An overview of energy minerals in the Springbok Flatsbasin, South Africa : implications for geochemical and geophysical exploration
- Authors: Ledwaba, Lebogang John
- Date: 2015
- Subjects: Energy minerals -- South Africa -- Springbok Flats (Limpopo) , Geochemistry , Prospecting -- Geophysical methods , Coal -- South Africa -- Springbok Flats (Limpopo) , Uranium -- South Africa -- Springbok Flats (Limpopo) , Coalbed methane -- South Africa -- Springbok Flats (Limpopo)
- Language: English
- Type: Thesis , Masters , MSc
- Identifier: vital:5092 , http://hdl.handle.net/10962/d1019880
- Description: This study is informed by the rising demand for power needs in South Africa and aims at understanding the geophysical and geochemical characteristics of the energy minerals in the Springbok Flats Basin and relating them to the prevailing geological and structural setting for improved exploration targeting. The Springbok Flats Basin is part of the Karoo sediments and host to uranium, coal and coal bed methane (CBM) resources. The lithology sections in the basin indicate presence of basaltic lavas at the top, underlain by mudrocks, siltstones, sandstones, conglomerates and diamictite, with interbedded coal beds occasionally. The coals are uraniferous and shale bounded and of lower Beaufort age at 250 Ma. The regional radiometric data identifies the regional extent of the Springbok Flats Basin as a basin with low total count values. This information is useful in exploration as it gives an idea of the limits of the area where to focus application for prospecting licenses. The reduced to pole of the total magnetic field, residuals and first vertical derivative maps clearly show the high magnetic susceptibility nature of the surrounding Bushveld rocks as compared to the low Karoo sediment susceptibility within the basin. There are distinct ring shaped picks within the basin possibly due to known Karoo dolerite sills in particular to the central south western part of the grid. The regional geochemical mapping program is a cost-effective way of providing an overview of the relative abundance levels, regional trends and anomalous patterns in the underlying lithological units. Background values of elements in soils over different lithological units and the identification of anomalous values relative to these elements can easily be identified. The geochemical results show an excellent correlation between soil chemistry and underlying geological formations. A few distinct gravity highs are clearly shown within the basin. Assuming the effect of the Letaba basalt to the gravity readings is uniform across the basin; these distinct anomalies could be due to Karoo dolerite sills as they coincide with areas of distinct high magnetic signature. A conceptual model was generated assuming that the Karoo sediments’ layering is uniform across the gravity profile but changes in the residual are due to an increased thickness of the sill supported by the gentle changes on the surface topography. Satellite imagery has got its challenges especially in areas of vegetation but it does provide a very useful tool in exploration. A number of spectral analysis techniques and band rations can be used to differentiate the areas underlain by the Letaba basalts, the Karoo sandstones/shale and Bushveld granites for mapping purposes. The priority focus will be on the shallower Karoo sediments because of the potential for cheaper mining. Exploration targeting needs to be guided by observed geochemical and geophysical characteristics in order to prioritize areas taking into account the presence of Karoo intrusives such as the dolerite sills that tend to devolatize the coal hence affecting the quality/rank. Structures and gravity signatures are very important in delineating areas with thick sediments that have a potential for CBM. The same understanding in targeting goes a long way in planning drill holes, resource modelling and pre-feasibility stages for mine planning. A high resolution airborne geophysical survey is recommended over the basin to better resolve structures. Geophysical borehole logging is recommended to be part of the exploration drilling programs in the Springbok Flats Basin in order to define the in-situ geophysical characteristics. Geophysical logging is useful in particular for the uranium reserves that cannot be delineated from the surface due to deep intersection.
- Full Text:
- Date Issued: 2015
- Authors: Ledwaba, Lebogang John
- Date: 2015
- Subjects: Energy minerals -- South Africa -- Springbok Flats (Limpopo) , Geochemistry , Prospecting -- Geophysical methods , Coal -- South Africa -- Springbok Flats (Limpopo) , Uranium -- South Africa -- Springbok Flats (Limpopo) , Coalbed methane -- South Africa -- Springbok Flats (Limpopo)
- Language: English
- Type: Thesis , Masters , MSc
- Identifier: vital:5092 , http://hdl.handle.net/10962/d1019880
- Description: This study is informed by the rising demand for power needs in South Africa and aims at understanding the geophysical and geochemical characteristics of the energy minerals in the Springbok Flats Basin and relating them to the prevailing geological and structural setting for improved exploration targeting. The Springbok Flats Basin is part of the Karoo sediments and host to uranium, coal and coal bed methane (CBM) resources. The lithology sections in the basin indicate presence of basaltic lavas at the top, underlain by mudrocks, siltstones, sandstones, conglomerates and diamictite, with interbedded coal beds occasionally. The coals are uraniferous and shale bounded and of lower Beaufort age at 250 Ma. The regional radiometric data identifies the regional extent of the Springbok Flats Basin as a basin with low total count values. This information is useful in exploration as it gives an idea of the limits of the area where to focus application for prospecting licenses. The reduced to pole of the total magnetic field, residuals and first vertical derivative maps clearly show the high magnetic susceptibility nature of the surrounding Bushveld rocks as compared to the low Karoo sediment susceptibility within the basin. There are distinct ring shaped picks within the basin possibly due to known Karoo dolerite sills in particular to the central south western part of the grid. The regional geochemical mapping program is a cost-effective way of providing an overview of the relative abundance levels, regional trends and anomalous patterns in the underlying lithological units. Background values of elements in soils over different lithological units and the identification of anomalous values relative to these elements can easily be identified. The geochemical results show an excellent correlation between soil chemistry and underlying geological formations. A few distinct gravity highs are clearly shown within the basin. Assuming the effect of the Letaba basalt to the gravity readings is uniform across the basin; these distinct anomalies could be due to Karoo dolerite sills as they coincide with areas of distinct high magnetic signature. A conceptual model was generated assuming that the Karoo sediments’ layering is uniform across the gravity profile but changes in the residual are due to an increased thickness of the sill supported by the gentle changes on the surface topography. Satellite imagery has got its challenges especially in areas of vegetation but it does provide a very useful tool in exploration. A number of spectral analysis techniques and band rations can be used to differentiate the areas underlain by the Letaba basalts, the Karoo sandstones/shale and Bushveld granites for mapping purposes. The priority focus will be on the shallower Karoo sediments because of the potential for cheaper mining. Exploration targeting needs to be guided by observed geochemical and geophysical characteristics in order to prioritize areas taking into account the presence of Karoo intrusives such as the dolerite sills that tend to devolatize the coal hence affecting the quality/rank. Structures and gravity signatures are very important in delineating areas with thick sediments that have a potential for CBM. The same understanding in targeting goes a long way in planning drill holes, resource modelling and pre-feasibility stages for mine planning. A high resolution airborne geophysical survey is recommended over the basin to better resolve structures. Geophysical borehole logging is recommended to be part of the exploration drilling programs in the Springbok Flats Basin in order to define the in-situ geophysical characteristics. Geophysical logging is useful in particular for the uranium reserves that cannot be delineated from the surface due to deep intersection.
- Full Text:
- Date Issued: 2015
Identification of novel SNPSTRs by 454 sequencing in Nguni and Sotho-Tswana populations
- Authors: Laurence, Jo-Anne Elizabeth
- Date: 2015
- Language: English
- Type: text , Thesis , Masters , MSc
- Identifier: http://hdl.handle.net/10962/55885 , vital:26752
- Description: DNA profiling is currently performed by analysis of the electropherogram that results following the amplification of a panel of Short Tandem Repeat (STR) loci. A need has arisen, however, for the development of a typing method that generates results which are compatible and comparable with existing databases, but that have a higher discrimination power by supplying sequence data as well as repeat-number data. Recent studies that explore these alternative typing methodologies have revealed the existence of a number of STR variants. There is, however, little information about the exact nature and prevalence of these sub-alleles. There have also been limited population studies of the genetic profiles of sub-Saharan African populations, despite the fact that evidence suggests that there is greater genetic structure and genetic diversity in these populations. In this study, a processing protocol for the generation of 454 sequencing-ready amplicons of vWA, D2S441, D3S1358, D13S317, D21S11 and D7S820 loci was developed. This protocol was applied to buccal swabs collected from 144 individuals of the Nguni and Sotho-Tswana population groups. A total of 145 485 reads were obtained from the sequencing of these amplicons, of which 97 400 and 48 085 reads were obtained for the Nguni and Sotho-Tswana populations respectively. The proportional representation for each locus ranged from 8-20%, and the allele calls and observed frequencies of these alleles suggested a high degree of relatedness between population groups. The sequencing results, furthermore, enabled the identification of a number of previously undescribed STR variants and SNPSTRs; with allele 13´ for D13S317 representing a SNP that may be predictive of Nguni-ancestry. The results also demonstrated the usefulness of next generation sequencing for increasing the number of discernible alleles for STR profiling.
- Full Text:
- Date Issued: 2015
- Authors: Laurence, Jo-Anne Elizabeth
- Date: 2015
- Language: English
- Type: text , Thesis , Masters , MSc
- Identifier: http://hdl.handle.net/10962/55885 , vital:26752
- Description: DNA profiling is currently performed by analysis of the electropherogram that results following the amplification of a panel of Short Tandem Repeat (STR) loci. A need has arisen, however, for the development of a typing method that generates results which are compatible and comparable with existing databases, but that have a higher discrimination power by supplying sequence data as well as repeat-number data. Recent studies that explore these alternative typing methodologies have revealed the existence of a number of STR variants. There is, however, little information about the exact nature and prevalence of these sub-alleles. There have also been limited population studies of the genetic profiles of sub-Saharan African populations, despite the fact that evidence suggests that there is greater genetic structure and genetic diversity in these populations. In this study, a processing protocol for the generation of 454 sequencing-ready amplicons of vWA, D2S441, D3S1358, D13S317, D21S11 and D7S820 loci was developed. This protocol was applied to buccal swabs collected from 144 individuals of the Nguni and Sotho-Tswana population groups. A total of 145 485 reads were obtained from the sequencing of these amplicons, of which 97 400 and 48 085 reads were obtained for the Nguni and Sotho-Tswana populations respectively. The proportional representation for each locus ranged from 8-20%, and the allele calls and observed frequencies of these alleles suggested a high degree of relatedness between population groups. The sequencing results, furthermore, enabled the identification of a number of previously undescribed STR variants and SNPSTRs; with allele 13´ for D13S317 representing a SNP that may be predictive of Nguni-ancestry. The results also demonstrated the usefulness of next generation sequencing for increasing the number of discernible alleles for STR profiling.
- Full Text:
- Date Issued: 2015
Prediction of interacting motifs within the protein subunits of Picornavirus capsids
- Authors: Ross, Caroline Jane
- Date: 2015
- Subjects: Picornaviruses , Antiviral agents , Poliovirus , Coxsackieviruses , Hepatitis A virus , Foot-and-mouth disease virus , Viral proteins
- Language: English
- Type: Thesis , Masters , MSc
- Identifier: vital:4151 , http://hdl.handle.net/10962/d1017912
- Description: The Picornaviridae family contains a number of pathogens which are economically important including Poliovirus, Coxsakievirus, Hepatitis A Virus, and Foot-and-Mouth-Disease-Virus. Recently the emergence of novel picornaviruses associated with gastrointestinal, neurological and respiratory diseases in humans has been reported. Although effective vaccines for viruses such as FMDV, PV and HAV have been developed there are currently no antivirals available for the treatment of picornavirus infections. Picornaviruses proteins are classified as: the structural proteins VP1, VP2, VP3 and VP4 which form the subunits of the viral capsid and the replication proteins which function as proteases, RNA-polymerases, primers and membrane binding proteins. Although the host specificity and viral pathogenicity varies across members of the family, the icosahedral capsid is highly conserved. The capsid consists of 60 protomers, each containing a single copy of VP1, VP2 and VP3. A fourth capsid protein, VP4, resides on the internal side of the capsid. Capsid assembly is integral to life-cycle of picornaviruses; however the process is complex and not fully-understood. The overall aim of the study was to broaden the understanding of the evolution and function of the structural proteins across the Picornaviridae family. Firstly a comprehensive analysis of the phylogenetic relationships amongst the individual structural proteins was performed. The functions of the structural proteins were further investigated by an exhaustive motif analysis. A subsequent structural analysis of highly conserved motifs was performed with respect to representative enteroviruses, Foot-and-Mouth-Disease-Virus and Theiler’s Virus. This was supplemented by the in silico prediction of interacting residues within the crystal structures of these protomers. Findings in this study suggest that the capsid proteins may be evolving independently from the replication proteins through possible inter-typic recombination of functional protein regions. Moreover the study predicts that protomer assembly may be facilitated through a network of multiple subunit-subunit interactions. Multiple conserved motifs and principle residues predicted to facilitate capsid subunit-subunit interactions were identified. It was also concluded that motif conservation may support the theory of inter-typic recombination between closely related virus sub-types. As capsid assembly is critical to the viral life-cycle, the principle interacting motifs may serve as novel drug targets for the antiviral treatment of picornavirus infections. Thus the findings in the study may be fundamental to the development of treatments which are more economically feasible or clinically effective than current vaccinations.
- Full Text:
- Date Issued: 2015
- Authors: Ross, Caroline Jane
- Date: 2015
- Subjects: Picornaviruses , Antiviral agents , Poliovirus , Coxsackieviruses , Hepatitis A virus , Foot-and-mouth disease virus , Viral proteins
- Language: English
- Type: Thesis , Masters , MSc
- Identifier: vital:4151 , http://hdl.handle.net/10962/d1017912
- Description: The Picornaviridae family contains a number of pathogens which are economically important including Poliovirus, Coxsakievirus, Hepatitis A Virus, and Foot-and-Mouth-Disease-Virus. Recently the emergence of novel picornaviruses associated with gastrointestinal, neurological and respiratory diseases in humans has been reported. Although effective vaccines for viruses such as FMDV, PV and HAV have been developed there are currently no antivirals available for the treatment of picornavirus infections. Picornaviruses proteins are classified as: the structural proteins VP1, VP2, VP3 and VP4 which form the subunits of the viral capsid and the replication proteins which function as proteases, RNA-polymerases, primers and membrane binding proteins. Although the host specificity and viral pathogenicity varies across members of the family, the icosahedral capsid is highly conserved. The capsid consists of 60 protomers, each containing a single copy of VP1, VP2 and VP3. A fourth capsid protein, VP4, resides on the internal side of the capsid. Capsid assembly is integral to life-cycle of picornaviruses; however the process is complex and not fully-understood. The overall aim of the study was to broaden the understanding of the evolution and function of the structural proteins across the Picornaviridae family. Firstly a comprehensive analysis of the phylogenetic relationships amongst the individual structural proteins was performed. The functions of the structural proteins were further investigated by an exhaustive motif analysis. A subsequent structural analysis of highly conserved motifs was performed with respect to representative enteroviruses, Foot-and-Mouth-Disease-Virus and Theiler’s Virus. This was supplemented by the in silico prediction of interacting residues within the crystal structures of these protomers. Findings in this study suggest that the capsid proteins may be evolving independently from the replication proteins through possible inter-typic recombination of functional protein regions. Moreover the study predicts that protomer assembly may be facilitated through a network of multiple subunit-subunit interactions. Multiple conserved motifs and principle residues predicted to facilitate capsid subunit-subunit interactions were identified. It was also concluded that motif conservation may support the theory of inter-typic recombination between closely related virus sub-types. As capsid assembly is critical to the viral life-cycle, the principle interacting motifs may serve as novel drug targets for the antiviral treatment of picornavirus infections. Thus the findings in the study may be fundamental to the development of treatments which are more economically feasible or clinically effective than current vaccinations.
- Full Text:
- Date Issued: 2015
Photo-physicochemical studies and photodynamic therapy activity of indium and gallium phthalocyanines
- Tshangana, Charmaine Sesethu
- Authors: Tshangana, Charmaine Sesethu
- Date: 2015
- Subjects: Quantum dots , Nanoparticles , Photochemotherapy , Phthalocyanines
- Language: English
- Type: Thesis , Masters , MSc
- Identifier: vital:4548 , http://hdl.handle.net/10962/d1017928
- Description: The potential toxicity of seven different types of quantum dots without shell (L-cysteine-CdTe, TGA-CdTe, MPA-CdTe, TGA-CdSe) and with the shell (GSH-CdSe@ZnS, GSH-CdTe@ZnS,) with different capping agents were evaluated. The growth inhibitory effects of the various quantum dots on human pancreatic BON cancerous cells were determined. The least cytotoxic of the various quantum dots synthesized and the one displaying the lowest growth inhibitory potential and no embryotoxicity was determined to be the GSH-CdSe@ZnS quantum dots. The GSH-CdSe@ZnS quantum dots were then conjugated to gallium, aluminium and indium octacarboxy phthalocyanine and the photophysical behaviour of the conjugates studied for potential use in photodynamic therapy and imaging applications. The sizes, morphology, thermal stability and confirmation of successful conjugation was determined using X-ray diffraction (XRD), transmission electron microscopy (TEM), thermogravimetric analysis (TGA) and Fourier transform infrared spectroscopy (FTIR), respectively. The study was extended by conjugating amino functionalized magnetic nanoparticles (Fe₃O₄) to indium octacarboxy phthalocyanine to study the photophysical behaviour of the conjugate as a potential bi-functional anti-cancer agent (hyperthermia and photodynamic therapy applications). A three-in-one multifunctional nanocomposite comprising of the quantum dots, magnetic nanoparticles and indium octacarboxy phthalocyanine was developed with the aim of developing a multifunctional composite that is able detect, monitor and treat cancer. All conjugates showed improved and enhanced photophysical behaviour. Finally, GSH-CdSe@ZnS conjugated to aluminium octacarboxy phthalocyanine was applied in human pancreatic carcinoid BON cells. The conjugates induced cell death dose-dependently.
- Full Text:
- Date Issued: 2015
- Authors: Tshangana, Charmaine Sesethu
- Date: 2015
- Subjects: Quantum dots , Nanoparticles , Photochemotherapy , Phthalocyanines
- Language: English
- Type: Thesis , Masters , MSc
- Identifier: vital:4548 , http://hdl.handle.net/10962/d1017928
- Description: The potential toxicity of seven different types of quantum dots without shell (L-cysteine-CdTe, TGA-CdTe, MPA-CdTe, TGA-CdSe) and with the shell (GSH-CdSe@ZnS, GSH-CdTe@ZnS,) with different capping agents were evaluated. The growth inhibitory effects of the various quantum dots on human pancreatic BON cancerous cells were determined. The least cytotoxic of the various quantum dots synthesized and the one displaying the lowest growth inhibitory potential and no embryotoxicity was determined to be the GSH-CdSe@ZnS quantum dots. The GSH-CdSe@ZnS quantum dots were then conjugated to gallium, aluminium and indium octacarboxy phthalocyanine and the photophysical behaviour of the conjugates studied for potential use in photodynamic therapy and imaging applications. The sizes, morphology, thermal stability and confirmation of successful conjugation was determined using X-ray diffraction (XRD), transmission electron microscopy (TEM), thermogravimetric analysis (TGA) and Fourier transform infrared spectroscopy (FTIR), respectively. The study was extended by conjugating amino functionalized magnetic nanoparticles (Fe₃O₄) to indium octacarboxy phthalocyanine to study the photophysical behaviour of the conjugate as a potential bi-functional anti-cancer agent (hyperthermia and photodynamic therapy applications). A three-in-one multifunctional nanocomposite comprising of the quantum dots, magnetic nanoparticles and indium octacarboxy phthalocyanine was developed with the aim of developing a multifunctional composite that is able detect, monitor and treat cancer. All conjugates showed improved and enhanced photophysical behaviour. Finally, GSH-CdSe@ZnS conjugated to aluminium octacarboxy phthalocyanine was applied in human pancreatic carcinoid BON cells. The conjugates induced cell death dose-dependently.
- Full Text:
- Date Issued: 2015
An analysis of malware evasion techniques against modern AV engines
- Authors: Haffejee, Jameel
- Date: 2015
- Language: English
- Type: Thesis , Masters , MSc
- Identifier: vital:20979 , http://hdl.handle.net/10962/5821
- Description: This research empirically tested the response of antivirus applications to binaries that use virus-like evasion techniques. In order to achieve this, a number of binaries are processed using a number of evasion methods and are then deployed against several antivirus engines. The research also documents the process of setting up an environment for testing antivirus engines, including building the evasion techniques used in the tests. The results of the empirical tests illustrate that an attacker can evade multiple antivirus engines without much effort using well-known evasion techniques. Furthermore, some antivirus engines may respond to the occurrence of an evasion technique instead of the presence of any malicious code. In practical terms, this shows that while antivirus applications are useful for protecting against known threats, their effectiveness against unknown or modified threats is limited.
- Full Text:
- Date Issued: 2015
- Authors: Haffejee, Jameel
- Date: 2015
- Language: English
- Type: Thesis , Masters , MSc
- Identifier: vital:20979 , http://hdl.handle.net/10962/5821
- Description: This research empirically tested the response of antivirus applications to binaries that use virus-like evasion techniques. In order to achieve this, a number of binaries are processed using a number of evasion methods and are then deployed against several antivirus engines. The research also documents the process of setting up an environment for testing antivirus engines, including building the evasion techniques used in the tests. The results of the empirical tests illustrate that an attacker can evade multiple antivirus engines without much effort using well-known evasion techniques. Furthermore, some antivirus engines may respond to the occurrence of an evasion technique instead of the presence of any malicious code. In practical terms, this shows that while antivirus applications are useful for protecting against known threats, their effectiveness against unknown or modified threats is limited.
- Full Text:
- Date Issued: 2015
Properties of traveling ionospheric disturbances (TIDs) over the Western Cape, South Africa
- Authors: Tyalimpi, Vumile Mike
- Date: 2015
- Subjects: Doppler radar , Geographic information systems , Traveling ionospheric disturbances -- south Africa , Ionospheric disturbances -- South Africa
- Language: English
- Type: Thesis , Masters , MSc
- Identifier: vital:5557 , http://hdl.handle.net/10962/d1017901
- Description: Travelling Ionospheric Disturbances (TIDs) are said to be produced by atmospheric gravitational waves propagating through the neutral ionosphere. These are smaller in amplitude and period when compared to most ionospheric disturbances and hence more difficult to measure. Very little is known about the properties of the travelling ionospheric disturbances (TIDs) over the Southern Hemisphere regions since studies have been conducted mostly over the Northern Hemisphere regions. This study presents a framework, using a High Frequency (HF) Doppler radar to investigate the physical properties and the possible driving mechanisms of TIDs. This research focuses on studying the characteristics of the TIDs, such as period, velocity and temporal variations, using HF Doppler measurements taken in South Africa. By making use of a Wavelet Analysis technique, the TIDs’ characteristics were determined. A statistical summary on speed and direction of propagation of the observed TIDs was performed. The winter medium scale travelling ionospheric disturbances (MSTIDs) observed are generally faster than the summer MSTIDs. For all seasons, the MSTIDs had a preferred south-southwest direction of propagation. Most of the large scale travelling ionospheric disturbances (LSTIDs) were observed during the night and of these, the spring LSTIDs were fastest when compared to autumn and summer LSTIDs. The general direction of travel of the observed LSTIDs is south-southeast. Total Electron Content (TEC), derived from Global Positioning System (GPS) measurements, were used to validate some of the TID results obtained from the HF Doppler data. The Horizontal Wind Model (HWM07), magnetic K index, and solar terminators were used to determine the possible sources of the observed TIDs. Only 41% of the observed TIDs were successfully linked to their possible sources of excitation. The information gathered from this study will be valuable in future radio communications and will serve as means to improve the existing ionospheric models over the South African region.
- Full Text:
- Date Issued: 2015
- Authors: Tyalimpi, Vumile Mike
- Date: 2015
- Subjects: Doppler radar , Geographic information systems , Traveling ionospheric disturbances -- south Africa , Ionospheric disturbances -- South Africa
- Language: English
- Type: Thesis , Masters , MSc
- Identifier: vital:5557 , http://hdl.handle.net/10962/d1017901
- Description: Travelling Ionospheric Disturbances (TIDs) are said to be produced by atmospheric gravitational waves propagating through the neutral ionosphere. These are smaller in amplitude and period when compared to most ionospheric disturbances and hence more difficult to measure. Very little is known about the properties of the travelling ionospheric disturbances (TIDs) over the Southern Hemisphere regions since studies have been conducted mostly over the Northern Hemisphere regions. This study presents a framework, using a High Frequency (HF) Doppler radar to investigate the physical properties and the possible driving mechanisms of TIDs. This research focuses on studying the characteristics of the TIDs, such as period, velocity and temporal variations, using HF Doppler measurements taken in South Africa. By making use of a Wavelet Analysis technique, the TIDs’ characteristics were determined. A statistical summary on speed and direction of propagation of the observed TIDs was performed. The winter medium scale travelling ionospheric disturbances (MSTIDs) observed are generally faster than the summer MSTIDs. For all seasons, the MSTIDs had a preferred south-southwest direction of propagation. Most of the large scale travelling ionospheric disturbances (LSTIDs) were observed during the night and of these, the spring LSTIDs were fastest when compared to autumn and summer LSTIDs. The general direction of travel of the observed LSTIDs is south-southeast. Total Electron Content (TEC), derived from Global Positioning System (GPS) measurements, were used to validate some of the TID results obtained from the HF Doppler data. The Horizontal Wind Model (HWM07), magnetic K index, and solar terminators were used to determine the possible sources of the observed TIDs. Only 41% of the observed TIDs were successfully linked to their possible sources of excitation. The information gathered from this study will be valuable in future radio communications and will serve as means to improve the existing ionospheric models over the South African region.
- Full Text:
- Date Issued: 2015
Natural resource use as a coping and adaptation strategy to floods of vulnerable populations in the Eastern Cape
- Sachikonye, Mwazvita Tapiwa Beatrice
- Authors: Sachikonye, Mwazvita Tapiwa Beatrice
- Date: 2015
- Subjects: Flood damage prevention -- South Africa -- Eastern Cape , Natural resources -- South Africa -- Eastern Cape , Land use -- South Africa -- Eastern Cape , Human ecology -- South Africa -- Eastern Cape , Nature -- Effect of human beings on -- South Africa -- Eastern Cape , Human beings -- Effect of environment on -- South Africa -- Eastern Cape
- Language: English
- Type: Thesis , Masters , MSc
- Identifier: vital:4786 , http://hdl.handle.net/10962/d1018194
- Description: Many of the anticipated increased occurances of natural hazards are not only a consequence of climate change, but rather of rapid and widespread land cover change and the subsequent loss of the buffering capacity provided by healthy ecosystems against natural hazards. Unplanned and unmanaged developments in informal settlements limit government’s ability to mitigate and manage, pointing towards natural resources as being integral for vulnerable communities in developing countries to cope with and mitigate flood disasters. There is a lack of understanding on how natural resources contribute to resilience of vulnerable populations in the Eastern Cape and how they are impacted by these populations before, during and after a flood shock. There also exists a gap in knowledge on how natural resources can mitigate the physical impacts of flooding in South Africa, more so in the Eastern Cape province. Using household questionnaires and GIS techniques, the strategies that households used to recover from the October 2012-February 2013 flood shocks were investigated in informal settlements of three towns (Grahamstown, Port Alfred and Port St Johns). Within the vulnerability paradigm and the sustainable livelihood framework, the study also quantified and evaluated the relative contribution of natural resources to recovery strategies, and lastly, the study investigated how patterns of land use, state of natural vegetation and household topographical location exacerbated or diminished the physical impacts of flooding. This study found that natural resources contributed up to 70 percent to recovery of households from the flood shock, most of this being to reconstruction of housing structures after the flood, less so to economic recovery. It was also found that at a settlement scale the buffering effect of vegetation, although variable amongst settlements, was significant. Settlements that were dominated by dense bush and small trees experienced up to 46 percent less impacts on their property than those surrounded by bare gravel and impervious roofs with degraded environments. The main findings of the research show that natural resources reduce the vulnerability of households in informal settlements to flooding in two significant ways; by physically mitigating against damage to shelters and by also providing an emergency-net function that substitutes financial capital in households. Their inclusion in disaster management has the potential to encourage the sustainable livelihoods of the urban poor in the Eastern Cape
- Full Text:
- Date Issued: 2015
- Authors: Sachikonye, Mwazvita Tapiwa Beatrice
- Date: 2015
- Subjects: Flood damage prevention -- South Africa -- Eastern Cape , Natural resources -- South Africa -- Eastern Cape , Land use -- South Africa -- Eastern Cape , Human ecology -- South Africa -- Eastern Cape , Nature -- Effect of human beings on -- South Africa -- Eastern Cape , Human beings -- Effect of environment on -- South Africa -- Eastern Cape
- Language: English
- Type: Thesis , Masters , MSc
- Identifier: vital:4786 , http://hdl.handle.net/10962/d1018194
- Description: Many of the anticipated increased occurances of natural hazards are not only a consequence of climate change, but rather of rapid and widespread land cover change and the subsequent loss of the buffering capacity provided by healthy ecosystems against natural hazards. Unplanned and unmanaged developments in informal settlements limit government’s ability to mitigate and manage, pointing towards natural resources as being integral for vulnerable communities in developing countries to cope with and mitigate flood disasters. There is a lack of understanding on how natural resources contribute to resilience of vulnerable populations in the Eastern Cape and how they are impacted by these populations before, during and after a flood shock. There also exists a gap in knowledge on how natural resources can mitigate the physical impacts of flooding in South Africa, more so in the Eastern Cape province. Using household questionnaires and GIS techniques, the strategies that households used to recover from the October 2012-February 2013 flood shocks were investigated in informal settlements of three towns (Grahamstown, Port Alfred and Port St Johns). Within the vulnerability paradigm and the sustainable livelihood framework, the study also quantified and evaluated the relative contribution of natural resources to recovery strategies, and lastly, the study investigated how patterns of land use, state of natural vegetation and household topographical location exacerbated or diminished the physical impacts of flooding. This study found that natural resources contributed up to 70 percent to recovery of households from the flood shock, most of this being to reconstruction of housing structures after the flood, less so to economic recovery. It was also found that at a settlement scale the buffering effect of vegetation, although variable amongst settlements, was significant. Settlements that were dominated by dense bush and small trees experienced up to 46 percent less impacts on their property than those surrounded by bare gravel and impervious roofs with degraded environments. The main findings of the research show that natural resources reduce the vulnerability of households in informal settlements to flooding in two significant ways; by physically mitigating against damage to shelters and by also providing an emergency-net function that substitutes financial capital in households. Their inclusion in disaster management has the potential to encourage the sustainable livelihoods of the urban poor in the Eastern Cape
- Full Text:
- Date Issued: 2015
A study of barred preferential arrangements with applications to numerical approximation in electric circuits
- Authors: Nkonkobe, Sithembele
- Date: 2015
- Subjects: Electric circuits , Numerical calculations , Sequences (Mathematics)
- Language: English
- Type: Thesis , Masters , MSc
- Identifier: vital:5433 , http://hdl.handle.net/10962/d1020394
- Description: In 1854 Cayley proposed an interesting sequence 1,1,3,13,75,541,... in connection with analytical forms called trees. Since then there has been various combinatorial interpretations of the sequence. The sequence has been interpreted as the number of preferential arrangements of members of a set with n elements. Alternatively the sequence has been interpreted as the number of ordered partitions; the outcomes in races in which ties are allowed or geometrically the number of vertices, edges and faces of simplicial objects. An interesting application of the sequence is found in combination locks. The idea of a preferential arrangement has been extended to a wider combinatorial object called barred preferential arrangement with multiple bars. In this thesis we study barred preferential arrangements combinatorially with application to resistance of certain electrical circuits. In the process we derive some results on cyclic properties of the last digit of the number of barred preferential arrangements. An algorithm in python has been developed to find the number of barred preferential arrangements.
- Full Text:
- Date Issued: 2015
- Authors: Nkonkobe, Sithembele
- Date: 2015
- Subjects: Electric circuits , Numerical calculations , Sequences (Mathematics)
- Language: English
- Type: Thesis , Masters , MSc
- Identifier: vital:5433 , http://hdl.handle.net/10962/d1020394
- Description: In 1854 Cayley proposed an interesting sequence 1,1,3,13,75,541,... in connection with analytical forms called trees. Since then there has been various combinatorial interpretations of the sequence. The sequence has been interpreted as the number of preferential arrangements of members of a set with n elements. Alternatively the sequence has been interpreted as the number of ordered partitions; the outcomes in races in which ties are allowed or geometrically the number of vertices, edges and faces of simplicial objects. An interesting application of the sequence is found in combination locks. The idea of a preferential arrangement has been extended to a wider combinatorial object called barred preferential arrangement with multiple bars. In this thesis we study barred preferential arrangements combinatorially with application to resistance of certain electrical circuits. In the process we derive some results on cyclic properties of the last digit of the number of barred preferential arrangements. An algorithm in python has been developed to find the number of barred preferential arrangements.
- Full Text:
- Date Issued: 2015
Statistical analysis of the ionospheric response during storm conditions over South Africa using ionosonde and GPS data
- Matamba, Tshimangadzo Merline
- Authors: Matamba, Tshimangadzo Merline
- Date: 2015
- Subjects: Ionospheric storms -- South Africa -- Grahamstown , Ionospheric storms -- South Africa -- Madimbo , Magnetic storms -- South Africa -- Grahamstown , Magnetic storms -- South Africa -- Madimbo , Ionosondes , Global Positioning System
- Language: English
- Type: Thesis , Masters , MSc
- Identifier: vital:5555 , http://hdl.handle.net/10962/d1017899
- Description: Ionospheric storms are an extreme form of space weather phenomena which affect space- and ground-based technological systems. Extreme solar activity may give rise to Coronal Mass Ejections (CME) and solar flares that may result in ionospheric storms. This thesis reports on a statistical analysis of the ionospheric response over the ionosonde stations Grahamstown (33.3◦S, 26.5◦E) and Madimbo (22.4◦S,30.9◦E), South Africa, during geomagnetic storm conditions which occurred during the period 1996 - 2011. Total Electron Content (TEC) derived from Global Positioning System (GPS) data by a dual Frequency receiver and an ionosonde at Grahamstown, was analysed for the storms that occurred during the period 2006 - 2011. A comprehensive analysis of the critical frequency of the F2 layer (foF2) and TEC was done. To identify the geomagnetically disturbed conditions the Disturbance storm time (Dst) index with a storm criteria of Dst ≤ −50 nT was used. The ionospheric disturbances were categorized into three responses, namely single disturbance, double disturbance and not significant (NS) ionospheric storms. Single disturbance ionospheric storms refer to positive (P) and negative (N) ionospheric storms observed separately, while double disturbance storms refer to negative and positive ionospheric storms observed during the same storm period. The statistics show the impact of geomagnetic storms on the ionosphere and indicate that negative ionospheric effects follow the solar cycle. In general, only a few ionospheric storms (0.11%) were observed during solar minimum. Positive ionospheric storms occurred most frequently (47.54%) during the declining phase of solar cycle 23. Seasonally, negative ionospheric storms occurred mostly during the summer (63.24%), while positive ionospheric storms occurred frequently during the winter (53.62%). An important finding is that only negative ionospheric storms were observed during great geomagnetic storm activity (Dst ≤ −350 nT). For periods when both ionosonde and GPS was available, the two data sets indicated similar ionospheric responses. Hence, GPS data can be used to effectively identify the ionospheric response in the absence of ionosonde data.
- Full Text:
- Date Issued: 2015
- Authors: Matamba, Tshimangadzo Merline
- Date: 2015
- Subjects: Ionospheric storms -- South Africa -- Grahamstown , Ionospheric storms -- South Africa -- Madimbo , Magnetic storms -- South Africa -- Grahamstown , Magnetic storms -- South Africa -- Madimbo , Ionosondes , Global Positioning System
- Language: English
- Type: Thesis , Masters , MSc
- Identifier: vital:5555 , http://hdl.handle.net/10962/d1017899
- Description: Ionospheric storms are an extreme form of space weather phenomena which affect space- and ground-based technological systems. Extreme solar activity may give rise to Coronal Mass Ejections (CME) and solar flares that may result in ionospheric storms. This thesis reports on a statistical analysis of the ionospheric response over the ionosonde stations Grahamstown (33.3◦S, 26.5◦E) and Madimbo (22.4◦S,30.9◦E), South Africa, during geomagnetic storm conditions which occurred during the period 1996 - 2011. Total Electron Content (TEC) derived from Global Positioning System (GPS) data by a dual Frequency receiver and an ionosonde at Grahamstown, was analysed for the storms that occurred during the period 2006 - 2011. A comprehensive analysis of the critical frequency of the F2 layer (foF2) and TEC was done. To identify the geomagnetically disturbed conditions the Disturbance storm time (Dst) index with a storm criteria of Dst ≤ −50 nT was used. The ionospheric disturbances were categorized into three responses, namely single disturbance, double disturbance and not significant (NS) ionospheric storms. Single disturbance ionospheric storms refer to positive (P) and negative (N) ionospheric storms observed separately, while double disturbance storms refer to negative and positive ionospheric storms observed during the same storm period. The statistics show the impact of geomagnetic storms on the ionosphere and indicate that negative ionospheric effects follow the solar cycle. In general, only a few ionospheric storms (0.11%) were observed during solar minimum. Positive ionospheric storms occurred most frequently (47.54%) during the declining phase of solar cycle 23. Seasonally, negative ionospheric storms occurred mostly during the summer (63.24%), while positive ionospheric storms occurred frequently during the winter (53.62%). An important finding is that only negative ionospheric storms were observed during great geomagnetic storm activity (Dst ≤ −350 nT). For periods when both ionosonde and GPS was available, the two data sets indicated similar ionospheric responses. Hence, GPS data can be used to effectively identify the ionospheric response in the absence of ionosonde data.
- Full Text:
- Date Issued: 2015
A Framework for using Open Source intelligence as a Digital Forensic Investigative tool
- Authors: Rule, Samantha Elizabeth
- Date: 2015
- Subjects: Open source intelligence , Criminal investigation , Electronic evidence
- Language: English
- Type: Thesis , Masters , MSc
- Identifier: vital:4715 , http://hdl.handle.net/10962/d1017937
- Description: The proliferation of the Internet has amplified the use of social networking sites by creating a platform that encourages individuals to share information. As a result there is a wealth of information that is publically and easily accessible. This research explores whether open source intelligence (OSINT), which is freely available, could be used as a digital forensic investigative tool. A survey was created and sent to digital forensic investigators to establish whether they currently use OSINT when performing investigations. The survey results confirm that OSINT is being used by digital forensic investigators when performing investigations but there are currently no guidelines or frameworks available to support the use thereof. Additionally, the survey results showed a belief amongst those surveyed that evidence gleaned from OSINT sources is considered supplementary rather than evidentiary. The findings of this research led to the development of a framework that identifies and recommends key processes to follow when conducting OSINT investigations. The framework can assist digital forensic investigators to follow a structured and rigorous process, which may lead to the unanimous acceptance of information obtained via OSINT sources as evidentiary rather than supplementary in the near future.
- Full Text:
- Date Issued: 2015
- Authors: Rule, Samantha Elizabeth
- Date: 2015
- Subjects: Open source intelligence , Criminal investigation , Electronic evidence
- Language: English
- Type: Thesis , Masters , MSc
- Identifier: vital:4715 , http://hdl.handle.net/10962/d1017937
- Description: The proliferation of the Internet has amplified the use of social networking sites by creating a platform that encourages individuals to share information. As a result there is a wealth of information that is publically and easily accessible. This research explores whether open source intelligence (OSINT), which is freely available, could be used as a digital forensic investigative tool. A survey was created and sent to digital forensic investigators to establish whether they currently use OSINT when performing investigations. The survey results confirm that OSINT is being used by digital forensic investigators when performing investigations but there are currently no guidelines or frameworks available to support the use thereof. Additionally, the survey results showed a belief amongst those surveyed that evidence gleaned from OSINT sources is considered supplementary rather than evidentiary. The findings of this research led to the development of a framework that identifies and recommends key processes to follow when conducting OSINT investigations. The framework can assist digital forensic investigators to follow a structured and rigorous process, which may lead to the unanimous acceptance of information obtained via OSINT sources as evidentiary rather than supplementary in the near future.
- Full Text:
- Date Issued: 2015
The effect of GH family affiliations of mannanolytic enzymes on their synergistic associations during the hydrolysis of mannan-containing substrates
- Authors: Malgas, Samkelo
- Date: 2015
- Subjects: Lignocellulose , Biomass energy , Ethanol as fuel , Polysaccharides , Sugar -- Inversion , Glycosidases , Galactoglucomannans , Oligosaccharides
- Language: English
- Type: Thesis , Masters , MSc
- Identifier: vital:4148 , http://hdl.handle.net/10962/d1017909
- Full Text:
- Date Issued: 2015
- Authors: Malgas, Samkelo
- Date: 2015
- Subjects: Lignocellulose , Biomass energy , Ethanol as fuel , Polysaccharides , Sugar -- Inversion , Glycosidases , Galactoglucomannans , Oligosaccharides
- Language: English
- Type: Thesis , Masters , MSc
- Identifier: vital:4148 , http://hdl.handle.net/10962/d1017909
- Full Text:
- Date Issued: 2015
In silico analysis of human Hsp90 for the identification of novel anti-cancer drug target sites and natural compound inhibitors
- Authors: Penkler, David Lawrence
- Date: 2015
- Subjects: Heat shock proteins , Cancer -- Treatment , Molecular chaperones , Homeostasis , Carcinogenesis , Chemotherapy , Ligand binding (Biochemistry) , Protein-protein interactions
- Language: English
- Type: Thesis , Masters , MSc
- Identifier: vital:4162 , http://hdl.handle.net/10962/d1018938
- Description: The 90-KDa heat shock protein (Hsp90) is part of the molecular chaperone family, and as such it is involved in the regulation of protein homeostasis within cells. Specifically, Hsp90 aids in the folding of nascent proteins and re-folding of denatured proteins. It also plays an important role in the prevention of protein aggregation. Hsp90’s functionality is attributed to its several staged, multi-conformational ATPase cycle, in which associated client proteins are bound and released. Hsp90 is known to be associated with a wide array of client proteins, some of which are thought to be involved in multiple oncogenic processes. Indeed Hsp90 is known to be directly involved in perpetuating the stability and function of multiple mutated, chimeric and over-expressed signalling proteins that are known to promote the growth and survival of cancer cells. Hsp90 inhibitors are thus thought to be promising therapeutic agents for cancer treatment. A lack of a 3D structure of human Hsp90 however has restricted Hsp90 inhibitor development in large to in vivo investigations. This study, aims to investigate and calculate hypothetical homology models of the full human Hsp90 protein, and to probe these structural models for novel drug target sites using several in silico techniques. A multi-template homology modelling methodology was developed and in conjunction with protein-protein docking techniques, two functionally important human Hsp90 structural models were calculated; the nucleotide free “v-like” open and nucleotide bound closed conformations. Based on the conservation of ligand binding, virtual screening experiments conducted on both models using 316 natural compounds indigenous to South Africa, revealed three novel putative target sites. Two binding pockets in close association with important Hsp90-Hop interaction residues and a single binding pocket on the dimerization interface in the C-terminal domain. Targeted molecular docking experiments at these sites revealed two compounds (721395-11-5 and 264624-39-7) as putative inhibitors, both showing strong binding affinities for at least one of the three investigated target sites. Furthermore both compounds were found to only violate one Lipinski’s rules, suggesting their potential as candidates for further drug development. The combined work described here provides a putative platform for the development of next generation inhibitors of human Hsp90.
- Full Text:
- Date Issued: 2015
- Authors: Penkler, David Lawrence
- Date: 2015
- Subjects: Heat shock proteins , Cancer -- Treatment , Molecular chaperones , Homeostasis , Carcinogenesis , Chemotherapy , Ligand binding (Biochemistry) , Protein-protein interactions
- Language: English
- Type: Thesis , Masters , MSc
- Identifier: vital:4162 , http://hdl.handle.net/10962/d1018938
- Description: The 90-KDa heat shock protein (Hsp90) is part of the molecular chaperone family, and as such it is involved in the regulation of protein homeostasis within cells. Specifically, Hsp90 aids in the folding of nascent proteins and re-folding of denatured proteins. It also plays an important role in the prevention of protein aggregation. Hsp90’s functionality is attributed to its several staged, multi-conformational ATPase cycle, in which associated client proteins are bound and released. Hsp90 is known to be associated with a wide array of client proteins, some of which are thought to be involved in multiple oncogenic processes. Indeed Hsp90 is known to be directly involved in perpetuating the stability and function of multiple mutated, chimeric and over-expressed signalling proteins that are known to promote the growth and survival of cancer cells. Hsp90 inhibitors are thus thought to be promising therapeutic agents for cancer treatment. A lack of a 3D structure of human Hsp90 however has restricted Hsp90 inhibitor development in large to in vivo investigations. This study, aims to investigate and calculate hypothetical homology models of the full human Hsp90 protein, and to probe these structural models for novel drug target sites using several in silico techniques. A multi-template homology modelling methodology was developed and in conjunction with protein-protein docking techniques, two functionally important human Hsp90 structural models were calculated; the nucleotide free “v-like” open and nucleotide bound closed conformations. Based on the conservation of ligand binding, virtual screening experiments conducted on both models using 316 natural compounds indigenous to South Africa, revealed three novel putative target sites. Two binding pockets in close association with important Hsp90-Hop interaction residues and a single binding pocket on the dimerization interface in the C-terminal domain. Targeted molecular docking experiments at these sites revealed two compounds (721395-11-5 and 264624-39-7) as putative inhibitors, both showing strong binding affinities for at least one of the three investigated target sites. Furthermore both compounds were found to only violate one Lipinski’s rules, suggesting their potential as candidates for further drug development. The combined work described here provides a putative platform for the development of next generation inhibitors of human Hsp90.
- Full Text:
- Date Issued: 2015
Characterisation of the HSP70-HSP90 organising protein gene and its link to cancer
- Authors: Weeks, Stacey
- Date: 2015
- Language: English
- Type: text , Thesis , Masters , MSc
- Identifier: http://hdl.handle.net/10962/56006 , vital:26764
- Description: HOP (Heat shock protein 70/ Heat shock protein 90 organising protein) is a co-chaperone essential for client protein transfer from HSP70 to HSP90 within the HSP90 chaperone machine and has been found to be up-regulated in various cancers. However, minimal in vitro information can be found on the regulation of HOP expression. The aim of this study was to analyse the HOP gene structure across known orthologues, identify and characterise the HOP promoter, and identify the regulatory mechanisms influencing the expression of HOP in cancer. We hypothesized that the expression of HOP in cancer cells is likely regulated by oncogenic signalling pathways linked to cis-elements within the HOP promoter. An initial study of the evolution of the HOP gene speciation was performed across identified orthologues using Mega5.2. The evolutionary pathway of the HOP gene was traced from the unicellular organisms to fish, to amphibian and then to land mammal. The synteny across the orthologues was identified and the co-expression profile of HOP analysed. We identified the putative promoter region for HOP in silico and in vitro. Luciferase reporter assays were utilized to demonstrate promoter activity of the upstream region in vitro. Bioinformatic analysis of the active promoter region identified a large CpG island and a range of putative cis-elements. Many of the cis-elements interact with transcription factors which are activated by oncogenic pathways. We therefore tested the regulation of HOP levels by rat sarcoma viral oncogene homologue (RAS). Cancer cell lines were transfected with mutated RAS to observe the effect of constitutively active RAS expression on the production of HOP using qRT-PCR and Western Blot analyses. Additionally, inhibitors of the RAS signalling pathway were utilised to confirm the regulatory effect of mutated RAS on HOP expression. In cancer cell lines containing mutated RAS (Hs578T), HOP was up-regulated via a mechanism involving the MAPK signalling pathway and the ETS-1 and C/EBPβ cis-elements within the HOP promoter. These findings suggest for the first time that Hop expression in cancer may be regulated by RAS activation of the HOP promoter. Additionally, this study allowed us to determine the murine system to be the most suited genetic model organism with which to study the function of human HOP.
- Full Text:
- Date Issued: 2015
- Authors: Weeks, Stacey
- Date: 2015
- Language: English
- Type: text , Thesis , Masters , MSc
- Identifier: http://hdl.handle.net/10962/56006 , vital:26764
- Description: HOP (Heat shock protein 70/ Heat shock protein 90 organising protein) is a co-chaperone essential for client protein transfer from HSP70 to HSP90 within the HSP90 chaperone machine and has been found to be up-regulated in various cancers. However, minimal in vitro information can be found on the regulation of HOP expression. The aim of this study was to analyse the HOP gene structure across known orthologues, identify and characterise the HOP promoter, and identify the regulatory mechanisms influencing the expression of HOP in cancer. We hypothesized that the expression of HOP in cancer cells is likely regulated by oncogenic signalling pathways linked to cis-elements within the HOP promoter. An initial study of the evolution of the HOP gene speciation was performed across identified orthologues using Mega5.2. The evolutionary pathway of the HOP gene was traced from the unicellular organisms to fish, to amphibian and then to land mammal. The synteny across the orthologues was identified and the co-expression profile of HOP analysed. We identified the putative promoter region for HOP in silico and in vitro. Luciferase reporter assays were utilized to demonstrate promoter activity of the upstream region in vitro. Bioinformatic analysis of the active promoter region identified a large CpG island and a range of putative cis-elements. Many of the cis-elements interact with transcription factors which are activated by oncogenic pathways. We therefore tested the regulation of HOP levels by rat sarcoma viral oncogene homologue (RAS). Cancer cell lines were transfected with mutated RAS to observe the effect of constitutively active RAS expression on the production of HOP using qRT-PCR and Western Blot analyses. Additionally, inhibitors of the RAS signalling pathway were utilised to confirm the regulatory effect of mutated RAS on HOP expression. In cancer cell lines containing mutated RAS (Hs578T), HOP was up-regulated via a mechanism involving the MAPK signalling pathway and the ETS-1 and C/EBPβ cis-elements within the HOP promoter. These findings suggest for the first time that Hop expression in cancer may be regulated by RAS activation of the HOP promoter. Additionally, this study allowed us to determine the murine system to be the most suited genetic model organism with which to study the function of human HOP.
- Full Text:
- Date Issued: 2015
The influence of the physical environment, topography and time on the inshore distribution of invertebrate larvae : a multi-taxon approach
- Authors: Duna, Oliver Olwethu
- Date: 2015
- Subjects: Benthic animals -- Larvae , Benthic animals -- Ecology , Plankton -- Larvae
- Language: English
- Type: Thesis , Masters , MSc
- Identifier: vital:5926 , http://hdl.handle.net/10962/d1017804
- Description: Coastal hydrodynamics regulate population dynamics through the distribution and dispersal of the meroplankton of many benthic invertebrates. I examined the hydrodynamics at four different sites on the south-east coast of South Africa and coupled them with larval sampling done at high temporal and spatial resolution. Day and night sampling was done at all four sites and a continuous 24 hour study was done in one site, both forms of sampling were carried out in autumn and spring. Samples were taken at two stations, 900 metres offshore and 300 metres apart, within each site. Water properties measured were depth, temperature and current velocity and direction. Plankton samples were collected using a plankton pump at various depths, from the surface, bottom and either side of the thermocline when present. A wide range of taxa (mostly bryozoans, bivalves, barnacles and decapods) was examined. 2-way ANOVAs were used to test the effects of time and depth on each taxon. In addition, multiple regression analyses were performed on each taxon to investigate the effects of hydrodynamics on the distribution of larvae. Bryozoanlarvae proved to be positively phototactic whilst bivalve veligers, barnacle larvae and decapod zoeae performed diel vertical migration. Turbulence and temperature had an effect on the vertical distribution/migration of decapod zoeae. These results highlight the role of taxon-specific responses to flow and the potential differential effects on larval retention and ultimately connectivity of benthic populations.
- Full Text:
- Date Issued: 2015
- Authors: Duna, Oliver Olwethu
- Date: 2015
- Subjects: Benthic animals -- Larvae , Benthic animals -- Ecology , Plankton -- Larvae
- Language: English
- Type: Thesis , Masters , MSc
- Identifier: vital:5926 , http://hdl.handle.net/10962/d1017804
- Description: Coastal hydrodynamics regulate population dynamics through the distribution and dispersal of the meroplankton of many benthic invertebrates. I examined the hydrodynamics at four different sites on the south-east coast of South Africa and coupled them with larval sampling done at high temporal and spatial resolution. Day and night sampling was done at all four sites and a continuous 24 hour study was done in one site, both forms of sampling were carried out in autumn and spring. Samples were taken at two stations, 900 metres offshore and 300 metres apart, within each site. Water properties measured were depth, temperature and current velocity and direction. Plankton samples were collected using a plankton pump at various depths, from the surface, bottom and either side of the thermocline when present. A wide range of taxa (mostly bryozoans, bivalves, barnacles and decapods) was examined. 2-way ANOVAs were used to test the effects of time and depth on each taxon. In addition, multiple regression analyses were performed on each taxon to investigate the effects of hydrodynamics on the distribution of larvae. Bryozoanlarvae proved to be positively phototactic whilst bivalve veligers, barnacle larvae and decapod zoeae performed diel vertical migration. Turbulence and temperature had an effect on the vertical distribution/migration of decapod zoeae. These results highlight the role of taxon-specific responses to flow and the potential differential effects on larval retention and ultimately connectivity of benthic populations.
- Full Text:
- Date Issued: 2015
The trophic ecology of the endangered endemic Barau's Petrel (Pterodroma baraui) from Reunion Island, south-western Indian Ocean
- Authors: Danckwerts, Daniel Keith
- Date: 2015
- Subjects: Petrels -- Réunion , Pterodroma baraui , Ecology -- Réunion
- Language: English
- Type: Thesis , Masters , MSc
- Identifier: vital:5925 , http://hdl.handle.net/10962/d1017803
- Description: Réunion is the only tropical island that supports two endemic gadfly petrels. Population modelling has indicated that the current threats to the Barau’s Petrel (Pterodroma baraui) may drive it to extinction; this fate is almost definite for the Mascarene Petrel (Pseudobulweria aterrima). Management interventions have therefore been implemented, but conservation potential is handicapped since virtually nothing is known about the former species’ at-sea biology. Thus, following numerous recommendations, this study aimed to combine stomach content, stable isotope, and fatty acid analyses so to provide new information on the at-sea ecology of Barau’s Petrel. Breeding colonies were repeatedly visited over the same season and samples gathered from adults, fledglings, and downy chicks. Stomach contents consisted mostly of accumulated cephalopod beaks whereas structures from fishes, molluscs, arthropods, and crustaceans were less frequently encountered. Fatty acid profiles of blood varied greatly among individuals and the lowincidences of monounsaturated and n-3 fatty acids discounted fish as an important dietary component. δ¹⁵N of blood indicated a niche between the fourth and fifth trophic levels, which proposes that these birds scavenge to a greater degree than other sympatric seabirds and suggests that adults are also reliant on their endogenous reserves during breeding. δ¹³C values confirmed the migratory behaviour of adults since birds returning from the non-breeding grounds were enriched relative to individuals sampled through the breeding period. Significant intra-breeding season variations in δ13C were also observed, which matched this species’ patterns of habitat use as have recently described. These results collectively indicate an opportunistic behaviour, which implies some degree of resilience against shifts in prey availability/accessibility, and suggest that this species’ reproduction isdependent on distant foraging areas. This breeding strategy is synonymous with great vulnerability as over-investing into a single breeding episode may jeopardize future survival and fecundity. Thus, in light of environmental conditions that are becoming increasingly more susceptible to dramatic changes, the birds could rather be prioritising adult survival, over reproductive output. Further work is obviously necessary and should benefit from databases of fatty acid profiles and isotope signatures of potential prey species.
- Full Text:
- Date Issued: 2015
- Authors: Danckwerts, Daniel Keith
- Date: 2015
- Subjects: Petrels -- Réunion , Pterodroma baraui , Ecology -- Réunion
- Language: English
- Type: Thesis , Masters , MSc
- Identifier: vital:5925 , http://hdl.handle.net/10962/d1017803
- Description: Réunion is the only tropical island that supports two endemic gadfly petrels. Population modelling has indicated that the current threats to the Barau’s Petrel (Pterodroma baraui) may drive it to extinction; this fate is almost definite for the Mascarene Petrel (Pseudobulweria aterrima). Management interventions have therefore been implemented, but conservation potential is handicapped since virtually nothing is known about the former species’ at-sea biology. Thus, following numerous recommendations, this study aimed to combine stomach content, stable isotope, and fatty acid analyses so to provide new information on the at-sea ecology of Barau’s Petrel. Breeding colonies were repeatedly visited over the same season and samples gathered from adults, fledglings, and downy chicks. Stomach contents consisted mostly of accumulated cephalopod beaks whereas structures from fishes, molluscs, arthropods, and crustaceans were less frequently encountered. Fatty acid profiles of blood varied greatly among individuals and the lowincidences of monounsaturated and n-3 fatty acids discounted fish as an important dietary component. δ¹⁵N of blood indicated a niche between the fourth and fifth trophic levels, which proposes that these birds scavenge to a greater degree than other sympatric seabirds and suggests that adults are also reliant on their endogenous reserves during breeding. δ¹³C values confirmed the migratory behaviour of adults since birds returning from the non-breeding grounds were enriched relative to individuals sampled through the breeding period. Significant intra-breeding season variations in δ13C were also observed, which matched this species’ patterns of habitat use as have recently described. These results collectively indicate an opportunistic behaviour, which implies some degree of resilience against shifts in prey availability/accessibility, and suggest that this species’ reproduction isdependent on distant foraging areas. This breeding strategy is synonymous with great vulnerability as over-investing into a single breeding episode may jeopardize future survival and fecundity. Thus, in light of environmental conditions that are becoming increasingly more susceptible to dramatic changes, the birds could rather be prioritising adult survival, over reproductive output. Further work is obviously necessary and should benefit from databases of fatty acid profiles and isotope signatures of potential prey species.
- Full Text:
- Date Issued: 2015
The effects of dietary soya and crystalline phytoestrogens on the growth, gonad development and histology of farmed abalone, Haliotis midae
- Wu, Yu
- Authors: Wu, Yu
- Date: 2015
- Subjects: Haliotis midae , Haliotis midae -- Feeding and feeds , Haliotis midae -- Growth , Haliotis midae -- Histology , Haliotis midae -- Effect of chemicals on , Soybean as feed , Phytoestrogens
- Language: English
- Type: Thesis , Masters , MSc
- Identifier: vital:5380 , http://hdl.handle.net/10962/d1017225
- Description: The inclusion of soya as a dietary protein source in the formulated feed, Abfeed® S34 (Marifeed Pty (Ltd), Hermanus) for farmed abalone, Haliotis midae has resulted in larger gonads during reproductive seasons compared to the gonads of abalone fed kelp or diets that included fishmeal as the only main protein source. The aim of this study was to determine if the isoflavones present in the soya were responsible for this increase in gonad size and the subsequent effects on farmed abalone growth. Animals weighing between 40-50 g were fed one of seven isonitrogenous and isoenergetic diets containing either 0, 25, 50 or 100 percent of the soya component of the commercial feed (Abfeed® S34, Marifeed Pty (Ltd), Hermanus) from September 2013 to March 2014. An additional three diets were formulated to include crystalline isoflavone (ISO). These diets were identical to the 0 percent soya diet (i.e. the fishmeal only diet - FM), only ISO was included at the same rate that ISO occurred in the three soya diets. Data were analysed using a multiple forward stepwise regression analysis (MSR) to test the effects of ISO concentration, soya concentration, time, sex, time by concentration interaction and sex by concentration interaction on growth and gonad development and to identify those variables that most contributed to the model. The inclusion of crystalline ISO failed to promote larger gonads and had no effect on abalone growth, while growth and gonad development was dose dependent on soya inclusion rates with sex and time contributing to the models. Mean monthly weight gain in males correlated with increasing soya concentrations (c) (MSR, y = 3.24 + 0.002c, r2 = 0.23, p = 0.03), ranging from 3.11 ± 0.55 g abalone-1 month-1 to 4.43 ± 0.46 g abalone-1 month-1, while both male and female monthly length gain was not influenced by soya concentration with an overall mean of 1.62 ± 0.05 mm abalone-1 month-1 (MSR, p = 0.05 and p = 0.81, respectively). By December, the whole body mass, meat mass and visceral mass in both males and females decreased with increasing soya levels. However, by February, female whole body mass, meat mass and visceral mass positively correlated with soya levels. At the end of the study, male abalone fed FM with soya equivalent to the commercial feed had the highest whole body mass (69.00 ± 2.48 g abalone-1), meat mass (41.80 ± 1.12 g abalone-1), visceral mass (9.00 ± 2.47 g abalone-1) and gonad bulk index (42.70 ± 9.82 g abalone-1), while females were not influenced by soya concentrations with an overall whole body mass of 63.46 ± 0.79 g abalone-1. Weight loss was observed in all treatments between February and March, probably due to a spawning event. The moisture content in the meat was not influenced by treatment, however, visceral water loss was effected by both ISO and soya concentration with time and sex contributing to the model. The visceral water loss of females fed graded levels of soya decreased as a function of soya from December to March, and from December to February for males, whereas females fed ISO-enriched diets decreased as a function of ISO concentration (c) at the end of the study from 74.98 ± 0.88 to 73.10 ± 0.75 percent (MSR, y = 74.97 – 0.0025c, r2 = 0.20, p = 0.048). The inclusion of crystalline ISO had no significant effect on oogenesis in female farmed Haliotis midae, while the distribution of the predominant oocyte stage, stage 7 (second last stage prior to spawning) was dose-dependent in abalone fed increasing soya concentration (c) (MSR, y = 33.38 + 0.03c, r2 = 0.32, F(1, 18) = 8.52, p = 0.01). The increase in stage 7 oocytes in abalone fed FM with soya did not reduce the number of oocytes (44.96 ± 3.01 oocytes mm-2) present within the lumen, while the number of oocytes (o) in abalone fed the FM-only based diets decreased with increasing abundance of stage 7 oocytes (MSR, y = 58.28 – 0.48c, r2 = 0.38, F(1, 18) = 12.51, p = 0.002), possibly due to the increase in size of the oocytes with thicker jelly coats. This study provided evidence that crystalline isoflavone had no influence on abalone gonad development over five months, while soya had a dose-dependent effect on growth, gonad mass and oogenesis in farmed Haliotis midae. Formulated abalone feed could be manipulated at certain times of the year to obtain maximum growth. These implications and further studies were discussed.
- Full Text:
- Date Issued: 2015
- Authors: Wu, Yu
- Date: 2015
- Subjects: Haliotis midae , Haliotis midae -- Feeding and feeds , Haliotis midae -- Growth , Haliotis midae -- Histology , Haliotis midae -- Effect of chemicals on , Soybean as feed , Phytoestrogens
- Language: English
- Type: Thesis , Masters , MSc
- Identifier: vital:5380 , http://hdl.handle.net/10962/d1017225
- Description: The inclusion of soya as a dietary protein source in the formulated feed, Abfeed® S34 (Marifeed Pty (Ltd), Hermanus) for farmed abalone, Haliotis midae has resulted in larger gonads during reproductive seasons compared to the gonads of abalone fed kelp or diets that included fishmeal as the only main protein source. The aim of this study was to determine if the isoflavones present in the soya were responsible for this increase in gonad size and the subsequent effects on farmed abalone growth. Animals weighing between 40-50 g were fed one of seven isonitrogenous and isoenergetic diets containing either 0, 25, 50 or 100 percent of the soya component of the commercial feed (Abfeed® S34, Marifeed Pty (Ltd), Hermanus) from September 2013 to March 2014. An additional three diets were formulated to include crystalline isoflavone (ISO). These diets were identical to the 0 percent soya diet (i.e. the fishmeal only diet - FM), only ISO was included at the same rate that ISO occurred in the three soya diets. Data were analysed using a multiple forward stepwise regression analysis (MSR) to test the effects of ISO concentration, soya concentration, time, sex, time by concentration interaction and sex by concentration interaction on growth and gonad development and to identify those variables that most contributed to the model. The inclusion of crystalline ISO failed to promote larger gonads and had no effect on abalone growth, while growth and gonad development was dose dependent on soya inclusion rates with sex and time contributing to the models. Mean monthly weight gain in males correlated with increasing soya concentrations (c) (MSR, y = 3.24 + 0.002c, r2 = 0.23, p = 0.03), ranging from 3.11 ± 0.55 g abalone-1 month-1 to 4.43 ± 0.46 g abalone-1 month-1, while both male and female monthly length gain was not influenced by soya concentration with an overall mean of 1.62 ± 0.05 mm abalone-1 month-1 (MSR, p = 0.05 and p = 0.81, respectively). By December, the whole body mass, meat mass and visceral mass in both males and females decreased with increasing soya levels. However, by February, female whole body mass, meat mass and visceral mass positively correlated with soya levels. At the end of the study, male abalone fed FM with soya equivalent to the commercial feed had the highest whole body mass (69.00 ± 2.48 g abalone-1), meat mass (41.80 ± 1.12 g abalone-1), visceral mass (9.00 ± 2.47 g abalone-1) and gonad bulk index (42.70 ± 9.82 g abalone-1), while females were not influenced by soya concentrations with an overall whole body mass of 63.46 ± 0.79 g abalone-1. Weight loss was observed in all treatments between February and March, probably due to a spawning event. The moisture content in the meat was not influenced by treatment, however, visceral water loss was effected by both ISO and soya concentration with time and sex contributing to the model. The visceral water loss of females fed graded levels of soya decreased as a function of soya from December to March, and from December to February for males, whereas females fed ISO-enriched diets decreased as a function of ISO concentration (c) at the end of the study from 74.98 ± 0.88 to 73.10 ± 0.75 percent (MSR, y = 74.97 – 0.0025c, r2 = 0.20, p = 0.048). The inclusion of crystalline ISO had no significant effect on oogenesis in female farmed Haliotis midae, while the distribution of the predominant oocyte stage, stage 7 (second last stage prior to spawning) was dose-dependent in abalone fed increasing soya concentration (c) (MSR, y = 33.38 + 0.03c, r2 = 0.32, F(1, 18) = 8.52, p = 0.01). The increase in stage 7 oocytes in abalone fed FM with soya did not reduce the number of oocytes (44.96 ± 3.01 oocytes mm-2) present within the lumen, while the number of oocytes (o) in abalone fed the FM-only based diets decreased with increasing abundance of stage 7 oocytes (MSR, y = 58.28 – 0.48c, r2 = 0.38, F(1, 18) = 12.51, p = 0.002), possibly due to the increase in size of the oocytes with thicker jelly coats. This study provided evidence that crystalline isoflavone had no influence on abalone gonad development over five months, while soya had a dose-dependent effect on growth, gonad mass and oogenesis in farmed Haliotis midae. Formulated abalone feed could be manipulated at certain times of the year to obtain maximum growth. These implications and further studies were discussed.
- Full Text:
- Date Issued: 2015
Variation in breeding systems, floral morphology and nectar properties in three co-occurring Erica species with contrasting pollination syndromes
- Authors: Lombardi, Giorgio Colombo
- Date: 2015
- Subjects: Ericas -- South Africa -- Western Cape , Ericas -- Morphology , Ericas -- Reproduction , Ericas -- Pollination , Pollination by animals , Pollination by insects , Nectar
- Language: English
- Type: Thesis , Masters , MSc
- Identifier: vital:4273 , http://hdl.handle.net/10962/d1018567
- Description: The genus Erica is the most species rich in the Cape Floristic Kingdom, yet there are limited data on the various flower-pollinator interactions and breeding systems for the majority of these species. Until recently research has focussed on predictive floral traits, including flower shape, length of corolla and corolla opening to identify likely pollinators in this genus. Field observations provide an empirical test of such predictions. This study investigated three species of Erica and compared their pollination and breeding systems and floral biology. Research, including field experiments and pollinator observations was undertaken in the Vogelgat Private Nature Reserve, Maanschynkop Nature Reserve and Boskloof farm in the vicinity of Hermanus in the Western Cape Province of South Africa. Field observations were conducted to determine what flower- visitor interactions occurred, while nectar volumes and sugar concentrations were measured to determine the value of the reward to the different visitors. Selective exclusion and breeding system experiments were carried out to determine whether these Erica species were capable of autonomous self-fertilization or whether they are pollinator dependent for breeding success. The unusual morphology of Erica lanuginosa suggested rodent-pollination. Field observations, including photographs of visits to plants in the field, the presence of pollen in scat sample and selective exclusion and breeding system experiments identified rodents, primarily Acomys subspinosus to be the primary pollinator. Long-proboscid flies of the family Nemestrinidae were found, on the basis of field observations to be responsible for pollination of the endemic Erica aristata. This was supported by with nectar volume and sugar concentration samples which are consistent with other long-proboscid fly-pollinated plant species. Selective exclusion and breeding system experiments undertaken confirmed that Erica aristata required a pollinator to set seed. Observations and breeding trials revealed bird-pollination in Erica sessiliflora. Nectar volume and sugar concentrations in Erica sessiliflora were in line with other sunbird-pollinated plant species, providing the necessary rewards for sunbirds visiting this species. Specialised pollination by single pollinators was found in all three species and results from breeding system experiments show that out-crossing is important. Further research into pollinator-flower interactions in the genus Erica is necessary, not least to understand more fully the conservation importance of specific pollinators.
- Full Text:
- Date Issued: 2015
- Authors: Lombardi, Giorgio Colombo
- Date: 2015
- Subjects: Ericas -- South Africa -- Western Cape , Ericas -- Morphology , Ericas -- Reproduction , Ericas -- Pollination , Pollination by animals , Pollination by insects , Nectar
- Language: English
- Type: Thesis , Masters , MSc
- Identifier: vital:4273 , http://hdl.handle.net/10962/d1018567
- Description: The genus Erica is the most species rich in the Cape Floristic Kingdom, yet there are limited data on the various flower-pollinator interactions and breeding systems for the majority of these species. Until recently research has focussed on predictive floral traits, including flower shape, length of corolla and corolla opening to identify likely pollinators in this genus. Field observations provide an empirical test of such predictions. This study investigated three species of Erica and compared their pollination and breeding systems and floral biology. Research, including field experiments and pollinator observations was undertaken in the Vogelgat Private Nature Reserve, Maanschynkop Nature Reserve and Boskloof farm in the vicinity of Hermanus in the Western Cape Province of South Africa. Field observations were conducted to determine what flower- visitor interactions occurred, while nectar volumes and sugar concentrations were measured to determine the value of the reward to the different visitors. Selective exclusion and breeding system experiments were carried out to determine whether these Erica species were capable of autonomous self-fertilization or whether they are pollinator dependent for breeding success. The unusual morphology of Erica lanuginosa suggested rodent-pollination. Field observations, including photographs of visits to plants in the field, the presence of pollen in scat sample and selective exclusion and breeding system experiments identified rodents, primarily Acomys subspinosus to be the primary pollinator. Long-proboscid flies of the family Nemestrinidae were found, on the basis of field observations to be responsible for pollination of the endemic Erica aristata. This was supported by with nectar volume and sugar concentration samples which are consistent with other long-proboscid fly-pollinated plant species. Selective exclusion and breeding system experiments undertaken confirmed that Erica aristata required a pollinator to set seed. Observations and breeding trials revealed bird-pollination in Erica sessiliflora. Nectar volume and sugar concentrations in Erica sessiliflora were in line with other sunbird-pollinated plant species, providing the necessary rewards for sunbirds visiting this species. Specialised pollination by single pollinators was found in all three species and results from breeding system experiments show that out-crossing is important. Further research into pollinator-flower interactions in the genus Erica is necessary, not least to understand more fully the conservation importance of specific pollinators.
- Full Text:
- Date Issued: 2015
Analysis of predictive power of binding affinity of PBM-derived sequences
- Authors: Matereke, Lavious Tapiwa
- Date: 2015
- Subjects: Transcription factors , Protein binding , DNA-binding proteins , Chromatin , Protein microarrays
- Language: English
- Type: Thesis , Masters , MSc
- Identifier: vital:4161 , http://hdl.handle.net/10962/d1018666
- Description: A transcription factor (TF) is a protein that binds to specific DNA sequences as part of the initiation stage of transcription. Various methods of finding these transcription factor binding sites (TFBS) have been developed. In vivo technologies analyze DNA binding regions known to have bound to a TF in a living cell. Most widely used in vivo methods at the moment are chromatin immunoprecipitation followed by deep sequencing (ChIP-seq) and DNase I hypersensitive sites sequencing. In vitro methods derive TFBS based on experiments with TFs and DNA usually in artificial settings or computationally. An example is the Protein Binding Microarray which uses artificially constructed DNA sequences to determine the short sequences that are most likely to bind to a TF. The major drawback of this approach is that binding of TFs in vivo is also dependent on other factors such as chromatin accessibility and the presence of cofactors. Therefore TFBS derived from the PBM technique might not resemble the true DNA binding sequences. In this work, we use PBM data from the UniPROBE motif database, ChIP-seq data and DNase I hypersensitive sites data. Using the Spearman’s rank correlation and area under receiver operating characteristic curve, we compare the enrichment scores which the PBM approach assigns to its identified sequences and the frequency of these sequences in likely binding regions and the human genome as a whole. We also use central motif enrichment analysis (CentriMo) to compare the enrichment of UniPROBE motifs with in vivo derived motifs (from the JASPAR CORE database) in their respective TF ChIP-seq peak region. CentriMo is applied to 14 TF ChIP-seq peak regions from different cell lines. We aim to establish if there is a relationship between the occurrences of UniPROBE 8-mer patterns in likely binding regions and their enrichment score and how well the in vitro derived motifs match in vivo binding specificity. We did not come out with a particular trend showing failure of the PBM approach to predict in vivo binding specificity. Our results show Ets1, Hnf4a and Tcf3 show prediction failure by the PBM technique in terms of our Spearman’s rank correlation for ChIP-seq data and central motif enrichment analysis. However, the PBM technique also matched the in vivo binding specificities of FoxA2, Pou2f2 and Mafk. Failure of the PBM approach was found to be a result of variability in the TF’s binding specificity, the presence of cofactors, narrow binding specificity and the presence ubiquitous binding patterns.
- Full Text:
- Date Issued: 2015
- Authors: Matereke, Lavious Tapiwa
- Date: 2015
- Subjects: Transcription factors , Protein binding , DNA-binding proteins , Chromatin , Protein microarrays
- Language: English
- Type: Thesis , Masters , MSc
- Identifier: vital:4161 , http://hdl.handle.net/10962/d1018666
- Description: A transcription factor (TF) is a protein that binds to specific DNA sequences as part of the initiation stage of transcription. Various methods of finding these transcription factor binding sites (TFBS) have been developed. In vivo technologies analyze DNA binding regions known to have bound to a TF in a living cell. Most widely used in vivo methods at the moment are chromatin immunoprecipitation followed by deep sequencing (ChIP-seq) and DNase I hypersensitive sites sequencing. In vitro methods derive TFBS based on experiments with TFs and DNA usually in artificial settings or computationally. An example is the Protein Binding Microarray which uses artificially constructed DNA sequences to determine the short sequences that are most likely to bind to a TF. The major drawback of this approach is that binding of TFs in vivo is also dependent on other factors such as chromatin accessibility and the presence of cofactors. Therefore TFBS derived from the PBM technique might not resemble the true DNA binding sequences. In this work, we use PBM data from the UniPROBE motif database, ChIP-seq data and DNase I hypersensitive sites data. Using the Spearman’s rank correlation and area under receiver operating characteristic curve, we compare the enrichment scores which the PBM approach assigns to its identified sequences and the frequency of these sequences in likely binding regions and the human genome as a whole. We also use central motif enrichment analysis (CentriMo) to compare the enrichment of UniPROBE motifs with in vivo derived motifs (from the JASPAR CORE database) in their respective TF ChIP-seq peak region. CentriMo is applied to 14 TF ChIP-seq peak regions from different cell lines. We aim to establish if there is a relationship between the occurrences of UniPROBE 8-mer patterns in likely binding regions and their enrichment score and how well the in vitro derived motifs match in vivo binding specificity. We did not come out with a particular trend showing failure of the PBM approach to predict in vivo binding specificity. Our results show Ets1, Hnf4a and Tcf3 show prediction failure by the PBM technique in terms of our Spearman’s rank correlation for ChIP-seq data and central motif enrichment analysis. However, the PBM technique also matched the in vivo binding specificities of FoxA2, Pou2f2 and Mafk. Failure of the PBM approach was found to be a result of variability in the TF’s binding specificity, the presence of cofactors, narrow binding specificity and the presence ubiquitous binding patterns.
- Full Text:
- Date Issued: 2015
The use of probiotics in the diet of farmed South African abalone Haliotis midae L
- Authors: Maliza, Siyabonga
- Date: 2015
- Subjects: Haliotis midae -- South Africa , Abalones -- South Africa , Haliotis midae -- Feeding and feeds , Haliotis midae -- Effect of chemicals on , Haliotis midae -- Growth , Haliotis midae -- Immunology , Probiotics
- Language: English
- Type: Thesis , Masters , MSc
- Identifier: vital:5382 , http://hdl.handle.net/10962/d1018178
- Description: Physiological stress in farmed abalone can lead to immunosuppression and increase the susceptibility to bacterial, viral and parasitic disease, often followed by mortality. Thus, handling and poor water quality can reduce farm production efficiency. Probiotics in aquaculture have been effective in a wide range of species in enhancing immunity, survival, improving feed utilisation and growth. Three putative probionts identified as a result of in vitro screening had been beneficial to laboratory-reared abalone in a previous study. The aim of this study was to produce an abalone feed that contains a suite of probionts that may promote abalone growth and health under farming conditions. The objectives were to compare growth and physiological responses (i.e., haemocyte and phagocytosis counts) of abalone fed a commercial feed (Abfeed®S 34, Marifeed, Hermanus) supplemented with probiotics (i.e., the probiotic diet) to abalone fed the commercial feed without probiotic supplementation as a control treatment in a factorial design with handling method as an independent variable. This experiment was conducted at HIK Abalone Farm (Pty Ltd) for a period of eight months with initial weight and length 36.1 ± 0.05 g and 58.6 ± 0.06 mm abalone-1. Another experiment was carried out at Roman Bay Sea Farm (Pty) Ltd with initial weight and length 34.7 ± 0.17 g and 62.3 ± 0.18 mm abalone-1, but this experiment included one factor only, i.e. the presence and absence of the probionts in the feed. At HIK there was no significant interaction between diet and handling on average length and weight gain month-1 after four (p=0.81 and p=0.32) and eight (p=0.51 and p=0.53) months, respectively. Average length (additional handling = 73.9 ± 0.52 mm, normal farm handling = 75.8 ± 0.57 mm) and weight gain (mean: additional handling = 68.5 ± 1.20 g, normal farm handling = 74.3 ± 1.86 g) increased significantly in animals that were handled under normal farm procedure and were either fed probiotic or control diet after eight months (p=0.03 and p=0.02, respectively). There was no iii difference in length gain or weight gain of abalone fed the probiotic diet and those fed the control diet (ANOVA: F(1,16)=0.04, p=0.84; F(1,16)=0.14, p=0.71, respectively). After four months phagocytotic count was significantly different between dietary treatments with mean values of 74.50 ± 10.52 and 63.52 ± 14.52 % phagocytosis count per sample for the probionts and control treatment, respectively (p=0.04), there was no difference after eight months at HIK Abalone Farm. There was no effect of stressor application (p=0.14) and no interaction between dietary treatment and stressor application for this variable i.e., phagocytosis count (p=0.61). There was no difference in feed conversion ratio between treatments with values ranging from 2.9 to 3.8. At Roman Bay Sea farm, there was no significant difference in mean length gain between abalone fed the probiotic and control diet after eight months (repeated measures ANOVA: F(4,28)=16.54. Mean weight gain of abalone fed the probiotic diet was significantly greater than those fed the control diet after eight months (repeated measures ANOVA: F(4,28)=39.82, p(0.00001). There was no significant difference in haemocyte counts between animals fed either probiotic or control diet after four and eight months at Roman Bay Sea farm (p>0.05).
- Full Text:
- Date Issued: 2015
- Authors: Maliza, Siyabonga
- Date: 2015
- Subjects: Haliotis midae -- South Africa , Abalones -- South Africa , Haliotis midae -- Feeding and feeds , Haliotis midae -- Effect of chemicals on , Haliotis midae -- Growth , Haliotis midae -- Immunology , Probiotics
- Language: English
- Type: Thesis , Masters , MSc
- Identifier: vital:5382 , http://hdl.handle.net/10962/d1018178
- Description: Physiological stress in farmed abalone can lead to immunosuppression and increase the susceptibility to bacterial, viral and parasitic disease, often followed by mortality. Thus, handling and poor water quality can reduce farm production efficiency. Probiotics in aquaculture have been effective in a wide range of species in enhancing immunity, survival, improving feed utilisation and growth. Three putative probionts identified as a result of in vitro screening had been beneficial to laboratory-reared abalone in a previous study. The aim of this study was to produce an abalone feed that contains a suite of probionts that may promote abalone growth and health under farming conditions. The objectives were to compare growth and physiological responses (i.e., haemocyte and phagocytosis counts) of abalone fed a commercial feed (Abfeed®S 34, Marifeed, Hermanus) supplemented with probiotics (i.e., the probiotic diet) to abalone fed the commercial feed without probiotic supplementation as a control treatment in a factorial design with handling method as an independent variable. This experiment was conducted at HIK Abalone Farm (Pty Ltd) for a period of eight months with initial weight and length 36.1 ± 0.05 g and 58.6 ± 0.06 mm abalone-1. Another experiment was carried out at Roman Bay Sea Farm (Pty) Ltd with initial weight and length 34.7 ± 0.17 g and 62.3 ± 0.18 mm abalone-1, but this experiment included one factor only, i.e. the presence and absence of the probionts in the feed. At HIK there was no significant interaction between diet and handling on average length and weight gain month-1 after four (p=0.81 and p=0.32) and eight (p=0.51 and p=0.53) months, respectively. Average length (additional handling = 73.9 ± 0.52 mm, normal farm handling = 75.8 ± 0.57 mm) and weight gain (mean: additional handling = 68.5 ± 1.20 g, normal farm handling = 74.3 ± 1.86 g) increased significantly in animals that were handled under normal farm procedure and were either fed probiotic or control diet after eight months (p=0.03 and p=0.02, respectively). There was no iii difference in length gain or weight gain of abalone fed the probiotic diet and those fed the control diet (ANOVA: F(1,16)=0.04, p=0.84; F(1,16)=0.14, p=0.71, respectively). After four months phagocytotic count was significantly different between dietary treatments with mean values of 74.50 ± 10.52 and 63.52 ± 14.52 % phagocytosis count per sample for the probionts and control treatment, respectively (p=0.04), there was no difference after eight months at HIK Abalone Farm. There was no effect of stressor application (p=0.14) and no interaction between dietary treatment and stressor application for this variable i.e., phagocytosis count (p=0.61). There was no difference in feed conversion ratio between treatments with values ranging from 2.9 to 3.8. At Roman Bay Sea farm, there was no significant difference in mean length gain between abalone fed the probiotic and control diet after eight months (repeated measures ANOVA: F(4,28)=16.54. Mean weight gain of abalone fed the probiotic diet was significantly greater than those fed the control diet after eight months (repeated measures ANOVA: F(4,28)=39.82, p(0.00001). There was no significant difference in haemocyte counts between animals fed either probiotic or control diet after four and eight months at Roman Bay Sea farm (p>0.05).
- Full Text:
- Date Issued: 2015
Building an E-health system for health awareness campaigns in poor areas
- Authors: Gremu, Chikumbutso David
- Date: 2015
- Subjects: National health services -- South Africa , Medical informatics , Public health -- Information services
- Language: English
- Type: Thesis , Masters , MSc
- Identifier: vital:4708 , http://hdl.handle.net/10962/d1017930
- Description: Appropriate e-services as well as revenue generation capabilities are key to the deployment and the sustainability for ICT installations in poor areas, particularly common in developing country. The area of e-Health is a promising area for e-services that are both important to the population in those areas and potentially of direct interest to National Health Organizations, which already spend money for Health campaigns there. This thesis focuses on the design, implementation, and full functional testing of HealthAware, an application that allows health organization to set up targeted awareness campaigns for poor areas. Requirements for such application are very specific, starting from the fact that the preparation of the campaign and its execution/consumption happen in two different environments from a technological and social point of view. Part of the research work done for this thesis was to make the above requirements explicit and then use them in the design. This phase of the research was facilitated by the fact that the thesis' work was executed within the context of the Siyakhula Living Lab (SLL; www.siyakhulaLL.org), which has accumulated multi-year experience of ICT deployment in such areas. As a result of the found requirements, HealthAware comprises two components, which are web-based, Java applications that run in a peer-to-peer fashion. The first component, the Dashboard, is used to create, manage, and publish information for conducting awareness campaigns or surveys. The second component, HealthMessenger, facilitates users' access to the campaigns or surveys that were created using the Dashboard. The HealthMessenger was designed to be hosted on TeleWeaver while the Dashboard is hosted independently of TeleWeaver and simply communicates with the HealthMessenger through webservices. TeleWeaver is an application integration platform developed within the SLL to host software applications for poor areas. Using a core service of TeleWeaver, the profile service, where all the users' defining elements are contained, campaigns and surveys can be easily and effectively targeted, for example to match specific demographics or geographic locations. Revenue generation is attained via the logging of the interactions of the target users in the communities with the applications in TeleWeaver, from which billing data is generated according to the specific contractual agreements with the National Health Organization. From a general point of view, HealthAware contributes to the concrete realizations of a bidirectional access channel between Health Organizations and users in poor communities, which not only allows the communication of appropriate content in both directions, but get 'monetized' and in so doing becomes a revenue generator.
- Full Text:
- Date Issued: 2015
- Authors: Gremu, Chikumbutso David
- Date: 2015
- Subjects: National health services -- South Africa , Medical informatics , Public health -- Information services
- Language: English
- Type: Thesis , Masters , MSc
- Identifier: vital:4708 , http://hdl.handle.net/10962/d1017930
- Description: Appropriate e-services as well as revenue generation capabilities are key to the deployment and the sustainability for ICT installations in poor areas, particularly common in developing country. The area of e-Health is a promising area for e-services that are both important to the population in those areas and potentially of direct interest to National Health Organizations, which already spend money for Health campaigns there. This thesis focuses on the design, implementation, and full functional testing of HealthAware, an application that allows health organization to set up targeted awareness campaigns for poor areas. Requirements for such application are very specific, starting from the fact that the preparation of the campaign and its execution/consumption happen in two different environments from a technological and social point of view. Part of the research work done for this thesis was to make the above requirements explicit and then use them in the design. This phase of the research was facilitated by the fact that the thesis' work was executed within the context of the Siyakhula Living Lab (SLL; www.siyakhulaLL.org), which has accumulated multi-year experience of ICT deployment in such areas. As a result of the found requirements, HealthAware comprises two components, which are web-based, Java applications that run in a peer-to-peer fashion. The first component, the Dashboard, is used to create, manage, and publish information for conducting awareness campaigns or surveys. The second component, HealthMessenger, facilitates users' access to the campaigns or surveys that were created using the Dashboard. The HealthMessenger was designed to be hosted on TeleWeaver while the Dashboard is hosted independently of TeleWeaver and simply communicates with the HealthMessenger through webservices. TeleWeaver is an application integration platform developed within the SLL to host software applications for poor areas. Using a core service of TeleWeaver, the profile service, where all the users' defining elements are contained, campaigns and surveys can be easily and effectively targeted, for example to match specific demographics or geographic locations. Revenue generation is attained via the logging of the interactions of the target users in the communities with the applications in TeleWeaver, from which billing data is generated according to the specific contractual agreements with the National Health Organization. From a general point of view, HealthAware contributes to the concrete realizations of a bidirectional access channel between Health Organizations and users in poor communities, which not only allows the communication of appropriate content in both directions, but get 'monetized' and in so doing becomes a revenue generator.
- Full Text:
- Date Issued: 2015