Analysis of bacterial Mur amide ligase enzymes for the identification of inhibitory compounds by in silico methods
- Chamboko, Chiratidzo Respina
- Authors: Chamboko, Chiratidzo Respina
- Date: 2020
- Subjects: Mur amide ligases , Ligases , Ligand binding (Biochemistry) , Antibacterial agents
- Language: English
- Type: Thesis , Masters , MSc
- Identifier: http://hdl.handle.net/10962/163430 , vital:41036
- Description: An increased emergence of resistant pathogenic bacterial strains over the years has resulted in many people dying of untreatable infections. This has become one of the most critical global public health problems, as resistant strains are complicating treatment of infectious diseases, increasing human morbidity, mortality, and health care costs. A very limited amount of effective antibiotics is currently available, but the development of novel classes of antibacterial agents is becoming a priority. Mur amide ligases are enzymes that have been identified as potentially good targets for antibiotics, as they are uniquely found in bacteria. They are responsible for the formation of peptide bonds in a growing peptidoglycan structure for bacterial cell walls. The current work presented here focused on characterizing these Mur amide ligase enzymes and obtaining inhibitory compounds that could potentially be of use in drug discovery of antibacterial agents. To do this, multiple sequence alignment, motif analysis and phylogenetic tree constructions were carried out, followed by docking studies and molecular dynamic simulations. Prior to docking, homology modelling of missing residues in the MurF structure (PDB 1GG4) was performed. Characterization results revealed the Mur amide ligase enzymes contained defined conservation in limited regions, that ultimately mapped towards the central domain responsible for ATP binding (presence of a conserved GKT motif). Further analysis of results further unraveled the unique patterns observed within each group of the family of enzymes. As a result of these findings, docking studies were carried out on each Mur amide ligase structure. At most, two ligands were identified to be sufficiently inhibiting each Mur amide ligase. The ligands obtained were SANC00574 and SANC00575 for MurC, SANC00290 and SANC00438 for MurD, SANC00290 and SANC00525 for MurE and SANC00290 and SANC00434 for MurF. The two best ligands identified for each enzyme had docked in the active site of their respective proteins, passed Lipinski’s rule of five and had substantially low binding energies. Molecular dynamic simulations were then performed to analyze the behavior of the proteins and protein-ligand complexes, to confirm the lead compounds as good inhibitors of the Mur amide ligases. In the case of MurC, MurD and MurE complexes, the identified ligands clearly impacted the behavior of the protein, as the ligand bound proteins became more compact and stable, while flexibility decreased. There was however an opposite effect on MurF complexes, that resulted in identified inhibitors being discarded. As a potential next step, in vivo and in vitro experiments can be performed with identified ligands from this research, to further support the information presented.
- Full Text:
- Authors: Chamboko, Chiratidzo Respina
- Date: 2020
- Subjects: Mur amide ligases , Ligases , Ligand binding (Biochemistry) , Antibacterial agents
- Language: English
- Type: Thesis , Masters , MSc
- Identifier: http://hdl.handle.net/10962/163430 , vital:41036
- Description: An increased emergence of resistant pathogenic bacterial strains over the years has resulted in many people dying of untreatable infections. This has become one of the most critical global public health problems, as resistant strains are complicating treatment of infectious diseases, increasing human morbidity, mortality, and health care costs. A very limited amount of effective antibiotics is currently available, but the development of novel classes of antibacterial agents is becoming a priority. Mur amide ligases are enzymes that have been identified as potentially good targets for antibiotics, as they are uniquely found in bacteria. They are responsible for the formation of peptide bonds in a growing peptidoglycan structure for bacterial cell walls. The current work presented here focused on characterizing these Mur amide ligase enzymes and obtaining inhibitory compounds that could potentially be of use in drug discovery of antibacterial agents. To do this, multiple sequence alignment, motif analysis and phylogenetic tree constructions were carried out, followed by docking studies and molecular dynamic simulations. Prior to docking, homology modelling of missing residues in the MurF structure (PDB 1GG4) was performed. Characterization results revealed the Mur amide ligase enzymes contained defined conservation in limited regions, that ultimately mapped towards the central domain responsible for ATP binding (presence of a conserved GKT motif). Further analysis of results further unraveled the unique patterns observed within each group of the family of enzymes. As a result of these findings, docking studies were carried out on each Mur amide ligase structure. At most, two ligands were identified to be sufficiently inhibiting each Mur amide ligase. The ligands obtained were SANC00574 and SANC00575 for MurC, SANC00290 and SANC00438 for MurD, SANC00290 and SANC00525 for MurE and SANC00290 and SANC00434 for MurF. The two best ligands identified for each enzyme had docked in the active site of their respective proteins, passed Lipinski’s rule of five and had substantially low binding energies. Molecular dynamic simulations were then performed to analyze the behavior of the proteins and protein-ligand complexes, to confirm the lead compounds as good inhibitors of the Mur amide ligases. In the case of MurC, MurD and MurE complexes, the identified ligands clearly impacted the behavior of the protein, as the ligand bound proteins became more compact and stable, while flexibility decreased. There was however an opposite effect on MurF complexes, that resulted in identified inhibitors being discarded. As a potential next step, in vivo and in vitro experiments can be performed with identified ligands from this research, to further support the information presented.
- Full Text:
Analysis of bacterial Mur amide ligase enzymes for the identification of inhibitory compounds by in silico methods
- Chamboko, Chiratidzo Respina
- Authors: Chamboko, Chiratidzo Respina
- Date: 2020
- Subjects: Pathogenic microorganisms -- Analysis , Drug resistance in microorganisms , Microorganisms -- Effect of drugs on , Antibiotics -- Effectiveness , Pathogenic bacteria , Drug tolerance , Enzymes -- Analysis , Peptide antibiotics
- Language: English
- Type: text , Thesis , Masters , MSc
- Identifier: http://hdl.handle.net/10962/161911 , vital:40690
- Description: An increased emergence of resistant pathogenic bacterial strains over the years has resulted in many people dying of untreatable infections. This has become one of the most critical global public health problems, as resistant strains are complicating treatment of infectious diseases, increasing human morbidity, mortality, and health care costs. A very limited amount of effective antibiotics is currently available, but the development of novel classes of antibacterial agents is becoming a priority. Mur amide ligases are enzymes that have been identified as potentially good targets for antibiotics, as they are uniquely found in bacteria. They are responsible for the formation of peptide bonds in a growing peptidoglycan structure for bacterial cell walls. The current work presented here focused on characterizing these Mur amide ligase enzymes and obtaining inhibitory compounds that could potentially be of use in drug discovery of antibacterial agents. To do this, multiple sequence alignment, motif analysis and phylogenetic tree constructions were carried out, followed by docking studies and molecular dynamic simulations. Prior to docking, homology modelling of missing residues in the MurF structure (PDB 1GG4) was performed. Characterization results revealed the Mur amide ligase enzymes contained defined conservation in limited regions, that ultimately mapped towards the central domain responsible for ATP binding (presence of a conserved GKT motif). Further analysis of results further unraveled the unique patterns observed within each group of the family of enzymes. As a result of these findings, docking studies were carried out on each Mur amide ligase structure. At most, two ligands were identified to be sufficiently inhibiting each Mur amide ligase. The ligands obtained were SANC00574 and SANC00575 for MurC, SANC00290 and SANC00438 for MurD, SANC00290 and SANC00525 for MurE and SANC00290 and SANC00434 for MurF. The two best ligands identified for each enzyme had docked in the active site of their respective proteins, passed Lipinski’s rule of five and had substantially low binding energies. Molecular dynamic simulations were then performed to analyze the behavior of the proteins and protein-ligand complexes, to confirm the lead compounds as good inhibitors of the Mur amide ligases. In the case of MurC, MurD and MurE complexes, the identified ligands clearly impacted the behavior of the protein, as the ligand bound proteins became more compact and stable, while flexibility decreased. There was however an opposite effect on MurF complexes, that resulted in identified inhibitors being discarded. As a potential next step, in vivo and in vitro experiments can be performed with identified ligands from this research, to further support the information presented.
- Full Text:
- Authors: Chamboko, Chiratidzo Respina
- Date: 2020
- Subjects: Pathogenic microorganisms -- Analysis , Drug resistance in microorganisms , Microorganisms -- Effect of drugs on , Antibiotics -- Effectiveness , Pathogenic bacteria , Drug tolerance , Enzymes -- Analysis , Peptide antibiotics
- Language: English
- Type: text , Thesis , Masters , MSc
- Identifier: http://hdl.handle.net/10962/161911 , vital:40690
- Description: An increased emergence of resistant pathogenic bacterial strains over the years has resulted in many people dying of untreatable infections. This has become one of the most critical global public health problems, as resistant strains are complicating treatment of infectious diseases, increasing human morbidity, mortality, and health care costs. A very limited amount of effective antibiotics is currently available, but the development of novel classes of antibacterial agents is becoming a priority. Mur amide ligases are enzymes that have been identified as potentially good targets for antibiotics, as they are uniquely found in bacteria. They are responsible for the formation of peptide bonds in a growing peptidoglycan structure for bacterial cell walls. The current work presented here focused on characterizing these Mur amide ligase enzymes and obtaining inhibitory compounds that could potentially be of use in drug discovery of antibacterial agents. To do this, multiple sequence alignment, motif analysis and phylogenetic tree constructions were carried out, followed by docking studies and molecular dynamic simulations. Prior to docking, homology modelling of missing residues in the MurF structure (PDB 1GG4) was performed. Characterization results revealed the Mur amide ligase enzymes contained defined conservation in limited regions, that ultimately mapped towards the central domain responsible for ATP binding (presence of a conserved GKT motif). Further analysis of results further unraveled the unique patterns observed within each group of the family of enzymes. As a result of these findings, docking studies were carried out on each Mur amide ligase structure. At most, two ligands were identified to be sufficiently inhibiting each Mur amide ligase. The ligands obtained were SANC00574 and SANC00575 for MurC, SANC00290 and SANC00438 for MurD, SANC00290 and SANC00525 for MurE and SANC00290 and SANC00434 for MurF. The two best ligands identified for each enzyme had docked in the active site of their respective proteins, passed Lipinski’s rule of five and had substantially low binding energies. Molecular dynamic simulations were then performed to analyze the behavior of the proteins and protein-ligand complexes, to confirm the lead compounds as good inhibitors of the Mur amide ligases. In the case of MurC, MurD and MurE complexes, the identified ligands clearly impacted the behavior of the protein, as the ligand bound proteins became more compact and stable, while flexibility decreased. There was however an opposite effect on MurF complexes, that resulted in identified inhibitors being discarded. As a potential next step, in vivo and in vitro experiments can be performed with identified ligands from this research, to further support the information presented.
- Full Text:
Analysis of the regulation of HSP90α expression upon differentiation of C2C12 cells
- Authors: Holm, Nathan Christopher
- Date: 2020
- Subjects: Uncatalogued
- Language: English
- Type: thesis , text , Masters , MSc
- Identifier: http://hdl.handle.net/10962/163318 , vital:41028
- Description: Thesis (MSc)--Rhodes University, Faculty of Science, Biochemistry and Microbiology, 2020.
- Full Text:
- Authors: Holm, Nathan Christopher
- Date: 2020
- Subjects: Uncatalogued
- Language: English
- Type: thesis , text , Masters , MSc
- Identifier: http://hdl.handle.net/10962/163318 , vital:41028
- Description: Thesis (MSc)--Rhodes University, Faculty of Science, Biochemistry and Microbiology, 2020.
- Full Text:
Assessing community structure and trophic interrelationships in three differently impacted headwater streams in the AmatholeWinterberg freshwater ecoregion, South Africa
- Authors: Matomela, Nonjabulo Happy
- Date: 2020
- Subjects: Stream ecology -- South Africa -- Eastern Cape , Freshwater animals -- Ecology -- South Africa -- Eastern Cape , Kat River (South Africa) -- , Lushington River (South Africa) , Elands River (South Africa) , Eyre River (South Africa) , Food chains (Ecology) -- South Africa -- Eastern Cape , Water quality -- South Africa -- Eastern Cape , Land use -- South Africa -- Eastern Cape
- Language: English
- Type: text , Thesis , Masters , MSc
- Identifier: http://hdl.handle.net/10962/147653 , vital:38658
- Description: Afromontane regions represent some of the highly threatened ecosystems on the planet as they harbour endemic and often relic freshwater fauna. These ecologically sensitive ecosystems have been altered by multiple impacts, including invasion by non-native fishes, replacement of diverse indigenous vegetation with monoculture plantations, agricultural and mining activities, hydrological modifications, and degradation of instream habitats, with potential detrimental effects on aquatic community structures and food web dynamics. The aim of the present study was to compare spatio-temporal patterns of macroinvertebrate and fish communities as well as food web dynamics in three differently impacted headwater tributaries of the Kat River in the Amathole-Winterberg freshwater ecoregion in the Eastern Cape Province of South Africa. The upper Kat River catchment was the ideal model for purposes of the present study as it contains streams with varying degrees of human impact. The streams considered in the present study were (i) the Eyre River which was considered to closely represent near-natural conditions as it is the least impacted stream in this catchment, with the riparian zone dominated by relatively intact and diverse native woody vegetation, (ii) the Elands River whose catchment has been altered by agricultural activities, and (iii) the Lushington River, whose riparian zone has been heavily invaded by black wattle. The three headwater streams were generally distinguished based on the physical-chemical variables. The Elands River was characterised by high conductivity and total dissolved solids (TDS). In addition, the Elands River was more alkaline and relatively warmer than the other two rivers. This suggested the negative influence of agriculture activities on the water quality in the Elands River. In general, the Lushington and Eyre rivers had comparable physical and chemical variables. However, the Lushington River was generally characterised by low streamflow, likely as a consequent of black wattle which is known for altering hydrological regimes of streams .The Eyre River and Lushington River were comparable in terms of macroinvertebrate richness and diversity, whereas the Elands River was characterised by low macroinvertebrate diversity and richness. Redundancy analysis indicated that the macroinvertebrate communities were mostly influenced by seasonality, with land-use accounting for a small but significant difference in community composition. In comparison, the generalised linear mixed-effects models (GLMMs) showed that chubbyhead barb abundance was significantly influenced by land-use patterns. Evaluation of food web dynamics using stable isotope analysis revealed that the food web structure in the three rivers differed substantially as a result of land-use. Specifically, the Eyre River was characterised by less variation in stable isotope values of basal food sources and consequently, the consumer groups had a narrow isotopic breadth. In contrast, the Elands River was characterised by a wide variation in basal food sources and therefore, a wider isotopic breadth for consumers. The Lushington River was spatially variable in terms of basal sources and isotopic breadth for consumers. The study concluded that food webs and trophic interrelationships were a more informative indicator of land-use than community structure was in evaluating the impact of land-use patterns on aquatic communities. In addition, future studies should seek to investigate food webs interrelationships in addition to community structure to infer a more conclusive river assessment.
- Full Text:
- Authors: Matomela, Nonjabulo Happy
- Date: 2020
- Subjects: Stream ecology -- South Africa -- Eastern Cape , Freshwater animals -- Ecology -- South Africa -- Eastern Cape , Kat River (South Africa) -- , Lushington River (South Africa) , Elands River (South Africa) , Eyre River (South Africa) , Food chains (Ecology) -- South Africa -- Eastern Cape , Water quality -- South Africa -- Eastern Cape , Land use -- South Africa -- Eastern Cape
- Language: English
- Type: text , Thesis , Masters , MSc
- Identifier: http://hdl.handle.net/10962/147653 , vital:38658
- Description: Afromontane regions represent some of the highly threatened ecosystems on the planet as they harbour endemic and often relic freshwater fauna. These ecologically sensitive ecosystems have been altered by multiple impacts, including invasion by non-native fishes, replacement of diverse indigenous vegetation with monoculture plantations, agricultural and mining activities, hydrological modifications, and degradation of instream habitats, with potential detrimental effects on aquatic community structures and food web dynamics. The aim of the present study was to compare spatio-temporal patterns of macroinvertebrate and fish communities as well as food web dynamics in three differently impacted headwater tributaries of the Kat River in the Amathole-Winterberg freshwater ecoregion in the Eastern Cape Province of South Africa. The upper Kat River catchment was the ideal model for purposes of the present study as it contains streams with varying degrees of human impact. The streams considered in the present study were (i) the Eyre River which was considered to closely represent near-natural conditions as it is the least impacted stream in this catchment, with the riparian zone dominated by relatively intact and diverse native woody vegetation, (ii) the Elands River whose catchment has been altered by agricultural activities, and (iii) the Lushington River, whose riparian zone has been heavily invaded by black wattle. The three headwater streams were generally distinguished based on the physical-chemical variables. The Elands River was characterised by high conductivity and total dissolved solids (TDS). In addition, the Elands River was more alkaline and relatively warmer than the other two rivers. This suggested the negative influence of agriculture activities on the water quality in the Elands River. In general, the Lushington and Eyre rivers had comparable physical and chemical variables. However, the Lushington River was generally characterised by low streamflow, likely as a consequent of black wattle which is known for altering hydrological regimes of streams .The Eyre River and Lushington River were comparable in terms of macroinvertebrate richness and diversity, whereas the Elands River was characterised by low macroinvertebrate diversity and richness. Redundancy analysis indicated that the macroinvertebrate communities were mostly influenced by seasonality, with land-use accounting for a small but significant difference in community composition. In comparison, the generalised linear mixed-effects models (GLMMs) showed that chubbyhead barb abundance was significantly influenced by land-use patterns. Evaluation of food web dynamics using stable isotope analysis revealed that the food web structure in the three rivers differed substantially as a result of land-use. Specifically, the Eyre River was characterised by less variation in stable isotope values of basal food sources and consequently, the consumer groups had a narrow isotopic breadth. In contrast, the Elands River was characterised by a wide variation in basal food sources and therefore, a wider isotopic breadth for consumers. The Lushington River was spatially variable in terms of basal sources and isotopic breadth for consumers. The study concluded that food webs and trophic interrelationships were a more informative indicator of land-use than community structure was in evaluating the impact of land-use patterns on aquatic communities. In addition, future studies should seek to investigate food webs interrelationships in addition to community structure to infer a more conclusive river assessment.
- Full Text:
Assessing invasive alien aquatic plant species, phytoremediation effects using biological indicators in the Swartkops River system
- Authors: Tshithukhe, Getrude
- Date: 2020
- Subjects: Aquatic weeds -- Biological control -- South Africa -- Eastern Cape , Alien plants -- Biological control -- South Africa -- Eastern Cape , Phytoremediation -- South Africa
- Language: English
- Type: text , Thesis , Masters , MSc
- Identifier: http://hdl.handle.net/10962/167665 , vital:41501
- Description: Pollution effluents in freshwater ecosystems are becoming increasingly ubiquitous as a result of cumulative anthropogenic activities, such as wastewater treatments works, and industrial, agricultural and mining activities. These activities are more noticeable in urban river atchments where there is greater human population densities and industrial developments. The ecological effects of anthropogenic activities on freshwater ecosystems include: excessive deposition of contaminants such as nutrients, pharmaceuticals, microplastics and other chemicals, which change physicochemical properties, causing a decline in aquatic biodiversity. These effects, impact negatively on the resilience of freshwater, making the systems vulnerable to invasion by alien aquatic plants. Ultimately, the loss of local biodiversity associated with the invasive alien aquatic plants (IAAP) results in a loss of some ecosystem goods and services. The Swartkops River system, Eastern Cape Province, drains most of the neighbouring formal and informal settlements, agricultural lands and industries, and hence is exposed to water pollution from human activities along the river catchment. Various water quality assessments are needed to evaluate the extent of pollutants and their impacts on the river ecosystem. Phytoremediation is one approach employed internationally for removing harmful nutrients and chemicals in freshwater ecosystems. Most studies measure the success of phytoremediation through measuring the reduction of contaminants in water or soil chemistry in mesocosm settings, which may not take into account all the important environmental factors that exist in the field. The present study assesses the phytoremediation potential of Pontederia (Eichhornia) crassipes and Salvinia molesta by evaluating water and sediment chemistry, periphyton and aquatic macroinvertebrate community recovery along seven field sites (excluding IAAP species mats sites) located upstream and downstream IAAP species mats on the Swartkops River between April and September 2018. Water and sediment samples were collected once monthly on ten seven field sites, including the IAAP species mat sites. Periphyton and aquatic macroinvertebrates were collected on seven sites, excluding the IAAP mat sites. Pontederia crassipes and S. molesta infestation in Swartkops River showed positive phytoremediation results and improved some water and sediment chemistry in the downstream treatments as compared to upstream treatments. Although there were some fluctuations with some variables, important water and sediment chemistry were reduced downstream. By contrast, biological assessment results did not show any response to the presence of IAAP species and phytoremediation. Periphyton and aquatic macroinvertebrates diversity and community assemblages were more influenced by water quality. Although IAAP species did provide improvement in water and sediments chemistry, multiple effluent point and non-point sources in Swartkops outpaced phytoremediation. Taxa evenness and relative taxa abundance showed significant differences between the upstream and downstream sites, however taxa richness and Shannon’s diversity showed no significant differences, indicating no relative recovery in biodiversity for either periphyton or aquatic macroinvertebrates. Similarly, the upstream and downstream sites showed similar periphyton and aquatic macroinvertebrates assemblages structure, all dominated by pollution tolerant taxa, thus indicating no functional diversity improvement down river; because of improvement in water chemistry downstream sites, it was expected that periphyton and aquatic macroinvertebrates assemblage structure would also improve at these downstream sites.It is possible that the phytoremediation process is outpaced by effluent discharges, given the multiple sources and distance between upstream and downstream mat sites. The study showed phytoremediation potential but the results were not indicated by biological indicators. A replica study conducted on a moderately disturbed river system is recommended to measure the success and recovery of biological indicators and assemblage composition following IAAP species phytoremediation; a moderately disturbed river compared to a largely disturbed river will broaden findings and look at differences for a wider application of phytoremediation.
- Full Text:
- Authors: Tshithukhe, Getrude
- Date: 2020
- Subjects: Aquatic weeds -- Biological control -- South Africa -- Eastern Cape , Alien plants -- Biological control -- South Africa -- Eastern Cape , Phytoremediation -- South Africa
- Language: English
- Type: text , Thesis , Masters , MSc
- Identifier: http://hdl.handle.net/10962/167665 , vital:41501
- Description: Pollution effluents in freshwater ecosystems are becoming increasingly ubiquitous as a result of cumulative anthropogenic activities, such as wastewater treatments works, and industrial, agricultural and mining activities. These activities are more noticeable in urban river atchments where there is greater human population densities and industrial developments. The ecological effects of anthropogenic activities on freshwater ecosystems include: excessive deposition of contaminants such as nutrients, pharmaceuticals, microplastics and other chemicals, which change physicochemical properties, causing a decline in aquatic biodiversity. These effects, impact negatively on the resilience of freshwater, making the systems vulnerable to invasion by alien aquatic plants. Ultimately, the loss of local biodiversity associated with the invasive alien aquatic plants (IAAP) results in a loss of some ecosystem goods and services. The Swartkops River system, Eastern Cape Province, drains most of the neighbouring formal and informal settlements, agricultural lands and industries, and hence is exposed to water pollution from human activities along the river catchment. Various water quality assessments are needed to evaluate the extent of pollutants and their impacts on the river ecosystem. Phytoremediation is one approach employed internationally for removing harmful nutrients and chemicals in freshwater ecosystems. Most studies measure the success of phytoremediation through measuring the reduction of contaminants in water or soil chemistry in mesocosm settings, which may not take into account all the important environmental factors that exist in the field. The present study assesses the phytoremediation potential of Pontederia (Eichhornia) crassipes and Salvinia molesta by evaluating water and sediment chemistry, periphyton and aquatic macroinvertebrate community recovery along seven field sites (excluding IAAP species mats sites) located upstream and downstream IAAP species mats on the Swartkops River between April and September 2018. Water and sediment samples were collected once monthly on ten seven field sites, including the IAAP species mat sites. Periphyton and aquatic macroinvertebrates were collected on seven sites, excluding the IAAP mat sites. Pontederia crassipes and S. molesta infestation in Swartkops River showed positive phytoremediation results and improved some water and sediment chemistry in the downstream treatments as compared to upstream treatments. Although there were some fluctuations with some variables, important water and sediment chemistry were reduced downstream. By contrast, biological assessment results did not show any response to the presence of IAAP species and phytoremediation. Periphyton and aquatic macroinvertebrates diversity and community assemblages were more influenced by water quality. Although IAAP species did provide improvement in water and sediments chemistry, multiple effluent point and non-point sources in Swartkops outpaced phytoremediation. Taxa evenness and relative taxa abundance showed significant differences between the upstream and downstream sites, however taxa richness and Shannon’s diversity showed no significant differences, indicating no relative recovery in biodiversity for either periphyton or aquatic macroinvertebrates. Similarly, the upstream and downstream sites showed similar periphyton and aquatic macroinvertebrates assemblages structure, all dominated by pollution tolerant taxa, thus indicating no functional diversity improvement down river; because of improvement in water chemistry downstream sites, it was expected that periphyton and aquatic macroinvertebrates assemblage structure would also improve at these downstream sites.It is possible that the phytoremediation process is outpaced by effluent discharges, given the multiple sources and distance between upstream and downstream mat sites. The study showed phytoremediation potential but the results were not indicated by biological indicators. A replica study conducted on a moderately disturbed river system is recommended to measure the success and recovery of biological indicators and assemblage composition following IAAP species phytoremediation; a moderately disturbed river compared to a largely disturbed river will broaden findings and look at differences for a wider application of phytoremediation.
- Full Text:
Azadipyrromethenes for applications in photodynamic antimicrobial chemotherapy, photodynamic therapy and optical limiting
- Authors: Dubazana, Nadine
- Date: 2020
- Subjects: Dyes and dyeing -- Chemistry , Photochemotherapy , Cancer -- Photochemotherapy , Anti-infective agents , Staphylococcus aureus , Nonlinear optics , Azadipyrromethenes , BODIPY
- Language: English
- Type: text , Thesis , Masters , MSc
- Identifier: http://hdl.handle.net/10962/166150 , vital:41333
- Description: Azadipyrromethenes, azaBODIPYs and zinc azadipyrromethene complexes were prepared and characterised to examine the effect on their photophysical properties of incorporating phenyl groups at the 1,3,5,7-positions with electron-donating and withdrawing groups at the para-positions. To enhance their ability to generate singlet oxygen, appropriate structural modifications were made through the addition of a Zn(II) ion or halogenation at the 2,6 positions. In vitro photodynamic therapy (PDT) studies targeting MCF-7 human breast cancer cells were carried out. To evaluate and understand the effectiveness of the dyes as photosensitisers, cellular uptake, phototoxicity and the half-maximal inhibitory concentration (IC50) values were analysed. Photodynamic antimicrobial chemotherapy (PACT) studies were also carried out to study the effectiveness of the dyes against Staphylococcus aureus (S. aureus). Dyes with donor-π-acceptor (D-π-A) properties were synthesised and tested against the second harmonic of the Nd:YAG laser in optical limiting (OL) studies. The second-order hyperpolarisability, third-order susceptibility and nonlinear absorption coefficient values were determined. The results suggest that 1,3,5,7-azaBODIPY dyes may be less suitable for use in this context than analogous D-π-A 3,5-distyrylBODIPY dyes. Molecular modelling was carried out to identify the structure-property relationships of the synthesised dyes by analysing trends in the energies of the frontier molecular orbitals (MOs) and spectroscopic properties.
- Full Text:
- Authors: Dubazana, Nadine
- Date: 2020
- Subjects: Dyes and dyeing -- Chemistry , Photochemotherapy , Cancer -- Photochemotherapy , Anti-infective agents , Staphylococcus aureus , Nonlinear optics , Azadipyrromethenes , BODIPY
- Language: English
- Type: text , Thesis , Masters , MSc
- Identifier: http://hdl.handle.net/10962/166150 , vital:41333
- Description: Azadipyrromethenes, azaBODIPYs and zinc azadipyrromethene complexes were prepared and characterised to examine the effect on their photophysical properties of incorporating phenyl groups at the 1,3,5,7-positions with electron-donating and withdrawing groups at the para-positions. To enhance their ability to generate singlet oxygen, appropriate structural modifications were made through the addition of a Zn(II) ion or halogenation at the 2,6 positions. In vitro photodynamic therapy (PDT) studies targeting MCF-7 human breast cancer cells were carried out. To evaluate and understand the effectiveness of the dyes as photosensitisers, cellular uptake, phototoxicity and the half-maximal inhibitory concentration (IC50) values were analysed. Photodynamic antimicrobial chemotherapy (PACT) studies were also carried out to study the effectiveness of the dyes against Staphylococcus aureus (S. aureus). Dyes with donor-π-acceptor (D-π-A) properties were synthesised and tested against the second harmonic of the Nd:YAG laser in optical limiting (OL) studies. The second-order hyperpolarisability, third-order susceptibility and nonlinear absorption coefficient values were determined. The results suggest that 1,3,5,7-azaBODIPY dyes may be less suitable for use in this context than analogous D-π-A 3,5-distyrylBODIPY dyes. Molecular modelling was carried out to identify the structure-property relationships of the synthesised dyes by analysing trends in the energies of the frontier molecular orbitals (MOs) and spectroscopic properties.
- Full Text:
Bayesian accelerated life tests for the Weibull distribution under non-informative priors
- Authors: Mostert, Philip
- Date: 2020
- Subjects: Accelerated life testing -- Statistical methods , Accelerated life testing -- Mathematical models , Failure time data analysis , Bayesian statistical decision theory , Monte Carlo method , Weibull distribution
- Language: English
- Type: text , Thesis , Masters , MSc
- Identifier: http://hdl.handle.net/10962/172181 , vital:42173
- Description: In a competitive world where products are designed to last for long periods of time, obtaining time-to-failure data is both difficult and costly. Hence for products with high reliability, accelerated life testing is required to obtain relevant life-data quickly. This is done by placing the products under higher-than-use stress levels, thereby causing the products to fail prematurely. Part of the analysis of accelerated life-data requires a life distribution that describes the lifetime of a product at a given stress level and a life-stress relationship – which is some function that describes the way in which the life distribution changes across different stress levels. In this thesis it is assumed that the underlying life distribution is the wellknown Weibull distribution, with shape parameter constant over all stress levels and scale parameter as a log-linear function of stress. The primary objective of this thesis is to obtain estimates from Bayesian analysis, and this thesis considers five types of non-informative prior distributions: Jeffreys’ prior, reference priors, maximal data information prior, uniform prior and probability matching priors. Since the associated posterior distribution under all the derived non-informative priors are of an unknown form, the propriety of the posterior distributions is assessed to ensure admissible results. For comparison purposes, estimates obtained via the method of maximum likelihood are also considered. Finding these estimates requires solving non-linear equations, hence the Newton-Raphson algorithm is used to obtain estimates. A simulation study based on the time-to-failure of accelerated data is conducted to compare results between maximum likelihood and Bayesian estimates. As a result of the Bayesian posterior distributions being analytically intractable, two methods to obtain Bayesian estimates are considered: Markov chain Monte Carlo methods and Lindley’s approximation technique. In the simulation study the posterior means and the root mean squared error values of the estimates under the symmetric squared error loss function and the two asymmetric loss functions: the LINEX loss function and general entropy loss function, are considered. Furthermore the coverage rates for the Bayesian Markov chain Monte Carlo and maximum likelihood estimates are found, and are compared by their average interval lengths. A case study using a dataset based on accelerated time-to-failure of an insulating fluid is considered. The fit of these data for the Weibull distribution is studied and is compared to that of other popular life distributions. A full simulation study is conducted to illustrate convergence of the proper posterior distributions. Both maximum likelihood and Bayesian estimates are found for these data. The deviance information criterion is used to compare Bayesian estimates between the prior distributions. The case study is concluded by finding reliability estimates of the data at use-stress levels.
- Full Text:
- Authors: Mostert, Philip
- Date: 2020
- Subjects: Accelerated life testing -- Statistical methods , Accelerated life testing -- Mathematical models , Failure time data analysis , Bayesian statistical decision theory , Monte Carlo method , Weibull distribution
- Language: English
- Type: text , Thesis , Masters , MSc
- Identifier: http://hdl.handle.net/10962/172181 , vital:42173
- Description: In a competitive world where products are designed to last for long periods of time, obtaining time-to-failure data is both difficult and costly. Hence for products with high reliability, accelerated life testing is required to obtain relevant life-data quickly. This is done by placing the products under higher-than-use stress levels, thereby causing the products to fail prematurely. Part of the analysis of accelerated life-data requires a life distribution that describes the lifetime of a product at a given stress level and a life-stress relationship – which is some function that describes the way in which the life distribution changes across different stress levels. In this thesis it is assumed that the underlying life distribution is the wellknown Weibull distribution, with shape parameter constant over all stress levels and scale parameter as a log-linear function of stress. The primary objective of this thesis is to obtain estimates from Bayesian analysis, and this thesis considers five types of non-informative prior distributions: Jeffreys’ prior, reference priors, maximal data information prior, uniform prior and probability matching priors. Since the associated posterior distribution under all the derived non-informative priors are of an unknown form, the propriety of the posterior distributions is assessed to ensure admissible results. For comparison purposes, estimates obtained via the method of maximum likelihood are also considered. Finding these estimates requires solving non-linear equations, hence the Newton-Raphson algorithm is used to obtain estimates. A simulation study based on the time-to-failure of accelerated data is conducted to compare results between maximum likelihood and Bayesian estimates. As a result of the Bayesian posterior distributions being analytically intractable, two methods to obtain Bayesian estimates are considered: Markov chain Monte Carlo methods and Lindley’s approximation technique. In the simulation study the posterior means and the root mean squared error values of the estimates under the symmetric squared error loss function and the two asymmetric loss functions: the LINEX loss function and general entropy loss function, are considered. Furthermore the coverage rates for the Bayesian Markov chain Monte Carlo and maximum likelihood estimates are found, and are compared by their average interval lengths. A case study using a dataset based on accelerated time-to-failure of an insulating fluid is considered. The fit of these data for the Weibull distribution is studied and is compared to that of other popular life distributions. A full simulation study is conducted to illustrate convergence of the proper posterior distributions. Both maximum likelihood and Bayesian estimates are found for these data. The deviance information criterion is used to compare Bayesian estimates between the prior distributions. The case study is concluded by finding reliability estimates of the data at use-stress levels.
- Full Text:
BODIPY dyes for application in the photo-oxidation of pollutants, photodynamic antimicrobial chemotherapy, and nonlinear optics
- Authors: Kelechi, Lebechi Augustus
- Date: 2020
- Subjects: Dyes and dyeing -- Chemistry , Fluorescent probes , Fluorescence spectroscopy
- Language: English
- Type: text , Thesis , Masters , MSc
- Identifier: http://hdl.handle.net/10962/140298 , vital:37859
- Description: The synthesis and structural characterization of a series of BODIPY dyes to analyze both the effects of halogenations at the 2,6-positions and the introduction of styryl groups at the 3,5-positions. The photophysical properties of these dyes were investigated to determine their suitability as singlet oxygen-generating photosensitiser dyes for application in photocatalytic degradation of azo dyes and in photodynamic antimicrobial chemotherapy (PACT). Upon halogenation, the dyes showed high to moderate singlet oxygen quantum yields. The potential utility of electrospun polystyrene (PS) nanofibres embedded with halogenated BODIPY dyes for the photocatalytic degradation of Orange G and Methyl Orange from textile industry effluents were investigated. A comparison of the singlet oxygen quantum yield of the BODIPY dyes in solution and when embedded in the PS nanofibres support demonstrates that its photosensitiser properties are maintained in the nanofibre mats. The photocatalytic degradation properties of the PS nanofibres for Orange G and Methyl Orange were determined by using a 530 nm and 660 nm light-emitting diodes. The rate of photodegradation increases with both the Orange G and Methyl Orange concentrations and follows pseudo-first-order kinetics. The PACT activities of brominated BODIPYs on Escherichia coli and Staphylococcus aureus were investigated. Log reduction values of over 9 were obtained during the photoinactivation of Staphylococcus aureus. To be able to red-shift the main spectral band of the BODIPY dyes into the therapeutic window, styryl groups were introduced at the 3,5-positions through a modified Knoevenagel condensation reaction. Because the red-shifted spectral band lies above 532 nm, the second harmonic of the Nd:YAG laser, there is very minute absorption at this wavelength. One of the novel brominated BODIPY dyes was investigated for its potential utility as optical limiting materials in nonlinear optics (NLO), and the dyes demonstrated typical nonlinear absorption behaviour characterised by reverse saturable absorption (RSA) in Z-scan measurements. Excellent optical limiting parameters were obtained for third-order susceptibility and hyperpolarisability.
- Full Text:
- Authors: Kelechi, Lebechi Augustus
- Date: 2020
- Subjects: Dyes and dyeing -- Chemistry , Fluorescent probes , Fluorescence spectroscopy
- Language: English
- Type: text , Thesis , Masters , MSc
- Identifier: http://hdl.handle.net/10962/140298 , vital:37859
- Description: The synthesis and structural characterization of a series of BODIPY dyes to analyze both the effects of halogenations at the 2,6-positions and the introduction of styryl groups at the 3,5-positions. The photophysical properties of these dyes were investigated to determine their suitability as singlet oxygen-generating photosensitiser dyes for application in photocatalytic degradation of azo dyes and in photodynamic antimicrobial chemotherapy (PACT). Upon halogenation, the dyes showed high to moderate singlet oxygen quantum yields. The potential utility of electrospun polystyrene (PS) nanofibres embedded with halogenated BODIPY dyes for the photocatalytic degradation of Orange G and Methyl Orange from textile industry effluents were investigated. A comparison of the singlet oxygen quantum yield of the BODIPY dyes in solution and when embedded in the PS nanofibres support demonstrates that its photosensitiser properties are maintained in the nanofibre mats. The photocatalytic degradation properties of the PS nanofibres for Orange G and Methyl Orange were determined by using a 530 nm and 660 nm light-emitting diodes. The rate of photodegradation increases with both the Orange G and Methyl Orange concentrations and follows pseudo-first-order kinetics. The PACT activities of brominated BODIPYs on Escherichia coli and Staphylococcus aureus were investigated. Log reduction values of over 9 were obtained during the photoinactivation of Staphylococcus aureus. To be able to red-shift the main spectral band of the BODIPY dyes into the therapeutic window, styryl groups were introduced at the 3,5-positions through a modified Knoevenagel condensation reaction. Because the red-shifted spectral band lies above 532 nm, the second harmonic of the Nd:YAG laser, there is very minute absorption at this wavelength. One of the novel brominated BODIPY dyes was investigated for its potential utility as optical limiting materials in nonlinear optics (NLO), and the dyes demonstrated typical nonlinear absorption behaviour characterised by reverse saturable absorption (RSA) in Z-scan measurements. Excellent optical limiting parameters were obtained for third-order susceptibility and hyperpolarisability.
- Full Text:
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:
- 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:
Combination ecosystem green engineering and early life history processes to enhance the intertidal biodiversity in the Port of East London
- Authors: Mafanya, Sandisiwer
- Date: 2020
- Subjects: Biotic communities -- South Africa -- East London , Perna -- Ecology --South Africa -- South Africa-- East London , Mexilhao mussel -- Ecology -- South Africa -- East London , Habitat (Ecology) -- Modification -- South Africa -- East London , Benthic animals -- Effect of habitat modification on -- South Africa -- East London , Harbors -- Environmental aspects -- South Africa -- East London
- Language: English
- Type: text , Thesis , Masters , MSc
- Identifier: http://hdl.handle.net/10962/166376 , vital:41357
- Description: Marine coastal ecosystems are highly impacted by anthropogenic activities, including the development of, and practices within, harbours and/or ports. Artificial structures associated with harbours have a different chemical composition, texture and orientation than that of the natural benthic habitats they have replaced, and are therefore not generally favourable for the settlement and occurrence of indigenous species. Attempts are being made to identify what structures and materials can be used to aid in the rehabilitation of native species within harbours. The aim of this study was to investigate the effects of utilising environmentally-friendly artificial structures (tiles) with varying complexity (crevices and ridges with different depths) with ecological engineers (the indigenous bivalve Perna perna), on the associated benthic biodiversity within an international port in South Africa (Port of East London). The objectives of the study were to test the effects of artificial habitat complexity and the presence of bivalves on 1) the growth, mortality and biomass of a selected model species of ecosystem engineer (P. perna), and 2) the associated intertidal biodiversity. Tiles seeded with bivalves (P. perna) were deployed at two sites in the Port of East London and monitored monthly over a period of 12 months (November 2016-October 2017) to assess survival, growth and associated biodiversity. Environmental variables were also measured every month. The results of the three-way repeated measures ANOVAs indicated that tile treatment (especially high complexity of 2.5 and 5 cm) had an effect on the diversity of mobile species, length, height and biomass of the bivalves used as model ecosystem engineer, indicating the potentials for protection from wave dislodgement and refuge provision. Treatment (especially flat tiles) also had an effect on sessile/sedentary species diversity, indicating the greater proportion of space provided by these non-complex tiles. In addition, month had an effect on the mortality, height and biomass of the bivalves. Mortality was highest in October 2017, while the growth in height and biomass of P. perna were largest in January and October 2017 respectively. The use of artificial tiles also had a positive effect on the survival, growth, and biomass of bivalves (especially the length, weight and dry weight in 2.5 cm and 5 cm complexity). Additionally, this research investigated patterns of settlement and recruitment of the local bivalve population (P. perna) in the Port of East London and adjacent natural coastline to understand the early life history temporal and spatial dynamics of this model ecosystem engineer species. Settlement and recruitment were assessed every month by deploying and replacing artificial collectors for a total period of 19 months (November 2016-May 2018). The results of the two-way ANOVAs indicated that month and site (port vs natural) had an effect on settlement and recruitment of bivalves. Settlement and recruitment of bivalves were highest in July 2017 (port) and March 2018 (natural rocky shore). This study has highlighted that the use of artificial concrete tiles with increased complexity, as well as the investigation of the early stages of mussel populations could be important to consider in a framework of rehabilitation of urban coastal environments such as the Port of East London. Ecological engineering (in terms of increased complexity and heterogeneity) has indeed the potentials to be incorporated in South African programmes aiming at improving natural biodiversity in coastal urban environments. Nonetheless, the spatio-temporal variability of early driver of mussel populations (settlement and recruitment) is also an important feature to be closely monitored if biodiversity in South African coastal armouring is to be enhanced effectively and in the long term.
- Full Text:
- Authors: Mafanya, Sandisiwer
- Date: 2020
- Subjects: Biotic communities -- South Africa -- East London , Perna -- Ecology --South Africa -- South Africa-- East London , Mexilhao mussel -- Ecology -- South Africa -- East London , Habitat (Ecology) -- Modification -- South Africa -- East London , Benthic animals -- Effect of habitat modification on -- South Africa -- East London , Harbors -- Environmental aspects -- South Africa -- East London
- Language: English
- Type: text , Thesis , Masters , MSc
- Identifier: http://hdl.handle.net/10962/166376 , vital:41357
- Description: Marine coastal ecosystems are highly impacted by anthropogenic activities, including the development of, and practices within, harbours and/or ports. Artificial structures associated with harbours have a different chemical composition, texture and orientation than that of the natural benthic habitats they have replaced, and are therefore not generally favourable for the settlement and occurrence of indigenous species. Attempts are being made to identify what structures and materials can be used to aid in the rehabilitation of native species within harbours. The aim of this study was to investigate the effects of utilising environmentally-friendly artificial structures (tiles) with varying complexity (crevices and ridges with different depths) with ecological engineers (the indigenous bivalve Perna perna), on the associated benthic biodiversity within an international port in South Africa (Port of East London). The objectives of the study were to test the effects of artificial habitat complexity and the presence of bivalves on 1) the growth, mortality and biomass of a selected model species of ecosystem engineer (P. perna), and 2) the associated intertidal biodiversity. Tiles seeded with bivalves (P. perna) were deployed at two sites in the Port of East London and monitored monthly over a period of 12 months (November 2016-October 2017) to assess survival, growth and associated biodiversity. Environmental variables were also measured every month. The results of the three-way repeated measures ANOVAs indicated that tile treatment (especially high complexity of 2.5 and 5 cm) had an effect on the diversity of mobile species, length, height and biomass of the bivalves used as model ecosystem engineer, indicating the potentials for protection from wave dislodgement and refuge provision. Treatment (especially flat tiles) also had an effect on sessile/sedentary species diversity, indicating the greater proportion of space provided by these non-complex tiles. In addition, month had an effect on the mortality, height and biomass of the bivalves. Mortality was highest in October 2017, while the growth in height and biomass of P. perna were largest in January and October 2017 respectively. The use of artificial tiles also had a positive effect on the survival, growth, and biomass of bivalves (especially the length, weight and dry weight in 2.5 cm and 5 cm complexity). Additionally, this research investigated patterns of settlement and recruitment of the local bivalve population (P. perna) in the Port of East London and adjacent natural coastline to understand the early life history temporal and spatial dynamics of this model ecosystem engineer species. Settlement and recruitment were assessed every month by deploying and replacing artificial collectors for a total period of 19 months (November 2016-May 2018). The results of the two-way ANOVAs indicated that month and site (port vs natural) had an effect on settlement and recruitment of bivalves. Settlement and recruitment of bivalves were highest in July 2017 (port) and March 2018 (natural rocky shore). This study has highlighted that the use of artificial concrete tiles with increased complexity, as well as the investigation of the early stages of mussel populations could be important to consider in a framework of rehabilitation of urban coastal environments such as the Port of East London. Ecological engineering (in terms of increased complexity and heterogeneity) has indeed the potentials to be incorporated in South African programmes aiming at improving natural biodiversity in coastal urban environments. Nonetheless, the spatio-temporal variability of early driver of mussel populations (settlement and recruitment) is also an important feature to be closely monitored if biodiversity in South African coastal armouring is to be enhanced effectively and in the long term.
- Full Text:
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:
- 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:
Cyclooxygenase-1 as an anti-stroke target: potential inhibitor identification and non-synonymous single nucleotide polymorphism analysis
- Authors: Muronzi, Tendai
- Date: 2020
- Subjects: Cerebrovascular disease , Cerebrovascular disease -- Treatment , Cerebrovascular disease -- Chemotherapy , Cyclooxygenases , High throughput screening (Drug development) , Drug development , Molecular dynamics , South African Natural Compounds Database , ZINC database
- Language: English
- Type: Thesis , Masters , MSc
- Identifier: http://hdl.handle.net/10962/143404 , vital:38243
- Description: Stroke is the third leading cause of death worldwide, with 87% of cases being ischemic stroke. The two primary therapeutic strategies to reduce post-ischemic brain damage are cellular and vascular approaches. The vascular strategy aims to rapidly re-open obstructed blood vessels, while the cellular approach aims to interfere with the signalling pathways that facilitate neuron damage and death. Unfortunately, popular vascular treatments have adverse side effects, necessitating the need for alternative chemotherapeutics. In this study, cyclooxygenase-1 (COX-1), which plays a significant role in the post- ischemic neuroinflammation and neuronal death, was targeted for identification of novel drug compounds and to assess the effect of nsSNPs on its structure and function. In a drug discovery part, ligands from the South African Natural Compounds Database (SANCDB-https://sancdb.rubi.ru.ac.za/) and ZINC database (http://zinc15.docking.org/) were used for high-throughput virtual screening (HVTS) against COX-1. Additionally, five nsSNPs were being investigated to assess their impact on protein structure and function. Three of these SNPs were in the COX-1 dimer interface. Molecular docking and molecular dynamics simulations revealed asymmetric nature of the protein. Several ligands, peculiar to each monomer, exhibited favourable binding energies in the respective active sites. SNP analysis indicated effects on inter-monomer interactions and protein stability.
- Full Text:
- Authors: Muronzi, Tendai
- Date: 2020
- Subjects: Cerebrovascular disease , Cerebrovascular disease -- Treatment , Cerebrovascular disease -- Chemotherapy , Cyclooxygenases , High throughput screening (Drug development) , Drug development , Molecular dynamics , South African Natural Compounds Database , ZINC database
- Language: English
- Type: Thesis , Masters , MSc
- Identifier: http://hdl.handle.net/10962/143404 , vital:38243
- Description: Stroke is the third leading cause of death worldwide, with 87% of cases being ischemic stroke. The two primary therapeutic strategies to reduce post-ischemic brain damage are cellular and vascular approaches. The vascular strategy aims to rapidly re-open obstructed blood vessels, while the cellular approach aims to interfere with the signalling pathways that facilitate neuron damage and death. Unfortunately, popular vascular treatments have adverse side effects, necessitating the need for alternative chemotherapeutics. In this study, cyclooxygenase-1 (COX-1), which plays a significant role in the post- ischemic neuroinflammation and neuronal death, was targeted for identification of novel drug compounds and to assess the effect of nsSNPs on its structure and function. In a drug discovery part, ligands from the South African Natural Compounds Database (SANCDB-https://sancdb.rubi.ru.ac.za/) and ZINC database (http://zinc15.docking.org/) were used for high-throughput virtual screening (HVTS) against COX-1. Additionally, five nsSNPs were being investigated to assess their impact on protein structure and function. Three of these SNPs were in the COX-1 dimer interface. Molecular docking and molecular dynamics simulations revealed asymmetric nature of the protein. Several ligands, peculiar to each monomer, exhibited favourable binding energies in the respective active sites. SNP analysis indicated effects on inter-monomer interactions and protein stability.
- Full Text:
Default in payment, an application of statistical learning techniques
- Authors: Gcakasi, Lulama
- Date: 2020
- Subjects: Credit -- South Africa -- Risk assessment , Risk management -- Statistical methods -- South Africa , Credit -- Management -- Statistical methods , Commercial statistics
- Language: English
- Type: text , Thesis , Masters , MSc
- Identifier: http://hdl.handle.net/10962/141547 , vital:37984
- Description: The ability of financial institutions to detect whether a customer will default on their credit card payment is essential for its profitability. To that effect, financial institutions have credit scoring systems in place to be able to estimate the credit risk associated with a customer. Various classification models are used to develop credit scoring systems such as k-nearest neighbours, logistic regression and classification trees. This study aims to assess the performance of different classification models on the prediction of credit card payment default. Credit data is usually of high dimension and as a result dimension reduction techniques, namely principal component analysis and linear discriminant analysis, are used in this study as a means to improve model performance. Two classification models are used, namely neural networks and support vector machines. Model performance is evaluated using accuracy and area under the curve (AUC). The neuarl network classifier performed better than the support vector machine classifier as it produced higher accuracy rates and AUC values. Dimension reduction techniques were not effective in improving model performance but did result in less computationally expensive models.
- Full Text:
- Authors: Gcakasi, Lulama
- Date: 2020
- Subjects: Credit -- South Africa -- Risk assessment , Risk management -- Statistical methods -- South Africa , Credit -- Management -- Statistical methods , Commercial statistics
- Language: English
- Type: text , Thesis , Masters , MSc
- Identifier: http://hdl.handle.net/10962/141547 , vital:37984
- Description: The ability of financial institutions to detect whether a customer will default on their credit card payment is essential for its profitability. To that effect, financial institutions have credit scoring systems in place to be able to estimate the credit risk associated with a customer. Various classification models are used to develop credit scoring systems such as k-nearest neighbours, logistic regression and classification trees. This study aims to assess the performance of different classification models on the prediction of credit card payment default. Credit data is usually of high dimension and as a result dimension reduction techniques, namely principal component analysis and linear discriminant analysis, are used in this study as a means to improve model performance. Two classification models are used, namely neural networks and support vector machines. Model performance is evaluated using accuracy and area under the curve (AUC). The neuarl network classifier performed better than the support vector machine classifier as it produced higher accuracy rates and AUC values. Dimension reduction techniques were not effective in improving model performance but did result in less computationally expensive models.
- Full Text:
Design, formulation and evalauation of liposomes co-loaded with human serum Albumin and Rifampicin
- Authors: Bapolisi, Alain Murhimalika
- Date: 2020
- Subjects: Liposomes , Serum albumin , Rifampin , Mycobacterium tuberculosis
- Language: English
- Type: text , Thesis , Masters , MSc
- Identifier: http://hdl.handle.net/10962/161780 , vital:40670
- Description: Tuberculosis (TB) is a devastating infectious disease caused by Mycobacterium tuberculosis and is the leading cause of death from a single infectious agent. The high morbidity and mortality rates of TB are partly due to factors such as the lengthy regimen (of 6–24 months), the development of drug resistance, and the pathogen location within the macrophages. These, with poor physiochemical properties of existing drugs hamper the effectiveness of the treatment despite the existence of potent antibiotics such as Rifampicin (Rif). Hydrophobicity plagues many drugs, including Rif, which are then particularly affected due to inherently poor intracellular availability. Novel drug delivery approaches are therefore needed in order to optimize the cytotoxic potential of said antitubercular drugs. To improve the bioavailability of hydrophobic drugs, numerous delivery strategies have been developed. Amongst these, the coordination of cytotoxic drugs to therapeutic proteins have shown some success for improved efficacy in the management of illnesses including infectious diseases. Of therapeutic proteins, Human Serum Albumin (HSA) is an attractive drug carrier with interestingbenefits such as low immunogenicity, antioxidant properties and improving cellular uptake ofdrugs through HSA-specific binding sites which are expressed on most cells including macrophages, where M. tuberculosis often resides. Hence, combination of Rif to HSA (Rif-HSA)seems a promising approach for improved intracellular delivery of Rif. However, the in vivo stability of colloidal protein-based therapeutics is mostly challenging and an effective vehicle is needed to control the biological fate of such conjugates.Liposomes seem to be appropriate carriers for the Rif-HSA complex due to their reputable applicability for encapsulating diverse materials (i.e., hydrophobic and hydrophilic compounds or small and complex molecules) and preventing chemical and biological degradation of the cargo. Therefore, the main objective of this study was to simultaneously encapsulate Rif and HSA in liposomes, which, to the best of our knowledge, has not been done before. The dual liposomes (Rif-HSA-lip) were made by a modified “Reverse Phase Evaporation” method (REV), following a Design of Experiments (DOE) approach to determine which factors impact the formulation. In addition, liposomes were made from crude soybean lecithin (CSL), rather than expensive and highly purified lipids. The liposomes were fully characterised, and the encapsulation efficiency (î) was monitored using high-performance liquid chromatography (HPLC). The results were correlated with factors such as organic and aqueous phase composition, as well as the in vitro release profile of Rif. Transmission electron microscopy (TEM) results confirmed the formation of spherical dual liposomes nanoparticles of roughly 200 nm. Dynamic light scattering (DLS) and Zeta potential measurements showed a negative charge (<–45 mV) and with satisfactory polydispersity (PDI<0.5). HSA dramatically improved the aqueous solubility of Rif (from1.9 mg/ml in water to around 4.3 mg/ml in HSA 10% solution) mainly due to Rif-HSA hydrophobic interactions. This resulted in a good î of almost 60% for Rif, despite the presence of bulky HSA in the lipid bilayer. These details were confirmed using proton nuclear magnetic resonance (1H NMR) and Fourier-transform infrared spectroscopy (FTIR). Furthermore, energy dispersive X-ray (EDX) and DLS data suggested the presence of HSA poking out on the surface of liposomes, which is encouraging for potential targeted delivery in the future. The in vitro release studies also depicted a substantial improvement in the diffusion of Rif in dual liposomes versus free Rif, from 65% after 12 hours for free Rif to 95% after only 5 hours for Rif- HSA-lip. Finally, stability studies conducted over 30 days at room temperature, showed that the freeze-dried formulations of Rif-HSA-lip exhibited good shelf stability over liposomes with no HSA. This study represents an illustrative example of co-loading of antibiotics and proteins into liposomes, which could encourage further development of novel nanoparticulate tools for the effective management of both drug-susceptible and -resistant infectious diseases such as TB.
- Full Text:
- Authors: Bapolisi, Alain Murhimalika
- Date: 2020
- Subjects: Liposomes , Serum albumin , Rifampin , Mycobacterium tuberculosis
- Language: English
- Type: text , Thesis , Masters , MSc
- Identifier: http://hdl.handle.net/10962/161780 , vital:40670
- Description: Tuberculosis (TB) is a devastating infectious disease caused by Mycobacterium tuberculosis and is the leading cause of death from a single infectious agent. The high morbidity and mortality rates of TB are partly due to factors such as the lengthy regimen (of 6–24 months), the development of drug resistance, and the pathogen location within the macrophages. These, with poor physiochemical properties of existing drugs hamper the effectiveness of the treatment despite the existence of potent antibiotics such as Rifampicin (Rif). Hydrophobicity plagues many drugs, including Rif, which are then particularly affected due to inherently poor intracellular availability. Novel drug delivery approaches are therefore needed in order to optimize the cytotoxic potential of said antitubercular drugs. To improve the bioavailability of hydrophobic drugs, numerous delivery strategies have been developed. Amongst these, the coordination of cytotoxic drugs to therapeutic proteins have shown some success for improved efficacy in the management of illnesses including infectious diseases. Of therapeutic proteins, Human Serum Albumin (HSA) is an attractive drug carrier with interestingbenefits such as low immunogenicity, antioxidant properties and improving cellular uptake ofdrugs through HSA-specific binding sites which are expressed on most cells including macrophages, where M. tuberculosis often resides. Hence, combination of Rif to HSA (Rif-HSA)seems a promising approach for improved intracellular delivery of Rif. However, the in vivo stability of colloidal protein-based therapeutics is mostly challenging and an effective vehicle is needed to control the biological fate of such conjugates.Liposomes seem to be appropriate carriers for the Rif-HSA complex due to their reputable applicability for encapsulating diverse materials (i.e., hydrophobic and hydrophilic compounds or small and complex molecules) and preventing chemical and biological degradation of the cargo. Therefore, the main objective of this study was to simultaneously encapsulate Rif and HSA in liposomes, which, to the best of our knowledge, has not been done before. The dual liposomes (Rif-HSA-lip) were made by a modified “Reverse Phase Evaporation” method (REV), following a Design of Experiments (DOE) approach to determine which factors impact the formulation. In addition, liposomes were made from crude soybean lecithin (CSL), rather than expensive and highly purified lipids. The liposomes were fully characterised, and the encapsulation efficiency (î) was monitored using high-performance liquid chromatography (HPLC). The results were correlated with factors such as organic and aqueous phase composition, as well as the in vitro release profile of Rif. Transmission electron microscopy (TEM) results confirmed the formation of spherical dual liposomes nanoparticles of roughly 200 nm. Dynamic light scattering (DLS) and Zeta potential measurements showed a negative charge (<–45 mV) and with satisfactory polydispersity (PDI<0.5). HSA dramatically improved the aqueous solubility of Rif (from1.9 mg/ml in water to around 4.3 mg/ml in HSA 10% solution) mainly due to Rif-HSA hydrophobic interactions. This resulted in a good î of almost 60% for Rif, despite the presence of bulky HSA in the lipid bilayer. These details were confirmed using proton nuclear magnetic resonance (1H NMR) and Fourier-transform infrared spectroscopy (FTIR). Furthermore, energy dispersive X-ray (EDX) and DLS data suggested the presence of HSA poking out on the surface of liposomes, which is encouraging for potential targeted delivery in the future. The in vitro release studies also depicted a substantial improvement in the diffusion of Rif in dual liposomes versus free Rif, from 65% after 12 hours for free Rif to 95% after only 5 hours for Rif- HSA-lip. Finally, stability studies conducted over 30 days at room temperature, showed that the freeze-dried formulations of Rif-HSA-lip exhibited good shelf stability over liposomes with no HSA. This study represents an illustrative example of co-loading of antibiotics and proteins into liposomes, which could encourage further development of novel nanoparticulate tools for the effective management of both drug-susceptible and -resistant infectious diseases such as TB.
- Full Text:
Design, formulation and evaluation of liposomes co-loaded with human serum albumin and rifampicin
- Authors: Bapolisi, Alain Murhimalika
- Date: 2020
- Subjects: Liposomes , Rifampin , Antitubercular agents , Serum albumin , Albumins , Tuberculosis -- Treatment
- Language: English
- Type: text , Thesis , Masters , MSc
- Identifier: http://hdl.handle.net/10962/163179 , vital:41016
- Description: Tuberculosis (TB) is a devastating infectious disease caused by Mycobacterium tuberculosis and is the leading cause of death from a single infectious agent. The high morbidity and mortality rates of TB are partly due to factors such as the lengthy regimen (of 6–24 months), the development of drug resistance, and the pathogen location within the macrophages. These, with poor physiochemical properties of existing drugs hamper the effectiveness of the treatment despite the existence of potent antibiotics such as Rifampicin (Rif). Hydrophobicity plagues many drugs, including Rif, which are then particularly affected due to inherently poor intracellular availability. Novel drug delivery approaches are therefore needed in order to optimize the cytotoxic potential of said antitubercular drugs. To improve the bioavailability of hydrophobic drugs, numerous delivery strategies have been developed. Amongst these, the coordination of cytotoxic drugs to therapeutic proteins have shown some success for improved efficacy in the management of illnesses including infectious diseases. Of therapeutic proteins, Human Serum Albumin (HSA) is an attractive drug carrier with interesting benefits such as low immunogenicity, antioxidant properties and improving cellular uptake of drugs through HSA-specific binding sites which are expressed on most cells including macrophages, where M. tuberculosis often resides. Hence, combination of Rif to HSA (Rif-HSA) seems a promising approach for improved intracellular delivery of Rif. However, the in vivo stability of colloidal protein-based therapeutics is mostly challenging and an effective vehicle is needed to control the biological fate of such conjugates. Liposomes seem to be appropriate carriers for the Rif-HSA complex due to their reputable applicability for encapsulating diverse materials (i.e., hydrophobic and hydrophilic compounds or small and complex molecules) and preventing chemical and biological degradation of the cargo. Therefore, the main objective of this study was to simultaneously encapsulate Rif and HSA in liposomes, which, to the best of our knowledge, has not been done before. The dual liposomes (Rif-HSA-lip) were made by a modified “Reverse Phase Evaporation” method (REV), following a Design of Experiments (DOE) approach to determine which factors impact the formulation. In addition, liposomes were made from crude soybean lecithin (CSL), rather than expensive and highly purified lipids. iv The liposomes were fully characterised, and the encapsulation efficiency (î) was monitored using high-performance liquid chromatography (HPLC). The results were correlated with factors such as organic and aqueous phase composition, as well as the in vitro release profile of Rif. Transmission electron microscopy (TEM) results confirmed the formation of spherical dual liposomes nanoparticles of roughly 200 nm. Dynamic light scattering (DLS) and Zeta potential measurements showed a negative charge (<–45 mV) and with satisfactory polydispersity (PDI<0.5). HSA dramatically improved the aqueous solubility of Rif (from1.9 mg/ml in water to around 4.3 mg/ml in HSA 10% solution) mainly due to Rif-HSA hydrophobic interactions. This resulted in a good î of almost 60% for Rif, despite the presence of bulky HSA in the lipid bilayer. These details were confirmed using proton nuclear magnetic resonance (1H NMR) and Fourier-transform infrared spectroscopy (FTIR). Furthermore, energy dispersive X-ray (EDX) and DLS data suggested the presence of HSA poking out on the surface of liposomes, which is encouraging for potential targeted delivery in the future. The in vitro release studies also depicted a substantial improvement in the diffusion of Rif in dual liposomes versus free Rif, from 65% after 12 hours for free Rif to 95% after only 5 hours for Rif- HSA-lip. Finally, stability studies conducted over 30 days at room temperature, showed that the freeze-dried formulations of Rif-HSA-lip exhibited good shelf stability over liposomes with no HSA. This study represents an illustrative example of co-loading of antibiotics and proteins into liposomes, which could encourage further development of novel nanoparticulate tools for the effective management of both drug-susceptible and -resistant infectious diseases such as TB.
- Full Text:
- Authors: Bapolisi, Alain Murhimalika
- Date: 2020
- Subjects: Liposomes , Rifampin , Antitubercular agents , Serum albumin , Albumins , Tuberculosis -- Treatment
- Language: English
- Type: text , Thesis , Masters , MSc
- Identifier: http://hdl.handle.net/10962/163179 , vital:41016
- Description: Tuberculosis (TB) is a devastating infectious disease caused by Mycobacterium tuberculosis and is the leading cause of death from a single infectious agent. The high morbidity and mortality rates of TB are partly due to factors such as the lengthy regimen (of 6–24 months), the development of drug resistance, and the pathogen location within the macrophages. These, with poor physiochemical properties of existing drugs hamper the effectiveness of the treatment despite the existence of potent antibiotics such as Rifampicin (Rif). Hydrophobicity plagues many drugs, including Rif, which are then particularly affected due to inherently poor intracellular availability. Novel drug delivery approaches are therefore needed in order to optimize the cytotoxic potential of said antitubercular drugs. To improve the bioavailability of hydrophobic drugs, numerous delivery strategies have been developed. Amongst these, the coordination of cytotoxic drugs to therapeutic proteins have shown some success for improved efficacy in the management of illnesses including infectious diseases. Of therapeutic proteins, Human Serum Albumin (HSA) is an attractive drug carrier with interesting benefits such as low immunogenicity, antioxidant properties and improving cellular uptake of drugs through HSA-specific binding sites which are expressed on most cells including macrophages, where M. tuberculosis often resides. Hence, combination of Rif to HSA (Rif-HSA) seems a promising approach for improved intracellular delivery of Rif. However, the in vivo stability of colloidal protein-based therapeutics is mostly challenging and an effective vehicle is needed to control the biological fate of such conjugates. Liposomes seem to be appropriate carriers for the Rif-HSA complex due to their reputable applicability for encapsulating diverse materials (i.e., hydrophobic and hydrophilic compounds or small and complex molecules) and preventing chemical and biological degradation of the cargo. Therefore, the main objective of this study was to simultaneously encapsulate Rif and HSA in liposomes, which, to the best of our knowledge, has not been done before. The dual liposomes (Rif-HSA-lip) were made by a modified “Reverse Phase Evaporation” method (REV), following a Design of Experiments (DOE) approach to determine which factors impact the formulation. In addition, liposomes were made from crude soybean lecithin (CSL), rather than expensive and highly purified lipids. iv The liposomes were fully characterised, and the encapsulation efficiency (î) was monitored using high-performance liquid chromatography (HPLC). The results were correlated with factors such as organic and aqueous phase composition, as well as the in vitro release profile of Rif. Transmission electron microscopy (TEM) results confirmed the formation of spherical dual liposomes nanoparticles of roughly 200 nm. Dynamic light scattering (DLS) and Zeta potential measurements showed a negative charge (<–45 mV) and with satisfactory polydispersity (PDI<0.5). HSA dramatically improved the aqueous solubility of Rif (from1.9 mg/ml in water to around 4.3 mg/ml in HSA 10% solution) mainly due to Rif-HSA hydrophobic interactions. This resulted in a good î of almost 60% for Rif, despite the presence of bulky HSA in the lipid bilayer. These details were confirmed using proton nuclear magnetic resonance (1H NMR) and Fourier-transform infrared spectroscopy (FTIR). Furthermore, energy dispersive X-ray (EDX) and DLS data suggested the presence of HSA poking out on the surface of liposomes, which is encouraging for potential targeted delivery in the future. The in vitro release studies also depicted a substantial improvement in the diffusion of Rif in dual liposomes versus free Rif, from 65% after 12 hours for free Rif to 95% after only 5 hours for Rif- HSA-lip. Finally, stability studies conducted over 30 days at room temperature, showed that the freeze-dried formulations of Rif-HSA-lip exhibited good shelf stability over liposomes with no HSA. This study represents an illustrative example of co-loading of antibiotics and proteins into liposomes, which could encourage further development of novel nanoparticulate tools for the effective management of both drug-susceptible and -resistant infectious diseases such as TB.
- Full Text:
Development and assessment of a fixed dose combination of perindopril arginine and indapamide loaded microparticles
- Authors: Mandava, Tavonga Tyomai
- Date: 2020
- Subjects: Uncatalogued
- Language: English
- Type: thesis , text , Masters , MSc
- Identifier: http://hdl.handle.net/10962/164413 , vital:41116
- Description: Thesis (MSc)--Rhodes University, Faculty of Pharmacy, Pharmaceutics, 2020
- Full Text:
- Authors: Mandava, Tavonga Tyomai
- Date: 2020
- Subjects: Uncatalogued
- Language: English
- Type: thesis , text , Masters , MSc
- Identifier: http://hdl.handle.net/10962/164413 , vital:41116
- Description: Thesis (MSc)--Rhodes University, Faculty of Pharmacy, Pharmaceutics, 2020
- Full Text:
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:
- 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:
Development of a protocol for extracting and quantifying the concentration of thiafentanil in blesbok (Damaliscus pygargus phillipsi) matrices 72-74 hours post administration
- Authors: Webber, Judith Tracy
- Date: 2020
- Subjects: Uncatalogued
- Language: English
- Type: thesis , text , Masters , MSc
- Identifier: http://hdl.handle.net/10962/164738 , vital:41159
- Description: Thesis (MSc)--Rhodes University, Faculty of Science, Chemistry, 2020
- Full Text:
- Authors: Webber, Judith Tracy
- Date: 2020
- Subjects: Uncatalogued
- Language: English
- Type: thesis , text , Masters , MSc
- Identifier: http://hdl.handle.net/10962/164738 , vital:41159
- Description: Thesis (MSc)--Rhodes University, Faculty of Science, Chemistry, 2020
- Full Text:
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:
- 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:
Distribution, habitat associations and conservation of the Eastern Cape rocky Sandelia bainsii (Perciform: Anabantidae) in the Great Fish River system
- Authors: Sifundza, Delsy Sindy
- Date: 2020
- Subjects: Anabantidae -- South Africa -- Great Fish River , Perciformes -- South Africa -- Great Fish River , Labyrinth fishes -- South Africa -- Great Fish River , Fishes -- Effect of human beings on -- South Africa -- Great Fish River , Fish populations -- South Africa -- Great Fish River , Fish declines -- South Africa -- Great Fish River , Fish populations -- Monitoring -- South Africa -- Great Fish River , Anabantidae -- Evolution -- South Africa -- Great Fish River , Gene flow , Mitochondrial DNA , Microsatellites (Genetics) , Eastern Cape rocky Sandelia bainsii , Freshwater ecology -- South Africa -- Great Fish River
- Language: English
- Type: Thesis , Masters , MSc
- Identifier: http://hdl.handle.net/10962/142692 , vital:38102
- Description: In South Africa, freshwater ecosystems are under pressure due to increasing anthropogenic factors degrading river systems. The Cape Fold, the lower Southern Temperate Highveld and the Amatolo – Winterberg Highlands freshwater ecoregions contain some of the heavily impacted river systems in the country. One such river system is the Great Fish River system, which has been affected by anthropogenic modification (hydrological modification, water pollution and invasion by non-native fish species). These modifications have raised conservation concerns on an imperilled anabantid fish, the Eastern Cape rocky Sandelia bainsii that is confined to the Kat and Koonap rivers, which are tributaries of the Great Fish River. Historically, the species was reportedly common and abundant, with a range spanning across seven river systems (Kowie, Great Fish, Keiskamma, Igoda, Gxulu, Buffalo and Nahoon rivers) in the Eastern Cape Province. However, surveys have indicated that the species has experienced decline in population size and distribution range, with localised extirpations being reported. This resulted in its listing on the IUCN Red List of threatened species as Endangered. The proposed shale gas exploration and potential infrastructure development in the Karoo basin, which encompasses the headwaters of the Kat River, represent a potential future threat to the remnant populations of this species. The aim of the present study was to review the past and present distribution range of S. bainsii, determine the habitat associations and assess the conservation of S. bainsii in the Great Fish River system. This information is essential for informing conservation and management decisions for this species in the Great Fish River system. This study undertook a comprehensive survey of the Kat and the Koonap rivers in 2017, and augmented this information with data from more recent surveys that were conducted from 2009 - 2014 to map the distributions freshwater fishes in the Great Fish River system. Data from these recent surveys (2009 – 2017) were compared with historical records (1961 – 2005) obtained from the South African Institute for Aquatic Biodiversity to evaluate changes in distribution patterns of S. bainsii. Historical records indicated that S. bainsii occurred at 11 localities in the Kat River and three localities in the Koonap River. Data from recent surveys indicated that the species has persisted at these historical localities, except one locality in the Koonap River where no individuals of S. bainsii were captured, despite the use of multiple sampling approaches and gears. Although the species still persists at two of the three historical localities in the Koonap River, the population sizes have considerably declined as the species was reportedly in high abundance at these localities in the 1980s. Factors threatening the continued existence of this species in the Koonap River likely include non-native species, extreme drought conditions and the associated excessive abstraction of water which has resulted in the drying of some of the refugia pools where the species was historically common and abundant. In contrast to the Koonap River, the 2017 survey indicated that in the Kat River, S. bainsii had a similar distribution range compared to historical records. The species occurred at 11 of the 41 localities that were sampled in the Kat River, and the sampled populations consisted of all size classes. Sandelia bainsii occurred with other native fish species in the system, including Labeo umbratus, Enteromius anoplus and Glossogobius callidus. A comparison of historical and recent data indicates that non-native fishes have likely not expanded their ranges in the Kat River. This is likely due to the presence of weirs and dams that have prevented upstream movement of non-native fish species L. aeneus, C. gariepinus and T. sparrmanii which are now abundant in the lower Kat and mainstem Great Fish River. Surveys from the present study indicated that although S. bainsii still persists within the Kat River, there are a number of factors that pose a considerable threat to the continued existence of this species in the Great Fish River system. Chapter 3 evaluated the habitat associations of S. bainsii based on 10 physical and chemical variables and distribution data collected from 30 localities in the Upper Kat River and seven of its tributaries. A non-metric multidimensional scaling model was used to assess the distribution patterns of S. bainsii in relation to environmental variables. Furthermore, a negative binomial generalised linear model (GLM) was used to assess the relationship between the abundance of S. bainsii and environmental variables. Results from the present study indicated that S. bainsii was a habitat generalist as the distribution of this species showed no specific association with any of the habitat variables that were considered in this study. The species occurred in a wide range of habitats, including rocky sections in the upper Kat River and its tributaries as well as the mainstem sections. The GLM however indicated that the abundance of S. bainsii was negatively associated with increasing conductivity. In addition, the Kat River contains multiple weirs of variable sizes. Future studies should therefore evaluate the effects of these weirs on population fragmentation, gene flow and long-term evolutionary potential of S. bainsii through the application of techniques such as mitochondrial DNA and microsatellites.
- Full Text:
- Authors: Sifundza, Delsy Sindy
- Date: 2020
- Subjects: Anabantidae -- South Africa -- Great Fish River , Perciformes -- South Africa -- Great Fish River , Labyrinth fishes -- South Africa -- Great Fish River , Fishes -- Effect of human beings on -- South Africa -- Great Fish River , Fish populations -- South Africa -- Great Fish River , Fish declines -- South Africa -- Great Fish River , Fish populations -- Monitoring -- South Africa -- Great Fish River , Anabantidae -- Evolution -- South Africa -- Great Fish River , Gene flow , Mitochondrial DNA , Microsatellites (Genetics) , Eastern Cape rocky Sandelia bainsii , Freshwater ecology -- South Africa -- Great Fish River
- Language: English
- Type: Thesis , Masters , MSc
- Identifier: http://hdl.handle.net/10962/142692 , vital:38102
- Description: In South Africa, freshwater ecosystems are under pressure due to increasing anthropogenic factors degrading river systems. The Cape Fold, the lower Southern Temperate Highveld and the Amatolo – Winterberg Highlands freshwater ecoregions contain some of the heavily impacted river systems in the country. One such river system is the Great Fish River system, which has been affected by anthropogenic modification (hydrological modification, water pollution and invasion by non-native fish species). These modifications have raised conservation concerns on an imperilled anabantid fish, the Eastern Cape rocky Sandelia bainsii that is confined to the Kat and Koonap rivers, which are tributaries of the Great Fish River. Historically, the species was reportedly common and abundant, with a range spanning across seven river systems (Kowie, Great Fish, Keiskamma, Igoda, Gxulu, Buffalo and Nahoon rivers) in the Eastern Cape Province. However, surveys have indicated that the species has experienced decline in population size and distribution range, with localised extirpations being reported. This resulted in its listing on the IUCN Red List of threatened species as Endangered. The proposed shale gas exploration and potential infrastructure development in the Karoo basin, which encompasses the headwaters of the Kat River, represent a potential future threat to the remnant populations of this species. The aim of the present study was to review the past and present distribution range of S. bainsii, determine the habitat associations and assess the conservation of S. bainsii in the Great Fish River system. This information is essential for informing conservation and management decisions for this species in the Great Fish River system. This study undertook a comprehensive survey of the Kat and the Koonap rivers in 2017, and augmented this information with data from more recent surveys that were conducted from 2009 - 2014 to map the distributions freshwater fishes in the Great Fish River system. Data from these recent surveys (2009 – 2017) were compared with historical records (1961 – 2005) obtained from the South African Institute for Aquatic Biodiversity to evaluate changes in distribution patterns of S. bainsii. Historical records indicated that S. bainsii occurred at 11 localities in the Kat River and three localities in the Koonap River. Data from recent surveys indicated that the species has persisted at these historical localities, except one locality in the Koonap River where no individuals of S. bainsii were captured, despite the use of multiple sampling approaches and gears. Although the species still persists at two of the three historical localities in the Koonap River, the population sizes have considerably declined as the species was reportedly in high abundance at these localities in the 1980s. Factors threatening the continued existence of this species in the Koonap River likely include non-native species, extreme drought conditions and the associated excessive abstraction of water which has resulted in the drying of some of the refugia pools where the species was historically common and abundant. In contrast to the Koonap River, the 2017 survey indicated that in the Kat River, S. bainsii had a similar distribution range compared to historical records. The species occurred at 11 of the 41 localities that were sampled in the Kat River, and the sampled populations consisted of all size classes. Sandelia bainsii occurred with other native fish species in the system, including Labeo umbratus, Enteromius anoplus and Glossogobius callidus. A comparison of historical and recent data indicates that non-native fishes have likely not expanded their ranges in the Kat River. This is likely due to the presence of weirs and dams that have prevented upstream movement of non-native fish species L. aeneus, C. gariepinus and T. sparrmanii which are now abundant in the lower Kat and mainstem Great Fish River. Surveys from the present study indicated that although S. bainsii still persists within the Kat River, there are a number of factors that pose a considerable threat to the continued existence of this species in the Great Fish River system. Chapter 3 evaluated the habitat associations of S. bainsii based on 10 physical and chemical variables and distribution data collected from 30 localities in the Upper Kat River and seven of its tributaries. A non-metric multidimensional scaling model was used to assess the distribution patterns of S. bainsii in relation to environmental variables. Furthermore, a negative binomial generalised linear model (GLM) was used to assess the relationship between the abundance of S. bainsii and environmental variables. Results from the present study indicated that S. bainsii was a habitat generalist as the distribution of this species showed no specific association with any of the habitat variables that were considered in this study. The species occurred in a wide range of habitats, including rocky sections in the upper Kat River and its tributaries as well as the mainstem sections. The GLM however indicated that the abundance of S. bainsii was negatively associated with increasing conductivity. In addition, the Kat River contains multiple weirs of variable sizes. Future studies should therefore evaluate the effects of these weirs on population fragmentation, gene flow and long-term evolutionary potential of S. bainsii through the application of techniques such as mitochondrial DNA and microsatellites.
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