Technology in conservation: towards a system for in-field drone detection of invasive vegetation
- James, Katherine Margaret Frances
- 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.
- Full Text:
- Date Issued: 2020
- 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.
- Full Text:
- Date Issued: 2020
Livelihood implications of a possible Ramsar declaration of the Swartkops estuary, Eastern Cape, South Africa
- Authors: Vembo, Glen Muchengeti
- Date: 2020
- Subjects: Uncatalogued
- Language: English
- Type: thesis , text , Masters , MSc
- Identifier: http://hdl.handle.net/10962/164715 , vital:41157
- Description: Thesis (MSc)--Rhodes University, Faculty of Science, Environmental Science, 2020
- Full Text:
- Date Issued: 2020
- Authors: Vembo, Glen Muchengeti
- Date: 2020
- Subjects: Uncatalogued
- Language: English
- Type: thesis , text , Masters , MSc
- Identifier: http://hdl.handle.net/10962/164715 , vital:41157
- Description: Thesis (MSc)--Rhodes University, Faculty of Science, Environmental Science, 2020
- Full Text:
- Date Issued: 2020
Initiating biological control for Nymphaea mexicana zuccarini (Nymphaeaceae) in South Africa
- Authors: Reid, Megan
- Date: 2020
- Subjects: Nymphaea mexicana zuccarini -- Biological control -- South Africa , Nymphaeaceae -- Biological control -- South Africa , Invasive plants -- Biological control -- South Africa
- Language: English
- Type: text , Thesis , Masters , MSc
- Identifier: http://hdl.handle.net/10962/144510 , vital:38352
- Description: Nymphaea mexicana Zuccarini (Nymphaeaceae) is an aquatic plant originating from south-eastern USA that is becoming increasingly invasive in South Africa as other invasive aquatic plants are being managed successfully through biological control. Mechanical and chemical control of aquatic weeds is expensive, damaging to the environment, and only effective in the short term, so biological control is more desirable as a management strategy for N. mexicana. The biological control of invasive alien plants requires that agents are host specific so that non-target risks are mitigated. For success to be achieved, it is important to ensure that the genetic structure of invasive populations is clarified so that agents can be collected from populations in the native range that match genetically to populations in the invasive range. This is especially important in cases where the morphology of invasive alien plants does not reflect genetic differences between populations. A previous study of the genetic structure of the invasive populations of N. mexicana in South Africa suggests the presence of hybrid forms of the plant in South Africa, with only one of these populations matching with samples from the native range. However, the study only used samples from two sites in the native range using amplified fragment length polymorphisms (AFLPs), so it was necessary to conduct further genetic analyses using samples from more sites in the native range. Hence, the first aim of this study was to develop a better understanding of the genetic structure of N. mexicana populations in the native and invaded range. Genetic samples were collected from sites in the native range during field surveys for potential biological control agents, and inter-simple sequence repeats (ISSRs) were used to compare the genetic structure of invasive and native populations of N. mexicana in South Africa. The results from these analyses suggest that seven of the 14 investigated invasive populations of N. mexicana in South Africa are genetically similar to populations in the native range, while the remaining seven populations are likely to be hybrid forms of the plant. This knowledge will be useful to target populations for biological control and highlights the need for further genetic analyses to determine the parentage of these hybrids so that biological control efforts are more likely to be successful. The initiation of a biological control programme requires that a series of steps are taken in order to maximise the likelihood that this form of intervention will be successful. The first few steps include: identification of the target weed and its genetic structure; exploration in the native range for potential biological control agents; and prioritisation of these agents based on factors such as climatic and genetic compatibility, feeding damage, abundance, and likely host range. Hence, the second aim of this study was to conduct surveys for potential biological control agents in the native range of N. mexicana, and to prioritise these agents. Field surveys were conducted between August and October in 2018 at 17 sites in Florida, Louisiana, and Texas, USA. Sites were selected based on climatic similarity of native sites compared to invasive sites by use of MaxEnt modelling. Native N. mexicana plants were searched for natural enemies, and these were prioritised based on feeding damage, abundance, incidence, and observations of field host range. Two species were prioritised: Bagous americanus LeConte (Coleoptera: Curculionidae) and Megamelus toddi Beamer (Hemiptera: Delphacidae). These species will be imported into quarantine facilities at Rhodes University for host specificity tests to be conducted. Understanding the factors that contribute to the successful establishment of biological control agents is important to improve the efficiency and reduce the costs incurred during the initiation of biological control programmes. Acquiring knowledge of the factors that predict the efficacy of biological control agents is similarly important, and these factors are discussed in the last chapter of this study. The challenges of the biological control of hybrids are also considered, and recommendations are made for the control of N. mexicana and other plants in South Africa.
- Full Text:
- Date Issued: 2020
- Authors: Reid, Megan
- Date: 2020
- Subjects: Nymphaea mexicana zuccarini -- Biological control -- South Africa , Nymphaeaceae -- Biological control -- South Africa , Invasive plants -- Biological control -- South Africa
- Language: English
- Type: text , Thesis , Masters , MSc
- Identifier: http://hdl.handle.net/10962/144510 , vital:38352
- Description: Nymphaea mexicana Zuccarini (Nymphaeaceae) is an aquatic plant originating from south-eastern USA that is becoming increasingly invasive in South Africa as other invasive aquatic plants are being managed successfully through biological control. Mechanical and chemical control of aquatic weeds is expensive, damaging to the environment, and only effective in the short term, so biological control is more desirable as a management strategy for N. mexicana. The biological control of invasive alien plants requires that agents are host specific so that non-target risks are mitigated. For success to be achieved, it is important to ensure that the genetic structure of invasive populations is clarified so that agents can be collected from populations in the native range that match genetically to populations in the invasive range. This is especially important in cases where the morphology of invasive alien plants does not reflect genetic differences between populations. A previous study of the genetic structure of the invasive populations of N. mexicana in South Africa suggests the presence of hybrid forms of the plant in South Africa, with only one of these populations matching with samples from the native range. However, the study only used samples from two sites in the native range using amplified fragment length polymorphisms (AFLPs), so it was necessary to conduct further genetic analyses using samples from more sites in the native range. Hence, the first aim of this study was to develop a better understanding of the genetic structure of N. mexicana populations in the native and invaded range. Genetic samples were collected from sites in the native range during field surveys for potential biological control agents, and inter-simple sequence repeats (ISSRs) were used to compare the genetic structure of invasive and native populations of N. mexicana in South Africa. The results from these analyses suggest that seven of the 14 investigated invasive populations of N. mexicana in South Africa are genetically similar to populations in the native range, while the remaining seven populations are likely to be hybrid forms of the plant. This knowledge will be useful to target populations for biological control and highlights the need for further genetic analyses to determine the parentage of these hybrids so that biological control efforts are more likely to be successful. The initiation of a biological control programme requires that a series of steps are taken in order to maximise the likelihood that this form of intervention will be successful. The first few steps include: identification of the target weed and its genetic structure; exploration in the native range for potential biological control agents; and prioritisation of these agents based on factors such as climatic and genetic compatibility, feeding damage, abundance, and likely host range. Hence, the second aim of this study was to conduct surveys for potential biological control agents in the native range of N. mexicana, and to prioritise these agents. Field surveys were conducted between August and October in 2018 at 17 sites in Florida, Louisiana, and Texas, USA. Sites were selected based on climatic similarity of native sites compared to invasive sites by use of MaxEnt modelling. Native N. mexicana plants were searched for natural enemies, and these were prioritised based on feeding damage, abundance, incidence, and observations of field host range. Two species were prioritised: Bagous americanus LeConte (Coleoptera: Curculionidae) and Megamelus toddi Beamer (Hemiptera: Delphacidae). These species will be imported into quarantine facilities at Rhodes University for host specificity tests to be conducted. Understanding the factors that contribute to the successful establishment of biological control agents is important to improve the efficiency and reduce the costs incurred during the initiation of biological control programmes. Acquiring knowledge of the factors that predict the efficacy of biological control agents is similarly important, and these factors are discussed in the last chapter of this study. The challenges of the biological control of hybrids are also considered, and recommendations are made for the control of N. mexicana and other plants in South Africa.
- Full Text:
- Date Issued: 2020
Combining DNA barcoding and morphology to identify larval fishes from the nearshore environment off the south-east coast of South Africa
- Authors: Somana, Zinzi Sinazo
- Date: 2020
- Subjects: Fishes -- Larvae -- South Africa -- Identification , Fishes -- Genetics -- Research -- Technique , Fishes -- South Africa -- Classification , Genetic markers
- Language: English
- Type: text , Thesis , Masters , MSc
- Identifier: http://hdl.handle.net/10962/144605 , vital:38362
- Description: The early life history stages of most marine fish species are undescribed. The problem is, most of these fishes have pelagic larvae which are minute, delicate forms. Linking the larval stage to an adult counterpart is extremely challenging as larvae are morphologically different from the adults. Historically, larval fish identification relied solely on distinguishing morphological characteristics and meristic measurements, which has resulted in taxonomic confusion and misidentification. The introduction of the deoxyribonucleic acid (DNA) barcoding technique as an alternative approach has been successful in positively identifying larval fishes. The correct identification of larval specimens is the key to a better understanding of larval ecology, which underpins the success of any adult fish population. This study aimed to positively identify larval fishes of the south-east coast of South Africa using morphological characteristics and DNA barcoding. Larval and eggs specimens for this study were collected from the shallow nearshore waters of the south-east coast of South Africa. A total of 177 larval specimens were used for morphological analysis. Body shape, gut shape, pigmentation and morphometric measurements (such as body depth, preanal length and total body length) were used to identify each specimen to the family level. In addition, a fragment of mitochondrial cytochrome c oxidase subunit 1 gene (COI) was adopted for sequencing to identify larval fish specimens and fish eggs. Sequences generated from this study were compared to those in the Barcode of Life Database (BOLD). When there were no close matches to a sequence, the GenBank nucleic acid sequence database, maintained by the National Center for Biotechnology Information (NCBI), was used as an alternative. A total of 18 different families were identified through morphology. Seventy-seven of the 177 larval specimens were not subjected to morphological identification due to physical damage. The majority of larvae identified using morphological characteristics belonged to either the Sparidae, Tripterygiidae or Gobiesocidae fish families. Through DNA barcoding, 12 fish families, 16 genera and 18 different species were identified. Ten DNA barcodes (categorised as ‘no match’) from 10 different larval specimens were not identified through any of the online databases. Therefore, the 2% threshold value was used to identify members of the same species. The K2P genetic distance relationships were calculated among the no match sequences and downloaded probability matches from NCBI. This resulted in two unknown specimens assigned to the Blenniidae and Gobiidae. All other taxa were identified to species level, except specimens representing the Gobiidae and Tripterygiidae families. Based on the K2P genetic distances Gobiidae representatives were categorised as members of the Caffrogobius genus. Twenty-eight barcodes represented specimens from the Tripterygiidae. DNA barcode data from COI was analysed using the standard phylogenetic procedures in MEGA6 to examine relationships and differentiation among sequences. These could not be identified to the lowest taxonomic rank due to limited sequence data to compare them with. The sequence data from these specimens gave different results in the two online databases. BOLD results were to family level (Tripterygiidae) and NCBI to the species level (Clinidae: Pavoclinus profundus). Results in this study confirmed the efficiency of the DNA barcoding technique in species level identification of fish larvae. The evidence from genetic barcodes of the Tripterygiidae specimens, supported by morphological characteristics, suggests the need for thorough research to identify the individuals to the species level. The fact that this study identified taxonomically problematic Gobiidae and Tripterygiidae specimens suggests that studies similar to this may highlight additional diversity and help to resolve the taxonomy of other species in these families. However, the lack of reference sequence data from the adult specimens, and especially those with cryptic diversity, were both shortcomings for the positive identification of larvae. With that being said, it shows the necessity for more research to be conducted on barcoding of larvae in general as to accommodate all kinds of species from biodiversity to economic perspectives.
- Full Text:
- Date Issued: 2020
- Authors: Somana, Zinzi Sinazo
- Date: 2020
- Subjects: Fishes -- Larvae -- South Africa -- Identification , Fishes -- Genetics -- Research -- Technique , Fishes -- South Africa -- Classification , Genetic markers
- Language: English
- Type: text , Thesis , Masters , MSc
- Identifier: http://hdl.handle.net/10962/144605 , vital:38362
- Description: The early life history stages of most marine fish species are undescribed. The problem is, most of these fishes have pelagic larvae which are minute, delicate forms. Linking the larval stage to an adult counterpart is extremely challenging as larvae are morphologically different from the adults. Historically, larval fish identification relied solely on distinguishing morphological characteristics and meristic measurements, which has resulted in taxonomic confusion and misidentification. The introduction of the deoxyribonucleic acid (DNA) barcoding technique as an alternative approach has been successful in positively identifying larval fishes. The correct identification of larval specimens is the key to a better understanding of larval ecology, which underpins the success of any adult fish population. This study aimed to positively identify larval fishes of the south-east coast of South Africa using morphological characteristics and DNA barcoding. Larval and eggs specimens for this study were collected from the shallow nearshore waters of the south-east coast of South Africa. A total of 177 larval specimens were used for morphological analysis. Body shape, gut shape, pigmentation and morphometric measurements (such as body depth, preanal length and total body length) were used to identify each specimen to the family level. In addition, a fragment of mitochondrial cytochrome c oxidase subunit 1 gene (COI) was adopted for sequencing to identify larval fish specimens and fish eggs. Sequences generated from this study were compared to those in the Barcode of Life Database (BOLD). When there were no close matches to a sequence, the GenBank nucleic acid sequence database, maintained by the National Center for Biotechnology Information (NCBI), was used as an alternative. A total of 18 different families were identified through morphology. Seventy-seven of the 177 larval specimens were not subjected to morphological identification due to physical damage. The majority of larvae identified using morphological characteristics belonged to either the Sparidae, Tripterygiidae or Gobiesocidae fish families. Through DNA barcoding, 12 fish families, 16 genera and 18 different species were identified. Ten DNA barcodes (categorised as ‘no match’) from 10 different larval specimens were not identified through any of the online databases. Therefore, the 2% threshold value was used to identify members of the same species. The K2P genetic distance relationships were calculated among the no match sequences and downloaded probability matches from NCBI. This resulted in two unknown specimens assigned to the Blenniidae and Gobiidae. All other taxa were identified to species level, except specimens representing the Gobiidae and Tripterygiidae families. Based on the K2P genetic distances Gobiidae representatives were categorised as members of the Caffrogobius genus. Twenty-eight barcodes represented specimens from the Tripterygiidae. DNA barcode data from COI was analysed using the standard phylogenetic procedures in MEGA6 to examine relationships and differentiation among sequences. These could not be identified to the lowest taxonomic rank due to limited sequence data to compare them with. The sequence data from these specimens gave different results in the two online databases. BOLD results were to family level (Tripterygiidae) and NCBI to the species level (Clinidae: Pavoclinus profundus). Results in this study confirmed the efficiency of the DNA barcoding technique in species level identification of fish larvae. The evidence from genetic barcodes of the Tripterygiidae specimens, supported by morphological characteristics, suggests the need for thorough research to identify the individuals to the species level. The fact that this study identified taxonomically problematic Gobiidae and Tripterygiidae specimens suggests that studies similar to this may highlight additional diversity and help to resolve the taxonomy of other species in these families. However, the lack of reference sequence data from the adult specimens, and especially those with cryptic diversity, were both shortcomings for the positive identification of larvae. With that being said, it shows the necessity for more research to be conducted on barcoding of larvae in general as to accommodate all kinds of species from biodiversity to economic perspectives.
- Full Text:
- Date Issued: 2020
Formulation and evaluation of liposomal films for buccal delivery of antiretroviral drug
- Authors: Okafor, Nnamdi Ikemefuna
- Date: 2020
- Subjects: Liposomes , Highly active antiretroviral therapy , Antiretroviral agents , HIV infections -- Prevention
- Language: English
- Type: text , Thesis , Masters , MSc
- Identifier: http://hdl.handle.net/10962/117161 , vital:34485
- Description: The human immune deficiency virus (HIV) infection has been ranked as one of the most devastating microbial infections in the world. This status is a result of the HIV rapid genetic variation, which limits discovery of a vaccine. Use application of antiretroviral therapy (ARVT) in treatment of the disease caused by the HIV infection (known as acquired immunodeficiency syndrome, HIV-AIDS) is frequently compromised by several factors such as the low bioavailability and severe adverse effects associated with the existing antiretroviral drugs (ARVDs). This underlines the need for controlling the pharmacokinetics profiles of ARVD using effective vehicles that can modify drug biodistribution. The same is true for many other conditions, where delivery systems can determine the success or failure of treatment by controlling pharmacokinetic and dynamic properties. The mucosal linings of the oral cavities in addition offer adorable route of administration for systematic drug delivery, improving drug therapeutic performance and often preferred by clinicians and patients. Liposomes are tiny spherical sacs of phospholipid molecules enclosing water droplets, formed (artificially) to carry drugs or other substances into the tissues by crossing and targeting to specific organelles. This work therefore focused on preparation of liposomes and liposomal buccal films (BFs) for potential buccal delivery of efavirenz, an ARVD model endowed with poor solubility and several side effects. The liposomes were prepared by thin film hydration method using crude soybean lecithin (CL) and cholesterol. Efavirenz loaded liposomes were evaluated for particle size, Zeta potential (ZP), morphology, encapsulation efficiency (EE%) and release kinetics studies. The physiochemical properties of the liposomes were also evaluated using Differential Scanning Calorimetry (DSC), X-ray diffraction (XRD), energy dispersity spectroscopy (EDS), and Fourier transform infrared (FTIR), while the formulation with the best encapsulation efficiency was used as the solvent medium for the buccal film formation. The buccal films were prepared using solvent casting method, where the liposomal suspension was used as the dispersing medium. The films were optimized for physical properties (thickness, weight variation and folding endurance) using digital Vernier calliper and digital weighing balance. The physiochemical properties of the selected BFs films made of Carbopol (CP) and its combination with Pluronic F127 (PF127) were further characterized using XRD, DSC, FTIR, Transmission Electron Microscopy (TEM), EDS and Scanning Electron Microscopy (SEM). The permeation study of the selected BFs was investigated using Franz diffusion cell. The BFs composed of CP alone or its combination with PF127 demonstrated much better bio-adhesive properties than the films made of other polymers (like Hydroxyl propyl methyl cellulose, HPMC) alone or in combination with PF127. The developed liposome formulation showed high encapsulation 98.8 ± 0.01 % in CL to cholesterol mass ratio of 1:1 and total lipid to drug mass ratio of 2:1. The average particle size 104.82 ± 2.29 nm and Zeta potential -50.33 ± 0.95 mV of these liposomes were found to be attractive for targeted delivery to the HIV infected cells. The CP based BFs (without and with PF127) exhibited good film thickness 0.88 ± 0.10 and 0.76 ± 0.14 mm, with weight uniformity 68.22 ± 1.04 and 86.28 ± 2. 16 mg, satisfactory flexibility values 258 and 321, and slightly acidic pH 6.43 ± 0.76 and 6.32 ± 0.01. The swelling percentage was found to be 50 % for CP film alone and 78 % for CP film with PF127. The cumulative amount of drug that permeated through the buccal epithelium over 24 hours was about 66 % from CP film alone and 75 % from CP film with PF127. Since no evidence of the liposomal encapsulation of EFV have been reported to our knowledge, we find the insights from the present study valuable as a set of preliminary data to encourage further investigations of the encapsulation and delivery of EFV like antiretrovirals for enhanced solubility, site targeting and prolonged release using crude soybean lecithin and mucoadhesive polymers, which holds some added economical values as naturally occurring lipid and polymeric mixtures as a promising delivery systems for buccal delivery of ARVDs.
- Full Text:
- Date Issued: 2020
- Authors: Okafor, Nnamdi Ikemefuna
- Date: 2020
- Subjects: Liposomes , Highly active antiretroviral therapy , Antiretroviral agents , HIV infections -- Prevention
- Language: English
- Type: text , Thesis , Masters , MSc
- Identifier: http://hdl.handle.net/10962/117161 , vital:34485
- Description: The human immune deficiency virus (HIV) infection has been ranked as one of the most devastating microbial infections in the world. This status is a result of the HIV rapid genetic variation, which limits discovery of a vaccine. Use application of antiretroviral therapy (ARVT) in treatment of the disease caused by the HIV infection (known as acquired immunodeficiency syndrome, HIV-AIDS) is frequently compromised by several factors such as the low bioavailability and severe adverse effects associated with the existing antiretroviral drugs (ARVDs). This underlines the need for controlling the pharmacokinetics profiles of ARVD using effective vehicles that can modify drug biodistribution. The same is true for many other conditions, where delivery systems can determine the success or failure of treatment by controlling pharmacokinetic and dynamic properties. The mucosal linings of the oral cavities in addition offer adorable route of administration for systematic drug delivery, improving drug therapeutic performance and often preferred by clinicians and patients. Liposomes are tiny spherical sacs of phospholipid molecules enclosing water droplets, formed (artificially) to carry drugs or other substances into the tissues by crossing and targeting to specific organelles. This work therefore focused on preparation of liposomes and liposomal buccal films (BFs) for potential buccal delivery of efavirenz, an ARVD model endowed with poor solubility and several side effects. The liposomes were prepared by thin film hydration method using crude soybean lecithin (CL) and cholesterol. Efavirenz loaded liposomes were evaluated for particle size, Zeta potential (ZP), morphology, encapsulation efficiency (EE%) and release kinetics studies. The physiochemical properties of the liposomes were also evaluated using Differential Scanning Calorimetry (DSC), X-ray diffraction (XRD), energy dispersity spectroscopy (EDS), and Fourier transform infrared (FTIR), while the formulation with the best encapsulation efficiency was used as the solvent medium for the buccal film formation. The buccal films were prepared using solvent casting method, where the liposomal suspension was used as the dispersing medium. The films were optimized for physical properties (thickness, weight variation and folding endurance) using digital Vernier calliper and digital weighing balance. The physiochemical properties of the selected BFs films made of Carbopol (CP) and its combination with Pluronic F127 (PF127) were further characterized using XRD, DSC, FTIR, Transmission Electron Microscopy (TEM), EDS and Scanning Electron Microscopy (SEM). The permeation study of the selected BFs was investigated using Franz diffusion cell. The BFs composed of CP alone or its combination with PF127 demonstrated much better bio-adhesive properties than the films made of other polymers (like Hydroxyl propyl methyl cellulose, HPMC) alone or in combination with PF127. The developed liposome formulation showed high encapsulation 98.8 ± 0.01 % in CL to cholesterol mass ratio of 1:1 and total lipid to drug mass ratio of 2:1. The average particle size 104.82 ± 2.29 nm and Zeta potential -50.33 ± 0.95 mV of these liposomes were found to be attractive for targeted delivery to the HIV infected cells. The CP based BFs (without and with PF127) exhibited good film thickness 0.88 ± 0.10 and 0.76 ± 0.14 mm, with weight uniformity 68.22 ± 1.04 and 86.28 ± 2. 16 mg, satisfactory flexibility values 258 and 321, and slightly acidic pH 6.43 ± 0.76 and 6.32 ± 0.01. The swelling percentage was found to be 50 % for CP film alone and 78 % for CP film with PF127. The cumulative amount of drug that permeated through the buccal epithelium over 24 hours was about 66 % from CP film alone and 75 % from CP film with PF127. Since no evidence of the liposomal encapsulation of EFV have been reported to our knowledge, we find the insights from the present study valuable as a set of preliminary data to encourage further investigations of the encapsulation and delivery of EFV like antiretrovirals for enhanced solubility, site targeting and prolonged release using crude soybean lecithin and mucoadhesive polymers, which holds some added economical values as naturally occurring lipid and polymeric mixtures as a promising delivery systems for buccal delivery of ARVDs.
- Full Text:
- Date Issued: 2020
Symmetry and asymmetry in electrocatalysis: enhancing the electrocatalytic activity of phthalocyanines through synergy with doped graphene quantum dots
- Nkhahle, Reitumetse Precious
- Authors: Nkhahle, Reitumetse Precious
- Date: 2020
- Subjects: Phthalocyanines , Quantum dots , Graphene
- Language: English
- Type: text , Thesis , Masters , MSc
- Identifier: http://hdl.handle.net/10962/117585 , vital:34529
- Description: An exploration on the enhancement of the electrocatalytic activity of phthalocyanines (Pcs) through coupling with a series of graphene quantum dots (GQDs) is undertaken. The preliminary studies using symmetrical Pcs, a cobalt and an iron chloride tetra substituted diethylaminophenoxy Pc (complexes 1 and 2), for the electro-oxidation of nitrite revealed through the various sequential modifications that doped GQDs fare better than their pristine counterparts with respect to improving the electrocatalytic behaviour of Pcs, in particular, the nitrogen-doped GQDs (NGQDs). Following up on this, a series of asymmetric Pc complexes; 2,9,16-tris-(4-tert-butylphenoxy) mono carboxyphenoxy phthalocyanato cobalt (II) (3), 2,9,16-tris-(4-tert-butylphenoxy) mono aminophenoxy phthalocyanato cobalt (II) (4), 2,9,16-tris-(3-diethylamino)phenoxy) mono carboxyphenoxy phthalocyanato cobalt (II) (5) and 2,9,16-tris-(3-diethylamino)phenoxy) mono aminophenoxy phthalocyanato cobalt (II) (6) was prepared in which push-pull systems were compared to other asymmetric complexes that lack this effect towards the electrocatalytic sensing of hydrazine. All asymmetric complexes (3-6) were π-stacked to the NGQDs while those with an NH2 group (4 and 6), were also covalently linked to the NGQDs. These complexes and their corresponding conjugates were characterized accordingly and applied as electrocatalysts in the oxidation of hydrazine. The electrochemical studies revealed that π π stacking yields better responses (higher sensitivities and lower limits of detection) than covalent linking because there are less forces acting on the graphene network. Covalent linking introduces both tensile and compressive forces which in turn results in an increase in the ID/IG ratio and that is unfavourable for electrocatalysis. In comparing the electrodes composed of the π-stacked conjugates to those altered through sequential modifications, despite the conditions not being the same, it can be inferred that the magnitude of the electrostatic forces between the Pcs and the GQDs also plays a significant role in electrocatalysis. The π-stacked conjugates, owing to the manner in which they were prepared, have stronger electrostatic forces acting between the Pc and GQDs hence they were able to elicit a better electrochemical response than the sequentially modified electrodes. In addition to that, it appears that asymmetric Pcs are better electrocatalysts in comparison to the symmetric Pcs.
- Full Text:
- Date Issued: 2020
- Authors: Nkhahle, Reitumetse Precious
- Date: 2020
- Subjects: Phthalocyanines , Quantum dots , Graphene
- Language: English
- Type: text , Thesis , Masters , MSc
- Identifier: http://hdl.handle.net/10962/117585 , vital:34529
- Description: An exploration on the enhancement of the electrocatalytic activity of phthalocyanines (Pcs) through coupling with a series of graphene quantum dots (GQDs) is undertaken. The preliminary studies using symmetrical Pcs, a cobalt and an iron chloride tetra substituted diethylaminophenoxy Pc (complexes 1 and 2), for the electro-oxidation of nitrite revealed through the various sequential modifications that doped GQDs fare better than their pristine counterparts with respect to improving the electrocatalytic behaviour of Pcs, in particular, the nitrogen-doped GQDs (NGQDs). Following up on this, a series of asymmetric Pc complexes; 2,9,16-tris-(4-tert-butylphenoxy) mono carboxyphenoxy phthalocyanato cobalt (II) (3), 2,9,16-tris-(4-tert-butylphenoxy) mono aminophenoxy phthalocyanato cobalt (II) (4), 2,9,16-tris-(3-diethylamino)phenoxy) mono carboxyphenoxy phthalocyanato cobalt (II) (5) and 2,9,16-tris-(3-diethylamino)phenoxy) mono aminophenoxy phthalocyanato cobalt (II) (6) was prepared in which push-pull systems were compared to other asymmetric complexes that lack this effect towards the electrocatalytic sensing of hydrazine. All asymmetric complexes (3-6) were π-stacked to the NGQDs while those with an NH2 group (4 and 6), were also covalently linked to the NGQDs. These complexes and their corresponding conjugates were characterized accordingly and applied as electrocatalysts in the oxidation of hydrazine. The electrochemical studies revealed that π π stacking yields better responses (higher sensitivities and lower limits of detection) than covalent linking because there are less forces acting on the graphene network. Covalent linking introduces both tensile and compressive forces which in turn results in an increase in the ID/IG ratio and that is unfavourable for electrocatalysis. In comparing the electrodes composed of the π-stacked conjugates to those altered through sequential modifications, despite the conditions not being the same, it can be inferred that the magnitude of the electrostatic forces between the Pcs and the GQDs also plays a significant role in electrocatalysis. The π-stacked conjugates, owing to the manner in which they were prepared, have stronger electrostatic forces acting between the Pc and GQDs hence they were able to elicit a better electrochemical response than the sequentially modified electrodes. In addition to that, it appears that asymmetric Pcs are better electrocatalysts in comparison to the symmetric Pcs.
- Full Text:
- Date Issued: 2020
Towards a capability maturity model for a cyber range
- Authors: Aschmann, Michael Joseph
- Date: 2020
- Subjects: Computer software -- Development , Computer security
- Language: English
- Type: text , Thesis , Masters , MSc
- Identifier: http://hdl.handle.net/10962/163142 , vital:41013
- Description: This work describes research undertaken towards the development of a Capability Maturity Model (CMM) for Cyber Ranges (CRs) focused on cyber security. Global cyber security needs are on the rise, and the need for attribution within the cyber domain is of particular concern. This has prompted major efforts to enhance cyber capabilities within organisations to increase their total cyber resilience posture. These efforts include, but are not limited to, the testing of computational devices, networks, and applications, and cyber skills training focused on prevention, detection and cyber attack response. A cyber range allows for the testing of the computational environment. By developing cyber events within a confined virtual or sand-boxed cyber environment, a cyber range can prepare the next generation of cyber security specialists to handle a variety of potential cyber attacks. Cyber ranges have different purposes, each designed to fulfil a different computational testing and cyber training goal; consequently, cyber ranges can vary greatly in the level of variety, capability, maturity and complexity. As cyber ranges proliferate and become more and more valued as tools for cyber security, a method to classify or rate them becomes essential. Yet while a universal criteria for measuring cyber ranges in terms of their capability maturity levels becomes more critical, there are currently very limited resources for researchers aiming to perform this kind of work. For this reason, this work proposes and describes a CMM, designed to give organisations the ability to benchmark the capability maturity of a given cyber range. This research adopted a synthesised approach to the development of a CMM, grounded in prior research and focused on the production of a conceptual model that provides a useful level of abstraction. In order to achieve this goal, the core capability elements of a cyber range are defined with their relative importance, allowing for the development of a proposed classification cyber range levels. An analysis of data gathered during the course of an expert review, together with other research, further supported the development of the conceptual model. In the context of cyber range capability, classification will include the ability of the cyber range to perform its functions optimally with different core capability elements, focusing on the Measurement of Capability (MoC) with its elements, namely effect, performance and threat ability. Cyber range maturity can evolve over time and can be defined through the Measurement of Maturity (MoM) with its elements, namely people, processes, technology. The combination of these measurements utilising the CMM for a CR determines the capability maturity level of a CR. The primary outcome of this research is the proposed level-based CMM framework for a cyber range, developed using adopted and synthesised CMMs, the analysis of an expert review, and the mapping of the results.
- Full Text:
- Date Issued: 2020
- Authors: Aschmann, Michael Joseph
- Date: 2020
- Subjects: Computer software -- Development , Computer security
- Language: English
- Type: text , Thesis , Masters , MSc
- Identifier: http://hdl.handle.net/10962/163142 , vital:41013
- Description: This work describes research undertaken towards the development of a Capability Maturity Model (CMM) for Cyber Ranges (CRs) focused on cyber security. Global cyber security needs are on the rise, and the need for attribution within the cyber domain is of particular concern. This has prompted major efforts to enhance cyber capabilities within organisations to increase their total cyber resilience posture. These efforts include, but are not limited to, the testing of computational devices, networks, and applications, and cyber skills training focused on prevention, detection and cyber attack response. A cyber range allows for the testing of the computational environment. By developing cyber events within a confined virtual or sand-boxed cyber environment, a cyber range can prepare the next generation of cyber security specialists to handle a variety of potential cyber attacks. Cyber ranges have different purposes, each designed to fulfil a different computational testing and cyber training goal; consequently, cyber ranges can vary greatly in the level of variety, capability, maturity and complexity. As cyber ranges proliferate and become more and more valued as tools for cyber security, a method to classify or rate them becomes essential. Yet while a universal criteria for measuring cyber ranges in terms of their capability maturity levels becomes more critical, there are currently very limited resources for researchers aiming to perform this kind of work. For this reason, this work proposes and describes a CMM, designed to give organisations the ability to benchmark the capability maturity of a given cyber range. This research adopted a synthesised approach to the development of a CMM, grounded in prior research and focused on the production of a conceptual model that provides a useful level of abstraction. In order to achieve this goal, the core capability elements of a cyber range are defined with their relative importance, allowing for the development of a proposed classification cyber range levels. An analysis of data gathered during the course of an expert review, together with other research, further supported the development of the conceptual model. In the context of cyber range capability, classification will include the ability of the cyber range to perform its functions optimally with different core capability elements, focusing on the Measurement of Capability (MoC) with its elements, namely effect, performance and threat ability. Cyber range maturity can evolve over time and can be defined through the Measurement of Maturity (MoM) with its elements, namely people, processes, technology. The combination of these measurements utilising the CMM for a CR determines the capability maturity level of a CR. The primary outcome of this research is the proposed level-based CMM framework for a cyber range, developed using adopted and synthesised CMMs, the analysis of an expert review, and the mapping of the results.
- Full Text:
- Date Issued: 2020
Development of graphene materials and phthalocyanines for application in dye-sensitized solar cells
- Authors: Chindeka, Francis
- Date: 2020
- Subjects: Dye-sensitized solar cells , Graphene , Phthalocyanines , Molecular orbitals , Impedance spectroscopy
- Language: English
- Type: text , Thesis , Masters , MSc
- Identifier: http://hdl.handle.net/10962/166092 , vital:41328
- Description: Two sets of dye-sensitized solar cells (DSSCs) were fabricated. In the first set, dye-sensitized solar cells (DSSC) were fabricated by incorporating graphene materials as catalysts at the counter electrode. Platinum was also used as a catalyst for comparative purposes. Different phthalocyanines: hydroxyl indium tetracarboxyphenoxy phthalocyanine (1), chloro indium octacarboxy phthalocyanine (2) and dibenzoic acid silicon phthalocyanine (3) were used as dyes. Complex 3 gave the highest power conversion efficiency (η) of 3.19% when using nitrogen doped reduced graphene oxide nanosheets (NrGONS) as a catalyst at the counter electrode, and TiO2 containing rGONS at the anode. The value obtained is close to 3.8% obtained when using Pt catalyst instead of NrGONS at the cathode, thus confirming that NrGONS is a promising candidate to replace the more expensive Pt. The study also shows that placing rGONS on both the anode and cathode improves efficiency. In the second set, DSSCs were fabricated by using 2(3,5-biscarboxyphenoxy), 9(10), 16(17), 23(24)-tri(tertbutyl) phthalocyaninato Cu (4) and Zn (5) complexes as dyes on the ITO-TiO2 photoanodes containing reduced graphene oxide nanosheets (rGONS) or nitrogen-doped rGONS (NrGONS). The evaluation of the assembled DSSCs revealed that using ITO-TiO2-NrGONS-CuPc (4) photoanode had the highest fill factor (FF) and power conversion efficiency (ɳ) of 69 % and 4.36 % respectively. These results show that the asymmetrical phthalocyanine complexes (4) and (5) showed significant improvement on the performance of the DSSC compared to previous work on symmetrical carboxylated phthalocyanines with ɳ = 3.19%.
- Full Text:
- Date Issued: 2020
- Authors: Chindeka, Francis
- Date: 2020
- Subjects: Dye-sensitized solar cells , Graphene , Phthalocyanines , Molecular orbitals , Impedance spectroscopy
- Language: English
- Type: text , Thesis , Masters , MSc
- Identifier: http://hdl.handle.net/10962/166092 , vital:41328
- Description: Two sets of dye-sensitized solar cells (DSSCs) were fabricated. In the first set, dye-sensitized solar cells (DSSC) were fabricated by incorporating graphene materials as catalysts at the counter electrode. Platinum was also used as a catalyst for comparative purposes. Different phthalocyanines: hydroxyl indium tetracarboxyphenoxy phthalocyanine (1), chloro indium octacarboxy phthalocyanine (2) and dibenzoic acid silicon phthalocyanine (3) were used as dyes. Complex 3 gave the highest power conversion efficiency (η) of 3.19% when using nitrogen doped reduced graphene oxide nanosheets (NrGONS) as a catalyst at the counter electrode, and TiO2 containing rGONS at the anode. The value obtained is close to 3.8% obtained when using Pt catalyst instead of NrGONS at the cathode, thus confirming that NrGONS is a promising candidate to replace the more expensive Pt. The study also shows that placing rGONS on both the anode and cathode improves efficiency. In the second set, DSSCs were fabricated by using 2(3,5-biscarboxyphenoxy), 9(10), 16(17), 23(24)-tri(tertbutyl) phthalocyaninato Cu (4) and Zn (5) complexes as dyes on the ITO-TiO2 photoanodes containing reduced graphene oxide nanosheets (rGONS) or nitrogen-doped rGONS (NrGONS). The evaluation of the assembled DSSCs revealed that using ITO-TiO2-NrGONS-CuPc (4) photoanode had the highest fill factor (FF) and power conversion efficiency (ɳ) of 69 % and 4.36 % respectively. These results show that the asymmetrical phthalocyanine complexes (4) and (5) showed significant improvement on the performance of the DSSC compared to previous work on symmetrical carboxylated phthalocyanines with ɳ = 3.19%.
- Full Text:
- Date Issued: 2020
Evaluation of an NADPH-dependent assay for inhibition screening of Salmonella enterica DOXP Reguctoisomerase for identification of novel drug hit compounds
- Authors: Ngcongco, Khanyisile
- Date: 2020
- Subjects: 1-Deoxy-D-xylulose 5-phosphate , Antibiotics , Drug development , Salmonella , Enterobacteriaceae , Vaccines , Plasmodium falciparum , Mycobacterium tuberculosis
- Language: English
- Type: text , Thesis , Masters , MSc
- Identifier: http://hdl.handle.net/10962/167132 , vital:41440
- Description: Invasive non-typhoidal Salmonella, caused by the intracellular pathogen Salmonella enterica, has emerged as a major cause of bloodstream infections. It remains a neglected infection responsible for many deaths in Africa, as it fails to receive the level of support that is given to most better known infections. There are currently no vaccines against invasive non-typhoidal Salmonella. First-line antibiotics have been used for treatment, however, the rise in the resistance of the bacteria against these antibiotics has made treatment of invasive salmonellosis into a clinical problem. Therefore, the discovery of new compounds for the development of antibiotic drugs is required. Central metabolic pathways can be a useful source for identifying drug targets and among these is the non-mevalonate pathway, one of the pathways used for the biosynthesis of isoprenoid precursors. The second step of the non-mevalonate pathway involves the NADPH-dependent reduction of 1-deoxy-D-xylulose 5-phosphate (DOXP) into 2-C-methyl-D-erythritol 4-phosphate (MEP). 1-Deoxy-D-xylulose 5-phosphate (DOXP) reductoisomerase plays a vital role in the catalysis of this reaction and requires NADPH and divalent metal cations as co-factors for its activity. In this investigation recombinant DOXP reductoisomerase from Salmonella enterica, Plasmodium falciparum and Mycobacterium tuberculosis were biochemically characterized as potential targets for developing drugs that could be used as treatment of the disease. The expression and nickel-chelate affinity purification of S. enterica DOXP reductoisomerase in a fully functional native state was successfully achieved. However, the expression and purification of P. falciparum DXR and M. tuberculosis DXR was unsuccessful due to the formation of insoluble inclusion bodies. Although alternative purification strategies were explored, including dialysis and slow dilution, these proteins remained insoluble, making their functional analysis not possible. An NADPH-dependent enzyme assay was used to determine the activity of S. enterica DXR. This assay monitors the reduction of DOXP to MEP by measuring the absorbance at 340 nm, which reflects the concentration of NADPH. An alternative assay, resazurin reduction, which monitors the NADPH-dependent reduction of resazurin to resorufin, was explored for detecting enzyme activity. The recombinant S. enterica DOXP reductoisomerase had a specific activity of 0.126 ± 0.0014 μmol/min/mg protein and a Km and Vmax of 881 μM and 0.249 μmol/min/mg respectively. FR900098, a derivative of fosmidomycin, is a well-known inhibitor of DXR, however, the sensitivity of S. enterica DXR towards FR900098 has not yet been reported. The NADPH dependent enzyme and resazurin reduction assays were used to determine whether FR900098 has enzyme inhibitory effects against S. enterica DXR. Upon confirming that FR900098 is able to inhibit S. enterica DXR, FR900098 was used as a control compound in the screening of novel compounds. The S. enterica DXR enzyme was screened for inhibition by the collection of compounds from the Pathogen Box. Compounds that exhibited the desired inhibitory activity, referred to as ‘hits’ were selected for further investigation. These hits were confirmed using the NADPH-dependent enzyme assay, resulting in the identification of two different DXR inhibitor compounds, MMV002816, also known as diethylcarbamazine, and MMV228911. The inhibitory concentration (IC50) values of FR900098, MMV002816 and MMV228911 against S. enterica DXR were 1.038 μM, 2.173 μM and 6.861 μM respectively. The binding mode of these compounds to S. enterica DXR could lead to the discovery of novel druggable sites on the enzyme and stimulate the development of new antibiotics that can be used for treating Salmonella infections.
- Full Text:
- Date Issued: 2020
- Authors: Ngcongco, Khanyisile
- Date: 2020
- Subjects: 1-Deoxy-D-xylulose 5-phosphate , Antibiotics , Drug development , Salmonella , Enterobacteriaceae , Vaccines , Plasmodium falciparum , Mycobacterium tuberculosis
- Language: English
- Type: text , Thesis , Masters , MSc
- Identifier: http://hdl.handle.net/10962/167132 , vital:41440
- Description: Invasive non-typhoidal Salmonella, caused by the intracellular pathogen Salmonella enterica, has emerged as a major cause of bloodstream infections. It remains a neglected infection responsible for many deaths in Africa, as it fails to receive the level of support that is given to most better known infections. There are currently no vaccines against invasive non-typhoidal Salmonella. First-line antibiotics have been used for treatment, however, the rise in the resistance of the bacteria against these antibiotics has made treatment of invasive salmonellosis into a clinical problem. Therefore, the discovery of new compounds for the development of antibiotic drugs is required. Central metabolic pathways can be a useful source for identifying drug targets and among these is the non-mevalonate pathway, one of the pathways used for the biosynthesis of isoprenoid precursors. The second step of the non-mevalonate pathway involves the NADPH-dependent reduction of 1-deoxy-D-xylulose 5-phosphate (DOXP) into 2-C-methyl-D-erythritol 4-phosphate (MEP). 1-Deoxy-D-xylulose 5-phosphate (DOXP) reductoisomerase plays a vital role in the catalysis of this reaction and requires NADPH and divalent metal cations as co-factors for its activity. In this investigation recombinant DOXP reductoisomerase from Salmonella enterica, Plasmodium falciparum and Mycobacterium tuberculosis were biochemically characterized as potential targets for developing drugs that could be used as treatment of the disease. The expression and nickel-chelate affinity purification of S. enterica DOXP reductoisomerase in a fully functional native state was successfully achieved. However, the expression and purification of P. falciparum DXR and M. tuberculosis DXR was unsuccessful due to the formation of insoluble inclusion bodies. Although alternative purification strategies were explored, including dialysis and slow dilution, these proteins remained insoluble, making their functional analysis not possible. An NADPH-dependent enzyme assay was used to determine the activity of S. enterica DXR. This assay monitors the reduction of DOXP to MEP by measuring the absorbance at 340 nm, which reflects the concentration of NADPH. An alternative assay, resazurin reduction, which monitors the NADPH-dependent reduction of resazurin to resorufin, was explored for detecting enzyme activity. The recombinant S. enterica DOXP reductoisomerase had a specific activity of 0.126 ± 0.0014 μmol/min/mg protein and a Km and Vmax of 881 μM and 0.249 μmol/min/mg respectively. FR900098, a derivative of fosmidomycin, is a well-known inhibitor of DXR, however, the sensitivity of S. enterica DXR towards FR900098 has not yet been reported. The NADPH dependent enzyme and resazurin reduction assays were used to determine whether FR900098 has enzyme inhibitory effects against S. enterica DXR. Upon confirming that FR900098 is able to inhibit S. enterica DXR, FR900098 was used as a control compound in the screening of novel compounds. The S. enterica DXR enzyme was screened for inhibition by the collection of compounds from the Pathogen Box. Compounds that exhibited the desired inhibitory activity, referred to as ‘hits’ were selected for further investigation. These hits were confirmed using the NADPH-dependent enzyme assay, resulting in the identification of two different DXR inhibitor compounds, MMV002816, also known as diethylcarbamazine, and MMV228911. The inhibitory concentration (IC50) values of FR900098, MMV002816 and MMV228911 against S. enterica DXR were 1.038 μM, 2.173 μM and 6.861 μM respectively. The binding mode of these compounds to S. enterica DXR could lead to the discovery of novel druggable sites on the enzyme and stimulate the development of new antibiotics that can be used for treating Salmonella infections.
- Full Text:
- Date Issued: 2020
Development of a low-cost bioprinting system for engineering of Human Tumour Models
- Authors: Fanucci, Sidne
- Date: 2020
- Subjects: Uncatalogued
- Language: English
- Type: thesis , text , Masters , MSc
- Identifier: http://hdl.handle.net/10962/163295 , vital:41026
- Description: Thesis (MSc)--Rhodes University, Faculty of Science, Biotechnology Innovation Centre, 2020.
- Full Text:
- Date Issued: 2020
- Authors: Fanucci, Sidne
- Date: 2020
- Subjects: Uncatalogued
- Language: English
- Type: thesis , text , Masters , MSc
- Identifier: http://hdl.handle.net/10962/163295 , vital:41026
- Description: Thesis (MSc)--Rhodes University, Faculty of Science, Biotechnology Innovation Centre, 2020.
- Full Text:
- Date Issued: 2020
Physical activity, physical fitness, sedentary behaviour and screen time profiles of primary school children in a school within the Makana Municipality, Eastern Cape, South Africa
- Authors: Kade, Andréa Gaby
- Date: 2021-04
- Subjects: Sedentary behavior in children -- South Africa -- Makana Municipality , Physical fitness for children -- South Africa -- Makana Municipality , Exercise -- Physiological aspects , Exercise -- Health aspects , Diabetes -- Risk factors , Heart -- Diseases -- Risk factors
- Language: English
- Type: thesis , text , Masters , MSc
- Identifier: http://hdl.handle.net/10962/177282 , vital:42806
- Description: There is a lack of data on the physical activity, physical fitness and sedentary behaviour of children in South Africa. Furthermore chronic diseases such as type II diabetes and coronary heart disease have been linked to childhood inactivity, and improving cardiorespiratory fitness and increasing levels of physical activity has been shown to be beneficial in reducing the risk of such diseases. In South Africa more broadly there is a lack of information on levels of physical activity and sedentary behaviour as well as physical fitness measures particularly in children. Objective: The purpose of this study was to enhance the existing body of knowledge on this, by measuring the prevalence of physical inactivity, sedentary behaviour and screen time of primary school children in a private school from the Makana Municipal region in the Eastern Cape Province of South Africa, where the evidence is most sparse. A secondary aim was to assess levels of physical fitness in this cohort, as well as to compare across grades and sexes. Method: After ethical approval was granted, stature and body mass measurements were taken and body mass index was computed for primary school children (Grade one to seven) from a private school in the Makana Municipality. Sitting stature was measured in order to determine each child’s peak height velocity and maturity offset. Five different physical fitness tests were conducted on the children and blood pressure and heart rate values were measured at rest. Physical activity and screen time questionnaires were completed by the children’s parents for a seven day period. Results: Females were found to mature faster than males. In addition females were more physically active (Females= 916 min/week; Males= 669 min/week) while also accumulating more sedentary time (Females= 1241 min/week; Males= 970 min/week) as compared to males, although no significant differences were found between males and females for these variables. The sample participated in more than 60 minutes of moderate-to-vigorous physical activity and less than two hours of screen time daily, which is in accordance with guidelines. No differences were found between grades and sexes for accumulated screen time. Strength increased significantly with grade and age, and there were also statistical differences between the sexes for all three strength measures with males being stronger than females. Females were more flexible than males and no statistical differences were found between sexes for the shuttle run test. Blood pressure correlated positively with mass, as did all the strength measures as well as maturity offset. No correlations were found between screen time and all other variables. A negative relationship was recorded between screen time and physical activity, although not significant. For females a strong positive correlation was found between sedentary behaviour and physical activity. Conclusion: The study was successful in adding to the body of knowledge regarding the prevalence of physical inactivity, sedentary behaviour and screen time within school children from the Makana Municipality in the Eastern Cape Province of South Africa. The sample was considered physically active as they accumulated on average more than 60 minutes of moderate-to-vigorous physical activity daily (Males= 96 min/day; Females 130 min/day), which is in accordance with guidelines recommended by the World Health Organization (World Health Organization, 2018). The sample accumulated more sedentary behaviour than physical activity, although not significant. Screen time was below regulations of two hours daily, indicating this population participated in more non screen related sedentary behaviour. More research is needed into the risks presented with different forms of sedentary behaviour. Physical fitness increased with increasing grade and age and males were considerably more fit. The current study did not present any concern with regards to the effects of increased physical activity and fitness levels within school aged children. More research into the current levels of physical activity, physical fitness and sedentary behaviour of school aged children in South Africa in general, and in the Eastern Cape Province, is needed. , Thesis (MSc) -- Faculty of Science, Human Kinetics and Ergonomics, 2021
- Full Text:
- Date Issued: 2021-04
- Authors: Kade, Andréa Gaby
- Date: 2021-04
- Subjects: Sedentary behavior in children -- South Africa -- Makana Municipality , Physical fitness for children -- South Africa -- Makana Municipality , Exercise -- Physiological aspects , Exercise -- Health aspects , Diabetes -- Risk factors , Heart -- Diseases -- Risk factors
- Language: English
- Type: thesis , text , Masters , MSc
- Identifier: http://hdl.handle.net/10962/177282 , vital:42806
- Description: There is a lack of data on the physical activity, physical fitness and sedentary behaviour of children in South Africa. Furthermore chronic diseases such as type II diabetes and coronary heart disease have been linked to childhood inactivity, and improving cardiorespiratory fitness and increasing levels of physical activity has been shown to be beneficial in reducing the risk of such diseases. In South Africa more broadly there is a lack of information on levels of physical activity and sedentary behaviour as well as physical fitness measures particularly in children. Objective: The purpose of this study was to enhance the existing body of knowledge on this, by measuring the prevalence of physical inactivity, sedentary behaviour and screen time of primary school children in a private school from the Makana Municipal region in the Eastern Cape Province of South Africa, where the evidence is most sparse. A secondary aim was to assess levels of physical fitness in this cohort, as well as to compare across grades and sexes. Method: After ethical approval was granted, stature and body mass measurements were taken and body mass index was computed for primary school children (Grade one to seven) from a private school in the Makana Municipality. Sitting stature was measured in order to determine each child’s peak height velocity and maturity offset. Five different physical fitness tests were conducted on the children and blood pressure and heart rate values were measured at rest. Physical activity and screen time questionnaires were completed by the children’s parents for a seven day period. Results: Females were found to mature faster than males. In addition females were more physically active (Females= 916 min/week; Males= 669 min/week) while also accumulating more sedentary time (Females= 1241 min/week; Males= 970 min/week) as compared to males, although no significant differences were found between males and females for these variables. The sample participated in more than 60 minutes of moderate-to-vigorous physical activity and less than two hours of screen time daily, which is in accordance with guidelines. No differences were found between grades and sexes for accumulated screen time. Strength increased significantly with grade and age, and there were also statistical differences between the sexes for all three strength measures with males being stronger than females. Females were more flexible than males and no statistical differences were found between sexes for the shuttle run test. Blood pressure correlated positively with mass, as did all the strength measures as well as maturity offset. No correlations were found between screen time and all other variables. A negative relationship was recorded between screen time and physical activity, although not significant. For females a strong positive correlation was found between sedentary behaviour and physical activity. Conclusion: The study was successful in adding to the body of knowledge regarding the prevalence of physical inactivity, sedentary behaviour and screen time within school children from the Makana Municipality in the Eastern Cape Province of South Africa. The sample was considered physically active as they accumulated on average more than 60 minutes of moderate-to-vigorous physical activity daily (Males= 96 min/day; Females 130 min/day), which is in accordance with guidelines recommended by the World Health Organization (World Health Organization, 2018). The sample accumulated more sedentary behaviour than physical activity, although not significant. Screen time was below regulations of two hours daily, indicating this population participated in more non screen related sedentary behaviour. More research is needed into the risks presented with different forms of sedentary behaviour. Physical fitness increased with increasing grade and age and males were considerably more fit. The current study did not present any concern with regards to the effects of increased physical activity and fitness levels within school aged children. More research into the current levels of physical activity, physical fitness and sedentary behaviour of school aged children in South Africa in general, and in the Eastern Cape Province, is needed. , Thesis (MSc) -- Faculty of Science, Human Kinetics and Ergonomics, 2021
- Full Text:
- Date Issued: 2021-04
Growth and photosynthetic responses of Acacia (Vachellia) seedlings to atmospheric CO2 increased from glacial to current concentrations: underlying mechanisms and ecological implications
- Authors: Anderson, Bruce Maurice
- Date: 2020
- Subjects: Acacia vachellia , Acacia vachellia -- Growth , Acacia -- South Africa
- Language: English
- Type: text , Thesis , Masters , MSc
- Identifier: http://hdl.handle.net/10962/138182 , vital:37604
- Description: The African Acacia species Vachellia karroo, V. robusta, V. nilotica, and V. tortilis are some of the most invasive species implicated in bush encroachment and woody thickening of historically open savannas in southern Africa. This is partially explained by historic increases in atmospheric CO2 concentrations, which are proposed to have promoted the growth and survivorship of C3 tree seedlings relative to C4 grasses. However, the uniformity of CO2 responsiveness and differences among Vachellia species remain largely undetermined. Here we investigate the growth and photosynthetic responses of four Vachellia species, all implicated in woody encroachment, but originating from distinct climatic niches. Exposing these species to a range of sub-ambient CO2 concentrations (12 – 40 Pa) showed that V. karroo, V. robusta, V. nilotica and V. tortilis all responded strongly and fairly consistently to increasing CO2 concentrations, acting as a ‘functional type’ despite being selected from different geographic regions and having different climatic niches. Combined average net CO2 assimilation rates increased by 130% despite significant, but low levels of down-regulation and decreased stomatal conductance. The increased photosynthetic rates stimulated growth and biomass production in all compartments, with no significant differences in interspecific above and below ground allocation. Growth rates and dry biomass increased by 50% and 186%, respectively, while leaf level water use efficiency (ratio of net CO2 assimilation rate to transpiration rate) increased by an average of 218%. When this was scaled to the whole plant level, this stimulation was decreased to 80%. The decrease was the result of the CO2 stimulated increase in canopy areas, which increased leaf area for water loss. The seedlings’ total number of spinescent physical defenses, as well as the average mass and spine mass fraction also increased with rising CO2. These thicker spines could act as better deterrents against vertebrate browsers. Spine density was unchanged, however, showing that the increased spine numbers were associated with larger seedlings at higher CO2 rather than an increase in the number of spines per stem length. The stimulatory effects of increasing CO2 concentrations since the last glacial maximum and resultant increases in seedling growth and biomass are likely to have had important consequences for the survival and establishment of Acacia seedlings. Tolerance of drought and disturbance has been related to seedling size, hence stimulating the growth rate could confer disturbance tolerance and this tolerance would develop more rapidly with increasing CO2 concentrations. Furthermore, increased nitrogen and water use efficiency have the potential to support seedling establishment in environments where these resources would otherwise be limited at lower atmospheric CO2 concentrations. Resulting in a larger proportion of CO2 fertilization responsive woody seedlings surviving the seedling size classes, and persisting within historically open savannas. Where interspecific differences occurred they are likely to have arisen from adaptation to specific climates where these species are native and selection would have been driven by factors such climate, resource availability, levels of disturbance and competitive interactions. V. karroo had the highest growth rates and strong CO2 driven increases in biomass accumulation, despite having the lowest inherent photosynthetic rates. V. karroo also had the lowest increase in water use efficiency and high transpiration rates could potentially increase access to soil nutrients through mass flow. This species had the highest mean spine mass and showed significant increases in spine mass fraction at elevated CO2 concentrations, which may be important for deterring herbivores. V. robusta’s distribution to the mesic east coast of Africa suggests that water is an important limitation to its distribution. Hence, the CO2 stimulated increase in water use efficiency at both leaf and whole canopy level allows speculation that this may be an important driver of this species’ range expansion, which might continue if increasing levels of CO2 continue to promote water use efficiency. V. nilotica occupies a broad range of habitats, inhabiting large areas of the subtropics both north and south of the equator, with the strongest climatic correlates being the precipitation of the wettest quarter followed by high temperature seasonality. In response to increasing CO2, V. nilotica showed overall strong increases in growth, water use efficiency, and physical defenses. These responses may explain why V. nilotica has been such a successful encroacher in a broad range of habitats where limitations are likely to include multiple climatic factors and disturbances. V. tortilis has the widest distribution of all the species studied, covering broad ranges of Africa and only being excluded from the wettest parts of the equator and driest parts of the deserts. In these experiments this species showed the lowest biomass responsiveness to CO2, but had especially large increases in water use efficiency at both the leaf and canopy level. This may have been an important driver for this species’ encroachment into the more arid parts of its distribution, however this link will need to be verified with further experimentation.
- Full Text:
- Date Issued: 2020
- Authors: Anderson, Bruce Maurice
- Date: 2020
- Subjects: Acacia vachellia , Acacia vachellia -- Growth , Acacia -- South Africa
- Language: English
- Type: text , Thesis , Masters , MSc
- Identifier: http://hdl.handle.net/10962/138182 , vital:37604
- Description: The African Acacia species Vachellia karroo, V. robusta, V. nilotica, and V. tortilis are some of the most invasive species implicated in bush encroachment and woody thickening of historically open savannas in southern Africa. This is partially explained by historic increases in atmospheric CO2 concentrations, which are proposed to have promoted the growth and survivorship of C3 tree seedlings relative to C4 grasses. However, the uniformity of CO2 responsiveness and differences among Vachellia species remain largely undetermined. Here we investigate the growth and photosynthetic responses of four Vachellia species, all implicated in woody encroachment, but originating from distinct climatic niches. Exposing these species to a range of sub-ambient CO2 concentrations (12 – 40 Pa) showed that V. karroo, V. robusta, V. nilotica and V. tortilis all responded strongly and fairly consistently to increasing CO2 concentrations, acting as a ‘functional type’ despite being selected from different geographic regions and having different climatic niches. Combined average net CO2 assimilation rates increased by 130% despite significant, but low levels of down-regulation and decreased stomatal conductance. The increased photosynthetic rates stimulated growth and biomass production in all compartments, with no significant differences in interspecific above and below ground allocation. Growth rates and dry biomass increased by 50% and 186%, respectively, while leaf level water use efficiency (ratio of net CO2 assimilation rate to transpiration rate) increased by an average of 218%. When this was scaled to the whole plant level, this stimulation was decreased to 80%. The decrease was the result of the CO2 stimulated increase in canopy areas, which increased leaf area for water loss. The seedlings’ total number of spinescent physical defenses, as well as the average mass and spine mass fraction also increased with rising CO2. These thicker spines could act as better deterrents against vertebrate browsers. Spine density was unchanged, however, showing that the increased spine numbers were associated with larger seedlings at higher CO2 rather than an increase in the number of spines per stem length. The stimulatory effects of increasing CO2 concentrations since the last glacial maximum and resultant increases in seedling growth and biomass are likely to have had important consequences for the survival and establishment of Acacia seedlings. Tolerance of drought and disturbance has been related to seedling size, hence stimulating the growth rate could confer disturbance tolerance and this tolerance would develop more rapidly with increasing CO2 concentrations. Furthermore, increased nitrogen and water use efficiency have the potential to support seedling establishment in environments where these resources would otherwise be limited at lower atmospheric CO2 concentrations. Resulting in a larger proportion of CO2 fertilization responsive woody seedlings surviving the seedling size classes, and persisting within historically open savannas. Where interspecific differences occurred they are likely to have arisen from adaptation to specific climates where these species are native and selection would have been driven by factors such climate, resource availability, levels of disturbance and competitive interactions. V. karroo had the highest growth rates and strong CO2 driven increases in biomass accumulation, despite having the lowest inherent photosynthetic rates. V. karroo also had the lowest increase in water use efficiency and high transpiration rates could potentially increase access to soil nutrients through mass flow. This species had the highest mean spine mass and showed significant increases in spine mass fraction at elevated CO2 concentrations, which may be important for deterring herbivores. V. robusta’s distribution to the mesic east coast of Africa suggests that water is an important limitation to its distribution. Hence, the CO2 stimulated increase in water use efficiency at both leaf and whole canopy level allows speculation that this may be an important driver of this species’ range expansion, which might continue if increasing levels of CO2 continue to promote water use efficiency. V. nilotica occupies a broad range of habitats, inhabiting large areas of the subtropics both north and south of the equator, with the strongest climatic correlates being the precipitation of the wettest quarter followed by high temperature seasonality. In response to increasing CO2, V. nilotica showed overall strong increases in growth, water use efficiency, and physical defenses. These responses may explain why V. nilotica has been such a successful encroacher in a broad range of habitats where limitations are likely to include multiple climatic factors and disturbances. V. tortilis has the widest distribution of all the species studied, covering broad ranges of Africa and only being excluded from the wettest parts of the equator and driest parts of the deserts. In these experiments this species showed the lowest biomass responsiveness to CO2, but had especially large increases in water use efficiency at both the leaf and canopy level. This may have been an important driver for this species’ encroachment into the more arid parts of its distribution, however this link will need to be verified with further experimentation.
- Full Text:
- Date Issued: 2020
An investigation into the application of Distributed Endpoint Processing to 3D Immersive Audio Rendering
- Authors: Devonport, Robin Sean
- Date: 2020
- Subjects: Uncatalogued
- Language: English
- Type: thesis , text , Masters , MSc
- Identifier: http://hdl.handle.net/10962/163258 , vital:41022
- Description: Thesis (MSc)--Rhodes University, Faculty of Science, Computer Science, 2020.
- Full Text:
- Date Issued: 2020
- Authors: Devonport, Robin Sean
- Date: 2020
- Subjects: Uncatalogued
- Language: English
- Type: thesis , text , Masters , MSc
- Identifier: http://hdl.handle.net/10962/163258 , vital:41022
- Description: Thesis (MSc)--Rhodes University, Faculty of Science, Computer Science, 2020.
- Full Text:
- Date Issued: 2020
The exploration of ARF1 screening assays to determine the drug status of ARF1 in cancer and malaria
- Authors: Ntlantsana, Apelele
- Date: 2020
- Subjects: ADP ribosylation , Golgi apparatus , Guanosine triphosphatase , G proteins , Malariotherapy , Malaria -- Research , Cancer -- Chemotherapy , Malaria -- Chemotherpay
- Language: English
- Type: text , Thesis , Masters , MSc
- Identifier: http://hdl.handle.net/10962/167232 , vital:41458
- Description: ARF GTPases are key regulators of the secretory and endocytic pathways. ARF1 is involved in the secretory pathway. ARF1 has been implicated in the endoplasmic reticulum to Golgi transport, function of the Golgi apparatus and transport from the trans-Golgi network to endosomes. ARFs cycle between active GTP-bound and inactive GDP-bound conformations. GDP/GTP cycling is regulated by large families of guanine nucleotide exchange factors (GEFs) and GTPase activating proteins (GAPs). ARF GEFs facilitate the activation of ARFs by mediating the exchange of GDP for GTP, while ARF GAPs terminate ARF function by stimulating the hydrolysis of the terminal phosphate group of GTP. Based on existing evidence gained from gene manipulation and cell biological investigations, ARF1 has been shown to be fundamentally important for cancer cell proliferation and metastasis and may be a promising target for the development of anti-cancer drugs. Additionally, the conservation of ARFs in eukaryotic organisms leads to an interesting question of whether a single drug target can be used to target multiple diseases. In this case, can a human cancer drug employed for cancer therapy be used in anti-malarial drug therapies? To confirm the drug target status of ARFs using chemical validation experiments, novel inhibitory compounds are needed. This requires the development of complex in vitro protein- protein interaction assays that can be used to screen chemical libraries for ARF GTPase inhibitors. In this study, we developed a fluorescence resonance energy transfer (FRET) assay and a novel in vitro colorimetric plate-based assay to detect the activation status of truncated human and Plasmodium falciparum ARF1. In the case of the FRET assay, active (GTP-bound) and inactive (GDP-bound) ARF1 could be distinguished with Z-factor values >0.5, suggesting that further development of the assay format to identify GEF and GAP inhibitors may be feasible. In the case of the colorimetric assay, robust signals could be detected and the assay was useful for detecting the activation status of ARF1. However, although the activation of ARF1 by the Sec7 domains of the BIG1 and ARNO was detectable, signals were not robust enough to employ in screening campaigns.
- Full Text:
- Date Issued: 2020
- Authors: Ntlantsana, Apelele
- Date: 2020
- Subjects: ADP ribosylation , Golgi apparatus , Guanosine triphosphatase , G proteins , Malariotherapy , Malaria -- Research , Cancer -- Chemotherapy , Malaria -- Chemotherpay
- Language: English
- Type: text , Thesis , Masters , MSc
- Identifier: http://hdl.handle.net/10962/167232 , vital:41458
- Description: ARF GTPases are key regulators of the secretory and endocytic pathways. ARF1 is involved in the secretory pathway. ARF1 has been implicated in the endoplasmic reticulum to Golgi transport, function of the Golgi apparatus and transport from the trans-Golgi network to endosomes. ARFs cycle between active GTP-bound and inactive GDP-bound conformations. GDP/GTP cycling is regulated by large families of guanine nucleotide exchange factors (GEFs) and GTPase activating proteins (GAPs). ARF GEFs facilitate the activation of ARFs by mediating the exchange of GDP for GTP, while ARF GAPs terminate ARF function by stimulating the hydrolysis of the terminal phosphate group of GTP. Based on existing evidence gained from gene manipulation and cell biological investigations, ARF1 has been shown to be fundamentally important for cancer cell proliferation and metastasis and may be a promising target for the development of anti-cancer drugs. Additionally, the conservation of ARFs in eukaryotic organisms leads to an interesting question of whether a single drug target can be used to target multiple diseases. In this case, can a human cancer drug employed for cancer therapy be used in anti-malarial drug therapies? To confirm the drug target status of ARFs using chemical validation experiments, novel inhibitory compounds are needed. This requires the development of complex in vitro protein- protein interaction assays that can be used to screen chemical libraries for ARF GTPase inhibitors. In this study, we developed a fluorescence resonance energy transfer (FRET) assay and a novel in vitro colorimetric plate-based assay to detect the activation status of truncated human and Plasmodium falciparum ARF1. In the case of the FRET assay, active (GTP-bound) and inactive (GDP-bound) ARF1 could be distinguished with Z-factor values >0.5, suggesting that further development of the assay format to identify GEF and GAP inhibitors may be feasible. In the case of the colorimetric assay, robust signals could be detected and the assay was useful for detecting the activation status of ARF1. However, although the activation of ARF1 by the Sec7 domains of the BIG1 and ARNO was detectable, signals were not robust enough to employ in screening campaigns.
- Full Text:
- Date Issued: 2020
Sexual attraction and mating compatibility between Thaumatotibia leucotreta populations and implications for semiochemical dependent technologies
- Authors: Upfold, Jennifer Kate
- Date: 2020
- Subjects: Cryptophlebia leucotreta -- South Africa , Cryptophlebia leucotreta -- Reproduction , Citrus -- Disease and pests -- Control -- South Africa , Insect sterilization -- South Africa , Pheromones , Pheromone traps
- Language: English
- Type: text , Thesis , Masters , MSc
- Identifier: http://hdl.handle.net/10962/148526 , vital:38747
- Description: False codling moth (FCM), Thaumatotibia leucotreta (Meyrick), is the most important pest for the cultivation of citrus in South Africa. False codling moth is indigenous to southern Africa and is a regulated pest of many international markets for phytosanitary concerns. Considerable research efforts have been invested in the past decades to develop semiochemcial technologies, such as monitoring with sex pheromones, attract-and-kill, mating disruption and the sterile insect technique. One of the potential obstacles identified with semiochemical control is the differences in the ratio of the compounds comprising the sex pheromone at different geographical locations, resulting in what is known as regional attraction. This has been identified in FCM populations from three different countries, however, regional attraction within South African FCM populations was unknown. Therefore, the study assessed the genetic integrity of five laboratory-reared FCM populations originating from geographically isolated populations in South Africa using the AFLP technique in order to assess regional attractiveness within the country. The results found isolated populations from Addo, Citrusdal, Marble Hall, Nelspruit and a fifth group found to be closely related to Addo and Citrusdal called the ‘Old’ colony. These five genetically isolated populations as well as a population from Xsit (Pty) Ltd, used for the sterile insect technique (SIT), were used in regional attractiveness trials. Males were significantly (P = <0.05) more attracted to females originating from the same population. No significant attraction could be determined from the sterile males, as the recapture rates in the trap were too low. Furthermore, regional attractiveness was assessed through choice/ no-choice mating compatibility trials. Significant sexual isolation (ISI) occurred between mating combinations Addo × Nelspruit (ISI = 0,13; t2 = 6.23; p = 0.02), Addo × Marble Hall (ISI = 0,11; t2 = 4.72; p = 0.04), Citrusdal × Nelspruit (ISI = 0,11; t2 = 4.95; p = 0.04), and Citrusdal × Marble Hall (ISI = 0,12; t2 = 4.31; p = 0.04). In these combinations, Addo and Citrusdal males were found to have outcompeted Nelspruit and Marble Hall males for more mating events. Significant sexual isolation was also recorded for Sterile × Marble Hall (ISI = 0.12; t2 = 4.98; p =0.01) and Sterile × Citrusdal (ISI = 0.13; t2 = 3.96; p = 0.01) populations. The male relative performance index was significant in both combinations, indicating that non-sterile laboratory males outcompeted the sterile males in these two combinations. When given no choice, evaluated as spermatophore transfer/ female/ 48h, all males (including sterile) were successful in transferring spermatophores to all FCM populations, with no significant differences. These results indicate that there may be incipient pre-isolation mechanisms affected by local natural selection, resulting in localised sexual attraction via differences in the sex pheromone ratios. These findings provide important information for semiochemical technologies and the implication of these results with regard to monitoring with sex pheromones, attract-and-kill, mating disruption and sterile insect technique are discussed.
- Full Text:
- Date Issued: 2020
- Authors: Upfold, Jennifer Kate
- Date: 2020
- Subjects: Cryptophlebia leucotreta -- South Africa , Cryptophlebia leucotreta -- Reproduction , Citrus -- Disease and pests -- Control -- South Africa , Insect sterilization -- South Africa , Pheromones , Pheromone traps
- Language: English
- Type: text , Thesis , Masters , MSc
- Identifier: http://hdl.handle.net/10962/148526 , vital:38747
- Description: False codling moth (FCM), Thaumatotibia leucotreta (Meyrick), is the most important pest for the cultivation of citrus in South Africa. False codling moth is indigenous to southern Africa and is a regulated pest of many international markets for phytosanitary concerns. Considerable research efforts have been invested in the past decades to develop semiochemcial technologies, such as monitoring with sex pheromones, attract-and-kill, mating disruption and the sterile insect technique. One of the potential obstacles identified with semiochemical control is the differences in the ratio of the compounds comprising the sex pheromone at different geographical locations, resulting in what is known as regional attraction. This has been identified in FCM populations from three different countries, however, regional attraction within South African FCM populations was unknown. Therefore, the study assessed the genetic integrity of five laboratory-reared FCM populations originating from geographically isolated populations in South Africa using the AFLP technique in order to assess regional attractiveness within the country. The results found isolated populations from Addo, Citrusdal, Marble Hall, Nelspruit and a fifth group found to be closely related to Addo and Citrusdal called the ‘Old’ colony. These five genetically isolated populations as well as a population from Xsit (Pty) Ltd, used for the sterile insect technique (SIT), were used in regional attractiveness trials. Males were significantly (P = <0.05) more attracted to females originating from the same population. No significant attraction could be determined from the sterile males, as the recapture rates in the trap were too low. Furthermore, regional attractiveness was assessed through choice/ no-choice mating compatibility trials. Significant sexual isolation (ISI) occurred between mating combinations Addo × Nelspruit (ISI = 0,13; t2 = 6.23; p = 0.02), Addo × Marble Hall (ISI = 0,11; t2 = 4.72; p = 0.04), Citrusdal × Nelspruit (ISI = 0,11; t2 = 4.95; p = 0.04), and Citrusdal × Marble Hall (ISI = 0,12; t2 = 4.31; p = 0.04). In these combinations, Addo and Citrusdal males were found to have outcompeted Nelspruit and Marble Hall males for more mating events. Significant sexual isolation was also recorded for Sterile × Marble Hall (ISI = 0.12; t2 = 4.98; p =0.01) and Sterile × Citrusdal (ISI = 0.13; t2 = 3.96; p = 0.01) populations. The male relative performance index was significant in both combinations, indicating that non-sterile laboratory males outcompeted the sterile males in these two combinations. When given no choice, evaluated as spermatophore transfer/ female/ 48h, all males (including sterile) were successful in transferring spermatophores to all FCM populations, with no significant differences. These results indicate that there may be incipient pre-isolation mechanisms affected by local natural selection, resulting in localised sexual attraction via differences in the sex pheromone ratios. These findings provide important information for semiochemical technologies and the implication of these results with regard to monitoring with sex pheromones, attract-and-kill, mating disruption and sterile insect technique are discussed.
- Full Text:
- Date Issued: 2020
Metallophthalocyanines linked to metal nanoparticles and folic acid for use in photodynamic therapy of cancer and photoinactivation of bacterial microorganisms.
- Authors: Matlou, Gauta Gold
- Date: 2020
- Subjects: Cancer -- Photochemotherapy , Nanoparticles , Phthalocyanines , Anti-infective agents -- Therapeutic use , Photochemotherapy , Photochemistry
- Language: English
- Type: text , Thesis , Masters , MSc
- Identifier: http://hdl.handle.net/10962/166540 , vital:41377
- Description: This thesis presents on the synthesis and characterization of novel asymmetric and symmetrical metallophthalocyanines (MPcs) substituted with carboxylic acid functional groups and centrally metallated with zinc and indium. The MPcs are further covalently linked to cysteine capped silver nanoparticles (cys-AgNPs), amino functionalized magnetic nanoparticles (AMNPs) and folic acid (FA) through an amide bond between the carboxylic group of MPcs and the amino group of FA, cys-AgNPs or AMNPs. The covalent linkage of MPcs to FA improved the water solubility of MPcs and allowed for singlet oxygen quantum yield determination in water. Asymmetric MPcs and their conjugates were found to have improved photochemical and photophysical properties compared to symmetrical MPcs and their conjugates. The heavy atom effect of AMNPs and AgNPs improved the triplet and singlet oxygen quantum yields of MPcs. MPcs and their conjugates (MPc-FA, MPc-AMNPs, MPc-AgNPs) were found to have lower in vitro dark cytotoxicity and higher photodynamic therapy (PDT) activity on MCF-7 breast cancer cells. The water soluble MPc-FA had better PDT activity when compared to MPc-AMNPs due to the active targeting of folic acid-folate binding on cancer cell surface. MPcs and MPc-AgNPs conjugates also showed excellent in vitro cytotoxicity on S. aureus under light irradiation compared to dark cytotoxicity. The photosensitizing properties of MPcs and their conjugates are demonstrated for the first time in this thesis, both on breast cancer cells (MCF-7) through photodynamic therapy and on microorganisms (S. aureus) through photodynamic antimicrobial chemotherapy.
- Full Text:
- Date Issued: 2020
- Authors: Matlou, Gauta Gold
- Date: 2020
- Subjects: Cancer -- Photochemotherapy , Nanoparticles , Phthalocyanines , Anti-infective agents -- Therapeutic use , Photochemotherapy , Photochemistry
- Language: English
- Type: text , Thesis , Masters , MSc
- Identifier: http://hdl.handle.net/10962/166540 , vital:41377
- Description: This thesis presents on the synthesis and characterization of novel asymmetric and symmetrical metallophthalocyanines (MPcs) substituted with carboxylic acid functional groups and centrally metallated with zinc and indium. The MPcs are further covalently linked to cysteine capped silver nanoparticles (cys-AgNPs), amino functionalized magnetic nanoparticles (AMNPs) and folic acid (FA) through an amide bond between the carboxylic group of MPcs and the amino group of FA, cys-AgNPs or AMNPs. The covalent linkage of MPcs to FA improved the water solubility of MPcs and allowed for singlet oxygen quantum yield determination in water. Asymmetric MPcs and their conjugates were found to have improved photochemical and photophysical properties compared to symmetrical MPcs and their conjugates. The heavy atom effect of AMNPs and AgNPs improved the triplet and singlet oxygen quantum yields of MPcs. MPcs and their conjugates (MPc-FA, MPc-AMNPs, MPc-AgNPs) were found to have lower in vitro dark cytotoxicity and higher photodynamic therapy (PDT) activity on MCF-7 breast cancer cells. The water soluble MPc-FA had better PDT activity when compared to MPc-AMNPs due to the active targeting of folic acid-folate binding on cancer cell surface. MPcs and MPc-AgNPs conjugates also showed excellent in vitro cytotoxicity on S. aureus under light irradiation compared to dark cytotoxicity. The photosensitizing properties of MPcs and their conjugates are demonstrated for the first time in this thesis, both on breast cancer cells (MCF-7) through photodynamic therapy and on microorganisms (S. aureus) through photodynamic antimicrobial chemotherapy.
- Full Text:
- Date Issued: 2020
Nutrient removal and biofuel potential of MaB-floc biomass from an integrated algal pond system treating domestic sewage
- Authors: Sibelo, Linda
- Date: 2020
- Subjects: Biomass energy , Waste products as fuel , Algal biofuels , Sewage -- Purification -- Nutrient removal
- Language: English
- Type: text , Thesis , Masters , MSc
- Identifier: http://hdl.handle.net/10962/144955 , vital:38395
- Description: Integrated algal pond systems (IAPS) are a passive water treatment technology derived from the Oswald designed advanced integrated wastewater pond systems (AIWPS®) and effect wastewater treatment based on biological activity of microorganisms within the system, solar energy and gravity. The technology consists of an advanced facultative pond (AFP), a series of interconnected high rate algal oxidation ponds (HRAOP) and algal settling ponds. The symbiotic relationship between microalgae and bacteria facilitated by paddlewheel mixing of HRAOP results in the formation of biomass aggregates known as MaB-flocs. MaB-floc formation enhances nutrient abstraction, gravitational sedimentation and separation from water hence forming two product streams; recyclable water and biomass, both with valorisation potential. This work aimed to determine the suitability of MaB-floc biomass generated in the HRAOP of an IAPS treating domestic sewage as feedstock for biofuel production based on the content of carbohydrate and lipid. Nutrient removal efficiency, biomass productivity and bulk lipid and carbohydrate concentration were monitored for two consecutive three-month periods in the winter and summer seasons of 2018/19. Maximum removal efficiencies of nitrogen and phosphorus were determined as 71% and 75% respectively, demonstrating the efficiency of IAPS as a wastewater treatment technology. MaB-floc biomass productivity in winter and summer was 9.4 g/m2/d and 16.5 g/m2/d respectively indicating the heavy influence of seasonal temperature, possibly day length, and solar irradiation on biomass productivity in the HRAOP. Summer productivity was lower than the maximum theoretical productivity of 25 g/m2/d possibly due to photoinhibition of photosynthesis as well as grazing pressures caused by the proliferation of rotifers mainly of the Brachionus genus. MaB-floc biomass consistently contained higher amounts of carbohydrate than lipid despite the changes in species dominance from Scenedesmus sp. and Desmodesmus sp. in winter to Pediastrum sp. in summer. Variations in MaB-floc biomass carbohydrate content were linked to changes in nitrogen concentration, mainly in the form of nitrates. Lower nitrogen concentration significantly increased the carbohydrate content of MaB-floc biomass from 17.5 ± 0.15% to 33.5 ± 0.3 % recorded in summer. In winter, biomass carbohydrate increased from 18.3 ± 1.2% to 35.8 ± 0.3%.To induce accumulation of carbohydrates through nitrogen starvation, isolated microalgal species native to the HRAOPs of the IAPS at Institute for Environmental Biotechnology Rhodes University(EBRU) were used. The outcome from the laboratory studies showed that carbon partitioning within isolated strains could be altered from carbohydrate to lipid which is more energy-rich. Hence, exploring the biodiesel production option using HRAOP MaB-floc biomass, which had a lipid content ranging between 12.1 ± 0.64 % and 13.9 ± 0.5 %, would require a preconditioning step in the form of nitrogen starvation to enhance its lipid content. Overall, the outcome of outdoor monitoring studies on biomass biochemical composition indicated that HRAOPs operating under natural environmental conditions preferentially generated a biomass rich in carbohydrate. Therefore, anaerobic digestion may be a more viable option for HRAOP MaB-floc biomass because of the high carbohydrate levels ranging between 24.9 ± 0.6 % and 25.6 ± 1.3 % of the dry MaB-floc biomass weight. Despite the low biomass C/N ratio (7.1 to 7.8), the MaB-floc biomass can be anaerobically co-digested with a higher C/N ratio (24) substrate such as in-pond digester sludge, to improve methane yields calculated to be between 0.31 m3 CH4/ kg MaB-floc biomass and 0.33 m3 CH4/ kg MaB-floc biomass. Anaerobic digestion of biomass also produces CO2 which can be recovered and added to HRAOPs to enhance MaB-floc biomass productivity while lowering greenhouse gas emissions from a wastewater treatment plant. The digestate from the anaerobic process, which is rich in nitrogen and phosphorus can be used as a biofertiliser. Thus, a potential MaB-floc biomass biorefinery consisting of biogas and bio-fertiliser pathways can be established using IAPS treating sewage as the platform technology. IAPS is a system designed to operate in a way that is passive and without substantial environmental impact but technological innovations and a reduction in the size of the system are required to make the technology more acceptable.
- Full Text:
- Date Issued: 2020
- Authors: Sibelo, Linda
- Date: 2020
- Subjects: Biomass energy , Waste products as fuel , Algal biofuels , Sewage -- Purification -- Nutrient removal
- Language: English
- Type: text , Thesis , Masters , MSc
- Identifier: http://hdl.handle.net/10962/144955 , vital:38395
- Description: Integrated algal pond systems (IAPS) are a passive water treatment technology derived from the Oswald designed advanced integrated wastewater pond systems (AIWPS®) and effect wastewater treatment based on biological activity of microorganisms within the system, solar energy and gravity. The technology consists of an advanced facultative pond (AFP), a series of interconnected high rate algal oxidation ponds (HRAOP) and algal settling ponds. The symbiotic relationship between microalgae and bacteria facilitated by paddlewheel mixing of HRAOP results in the formation of biomass aggregates known as MaB-flocs. MaB-floc formation enhances nutrient abstraction, gravitational sedimentation and separation from water hence forming two product streams; recyclable water and biomass, both with valorisation potential. This work aimed to determine the suitability of MaB-floc biomass generated in the HRAOP of an IAPS treating domestic sewage as feedstock for biofuel production based on the content of carbohydrate and lipid. Nutrient removal efficiency, biomass productivity and bulk lipid and carbohydrate concentration were monitored for two consecutive three-month periods in the winter and summer seasons of 2018/19. Maximum removal efficiencies of nitrogen and phosphorus were determined as 71% and 75% respectively, demonstrating the efficiency of IAPS as a wastewater treatment technology. MaB-floc biomass productivity in winter and summer was 9.4 g/m2/d and 16.5 g/m2/d respectively indicating the heavy influence of seasonal temperature, possibly day length, and solar irradiation on biomass productivity in the HRAOP. Summer productivity was lower than the maximum theoretical productivity of 25 g/m2/d possibly due to photoinhibition of photosynthesis as well as grazing pressures caused by the proliferation of rotifers mainly of the Brachionus genus. MaB-floc biomass consistently contained higher amounts of carbohydrate than lipid despite the changes in species dominance from Scenedesmus sp. and Desmodesmus sp. in winter to Pediastrum sp. in summer. Variations in MaB-floc biomass carbohydrate content were linked to changes in nitrogen concentration, mainly in the form of nitrates. Lower nitrogen concentration significantly increased the carbohydrate content of MaB-floc biomass from 17.5 ± 0.15% to 33.5 ± 0.3 % recorded in summer. In winter, biomass carbohydrate increased from 18.3 ± 1.2% to 35.8 ± 0.3%.To induce accumulation of carbohydrates through nitrogen starvation, isolated microalgal species native to the HRAOPs of the IAPS at Institute for Environmental Biotechnology Rhodes University(EBRU) were used. The outcome from the laboratory studies showed that carbon partitioning within isolated strains could be altered from carbohydrate to lipid which is more energy-rich. Hence, exploring the biodiesel production option using HRAOP MaB-floc biomass, which had a lipid content ranging between 12.1 ± 0.64 % and 13.9 ± 0.5 %, would require a preconditioning step in the form of nitrogen starvation to enhance its lipid content. Overall, the outcome of outdoor monitoring studies on biomass biochemical composition indicated that HRAOPs operating under natural environmental conditions preferentially generated a biomass rich in carbohydrate. Therefore, anaerobic digestion may be a more viable option for HRAOP MaB-floc biomass because of the high carbohydrate levels ranging between 24.9 ± 0.6 % and 25.6 ± 1.3 % of the dry MaB-floc biomass weight. Despite the low biomass C/N ratio (7.1 to 7.8), the MaB-floc biomass can be anaerobically co-digested with a higher C/N ratio (24) substrate such as in-pond digester sludge, to improve methane yields calculated to be between 0.31 m3 CH4/ kg MaB-floc biomass and 0.33 m3 CH4/ kg MaB-floc biomass. Anaerobic digestion of biomass also produces CO2 which can be recovered and added to HRAOPs to enhance MaB-floc biomass productivity while lowering greenhouse gas emissions from a wastewater treatment plant. The digestate from the anaerobic process, which is rich in nitrogen and phosphorus can be used as a biofertiliser. Thus, a potential MaB-floc biomass biorefinery consisting of biogas and bio-fertiliser pathways can be established using IAPS treating sewage as the platform technology. IAPS is a system designed to operate in a way that is passive and without substantial environmental impact but technological innovations and a reduction in the size of the system are required to make the technology more acceptable.
- Full Text:
- Date Issued: 2020
Building a flexible and inexpensive multi-layer switch for software-defined networks
- Authors: Magwenzi, Tinashe
- Date: 2020
- Subjects: Software-defined networking (Computer network technology) , Telecommunication -- Switching systems , OpenFlow (Computer network protocol) , Local area networks (Computer networks)
- Language: English
- Type: text , Thesis , Masters , MSc
- Identifier: http://hdl.handle.net/10962/142841 , vital:38122
- Description: Software-Defined Networking (SDN) is a paradigm which enables the realisation of programmable network through the separation of the control logic from the forwarding functions. This separation is a departure from the traditional architecture. Much of the work done in SDN enabled devices has concentrated on higher end, high speed networks (10s GBit/s 100s GBit/s), rather than the relatively low bandwidth links (10s MBit/s to a few GBit/s) which are seen, for example, in South Africa. As SDN is increasingly becoming more accepted, due to its advantages over the traditional networks, it has been adopted for industrial purposes such as networking in data centres and network providers. The demand for programmable networks is increasing but is limited by the ability of providers to upgrade their infrastructure. In addition, as access to the Internet has become less expensive, the use of Internet is increasing in academic institutions, NGOs, and small to medium enterprises. This thesis details a means of building and managing a small scale Software-Defined Network using commodity hardware and open source tools. Core to the SDN Network illustrated in this thesis is the prototype of a multi-layer SDN switch. The proposed device is targeted to serve lower bandwidth communication (in relation to commercially produced high speed SDN-enabled devices). The performance of the prototype multilayer switch had shown to achieve: data-rates of up to 99.998%, average latencies that are under 40µs during forwarding/switching and under 100µs during routing while using packet sizes between 64 bytes and 1518 bytes, and a jitter of less than 15µs during all tests. This research explores in detail the design, development, and management of a multi-layer switch and its placement and integration in small scale SDN network. This includes testing of Layer 2 forwarding and Layer 3 routing, OpenFlow compliance testing, the management of the switch using created SDN applications, and real life network functionality such as forwarding, routing and VLAN networking to demonstrate its real world applicability.
- Full Text:
- Date Issued: 2020
- Authors: Magwenzi, Tinashe
- Date: 2020
- Subjects: Software-defined networking (Computer network technology) , Telecommunication -- Switching systems , OpenFlow (Computer network protocol) , Local area networks (Computer networks)
- Language: English
- Type: text , Thesis , Masters , MSc
- Identifier: http://hdl.handle.net/10962/142841 , vital:38122
- Description: Software-Defined Networking (SDN) is a paradigm which enables the realisation of programmable network through the separation of the control logic from the forwarding functions. This separation is a departure from the traditional architecture. Much of the work done in SDN enabled devices has concentrated on higher end, high speed networks (10s GBit/s 100s GBit/s), rather than the relatively low bandwidth links (10s MBit/s to a few GBit/s) which are seen, for example, in South Africa. As SDN is increasingly becoming more accepted, due to its advantages over the traditional networks, it has been adopted for industrial purposes such as networking in data centres and network providers. The demand for programmable networks is increasing but is limited by the ability of providers to upgrade their infrastructure. In addition, as access to the Internet has become less expensive, the use of Internet is increasing in academic institutions, NGOs, and small to medium enterprises. This thesis details a means of building and managing a small scale Software-Defined Network using commodity hardware and open source tools. Core to the SDN Network illustrated in this thesis is the prototype of a multi-layer SDN switch. The proposed device is targeted to serve lower bandwidth communication (in relation to commercially produced high speed SDN-enabled devices). The performance of the prototype multilayer switch had shown to achieve: data-rates of up to 99.998%, average latencies that are under 40µs during forwarding/switching and under 100µs during routing while using packet sizes between 64 bytes and 1518 bytes, and a jitter of less than 15µs during all tests. This research explores in detail the design, development, and management of a multi-layer switch and its placement and integration in small scale SDN network. This includes testing of Layer 2 forwarding and Layer 3 routing, OpenFlow compliance testing, the management of the switch using created SDN applications, and real life network functionality such as forwarding, routing and VLAN networking to demonstrate its real world applicability.
- Full Text:
- Date Issued: 2020
A study of why some physic concepts in the South African Physical Science curriculum are poorly understood in order to develop a targeted action-research intervention for Newton’s second law
- Authors: Cobbing, Kathleen Margaret
- Date: 2020
- Subjects: Physics -- Study and teaching (Secondary) -- South Africa , Physics -- Examinations, questions, etc. -- South Africa , Motion -- Study and teaching (Secondary) -- South Africa
- Language: English
- Type: text , Thesis , Masters , MSc
- Identifier: http://hdl.handle.net/10962/146903 , vital:38575
- Description: Globally, many students show a poor understanding of concepts in high school physics and lack the necessary problem-solving skills that the course demands. The application of Newton’s second law was found to be particularly problematic through document analysis of South African examination feedback reports, as well as from an analysis of the physics examinations at a pair of well-resourced South African independent schools that follow the Independent Examination Board curriculum. Through an action-research approach, a resource for use by students was designed and modified to improve students’ understanding of this concept, while modelling problemsolving methods. The resource consisted of brief revision notes, worked examples and scaffolded exercises. The design of the resource was influenced by the theory of cognitive apprenticeship, cognitive load theory and conceptual change theory. One of the aims of the resource was to encourage students to translate between the different representations of a problem situation: symbolic, abstract, model and concrete. The impact of this resource was evaluated at a pair of schools using a mixed methods approach. This incorporated pre- and post-tests for a quantitative assessment, qualitative student evaluations and the analysis of examination scripts. There was an improvement from pre- to post-test for all four iterations of the intervention and these improvements were shown to be significant. The use of the resource led to an increase in the quality and quantity of diagrams drawn by students in subsequent assessments.
- Full Text:
- Date Issued: 2020
- Authors: Cobbing, Kathleen Margaret
- Date: 2020
- Subjects: Physics -- Study and teaching (Secondary) -- South Africa , Physics -- Examinations, questions, etc. -- South Africa , Motion -- Study and teaching (Secondary) -- South Africa
- Language: English
- Type: text , Thesis , Masters , MSc
- Identifier: http://hdl.handle.net/10962/146903 , vital:38575
- Description: Globally, many students show a poor understanding of concepts in high school physics and lack the necessary problem-solving skills that the course demands. The application of Newton’s second law was found to be particularly problematic through document analysis of South African examination feedback reports, as well as from an analysis of the physics examinations at a pair of well-resourced South African independent schools that follow the Independent Examination Board curriculum. Through an action-research approach, a resource for use by students was designed and modified to improve students’ understanding of this concept, while modelling problemsolving methods. The resource consisted of brief revision notes, worked examples and scaffolded exercises. The design of the resource was influenced by the theory of cognitive apprenticeship, cognitive load theory and conceptual change theory. One of the aims of the resource was to encourage students to translate between the different representations of a problem situation: symbolic, abstract, model and concrete. The impact of this resource was evaluated at a pair of schools using a mixed methods approach. This incorporated pre- and post-tests for a quantitative assessment, qualitative student evaluations and the analysis of examination scripts. There was an improvement from pre- to post-test for all four iterations of the intervention and these improvements were shown to be significant. The use of the resource led to an increase in the quality and quantity of diagrams drawn by students in subsequent assessments.
- Full Text:
- Date Issued: 2020
Identification of SANCDB compounds against G2019S and I2020T variants of leucine-rich repeat Kinase 2 (LRRK2) for the development of drugs against Parkinson’s Disease
- Authors: Baye, Bertha Cinthia
- Date: 2020
- Subjects: Antiparkinsonian agents , Parkinson's disease -- Treatment , Protein kinases , Parkinson's disease -- Chemotherapy , Molecules -- Models
- Language: English
- Type: text , Thesis , Masters , MSc
- Identifier: http://hdl.handle.net/10962/138764 , vital:37671
- Description: Parkinson’s disease is a type of movement disorder that occurs when nerve cells in the brain stop producing dopamine. It is the second neurodegenerative disease affecting 1-2% of people above the ages of 65 years old. There is a worldwide prevalence of 7 to 10 million affected people of all cultures and race. Studies have shown that mutation that causes Parkinson’s disease result in increased kinase activity. The c.6055 G > A in exon 41 is the most prevalent LRRK2 variation which causes a substitution of glycine to serine in G2019S in the highly activated loop of its MAP kinase domain. The LRRK2 G2019S variant is the most common genetic determinant of Parkinson’s disease identified to date. This work focused on building accurate 3D models of the LRRK2 kinase domain, that were used for large-scale in silico docking against South African natural compounds from the South African Natural Compounds Database (SANCDB; https://sancdb.rubi.ru.ac.za/). Molecular docking was performed to identify compounds that formed interactions with the active site of the protein and had the lowest binding energy scores. Molecular dynamics simulations showed different movements of the protein-ligand complexes and behavioural difference of the wildtype and the variants, all three structures proved to be compact. Network analysis was done to study residue interactions, contact maps, dynamic cross correlations, average BC and average L were used to study the residue interactions and general residue contribution to the functioning of the protein..
- Full Text:
- Date Issued: 2020
- Authors: Baye, Bertha Cinthia
- Date: 2020
- Subjects: Antiparkinsonian agents , Parkinson's disease -- Treatment , Protein kinases , Parkinson's disease -- Chemotherapy , Molecules -- Models
- Language: English
- Type: text , Thesis , Masters , MSc
- Identifier: http://hdl.handle.net/10962/138764 , vital:37671
- Description: Parkinson’s disease is a type of movement disorder that occurs when nerve cells in the brain stop producing dopamine. It is the second neurodegenerative disease affecting 1-2% of people above the ages of 65 years old. There is a worldwide prevalence of 7 to 10 million affected people of all cultures and race. Studies have shown that mutation that causes Parkinson’s disease result in increased kinase activity. The c.6055 G > A in exon 41 is the most prevalent LRRK2 variation which causes a substitution of glycine to serine in G2019S in the highly activated loop of its MAP kinase domain. The LRRK2 G2019S variant is the most common genetic determinant of Parkinson’s disease identified to date. This work focused on building accurate 3D models of the LRRK2 kinase domain, that were used for large-scale in silico docking against South African natural compounds from the South African Natural Compounds Database (SANCDB; https://sancdb.rubi.ru.ac.za/). Molecular docking was performed to identify compounds that formed interactions with the active site of the protein and had the lowest binding energy scores. Molecular dynamics simulations showed different movements of the protein-ligand complexes and behavioural difference of the wildtype and the variants, all three structures proved to be compact. Network analysis was done to study residue interactions, contact maps, dynamic cross correlations, average BC and average L were used to study the residue interactions and general residue contribution to the functioning of the protein..
- Full Text:
- Date Issued: 2020