Quantification of pre-competitive sleep/wake behaviour in a sample of South African cyclists
- Authors: Steenekamp, Travis
- Date: 2018
- Subjects: Sleep deprivation , Cyclists Health and hygiene South Africa , Sleep Physiological aspects , Performance , Performance anxiety
- Language: English
- Type: text , Thesis , Masters , MSc
- Identifier: http://hdl.handle.net/10962/59015 , vital:27408
- Description: The quantification of athlete pre-competitive sleep behaviour is of interest owing to the possibility that sleep loss may have a negative effect on health and performance. The purpose of this study was to monitor and quantify the sleep/wake patterns of South African cyclists prior to competitive races. A total of 336 cyclists, male and female and of differing competition levels, cycling in either the 2015 Tsogo Sun Amashova or the 2016 Telkom 94.7 Cycle Challenge completed an altered version of the Competitive Sports and Sleep Questionnaire. The questionnaire asked cyclists to report on precompetitive sleep over the past year. A subset of 92 cyclists also recorded a Core Consensus Sleep Diary for the three nights leading up to the races. The questionnaire showed that 67% of the cyclists reported worsened sleep at least once prior to competition within the past 12 months. The sleep diary found that the cyclists’ average sleep duration the night before the races was 6h19min (±1h38min), which was significantly less than two and three nights prior to the races. Sleep quality was also shown to deteriorate significantly the night before the races. The contributing factors leading to worsened pre-competitive sleep were the time the cyclists had to wake-up as well as perceived increases in sleep latency and awakenings after sleep onset. Anxiety was found to be the major cause of sleep disturbances. While females were found to be significantly more likely to report having experienced poorer sleep before competition in the past year, the sleep diary showed no difference in sleep the night before the races between the sexes. Females were significantly more likely to report instances of unpleasant dreams and waking up during the night. Again, the sleep diary data did not corroborate these findings. Females were also found to report significantly more accounts of nervousness or thoughts about competition as being the cause of sleep problems. There was no difference in sleep loss the night before competition when comparing competition-level groups. The only significant difference was that recreational cyclists were more likely to report sleeping in foreign environments as a cause of sleep disturbances. Despite a large percentage of cyclists experiencing pre-competitive sleep loss, over half (55%) perceived sleep loss to have no impact on their performance. Analysis of pre-sleep behaviour also revealed that the cyclists engaged in several practices that may have a negative effect on subsequent sleep. The vast majority of the cyclists (61%) indicated having no specific strategy to help them sleep the night before competition. Fifteen percent of cyclists reporting using media devices to help them fall asleep, a practice that has been shown to disrupt sleep. In conclusion, most cyclists, regardless of sex and level of competition experience precompetitive sleep loss attributed largely to anxiety but with the perception that this loss in sleep does not negatively impact their performance.
- Full Text:
- Date Issued: 2018
- Authors: Steenekamp, Travis
- Date: 2018
- Subjects: Sleep deprivation , Cyclists Health and hygiene South Africa , Sleep Physiological aspects , Performance , Performance anxiety
- Language: English
- Type: text , Thesis , Masters , MSc
- Identifier: http://hdl.handle.net/10962/59015 , vital:27408
- Description: The quantification of athlete pre-competitive sleep behaviour is of interest owing to the possibility that sleep loss may have a negative effect on health and performance. The purpose of this study was to monitor and quantify the sleep/wake patterns of South African cyclists prior to competitive races. A total of 336 cyclists, male and female and of differing competition levels, cycling in either the 2015 Tsogo Sun Amashova or the 2016 Telkom 94.7 Cycle Challenge completed an altered version of the Competitive Sports and Sleep Questionnaire. The questionnaire asked cyclists to report on precompetitive sleep over the past year. A subset of 92 cyclists also recorded a Core Consensus Sleep Diary for the three nights leading up to the races. The questionnaire showed that 67% of the cyclists reported worsened sleep at least once prior to competition within the past 12 months. The sleep diary found that the cyclists’ average sleep duration the night before the races was 6h19min (±1h38min), which was significantly less than two and three nights prior to the races. Sleep quality was also shown to deteriorate significantly the night before the races. The contributing factors leading to worsened pre-competitive sleep were the time the cyclists had to wake-up as well as perceived increases in sleep latency and awakenings after sleep onset. Anxiety was found to be the major cause of sleep disturbances. While females were found to be significantly more likely to report having experienced poorer sleep before competition in the past year, the sleep diary showed no difference in sleep the night before the races between the sexes. Females were significantly more likely to report instances of unpleasant dreams and waking up during the night. Again, the sleep diary data did not corroborate these findings. Females were also found to report significantly more accounts of nervousness or thoughts about competition as being the cause of sleep problems. There was no difference in sleep loss the night before competition when comparing competition-level groups. The only significant difference was that recreational cyclists were more likely to report sleeping in foreign environments as a cause of sleep disturbances. Despite a large percentage of cyclists experiencing pre-competitive sleep loss, over half (55%) perceived sleep loss to have no impact on their performance. Analysis of pre-sleep behaviour also revealed that the cyclists engaged in several practices that may have a negative effect on subsequent sleep. The vast majority of the cyclists (61%) indicated having no specific strategy to help them sleep the night before competition. Fifteen percent of cyclists reporting using media devices to help them fall asleep, a practice that has been shown to disrupt sleep. In conclusion, most cyclists, regardless of sex and level of competition experience precompetitive sleep loss attributed largely to anxiety but with the perception that this loss in sleep does not negatively impact their performance.
- Full Text:
- Date Issued: 2018
Treatment of anaerobically digested brewery effluent in high rate algal ponds: an understanding of the microbial community structure in the ponds and the underlying mechanisms responsible for nutrient removal from the effluent
- Authors: Mogane, Mmathabo Lucretia
- Date: 2017
- Subjects: Brewing industry -- Waste disposal -- South Africa , Breweries -- Waste displosal -- South Africa , Algae culture -- South Africa , Water -- Purification -- South Africa , Sewage lagoons -- South Africa
- Language: English
- Type: Thesis , Masters , MSc
- Identifier: http://hdl.handle.net/10962/5026 , vital:20754
- Full Text:
- Date Issued: 2017
- Authors: Mogane, Mmathabo Lucretia
- Date: 2017
- Subjects: Brewing industry -- Waste disposal -- South Africa , Breweries -- Waste displosal -- South Africa , Algae culture -- South Africa , Water -- Purification -- South Africa , Sewage lagoons -- South Africa
- Language: English
- Type: Thesis , Masters , MSc
- Identifier: http://hdl.handle.net/10962/5026 , vital:20754
- Full Text:
- Date Issued: 2017
Reliability analysis: assessment of hardware and human reliability
- Authors: Mafu, Masakheke
- Date: 2017
- Subjects: Bayesian statistical decision theory , Reliability (Engineering) , Human machine systems , Probabilities , Markov processes
- Language: English
- Type: Thesis , Masters , MSc
- Identifier: http://hdl.handle.net/10962/6280 , vital:21077
- Description: Most reliability analyses involve the analysis of binary data. Practitioners in the field of reliability place great emphasis on analysing the time periods over which items or systems function (failure time analyses), which make use of different statistical models. This study intends to introduce, review and investigate four statistical models for modeling failure times of non-repairable items, and to utilise a Bayesian methodology to achieve this. The exponential, Rayleigh, gamma and Weibull distributions will be considered. The performance of the two non-informative priors will be investigated. An application of two failure time distributions will be carried out. To meet these objectives, the failure rate and the reliability functions of failure time distributions are calculated. Two non-informative priors, the Jeffreys prior and the general divergence prior, and the corresponding posteriors are derived for each distribution. Simulation studies for each distribution are carried out, where the coverage rates and credible intervals lengths are calculated and the results of these are discussed. The gamma distribution and the Weibull distribution are applied to failure time data.The Jeffreys prior is found to have better coverage rate than the general divergence prior. The general divergence shows undercoverage when used with the Rayleigh distribution. The Jeffreys prior produces coverage rates that are conservative when used with the exponential distribution. These priors give, on average, the same average interval lengths and increase as the value of the parameter increases. Both priors perform similar when used with the gamma distribution and the Weibull distribution. A thorough discussion and review of human reliability analysis (HRA) techniques will be considered. Twenty human reliability analysis (HRA) techniques are discussed; providing a background, description and advantages and disadvantages for each. Case studies in the nuclear industry, railway industry, and aviation industry are presented to show the importance and applications of HRA. Human error has been shown to be the major contributor to system failure.
- Full Text:
- Date Issued: 2017
- Authors: Mafu, Masakheke
- Date: 2017
- Subjects: Bayesian statistical decision theory , Reliability (Engineering) , Human machine systems , Probabilities , Markov processes
- Language: English
- Type: Thesis , Masters , MSc
- Identifier: http://hdl.handle.net/10962/6280 , vital:21077
- Description: Most reliability analyses involve the analysis of binary data. Practitioners in the field of reliability place great emphasis on analysing the time periods over which items or systems function (failure time analyses), which make use of different statistical models. This study intends to introduce, review and investigate four statistical models for modeling failure times of non-repairable items, and to utilise a Bayesian methodology to achieve this. The exponential, Rayleigh, gamma and Weibull distributions will be considered. The performance of the two non-informative priors will be investigated. An application of two failure time distributions will be carried out. To meet these objectives, the failure rate and the reliability functions of failure time distributions are calculated. Two non-informative priors, the Jeffreys prior and the general divergence prior, and the corresponding posteriors are derived for each distribution. Simulation studies for each distribution are carried out, where the coverage rates and credible intervals lengths are calculated and the results of these are discussed. The gamma distribution and the Weibull distribution are applied to failure time data.The Jeffreys prior is found to have better coverage rate than the general divergence prior. The general divergence shows undercoverage when used with the Rayleigh distribution. The Jeffreys prior produces coverage rates that are conservative when used with the exponential distribution. These priors give, on average, the same average interval lengths and increase as the value of the parameter increases. Both priors perform similar when used with the gamma distribution and the Weibull distribution. A thorough discussion and review of human reliability analysis (HRA) techniques will be considered. Twenty human reliability analysis (HRA) techniques are discussed; providing a background, description and advantages and disadvantages for each. Case studies in the nuclear industry, railway industry, and aviation industry are presented to show the importance and applications of HRA. Human error has been shown to be the major contributor to system failure.
- Full Text:
- Date Issued: 2017
The exploration of ARF1 screening assays to determine the drug status of ARF1 in cancer and malaria
- Authors: Ntlantsana, Apelele
- Date: 2020
- Subjects: ADP ribosylation , Golgi apparatus , Guanosine triphosphatase , G proteins , Malariotherapy , Malaria -- Research , Cancer -- Chemotherapy , Malaria -- Chemotherpay
- Language: English
- Type: text , Thesis , Masters , MSc
- Identifier: http://hdl.handle.net/10962/167232 , vital:41458
- Description: ARF GTPases are key regulators of the secretory and endocytic pathways. ARF1 is involved in the secretory pathway. ARF1 has been implicated in the endoplasmic reticulum to Golgi transport, function of the Golgi apparatus and transport from the trans-Golgi network to endosomes. ARFs cycle between active GTP-bound and inactive GDP-bound conformations. GDP/GTP cycling is regulated by large families of guanine nucleotide exchange factors (GEFs) and GTPase activating proteins (GAPs). ARF GEFs facilitate the activation of ARFs by mediating the exchange of GDP for GTP, while ARF GAPs terminate ARF function by stimulating the hydrolysis of the terminal phosphate group of GTP. Based on existing evidence gained from gene manipulation and cell biological investigations, ARF1 has been shown to be fundamentally important for cancer cell proliferation and metastasis and may be a promising target for the development of anti-cancer drugs. Additionally, the conservation of ARFs in eukaryotic organisms leads to an interesting question of whether a single drug target can be used to target multiple diseases. In this case, can a human cancer drug employed for cancer therapy be used in anti-malarial drug therapies? To confirm the drug target status of ARFs using chemical validation experiments, novel inhibitory compounds are needed. This requires the development of complex in vitro protein- protein interaction assays that can be used to screen chemical libraries for ARF GTPase inhibitors. In this study, we developed a fluorescence resonance energy transfer (FRET) assay and a novel in vitro colorimetric plate-based assay to detect the activation status of truncated human and Plasmodium falciparum ARF1. In the case of the FRET assay, active (GTP-bound) and inactive (GDP-bound) ARF1 could be distinguished with Z-factor values >0.5, suggesting that further development of the assay format to identify GEF and GAP inhibitors may be feasible. In the case of the colorimetric assay, robust signals could be detected and the assay was useful for detecting the activation status of ARF1. However, although the activation of ARF1 by the Sec7 domains of the BIG1 and ARNO was detectable, signals were not robust enough to employ in screening campaigns.
- Full Text:
- Date Issued: 2020
- Authors: Ntlantsana, Apelele
- Date: 2020
- Subjects: ADP ribosylation , Golgi apparatus , Guanosine triphosphatase , G proteins , Malariotherapy , Malaria -- Research , Cancer -- Chemotherapy , Malaria -- Chemotherpay
- Language: English
- Type: text , Thesis , Masters , MSc
- Identifier: http://hdl.handle.net/10962/167232 , vital:41458
- Description: ARF GTPases are key regulators of the secretory and endocytic pathways. ARF1 is involved in the secretory pathway. ARF1 has been implicated in the endoplasmic reticulum to Golgi transport, function of the Golgi apparatus and transport from the trans-Golgi network to endosomes. ARFs cycle between active GTP-bound and inactive GDP-bound conformations. GDP/GTP cycling is regulated by large families of guanine nucleotide exchange factors (GEFs) and GTPase activating proteins (GAPs). ARF GEFs facilitate the activation of ARFs by mediating the exchange of GDP for GTP, while ARF GAPs terminate ARF function by stimulating the hydrolysis of the terminal phosphate group of GTP. Based on existing evidence gained from gene manipulation and cell biological investigations, ARF1 has been shown to be fundamentally important for cancer cell proliferation and metastasis and may be a promising target for the development of anti-cancer drugs. Additionally, the conservation of ARFs in eukaryotic organisms leads to an interesting question of whether a single drug target can be used to target multiple diseases. In this case, can a human cancer drug employed for cancer therapy be used in anti-malarial drug therapies? To confirm the drug target status of ARFs using chemical validation experiments, novel inhibitory compounds are needed. This requires the development of complex in vitro protein- protein interaction assays that can be used to screen chemical libraries for ARF GTPase inhibitors. In this study, we developed a fluorescence resonance energy transfer (FRET) assay and a novel in vitro colorimetric plate-based assay to detect the activation status of truncated human and Plasmodium falciparum ARF1. In the case of the FRET assay, active (GTP-bound) and inactive (GDP-bound) ARF1 could be distinguished with Z-factor values >0.5, suggesting that further development of the assay format to identify GEF and GAP inhibitors may be feasible. In the case of the colorimetric assay, robust signals could be detected and the assay was useful for detecting the activation status of ARF1. However, although the activation of ARF1 by the Sec7 domains of the BIG1 and ARNO was detectable, signals were not robust enough to employ in screening campaigns.
- Full Text:
- Date Issued: 2020
Strength and conditioning practices of high school rugby coaches: a South African context
- Authors: Robinson, Bradley Charles
- Date: 2018
- Subjects: Rugby football coaches South Africa , Rugby football Coaching , Rugby football Physiological aspects , Rugby football Training , High school students Social conditions
- Language: English
- Type: text , Thesis , Masters , MSc
- Identifier: http://hdl.handle.net/10962/63459 , vital:28413
- Description: Although the sport of rugby union is well established, the strength and conditioning practices of high school level players are not well known. Therefore, the purpose of this study was to examine the current strength and conditioning practices that coaches implement at South African high school level rugby. A secondary purpose was to compare practices between different types of schooling systems available in South Africa. An online survey or in person interview (depending on the school), adapted from previous strength and conditioning questionnaires, was conducted with 43 responses; including 28 schools among the top 100 rugby schools in South Africa for 2016 and 15 no-fee paying public schools in the Eastern Cape Province of South Africa. Results indicated that the top 100 rugby schools implement conditioning practices similar to the best-known international practices compared to no-fee paying schools who lacked the knowledge and skills in various strength and conditioning principles. It was found that all no-fee paying school coaches had insufficient qualifications to administer the correct training techniques. Coaches at all schools lacked the appropriate knowledge on injury prevention and scientifically based training programmes. It was concluded that education and skills around the best strength and conditioning practices for school level coaches needs to be improved and particularly in less privileged schools. The main goal being to reduce the risk of injury and improve performance across all sectors of the rugby playing population within the country. This was deemed crucial to the transformation goals set out by the South African Rugby Union, which would benefit from player development in lower socioeconomic schools.
- Full Text:
- Date Issued: 2018
- Authors: Robinson, Bradley Charles
- Date: 2018
- Subjects: Rugby football coaches South Africa , Rugby football Coaching , Rugby football Physiological aspects , Rugby football Training , High school students Social conditions
- Language: English
- Type: text , Thesis , Masters , MSc
- Identifier: http://hdl.handle.net/10962/63459 , vital:28413
- Description: Although the sport of rugby union is well established, the strength and conditioning practices of high school level players are not well known. Therefore, the purpose of this study was to examine the current strength and conditioning practices that coaches implement at South African high school level rugby. A secondary purpose was to compare practices between different types of schooling systems available in South Africa. An online survey or in person interview (depending on the school), adapted from previous strength and conditioning questionnaires, was conducted with 43 responses; including 28 schools among the top 100 rugby schools in South Africa for 2016 and 15 no-fee paying public schools in the Eastern Cape Province of South Africa. Results indicated that the top 100 rugby schools implement conditioning practices similar to the best-known international practices compared to no-fee paying schools who lacked the knowledge and skills in various strength and conditioning principles. It was found that all no-fee paying school coaches had insufficient qualifications to administer the correct training techniques. Coaches at all schools lacked the appropriate knowledge on injury prevention and scientifically based training programmes. It was concluded that education and skills around the best strength and conditioning practices for school level coaches needs to be improved and particularly in less privileged schools. The main goal being to reduce the risk of injury and improve performance across all sectors of the rugby playing population within the country. This was deemed crucial to the transformation goals set out by the South African Rugby Union, which would benefit from player development in lower socioeconomic schools.
- Full Text:
- Date Issued: 2018
A study of South African computer users' password usage habits and attitude towards password security
- Authors: Friendman, Brandon
- Date: 2014
- Subjects: Computers -- Access control -- Passwords , Computer users -- Attitudes , Internet -- Access control , Internet -- Security measures , Internet -- Management , Data protection
- Language: English
- Type: text , Thesis , Masters , MSc
- Identifier: vital:4700
- Description: The challenge of having to create and remember a secure password for each user account has become a problem for many computer users and can lead to bad password management practices. Simpler and less secure passwords are often selected and are regularly reused across multiple user accounts. Computer users within corporations and institutions are subject to password policies, policies which require users to create passwords of a specified length and composition and change passwords regularly. These policies often prevent users from reusing previous selected passwords. Security vendors and professionals have sought to improve or even replace password authentication. Technologies such as multi-factor authentication and single sign-on have been developed to complement or even replace password authentication. The objective of the study was to investigate the password habits of South African computer and internet users. The aim was to assess their attitudes toward password security, to determine whether password policies a↵ect the manner in which they manage their passwords and to investigate their exposure to alternate authentication technologies. The results from the online survey demonstrated that password practices of the participants across their professional and personal contexts were generally insecure. Participants often used shorter, simpler and ultimately less secure passwords. Participants would try to memorise all of their passwords or reuse the same password on most of their accounts. Many participants had not received any security awareness training, and additional security technologies (such as multi-factor authentication or password managers) were seldom used or provided to them. The password policies encountered by the participants in their organisations did little towards encouraging the users to apply more secure password practices. Users lack the knowledge and understanding about password security as they had received little or no training pertaining to it.
- Full Text:
- Date Issued: 2014
- Authors: Friendman, Brandon
- Date: 2014
- Subjects: Computers -- Access control -- Passwords , Computer users -- Attitudes , Internet -- Access control , Internet -- Security measures , Internet -- Management , Data protection
- Language: English
- Type: text , Thesis , Masters , MSc
- Identifier: vital:4700
- Description: The challenge of having to create and remember a secure password for each user account has become a problem for many computer users and can lead to bad password management practices. Simpler and less secure passwords are often selected and are regularly reused across multiple user accounts. Computer users within corporations and institutions are subject to password policies, policies which require users to create passwords of a specified length and composition and change passwords regularly. These policies often prevent users from reusing previous selected passwords. Security vendors and professionals have sought to improve or even replace password authentication. Technologies such as multi-factor authentication and single sign-on have been developed to complement or even replace password authentication. The objective of the study was to investigate the password habits of South African computer and internet users. The aim was to assess their attitudes toward password security, to determine whether password policies a↵ect the manner in which they manage their passwords and to investigate their exposure to alternate authentication technologies. The results from the online survey demonstrated that password practices of the participants across their professional and personal contexts were generally insecure. Participants often used shorter, simpler and ultimately less secure passwords. Participants would try to memorise all of their passwords or reuse the same password on most of their accounts. Many participants had not received any security awareness training, and additional security technologies (such as multi-factor authentication or password managers) were seldom used or provided to them. The password policies encountered by the participants in their organisations did little towards encouraging the users to apply more secure password practices. Users lack the knowledge and understanding about password security as they had received little or no training pertaining to it.
- Full Text:
- Date Issued: 2014
Understanding the underlying resistance mechanism of Mycobacterium tuberculosis against Rifampicin by analyzing mutant DNA - directed RNA polymerase proteins via bioinformatics approaches
- Authors: Monama, Mokgerwa Zacharia
- Date: 2020
- Subjects: Mycobacterium tuberculosis , Rifampin , Drug resistance , Homology (Biology) , Tuberculosis -- Chemotherapy
- Language: English
- Type: text , Thesis , Masters , MSc
- Identifier: http://hdl.handle.net/10962/167508 , vital:41487
- Description: Tuberculosis or TB is an airborne disease caused by the non-motile bacilli, Mycobacterium tuberculosis (MTB). There are two main forms of TB, namely, latent TB or LTB, asymptomatic and non-contagious version which according to the World Health Organization (WHO) is estimated to afflict over a third of the world’s population; and active TB or ATB, a symptomatic and contagious version which continues to spread, affecting millions worldwide. With the already high reported prevalence of TB, the emergence of drug-resistant strains has prompted the development of novel approaches to enhance the efficacy of known drugs and a desperate search for novel compounds to combat MTB infections. It was for this very purpose that this study was conducted. A look into the resistance mechanism of Rifampicin (Rifampin or RIF), one of the more potent first-line drugs, might prove beneficial in predicting the consequence of an introduced mutation (which usually occur as single nucleotide polymorphisms or SNPs) and perhaps even overcome it using appropriate therapeutic interventions that improve RIF’s efficacy. To accomplish this task, models of acceptable quality were generated for the WT and clinically relevant, RIF resistance conferring, SNPs occurring at codon positions D516, H526 and S531 (E .coli numbering system) using MODELLER. The models were accordingly ranked using GA341 and z-DOPE score, and subsequently validated with QMEAN, PROCHECK and VERIFY3D. MD simulations spanning 100 ns were run for RIF-bound (complex) and RIF-free (holo) DNA-directed RNA polymerase (DDRP) protein systems for the WT and SNP mutants using GROMACS. The MD frames were analyzed using RMSD, Rg and RMSF. For further analysis, MD-TASK was used to analyze the calculated dynamic residue networks (DRNs) from the generated MD frames, determining both change in average shortest path (ΔL) and betweenness centrality (ΔBC). The RMSD analysis revealed that all of the SNP complex models displayed a level instability higher than that of the WT complex. A majority of the SNP complex models were also observed to have similar compactness to the WT holo when looking at the calculated Rg. The RMSF results also hinted towards possible physiological consequences of the mutations (generally referred to as a fitness cost) highlighted by the increased fluctuations of the zinc-binding domain and the MTB SI α helical coiled coil. For the first time, to the knowledge of the authors, DRN analysis was employed for the DDRP protein for both holo and complex systems, revealing insightful information about the residues that play a key role in the change in distance between residue pairs along with residues that play an essential role in protein communication within the calculated RIN. Overall, the data supported the conclusions drawn by a recent study that only concentrated on RIF-resistance in rpoB models which suggested that the binding pocket for the SNP models may result in the changed coordination of RIF which may be the main contributor to its impaired efficacy.
- Full Text:
- Date Issued: 2020
- Authors: Monama, Mokgerwa Zacharia
- Date: 2020
- Subjects: Mycobacterium tuberculosis , Rifampin , Drug resistance , Homology (Biology) , Tuberculosis -- Chemotherapy
- Language: English
- Type: text , Thesis , Masters , MSc
- Identifier: http://hdl.handle.net/10962/167508 , vital:41487
- Description: Tuberculosis or TB is an airborne disease caused by the non-motile bacilli, Mycobacterium tuberculosis (MTB). There are two main forms of TB, namely, latent TB or LTB, asymptomatic and non-contagious version which according to the World Health Organization (WHO) is estimated to afflict over a third of the world’s population; and active TB or ATB, a symptomatic and contagious version which continues to spread, affecting millions worldwide. With the already high reported prevalence of TB, the emergence of drug-resistant strains has prompted the development of novel approaches to enhance the efficacy of known drugs and a desperate search for novel compounds to combat MTB infections. It was for this very purpose that this study was conducted. A look into the resistance mechanism of Rifampicin (Rifampin or RIF), one of the more potent first-line drugs, might prove beneficial in predicting the consequence of an introduced mutation (which usually occur as single nucleotide polymorphisms or SNPs) and perhaps even overcome it using appropriate therapeutic interventions that improve RIF’s efficacy. To accomplish this task, models of acceptable quality were generated for the WT and clinically relevant, RIF resistance conferring, SNPs occurring at codon positions D516, H526 and S531 (E .coli numbering system) using MODELLER. The models were accordingly ranked using GA341 and z-DOPE score, and subsequently validated with QMEAN, PROCHECK and VERIFY3D. MD simulations spanning 100 ns were run for RIF-bound (complex) and RIF-free (holo) DNA-directed RNA polymerase (DDRP) protein systems for the WT and SNP mutants using GROMACS. The MD frames were analyzed using RMSD, Rg and RMSF. For further analysis, MD-TASK was used to analyze the calculated dynamic residue networks (DRNs) from the generated MD frames, determining both change in average shortest path (ΔL) and betweenness centrality (ΔBC). The RMSD analysis revealed that all of the SNP complex models displayed a level instability higher than that of the WT complex. A majority of the SNP complex models were also observed to have similar compactness to the WT holo when looking at the calculated Rg. The RMSF results also hinted towards possible physiological consequences of the mutations (generally referred to as a fitness cost) highlighted by the increased fluctuations of the zinc-binding domain and the MTB SI α helical coiled coil. For the first time, to the knowledge of the authors, DRN analysis was employed for the DDRP protein for both holo and complex systems, revealing insightful information about the residues that play a key role in the change in distance between residue pairs along with residues that play an essential role in protein communication within the calculated RIN. Overall, the data supported the conclusions drawn by a recent study that only concentrated on RIF-resistance in rpoB models which suggested that the binding pocket for the SNP models may result in the changed coordination of RIF which may be the main contributor to its impaired efficacy.
- Full Text:
- Date Issued: 2020
Changes in energy use patterns in the Bushbuckridge Lowveld of the Limpopo Province, South Africa: eleven years on
- Authors: Madubansi, Mainza
- Date: 2004
- Subjects: Energy consumption -- South Africa -- Limpopo
- Language: English
- Type: Thesis , Masters , MSc
- Identifier: vital:4756 , http://hdl.handle.net/10962/d1007139 , Energy consumption -- South Africa -- Limpopo
- Description: This research reports on the energy transition that has taken place in the Bushbuckridge district between 1991 and 2002. It is a follow up to a similar study that was done in 1991 investigating a number of aspects of energy use. It uses the 1991 study as a baseline and aims to explore how the passage of time, growth of the local population and changes in incomes and the availability of fuels have affected the patterns of fuel use in the region in the past eleven years. A structured interview approach was used for most aspects of the study. The interview schedule included sections on types, amounts and reasons for use and non-use of 13 different energy sources as well as data on income levels, household size and other economic parameters. Analysis of the consumption patterns of the different fuel types revealed that between the two survey periods, households in the sample settlements went through some pronounced changes in patterns of fuel use, particularly those that had acquired electricity. The introduction of electricity in the region had certainly played a major role in spurring the energy transition. Fuels that were previously used for lighting, powering entertainment appliances and refrigeration had been displaced by electricity. In terms of cooking and other thermal application, however, the vast majority of households in all the sample settlements continued using fuelwood and complemented it to a lesser extent with paraffin and electricity. In both surveys, the use or non-use of available fuels in the region was influenced by several factors. Common reasons for non-use of certain fuel types included expense, lack of appliances, the risk involved in using such fuels and the preference for other fuels. Reasons for use were mainly related to the low cost of the fuel and the fuel’s ability to meet particular end uses. Although incomes in the region had increased between 1991 and 2002, they were still below the poverty line. Activities from which households obtained their income remained the same. Old age pension, migrant wages and the informal sector remained the largest contributors of income to most households. Other indicators of relative wealth and poverty, like ownership of vehicles, bicycles and beds remained the same.
- Full Text:
- Date Issued: 2004
- Authors: Madubansi, Mainza
- Date: 2004
- Subjects: Energy consumption -- South Africa -- Limpopo
- Language: English
- Type: Thesis , Masters , MSc
- Identifier: vital:4756 , http://hdl.handle.net/10962/d1007139 , Energy consumption -- South Africa -- Limpopo
- Description: This research reports on the energy transition that has taken place in the Bushbuckridge district between 1991 and 2002. It is a follow up to a similar study that was done in 1991 investigating a number of aspects of energy use. It uses the 1991 study as a baseline and aims to explore how the passage of time, growth of the local population and changes in incomes and the availability of fuels have affected the patterns of fuel use in the region in the past eleven years. A structured interview approach was used for most aspects of the study. The interview schedule included sections on types, amounts and reasons for use and non-use of 13 different energy sources as well as data on income levels, household size and other economic parameters. Analysis of the consumption patterns of the different fuel types revealed that between the two survey periods, households in the sample settlements went through some pronounced changes in patterns of fuel use, particularly those that had acquired electricity. The introduction of electricity in the region had certainly played a major role in spurring the energy transition. Fuels that were previously used for lighting, powering entertainment appliances and refrigeration had been displaced by electricity. In terms of cooking and other thermal application, however, the vast majority of households in all the sample settlements continued using fuelwood and complemented it to a lesser extent with paraffin and electricity. In both surveys, the use or non-use of available fuels in the region was influenced by several factors. Common reasons for non-use of certain fuel types included expense, lack of appliances, the risk involved in using such fuels and the preference for other fuels. Reasons for use were mainly related to the low cost of the fuel and the fuel’s ability to meet particular end uses. Although incomes in the region had increased between 1991 and 2002, they were still below the poverty line. Activities from which households obtained their income remained the same. Old age pension, migrant wages and the informal sector remained the largest contributors of income to most households. Other indicators of relative wealth and poverty, like ownership of vehicles, bicycles and beds remained the same.
- Full Text:
- Date Issued: 2004
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