The petrology of the Khale dolerite sheet
- Authors: Eales, Hugh V
- Date: 1953
- Subjects: Petrology -- Botswana , Diabase -- Botswana
- Language: English
- Type: Thesis , Masters , MSc
- Identifier: vital:5076 , http://hdl.handle.net/10962/d1014853
- Description: In the hills and in the plain of the Khale area are exposed two sheets of quartz-dolerite, the upper sheet being locally mushroom-shaped. The rock corresponds loosely with the Downes mountain type of dolorite, and contains numerous horizons of coarse-grained dolorite-pegmatite. The plagioclase felspars are described with special reference to the variation of grain-size, the features of zoned crystals, and the possible causes of a peculiar brown clouding in the basic zones of the crystals. Phenocrysts of augite and pigeonite, as well as plagioclase are recorded in the chilled contact rock. The micrometric data indicate that the mineral composition of the specimens is largely governed by the oxidation state of the iron, and that the Soret effect has caused the marginal rock to be enriched in basic elements. Hydrothermal veinlets composed largely of chlorite occur in both the dolorite and the country rock, and evidence suggests that veins of both residual material and mobilised granite occur in the upper finer-grained dolorite.
- Full Text:
- Date Issued: 1953
- Authors: Eales, Hugh V
- Date: 1953
- Subjects: Petrology -- Botswana , Diabase -- Botswana
- Language: English
- Type: Thesis , Masters , MSc
- Identifier: vital:5076 , http://hdl.handle.net/10962/d1014853
- Description: In the hills and in the plain of the Khale area are exposed two sheets of quartz-dolerite, the upper sheet being locally mushroom-shaped. The rock corresponds loosely with the Downes mountain type of dolorite, and contains numerous horizons of coarse-grained dolorite-pegmatite. The plagioclase felspars are described with special reference to the variation of grain-size, the features of zoned crystals, and the possible causes of a peculiar brown clouding in the basic zones of the crystals. Phenocrysts of augite and pigeonite, as well as plagioclase are recorded in the chilled contact rock. The micrometric data indicate that the mineral composition of the specimens is largely governed by the oxidation state of the iron, and that the Soret effect has caused the marginal rock to be enriched in basic elements. Hydrothermal veinlets composed largely of chlorite occur in both the dolorite and the country rock, and evidence suggests that veins of both residual material and mobilised granite occur in the upper finer-grained dolorite.
- Full Text:
- Date Issued: 1953
The development of techniques for the identification of novel viruses associated with acute infantile gastroenteritis in South Africa
- Authors: Jaquet, Brittany J
- Date: 2017
- Subjects: Gastroenteritis in children -- Treatment , Gastroenteritis in children -- Treatment -- South Africa , Antiviral agents , Viral vaccines , Rotaviruses , Virus diseases in children
- Language: English
- Type: Thesis , Masters , MSc
- Identifier: http://hdl.handle.net/10962/38013 , vital:24725
- Description: Gastroenteritis is a serious disease affecting both children and adults globally, but is more predominant in children with over half a million deaths reported each year. The leading cause of this disease is rotavirus, which accounts for 38% of all hospitalised cases. There has, however, been a significant decrease in the number of deaths associated with rotavirus worldwide since the introduction of the two vaccines, Rotarix® and RotaTeq®. A large number of cases are therefore either associated with other viruses, such as norovirus, Aichi virus (AiV) or Saffold virus (SAFV), or are of unknown aetiology. This study thus aims to develop techniques for the identification of viruses associated with gastroenteritis. Theiler’s murine encephalomyelitis virus (TMEV) was used to develop the sample preparation, transmission electron microscopy and RT-PCR techniques used in this study. This virus was chosen as a replication system using baby hamster kidney cells can be used to create high concentrations of viral particles from which RNA can be extracted preventing the waste of the limited samples. The virus particles are also similar in size and morphology to the viruses to be identified in this study, as it belongs to the same family. After sample preparation, TEM analysis showed the presence of small, round, non-enveloped virus particles in the TMEV sample. Due to the low concentration of virus particles, PEG precipitation was performed using both 0.15 M and 0.25 M NaCl and 8% (w/v) PEG 6000. TEM analysis then showed an increase in viral particle concentration, with the highest concentration observed at 0.25 M NaCl and 8% PEG 6000. RNA was successfully extracted and RT-PCR assays were performed for both the VP1 and 2B coding regions of TMEV. A method for creating a positive control for the RT-PCR assay was developed by the in vitro transcription of RNA from pTMEV, which contains the cDNA of TMEV. The RNA was then used as the template for the 2B two-step RT-PCR assay. A product of 412 bp was successfully amplified from the in vitro transcribed RNA and the sensitivity of the RT-PCR assay was determined. Using a Norovirus GII positive stool sample provided by Maureen Taylor, a nested RT-PCR assay was developed for the NoV GII N/S domain using a previously-published primer set and cycling parameters. A 342 bp product was successfully amplified from the RNA extracted from the stool sample and cloned into pGEM®-T Easy to produce pNoVGII. Using the plasmid containing the AiV 5’UTR and the PCR amplicon for AiV 3CD, RT-PCR assays were developed for AiV 5’UTR and partial 3CD. The RT-PCR assays produced a 1008 bp product for AiV 5’UTR and 266 bp for AiV 3CD, which were cloned into pGEM®-T Easy to produce pAiV5’UTR and pAiV3CD, respectively. Using in vitro transcribed RNA from pNoVGII, pAiV5’UTR, pAiV3CD and pSAFV, which contains the SAFV cDNA, positive controls were developed for the RT-PCR assays for NoV GII, AiV 5’UTR, AiV 3CD and SAFV 2C. The sensitivity of these assays was determined. The samples chosen for this study include wastewater collected from the Belmont Valley water treatment plant, oysters suspected to be infected with viruses collected from Port Elizabeth, South Africa and 30 stool samples from symptomatic patients. With the methods developed using TMEV, the wastewater, oysters and 30 stool samples were filter-sterilised, concentrated and screened by TEM. All samples showed the presence of virus particles. RNA was successfully extracted and the wastewater, oyster and 30 stool samples were screened for NoV GII using the NoV GII RT-PCR assay. The wastewater, oysters and 11 of the stool samples produced the 342 bp NoV GII PCR product and BLAST analysis determined the nucleotide sequences to be NoV GII.4. This shows that this study was able to develop sample preparation techniques and TEM analysis for selected samples and RT-PCR assays for NoV GII, AiV and SAFV. The NoV GII RT-PCR assay was successfully used for the screening of the wastewater, oysters and 30 stool samples for NoV GII. Due to the high number of gastroenteritis cases with unknown aetiology in South Africa, the development of techniques for the identification of NoV, AiV, SAFV and other viruses is very important. The identification of these viruses will allow for better surveillance, treatment and prevention of gastroenteritis in South Africa.
- Full Text:
- Date Issued: 2017
- Authors: Jaquet, Brittany J
- Date: 2017
- Subjects: Gastroenteritis in children -- Treatment , Gastroenteritis in children -- Treatment -- South Africa , Antiviral agents , Viral vaccines , Rotaviruses , Virus diseases in children
- Language: English
- Type: Thesis , Masters , MSc
- Identifier: http://hdl.handle.net/10962/38013 , vital:24725
- Description: Gastroenteritis is a serious disease affecting both children and adults globally, but is more predominant in children with over half a million deaths reported each year. The leading cause of this disease is rotavirus, which accounts for 38% of all hospitalised cases. There has, however, been a significant decrease in the number of deaths associated with rotavirus worldwide since the introduction of the two vaccines, Rotarix® and RotaTeq®. A large number of cases are therefore either associated with other viruses, such as norovirus, Aichi virus (AiV) or Saffold virus (SAFV), or are of unknown aetiology. This study thus aims to develop techniques for the identification of viruses associated with gastroenteritis. Theiler’s murine encephalomyelitis virus (TMEV) was used to develop the sample preparation, transmission electron microscopy and RT-PCR techniques used in this study. This virus was chosen as a replication system using baby hamster kidney cells can be used to create high concentrations of viral particles from which RNA can be extracted preventing the waste of the limited samples. The virus particles are also similar in size and morphology to the viruses to be identified in this study, as it belongs to the same family. After sample preparation, TEM analysis showed the presence of small, round, non-enveloped virus particles in the TMEV sample. Due to the low concentration of virus particles, PEG precipitation was performed using both 0.15 M and 0.25 M NaCl and 8% (w/v) PEG 6000. TEM analysis then showed an increase in viral particle concentration, with the highest concentration observed at 0.25 M NaCl and 8% PEG 6000. RNA was successfully extracted and RT-PCR assays were performed for both the VP1 and 2B coding regions of TMEV. A method for creating a positive control for the RT-PCR assay was developed by the in vitro transcription of RNA from pTMEV, which contains the cDNA of TMEV. The RNA was then used as the template for the 2B two-step RT-PCR assay. A product of 412 bp was successfully amplified from the in vitro transcribed RNA and the sensitivity of the RT-PCR assay was determined. Using a Norovirus GII positive stool sample provided by Maureen Taylor, a nested RT-PCR assay was developed for the NoV GII N/S domain using a previously-published primer set and cycling parameters. A 342 bp product was successfully amplified from the RNA extracted from the stool sample and cloned into pGEM®-T Easy to produce pNoVGII. Using the plasmid containing the AiV 5’UTR and the PCR amplicon for AiV 3CD, RT-PCR assays were developed for AiV 5’UTR and partial 3CD. The RT-PCR assays produced a 1008 bp product for AiV 5’UTR and 266 bp for AiV 3CD, which were cloned into pGEM®-T Easy to produce pAiV5’UTR and pAiV3CD, respectively. Using in vitro transcribed RNA from pNoVGII, pAiV5’UTR, pAiV3CD and pSAFV, which contains the SAFV cDNA, positive controls were developed for the RT-PCR assays for NoV GII, AiV 5’UTR, AiV 3CD and SAFV 2C. The sensitivity of these assays was determined. The samples chosen for this study include wastewater collected from the Belmont Valley water treatment plant, oysters suspected to be infected with viruses collected from Port Elizabeth, South Africa and 30 stool samples from symptomatic patients. With the methods developed using TMEV, the wastewater, oysters and 30 stool samples were filter-sterilised, concentrated and screened by TEM. All samples showed the presence of virus particles. RNA was successfully extracted and the wastewater, oyster and 30 stool samples were screened for NoV GII using the NoV GII RT-PCR assay. The wastewater, oysters and 11 of the stool samples produced the 342 bp NoV GII PCR product and BLAST analysis determined the nucleotide sequences to be NoV GII.4. This shows that this study was able to develop sample preparation techniques and TEM analysis for selected samples and RT-PCR assays for NoV GII, AiV and SAFV. The NoV GII RT-PCR assay was successfully used for the screening of the wastewater, oysters and 30 stool samples for NoV GII. Due to the high number of gastroenteritis cases with unknown aetiology in South Africa, the development of techniques for the identification of NoV, AiV, SAFV and other viruses is very important. The identification of these viruses will allow for better surveillance, treatment and prevention of gastroenteritis in South Africa.
- Full Text:
- Date Issued: 2017
Mesoscale alongshore and cross-shore transport and settlement of invertebrate larvae on the south east coast of South Africa
- Authors: Dyantyi, Siphelele Buntu
- Date: 2019
- Subjects: Marine invertebrates -- Larvae -- Dispersal -- South Africa -- Eastern Cape , Benthic animals -- Larvae -- Dispersal -- South Africa -- Eastern Cape , Mexilhao mussel -- Larvae -- Dispersal -- South Africa -- Eastern Cape , Mytilus galloprovincialis -- Larvae -- Dispersal -- South Africa -- Eastern Cape , Oysters -- Larvae -- Dispersal -- South Africa -- Eastern Cape
- Language: English
- Type: text , Thesis , Masters , MSc
- Identifier: http://hdl.handle.net/10962/97007 , vital:31386
- Description: Pelagic larval stages of most marine benthic species are important in maintaining coastal populations of adults. Several physio-chemical factors such as currents, winds, larval behaviour and time have an influence on the dispersal and transport of larvae to the adult habitat but their role is however still poorly understood. The aim of this study was to investigate the alongshore and cross-shore transport and temporal delivery of invertebrate larvae at four sites (Kenton on Sea, Cannon Rocks, Schoenmakerskop and Cape St Francis) along the south east coast of Eastern Cape, South Africa. Larval distribution of several taxa was determined during two sampling periods, by collecting water samples at nearshore line transects (3 distances: 900m, 1500m and 2400m – perpendicular to the shore) and at three depths (surface, thermocline/middle, bottom), which ranged from 15m (inshore) to 50m (offshore). Physical properties (current speed and direction, dissolved oxygen, fluorescence, turbidity, temperature, salinity, pH, pressure, density and conductivity) were measured and coupled in order to further understand larval distribution. The larvae were analysed as both total abundance and separately as the abundances of a variety of taxa which were: Perna perna, Mytilus galloprovincialis, oysters, early and late nauplii and cyprids. Larval settlement and recruitment on the rocky shores were measured by monthly deployment and collection of 20 (10 each for barnacles and mussels) artificial collectors at each site, which were preserved in ethanol or frozen for further processing. Multiple Permutational Multivariate Analysis of Variance (PERMANOVA) analyses were used to test the effects of site, depth and distance from the shore for the nearshore larvae (taxa analysed separately). In addition, a distance based linear model (distLM) was performed to analyse the relationship between the total larval abundance and the above mentioned physical variables. Multiple two-way analyses of variance (ANOVA) were performed to test the effects of months and sites on the settlement and recruitment of the larvae (P. perna, M. galloprovincialis, other bivalves, cyprids and juvenile barnacles) arriving on the shore. For the nearshore larval distribution, results from the PERMANOVAs revealed that most taxa showed a significant site and depth interactions with the exception of ‘early nauplii’ taxon. Also nearly all taxa were found within the thermocline, besides ‘oyster’ and ‘cyprids’ which were located at thermocline or bottom. Larvae were also located at variable distances from the shore, with most occurring at the offshore stations. Furthermore, there was a geographical separation of larval abundance according to sites, with most larvae located at Cannon Rocks and Kenton on Sea and least at Schoenmakerskop and Cape St Francis. For the settlement and recruitment, most taxa showed a seasonal trend, with the highest abundance of settlers and recruits expectedly appearing during the summer months of the sampling period. Additionally there was a site effect for most taxa (P. perna, M. galloprovincialis, other bivalves and juvenile barnacles), where settlers and recruits were mostly found at Cannon Rocks. Significant differences in abundance of settlers and recruits amongst the four sites indicate spatial and temporal variability for the targeted 180km stretch of coast. Overall for this study, taxon and ontogenetic stage of larvae were important in the distribution and abundance of larvae. Throughout the time frame of nearshore and intertidal sampling, Cannon Rocks consistently resulted as a ‘hot spot’ for larval abundance, settlement and recruitment, while a broad west to east separation was also observed. These results hence highlight that within this stretch of c.180km coast, time, taxon, ontogeny and post-settlement factors influence early dynamics of benthic populations.
- Full Text:
- Date Issued: 2019
- Authors: Dyantyi, Siphelele Buntu
- Date: 2019
- Subjects: Marine invertebrates -- Larvae -- Dispersal -- South Africa -- Eastern Cape , Benthic animals -- Larvae -- Dispersal -- South Africa -- Eastern Cape , Mexilhao mussel -- Larvae -- Dispersal -- South Africa -- Eastern Cape , Mytilus galloprovincialis -- Larvae -- Dispersal -- South Africa -- Eastern Cape , Oysters -- Larvae -- Dispersal -- South Africa -- Eastern Cape
- Language: English
- Type: text , Thesis , Masters , MSc
- Identifier: http://hdl.handle.net/10962/97007 , vital:31386
- Description: Pelagic larval stages of most marine benthic species are important in maintaining coastal populations of adults. Several physio-chemical factors such as currents, winds, larval behaviour and time have an influence on the dispersal and transport of larvae to the adult habitat but their role is however still poorly understood. The aim of this study was to investigate the alongshore and cross-shore transport and temporal delivery of invertebrate larvae at four sites (Kenton on Sea, Cannon Rocks, Schoenmakerskop and Cape St Francis) along the south east coast of Eastern Cape, South Africa. Larval distribution of several taxa was determined during two sampling periods, by collecting water samples at nearshore line transects (3 distances: 900m, 1500m and 2400m – perpendicular to the shore) and at three depths (surface, thermocline/middle, bottom), which ranged from 15m (inshore) to 50m (offshore). Physical properties (current speed and direction, dissolved oxygen, fluorescence, turbidity, temperature, salinity, pH, pressure, density and conductivity) were measured and coupled in order to further understand larval distribution. The larvae were analysed as both total abundance and separately as the abundances of a variety of taxa which were: Perna perna, Mytilus galloprovincialis, oysters, early and late nauplii and cyprids. Larval settlement and recruitment on the rocky shores were measured by monthly deployment and collection of 20 (10 each for barnacles and mussels) artificial collectors at each site, which were preserved in ethanol or frozen for further processing. Multiple Permutational Multivariate Analysis of Variance (PERMANOVA) analyses were used to test the effects of site, depth and distance from the shore for the nearshore larvae (taxa analysed separately). In addition, a distance based linear model (distLM) was performed to analyse the relationship between the total larval abundance and the above mentioned physical variables. Multiple two-way analyses of variance (ANOVA) were performed to test the effects of months and sites on the settlement and recruitment of the larvae (P. perna, M. galloprovincialis, other bivalves, cyprids and juvenile barnacles) arriving on the shore. For the nearshore larval distribution, results from the PERMANOVAs revealed that most taxa showed a significant site and depth interactions with the exception of ‘early nauplii’ taxon. Also nearly all taxa were found within the thermocline, besides ‘oyster’ and ‘cyprids’ which were located at thermocline or bottom. Larvae were also located at variable distances from the shore, with most occurring at the offshore stations. Furthermore, there was a geographical separation of larval abundance according to sites, with most larvae located at Cannon Rocks and Kenton on Sea and least at Schoenmakerskop and Cape St Francis. For the settlement and recruitment, most taxa showed a seasonal trend, with the highest abundance of settlers and recruits expectedly appearing during the summer months of the sampling period. Additionally there was a site effect for most taxa (P. perna, M. galloprovincialis, other bivalves and juvenile barnacles), where settlers and recruits were mostly found at Cannon Rocks. Significant differences in abundance of settlers and recruits amongst the four sites indicate spatial and temporal variability for the targeted 180km stretch of coast. Overall for this study, taxon and ontogenetic stage of larvae were important in the distribution and abundance of larvae. Throughout the time frame of nearshore and intertidal sampling, Cannon Rocks consistently resulted as a ‘hot spot’ for larval abundance, settlement and recruitment, while a broad west to east separation was also observed. These results hence highlight that within this stretch of c.180km coast, time, taxon, ontogeny and post-settlement factors influence early dynamics of benthic populations.
- Full Text:
- Date Issued: 2019
Sulphide textures and compositions associated with the hydrothermal/magmatic system of the Twangiza gold deposit (South Kivu, DRC)
- Authors: Busane, Emmanuel Aganze
- Date: 2019
- Subjects: Gold mines and mining -- Congo (Democratic Republic) , Geology -- Congo (Democratic Republic) , Hydrothermal alteration -- Congo (Democratic Republic) , Sulphide minerals -- Congo (Democratic Republic) , Gold ores -- Geology -- Congo (Democratic Republic) , Geochemistry -- Congo (Democratic Republic) , Twangiza Mine (Congo (Democratic Republic))
- Language: English
- Type: text , Thesis , Masters , MSc
- Identifier: http://hdl.handle.net/10962/76588 , vital:30610
- Description: Twangiza mine is a gold deposit situated in the eastern Democratic Republic of Congo. The rock types at the Twangiza Mine consist of black shale, including carbonaceous mudstone and thin intercalated layers of siltstone, and feldspar-rich granitoid intrusive sills, referred to as albitite, folded into a major antiformal structure. The gold mineralization at the mine is commonly found associated with sulphides. The sulphide textures and compositions of mineralized and unmineralized samples of black shales, albitite sills and hydrothermal veins in the mine are considered for the understanding of the spatial association of gold with sulphides and gold mineralization history of the mine. The sulphides within the Twangiza mine consist of pyrite, arsenopyrite, pyrrhotite, chalcopyrite and rare cobaltite. The primary pyrite texture occurs in unmineralized black shale and is interpreted to be diagenetic. It consists of fine-grained anhedral pyrite crystals aggregating into spherical nodules and formed in replacement of organic material during the diagenesis process. The secondary pyrite textures resulted from the hydrothermal fluids activity and include (i) aggregates of annealed anhedral crystals into sulphide-rich lenses; (ii) elongated anhedral pyrite in the form of short stringers; (iii) fine-grained subhedral to euhedral pyrite randomly distributed within the rock matrix; (iv) euhedral zoned pyrite crystals occurring within veins; (v) aggregations of fine-grained anhedral pyrite, locally distributed in the matrix; (vi) abundant dissemination of fine-grained subhedral to anhedral pyrite crystals within the vein selvedge in the host rock; (vii) and coarse-grained massive pyrite bodies. The pyrite major elemental composition does not vary significantly in the different textures and sample types. The Fe content ranges from 44.57 to 46.40 wt. %, and the S content ranges from 53.75 to 55.25 wt. %. Pyrite from mineralized black shale and hydrothermal veins contains relatively higher concentrations of As (~ 1 wt. %) than pyrite from other sample types. The arsenopyrite commonly occurs as fine-grained anhedral crystals as inclusions within pyrite, medium-grained crystal intergrowing with pyrite and/or as coarse-grained massive arsenopyrite bodies in the massive sulphide veins. The arsenopyrite composition is uniform in all textural and sample type with Fe content ranging from 33.44 to 35.20 wt. %, S content ranging from 21.13 to 22.55 wt. % and As content ranging from 42.20 to 43.97 wt. %. In mineralized black shale and unmineralized black shale, the arsenopyrite shows, however, minor concentrations of Ni with 0.39 and 0.70 wt. % respectively. The pyrrhotite occurs as fine-grained anhedral patchy crystals randomly distributed within the rock matrix of unmineralized black shale and unmineralized granitoid, and / or as inclusions within pyrite in mineralized granitoid. The pyrrhotite shows a uniform composition in all samples and textural types, though minor concentrations of Ni (2.06 wt. %) content are reported in unmineralized granitoid. Chalcopyrite occurs as fine-grained crystals in inclusions within pyrite; and cobaltite occurs as rare fine-grained anhedral crystals occasionally disseminated in the albitite sill matrix. The chalcopyrite composition does not vary considerably in all sample and textural types, and cobaltite shows minor concentrations of Ni (4.55 wt. %) and Fe (3.45 wt. %). Native gold grains are commonly found associated with the secondary pyrite texture especially within the sulphide-rich lenses and in the massive sulphide veins, and are almost pure with ~97 wt. %. A Na-rich hydrothermal fluid from low-grade metamorphism associated with the E-W compressive tectonic event, which caused formation of the antiform structure which control the mineralization in the deposit area, led to the albitization of the deposit rocks and specially the alteration of the granitic assemblage to form albitite, and the deposition of aggregates of fine-grained anhedral crystals and growth and annealing of pyrite in sulphide-rich lenses. Afterward, the CO2-rich hydrothermal fluids influx circulated through reactivated structures, including quartz veins, and led to the precipitation of dolomite, ankerite, siderite and magnesite. They also led to the precipitation of pyrite of secondary textures as well as arsenopyrite, chalcopyrite and formation of pyrrhotite from the desulphurization of early pyrite. The CO2-rich hydrothermal fluids probably leached gold and other trace elements such as As, Co, etc. from the sedimentary host rocks and deposited them into suitable traps, such as the sulphide-rich lenses and massive sulphide bodies, preferably within the hinge zone of anticline axis constituting a hydrothermal fluid pathway.
- Full Text:
- Date Issued: 2019
- Authors: Busane, Emmanuel Aganze
- Date: 2019
- Subjects: Gold mines and mining -- Congo (Democratic Republic) , Geology -- Congo (Democratic Republic) , Hydrothermal alteration -- Congo (Democratic Republic) , Sulphide minerals -- Congo (Democratic Republic) , Gold ores -- Geology -- Congo (Democratic Republic) , Geochemistry -- Congo (Democratic Republic) , Twangiza Mine (Congo (Democratic Republic))
- Language: English
- Type: text , Thesis , Masters , MSc
- Identifier: http://hdl.handle.net/10962/76588 , vital:30610
- Description: Twangiza mine is a gold deposit situated in the eastern Democratic Republic of Congo. The rock types at the Twangiza Mine consist of black shale, including carbonaceous mudstone and thin intercalated layers of siltstone, and feldspar-rich granitoid intrusive sills, referred to as albitite, folded into a major antiformal structure. The gold mineralization at the mine is commonly found associated with sulphides. The sulphide textures and compositions of mineralized and unmineralized samples of black shales, albitite sills and hydrothermal veins in the mine are considered for the understanding of the spatial association of gold with sulphides and gold mineralization history of the mine. The sulphides within the Twangiza mine consist of pyrite, arsenopyrite, pyrrhotite, chalcopyrite and rare cobaltite. The primary pyrite texture occurs in unmineralized black shale and is interpreted to be diagenetic. It consists of fine-grained anhedral pyrite crystals aggregating into spherical nodules and formed in replacement of organic material during the diagenesis process. The secondary pyrite textures resulted from the hydrothermal fluids activity and include (i) aggregates of annealed anhedral crystals into sulphide-rich lenses; (ii) elongated anhedral pyrite in the form of short stringers; (iii) fine-grained subhedral to euhedral pyrite randomly distributed within the rock matrix; (iv) euhedral zoned pyrite crystals occurring within veins; (v) aggregations of fine-grained anhedral pyrite, locally distributed in the matrix; (vi) abundant dissemination of fine-grained subhedral to anhedral pyrite crystals within the vein selvedge in the host rock; (vii) and coarse-grained massive pyrite bodies. The pyrite major elemental composition does not vary significantly in the different textures and sample types. The Fe content ranges from 44.57 to 46.40 wt. %, and the S content ranges from 53.75 to 55.25 wt. %. Pyrite from mineralized black shale and hydrothermal veins contains relatively higher concentrations of As (~ 1 wt. %) than pyrite from other sample types. The arsenopyrite commonly occurs as fine-grained anhedral crystals as inclusions within pyrite, medium-grained crystal intergrowing with pyrite and/or as coarse-grained massive arsenopyrite bodies in the massive sulphide veins. The arsenopyrite composition is uniform in all textural and sample type with Fe content ranging from 33.44 to 35.20 wt. %, S content ranging from 21.13 to 22.55 wt. % and As content ranging from 42.20 to 43.97 wt. %. In mineralized black shale and unmineralized black shale, the arsenopyrite shows, however, minor concentrations of Ni with 0.39 and 0.70 wt. % respectively. The pyrrhotite occurs as fine-grained anhedral patchy crystals randomly distributed within the rock matrix of unmineralized black shale and unmineralized granitoid, and / or as inclusions within pyrite in mineralized granitoid. The pyrrhotite shows a uniform composition in all samples and textural types, though minor concentrations of Ni (2.06 wt. %) content are reported in unmineralized granitoid. Chalcopyrite occurs as fine-grained crystals in inclusions within pyrite; and cobaltite occurs as rare fine-grained anhedral crystals occasionally disseminated in the albitite sill matrix. The chalcopyrite composition does not vary considerably in all sample and textural types, and cobaltite shows minor concentrations of Ni (4.55 wt. %) and Fe (3.45 wt. %). Native gold grains are commonly found associated with the secondary pyrite texture especially within the sulphide-rich lenses and in the massive sulphide veins, and are almost pure with ~97 wt. %. A Na-rich hydrothermal fluid from low-grade metamorphism associated with the E-W compressive tectonic event, which caused formation of the antiform structure which control the mineralization in the deposit area, led to the albitization of the deposit rocks and specially the alteration of the granitic assemblage to form albitite, and the deposition of aggregates of fine-grained anhedral crystals and growth and annealing of pyrite in sulphide-rich lenses. Afterward, the CO2-rich hydrothermal fluids influx circulated through reactivated structures, including quartz veins, and led to the precipitation of dolomite, ankerite, siderite and magnesite. They also led to the precipitation of pyrite of secondary textures as well as arsenopyrite, chalcopyrite and formation of pyrrhotite from the desulphurization of early pyrite. The CO2-rich hydrothermal fluids probably leached gold and other trace elements such as As, Co, etc. from the sedimentary host rocks and deposited them into suitable traps, such as the sulphide-rich lenses and massive sulphide bodies, preferably within the hinge zone of anticline axis constituting a hydrothermal fluid pathway.
- Full Text:
- Date Issued: 2019
A Bayesian approach to tilted-ring modelling of galaxies
- Authors: Maina, Eric Kamau
- Date: 2020
- Subjects: Bayesian statistical decision theory , Galaxies , Radio astronomy , TiRiFiC (Tilted Ring Fitting Code) , Neutral hydrogen , Spectroscopic data cubes , Galaxy parametrisation
- Language: English
- Type: text , Thesis , Masters , MSc
- Identifier: http://hdl.handle.net/10962/145783 , vital:38466
- Description: The orbits of neutral hydrogen (H I) gas found in most disk galaxies are circular and also exhibit long-lived warps at large radii where the restoring gravitational forces of the inner disk become weak (Spekkens and Giovanelli 2006). These warps make the tilted-ring model an ideal choice for galaxy parametrisation. Analysis software utilizing the tilted-ring-model can be grouped into two and three-dimensional based software. Józsa et al. (2007b) demonstrated that three dimensional based software is better suited for galaxy parametrisation because it is affected by the effect of beam smearing only by increasing the uncertainty of parameters but not with the notorious systematic effects observed for two-dimensional fitting techniques. TiRiFiC, The Tilted Ring Fitting Code (Józsa et al. 2007b), is a software to construct parameterised models of high-resolution data cubes of rotating galaxies. It uses the tilted-ring model, and with that, a combination of some parameters such as surface brightness, position angle, rotation velocity and inclination, to describe galaxies. TiRiFiC works by directly fitting tilted-ring models to spectroscopic data cubes and hence is not affected by beam smearing or line-of-site-effects, e.g. strong warps. Because of that, the method is unavoidable as an analytic method in future Hi surveys. In the current implementation, though, there are several drawbacks. The implemented optimisers search for local solutions in parameter space only, do not quantify correlations between parameters and cannot find errors of single parameters. In theory, these drawbacks can be overcome by using Bayesian statistics, implemented in Multinest (Feroz et al. 2008), as it allows for sampling a posterior distribution irrespective of its multimodal nature resulting in parameter samples that correspond to the maximum in the posterior distribution. These parameter samples can be used as well to quantify correlations and find errors of single parameters. Since this method employs Bayesian statistics, it also allows the user to leverage any prior information they may have on parameter values.
- Full Text:
- Date Issued: 2020
- Authors: Maina, Eric Kamau
- Date: 2020
- Subjects: Bayesian statistical decision theory , Galaxies , Radio astronomy , TiRiFiC (Tilted Ring Fitting Code) , Neutral hydrogen , Spectroscopic data cubes , Galaxy parametrisation
- Language: English
- Type: text , Thesis , Masters , MSc
- Identifier: http://hdl.handle.net/10962/145783 , vital:38466
- Description: The orbits of neutral hydrogen (H I) gas found in most disk galaxies are circular and also exhibit long-lived warps at large radii where the restoring gravitational forces of the inner disk become weak (Spekkens and Giovanelli 2006). These warps make the tilted-ring model an ideal choice for galaxy parametrisation. Analysis software utilizing the tilted-ring-model can be grouped into two and three-dimensional based software. Józsa et al. (2007b) demonstrated that three dimensional based software is better suited for galaxy parametrisation because it is affected by the effect of beam smearing only by increasing the uncertainty of parameters but not with the notorious systematic effects observed for two-dimensional fitting techniques. TiRiFiC, The Tilted Ring Fitting Code (Józsa et al. 2007b), is a software to construct parameterised models of high-resolution data cubes of rotating galaxies. It uses the tilted-ring model, and with that, a combination of some parameters such as surface brightness, position angle, rotation velocity and inclination, to describe galaxies. TiRiFiC works by directly fitting tilted-ring models to spectroscopic data cubes and hence is not affected by beam smearing or line-of-site-effects, e.g. strong warps. Because of that, the method is unavoidable as an analytic method in future Hi surveys. In the current implementation, though, there are several drawbacks. The implemented optimisers search for local solutions in parameter space only, do not quantify correlations between parameters and cannot find errors of single parameters. In theory, these drawbacks can be overcome by using Bayesian statistics, implemented in Multinest (Feroz et al. 2008), as it allows for sampling a posterior distribution irrespective of its multimodal nature resulting in parameter samples that correspond to the maximum in the posterior distribution. These parameter samples can be used as well to quantify correlations and find errors of single parameters. Since this method employs Bayesian statistics, it also allows the user to leverage any prior information they may have on parameter values.
- Full Text:
- Date Issued: 2020
Structure and interaction studies of beta-amyloid in the search for new lead compounds for the treatment of Alzheimer’s disease
- Authors: Mtini, Onke
- Date: 2020
- Subjects: Alzheimer's disease -- Chemotherapy , Alzheimer's disease -- Treatment , Amyloid beta-protein , Oxidative stress , Protein binding , South African Natural Compounds Database
- Language: English
- Type: Thesis , Masters , MSc
- Identifier: http://hdl.handle.net/10962/167574 , vital:41493
- Description: Alzheimer’s disease (AD) is the most devastating neurodegenerative disorder that effects the aging population worldwide. In this study three hypotheses of AD are explored, the β-amyloid cascade hypothesis, the β-amyloid metal binding hypothesis and the oxidative stress hypothesis are explored. In the first case compounds from the South African Natural Compounds Database (SANCDB) are docked to models of β-amyloid fibrils and the properties of these fibrils under pulling simulations are compared to a known small molecule disruptor of β-amyloid, wgx-50. In these simulations SANCDB compounds are identified that disrupt β-amyloid in a similar manner to wgx-50. In these simulations the disruption to the free energy of binding of chains to the fibrils is quantified. For metal binding and oxidative stress hypotheses, problems in simulation arise due to only fragments of β-amyloid being present in the Research Collaboratory for Structural Bioinformatics protein data bank (RCSB PDB), as determined from NMR experiments. In this work, β-amyloid is set up under periodic boundary conditions to simulate a fibril under reasonable computational time. Within these periodic boundary conditions, β-amyloid has been solvated in copper and zinc rich environments and diffusion of these metals around the fibrils has been explored. The localization of these metals (in simulation only using van der Waal’s and electrostatic terms) around the fibril has led us to explore other possible metal binding sites. Metal bound to the infinite fibril has been optimized at the QM/MM level and some of the reactive oxygen species in the presence of the fibril are quantified.
- Full Text:
- Date Issued: 2020
- Authors: Mtini, Onke
- Date: 2020
- Subjects: Alzheimer's disease -- Chemotherapy , Alzheimer's disease -- Treatment , Amyloid beta-protein , Oxidative stress , Protein binding , South African Natural Compounds Database
- Language: English
- Type: Thesis , Masters , MSc
- Identifier: http://hdl.handle.net/10962/167574 , vital:41493
- Description: Alzheimer’s disease (AD) is the most devastating neurodegenerative disorder that effects the aging population worldwide. In this study three hypotheses of AD are explored, the β-amyloid cascade hypothesis, the β-amyloid metal binding hypothesis and the oxidative stress hypothesis are explored. In the first case compounds from the South African Natural Compounds Database (SANCDB) are docked to models of β-amyloid fibrils and the properties of these fibrils under pulling simulations are compared to a known small molecule disruptor of β-amyloid, wgx-50. In these simulations SANCDB compounds are identified that disrupt β-amyloid in a similar manner to wgx-50. In these simulations the disruption to the free energy of binding of chains to the fibrils is quantified. For metal binding and oxidative stress hypotheses, problems in simulation arise due to only fragments of β-amyloid being present in the Research Collaboratory for Structural Bioinformatics protein data bank (RCSB PDB), as determined from NMR experiments. In this work, β-amyloid is set up under periodic boundary conditions to simulate a fibril under reasonable computational time. Within these periodic boundary conditions, β-amyloid has been solvated in copper and zinc rich environments and diffusion of these metals around the fibrils has been explored. The localization of these metals (in simulation only using van der Waal’s and electrostatic terms) around the fibril has led us to explore other possible metal binding sites. Metal bound to the infinite fibril has been optimized at the QM/MM level and some of the reactive oxygen species in the presence of the fibril are quantified.
- Full Text:
- Date Issued: 2020
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