17 were done to test the binding affinity of the isolated compounds to the proteins which are well known to be overexpressed in some types of cancer. Flavonoids isolated from Erythrina species have been reported to possess good antiplasmodial activity. However, due to the minute amounts isolated in the present study in-vitro assays could not be carried out. Nevertheless, in-silico assays were conducted on the most prominent protozoal parasite which causes malaria in the majority of African countries. In-silico simulations were done against Plasmodium falciparum protein (PDB ID: 7KJH), of the tested compounds Abyssinone V’ 4-methyl-ether (3) was found possess the best docking score of -4.4 Kcal/mol. The molecular docking of 7KJH was done to assess the inhibitory potential of the isolated compounds on protozoal parasites. Pharmacokinetic properties of the isolated compounds were also assessed in silico to assist in evaluating the drug likeness of these compounds. The compounds showed a percent human oral absorption of 100% except for Abyssinone V’ 4-methyl-ether (3), which showed 93.83%, this indicates a remarkable oral bioavailability. Stigamsterol (2) exhibited a Caco-2 cell permeability (QPPCaco) greater than 500 which indicates outstanding results for good intestinal absorption. The compounds also displayed a blood-brain partition co-efficient (QPlogBB) ranging from -1.433 to 0.128 suggesting they will have less potential to cross the blood-brain barrier, thus reducing any CNS related toxicity. Molecular networking of the crude extracts and the fractions was done through GNPS which allowed the identification of known compounds including one isolated in the present study, Abyssinone V’ 4-methyl-ether (3). Possible derivatives that have not been isolated from this plant before were also putatively identified. , Thesis (MSc) -- Faculty of Science, Chemistry, 2023
- Full Text:
- Authors: Nogqala, Simnikiwe
- Date: 2023-03-29
- Subjects: Coast coral tree , Traditional medicine South Africa , Antibacterial agents , Antineoplastic agents , Organic compounds
- Language: English
- Type: Academic theses , Master's theses , text
- Identifier: http://hdl.handle.net/10962/422459 , vital:71944
- Description: In this study, secondary metabolites isolated from Erythrina caffra, a medicinal plant indigenous to South Africa, were investigated. E. caffra is well-known for its healing properties and it is traditionally used for treating bacterial infections like tuberculosis (TB), abscesses, tooth aches and ear infections. Its extracts have also been used to treat cancer. Though many studies have been done on this plant, most of them tended to focus solely on the isolated compounds. In the present study however, extracts, fractions and isolated compounds from E. caffra were evaluated for their anticancer, anti-oxidant, anti-enzymatic, antibacterial and cytotoxicity. The methanol crude extract (B1) from the stem bark of E. caffra was used to extract alkaloidic fractions (B2 and B3) using ethyl acetate and n-butanol respectively, a third fraction (B4) was also extracted using ethyl acetate this fraction was called a neutral fraction. The neutral fraction (B4) was fractionated and through a sequence of column chromatography three active secondary metabolites were isolated. The isolated compounds included Lupeol (1), stigmasterol (2) and 5,7-Dihydroxy-4'-methoxy-3',5'-diprenylflavanone (3). These isolated compounds were characterized and identified using spectroscopic techniques including IR, NMR and high-resolution Mass Spectrometry. Using the cell line HCC-70, isolated from a primary ductal carcinoma, in vitro anticancer assays were carried out on the crude extract from the bark, fractions, isolated compounds and an unseparated mixture of two compounds. These samples were also evaluated for their anti-oxidant, anti-enzymatic, antibacterial and cytotoxicity activities. The crude extract inhibited the cell viability by over 30% and had no effect on the HeLa cells at concentrations of 20μM. Abyssinone V’ 4-methyl-ether (3) and the mixture of stigmasterol (2) and an unidentified compound exhibited potent anticancer activity against the HCC-70 cell line with IC50 of 18.05μM and 9.04μM respectively. Antibacterial assays were also carried out on the crude extracts, fractions and concoctions made from the fractions with the best activity combined with the ones that performed poorly. The concoctions were prepared as two separate series (S and N series). The crude extract inhibited more than 80% of the Staphylococcus aureus cells at a concentration of 20μM with only minimal damage to the HeLa cells. In the concoctions however, the N series managed to inhibit over 96% of the S. aureus while exhibiting no cytotoxicity towards HeLa cells. The extract and its fractions also showed good anti-oxidant activities. Molecular docking of these compounds was done on the Human estrogen receptor (PDB ID:3ERT) and Abyssinone V’ 4-methyl-ether (3) showed the best docking score of -6.6 Kcal/mol, for the simulation against Epidermal growth factor receptor (PDB ID: 1M17) Stigmasterol (2) showed the best docking score of -3.8 Kcal/mol. In silico docking on 3ERT and 1M17 were done to test the binding affinity of the isolated compounds to the proteins which are well known to be overexpressed in some types of cancer. Flavonoids isolated from Erythrina species have been reported to possess good antiplasmodial activity. However, due to the minute amounts isolated in the present study in-vitro assays could not be carried out. Nevertheless, in-silico assays were conducted on the most prominent protozoal parasite which causes malaria in the majority of African countries. In-silico simulations were done against Plasmodium falciparum protein (PDB ID: 7KJH), of the tested compounds Abyssinone V’ 4-methyl-ether (3) was found possess the best docking score of -4.4 Kcal/mol. The molecular docking of 7KJH was done to assess the inhibitory potential of the isolated compounds on protozoal parasites. Pharmacokinetic properties of the isolated compounds were also assessed in silico to assist in evaluating the drug likeness of these compounds. The compounds showed a percent human oral absorption of 100% except for Abyssinone V’ 4-methyl-ether (3), which showed 93.83%, this indicates a remarkable oral bioavailability. Stigamsterol (2) exhibited a Caco-2 cell permeability (QPPCaco) greater than 500 which indicates outstanding results for good intestinal absorption. The compounds also displayed a blood-brain partition co-efficient (QPlogBB) ranging from -1.433 to 0.128 suggesting they will have less potential to cross the blood-brain barrier, thus reducing any CNS related toxicity. Molecular networking of the crude extracts and the fractions was done through GNPS which allowed the identification of known compounds including one isolated in the present study, Abyssinone V’ 4-methyl-ether (3). Possible derivatives that have not been isolated from this plant before were also putatively identified. , Thesis (MSc) -- Faculty of Science, Chemistry, 2023
- Full Text:
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