Assessing the invasive status and reproductive ecology of two Crataegus species in South Africa; Crataegus monogyna Jacq and C. mexicana DC
- Authors: Tshilingalinga, Sydney
- Date: 2021-03
- Subjects: Crataegus monogyna , Nonindigenous pests , Biological invasions
- Language: English
- Type: Master's theses , text
- Identifier: http://hdl.handle.net/10353/20904 , vital:46740
- Description: In South Africa different species, from the genus Crataegus, including Crataegus monogyna Jacq and C. mexicana DC have been introduced for various reasons in the past. Populations of these plants have now established in multiple provinces. However, the invasive status, risk and insect pollinators that promote their reproduction and dispersal have never been studied in South Africa. This study was aimed at 1) Assessing the risk of, and mapping two Crataegus species, Crataegus monogyna Jacq and C. mexicana DC in South Africa, 2) Determining the role and effectiveness of insects pollinators to fruiting of C. monogyna and C. mexicana, 3) Identifying flower visitors of C. monogyna and C. mexicana, and 4) documenting potential dispersal vectors for both species in the Eastern Cape Province. A framework entitled “Framework and guideline for conducting risk analysis under NEM: BA Alien and Invasive Species Regulation of 2014” was used to assess the risk of the two Crataegus spp, and we conducted field trips to various provinces in SA to map their distribution. The author conducted an exclusion experiment to determine the role and effectiveness of insect pollinators. Observations were conducted to identify flower visitors and potential dispersal vectors for both species. The risk analysis results suggested that both species pose a high risk of becoming invasive in South Africa. The eradication feasibility of both species was found to be medium with C. monogyna having an eradication feasibility score of 5 and C. mexicana having an eradication feasibility score of 4. This meant that there was a 50 percent chance for both species to be eradicated in South Africa currently. After a thorough risk analysis, it was recommended that both species be listed under category 1b on the National Environmental Management Biodiversity Act. Category 1b species are invasive species that need to be controlled, and if possible, they must be eradicated, trading of species from this category is not allowed. Crataegus mexicana was found to be widespread in South Africa with ten relatively small populations distributed in 5 provinces; Limpopo, Mpumalanga, KwaZulu-Natal, Free State and Eastern Cape Province. Crataegus monogyna was found not to be widespread in South Africa, with only three populations found in the Eastern Cape Province. Insect pollinators contribute to the fruiting of both species in SA. However, the exotic plants were also observed to be able to self-pollinate when insects are excluded. Flowers of C. monogyna were visited by various insect species from orders Lepidoptera, Hymenoptera, Coleoptera and Diptera, while C. mexicana is visited by species from the order Hymenoptera, Diptera, Lepidoptera and Coleoptera. Seventy-seven percent (77 percent) of potential dispersal vectors observed for C. monogyna were birds, and 15 percent were mammals. For C. mexicana, 71 percent of potential dispersal vectors observed were mammals, and 29 percent were birds. Crataegus monogyna and C. mexicana are emerging invasive alien species in South Africa, and not much is known about them. Although the two species are listed as invasive weeds in South Africa, very little is known about their invasive status in other parts of the world. This study has managed to give baseline information and data about both species which are already in South Africa. The baseline information and data include the population structure of both species, their distribution, the risk they pose to South Africa biodiversity and their reproduction ecology. Currently, there are no management plans in place for both species in South Africa, and this is because they are not listed yet in the National Environmental Management Biodiversity Act of South Africa. However, this study recommends that current populations continue to be monitored, awareness of both species in various provinces be initiated to help in the discovery of new and emerging populations, and management options of large populations developed in the future. , Thesis (MSc) (Entomology) -- University of Fort Hare, 2021
- Full Text:
- Date Issued: 2021-03
Assessing the local awareness and perception of invasive alien plants: A case study of Port St Johns Local Municipality, Eastern Cape Province, South Africa
- Authors: Somkala, Avela Abongile
- Date: 2021-10
- Subjects: Alien plants , Invasive plants
- Language: English
- Type: Master's theses , text
- Identifier: http://hdl.handle.net/10353/22600 , vital:52595
- Description: Invasive alien plants (IAPs) are introduced species that constitute a self-sustaining population, consistently producing offspring in large numbers and at considerable distances from the parent plants with the potential to spread over a large area. Species invasions are one of the main conservation threats today and have caused modification of ecosystems, particularly in coastal areas. Therefore, Port St Johns Local Municipality (PSJ LM) was an appropriate study site to evaluate the local awareness and perceptions of IAPs. The study investigated the local community’s perceptions of invasive alien plants' uses and ecological impacts. Information about the local awareness and perceptions of invasive alien plant species in PSJ LM was gathered through semi-structured interviews, observation and guided field walks with 120 participants between February and April 2021. The participants included 30 people working on the alien plant eradication project in PSJ LM (Wards 1, 2 and 3) and 90 randomly selected community members. The data collected were entered in Microsoft Excel 2016 programme and analyzed for descriptive statistical patterns using Statistical Package for Social Studies (SPSS) version 22.0. Biological invasion by IAPs was ubiquitously perceived, with participants working on invasive alien plant eradication project in the area exhibiting more scientifically based knowledge on IAPs than ordinary community members. Invasive alien plants in the area appear to have adverse environmental and socio-economic impacts, as the participants are not benefiting from these plant species. Similarly, costs of eradicating these species were also acknowledged. The ability of local community members to identify IAPs is vital in effective management of the spread of these species. A total of seven invasive IAPs were recorded. Evaluating the perceptions of local people towards IAPs provides valuable insights for development planning and future management programmes focusing on biological invasions. The study will provide a basis for an enabling policy and institutional environment that provides a coherent framework for the sustainable management of IAPs in the Eastern Cape Province. , Thesis (MPhil) -- Faculty of Science and Agriculture, 2021
- Full Text:
- Date Issued: 2021-10
Assessment of anti-urease and consequential inhibitory potential of South African honey extracts on the multiplication of drug-resistant, vacA and cagA positive helicobacter pylori strains under acidic conditions
- Authors: Dube, Callote
- Date: 2017
- Subjects: Helicobacter pylori Drug resistance in microorganisms Honey -- Therapeutic use
- Language: English
- Type: Thesis , Doctoral , PhD
- Identifier: http://hdl.handle.net/10353/7787 , vital:30764
- Description: Helicobacter pylori, a neutralophile chronically infects the gastric stomach of more than half of the world’s population. Infection with the organism is associated with acute or chronic duodenal/gastric ulcer disease, gastritis, gastric adenocarcinoma, mucosa-associated tissue lymphoma (MALT) and primary B-cell gastric lymphoma and has been grouped as a class one carcinogen by the World Health Organisation (WHO). Prevalence of this organism is very high in developing countries especially in Africa, including South Africa. H. pylori treatment using the common first and second line regimens, triple therapy with two antibiotics and a proton pump inhibitor (PPI) is showing inefficiency due to increasing drug resistance. However, newly developed treatment regimens seem to be more expensive and are accompanied by more side effects. Honey contains phytochemicals which are a wealthy source of biologically active compounds some of which have been put into good use in the pharmaceutical industry. Pathogenesis of H. pylori infection in the human stomach relies on several virulence factors which include the urease enzyme, cagA and vacA. The urease enzyme actively hydrolyses urea to produce ammonia an important by-product involved in pH regulation favouring the survival of the organism in the acidic human stomach. This study therefore focuses on screening for anti-urease solvent extracts of South African honey, and evaluate whether inhibition of urease offsets the growth of H. pylori under acidic conditions. Locally produced natural honeys; Bush honey, Raw honey, Gold Crest honey, Q Bee honey, Little Bee honey, Fleures honey-radurised, Siyakholwa pure honey and Manuka honey; an import from New Zealand were purchased and the method by Syazana et al. (2010) was used for the extraction of compounds in honey. A standard strain ATCC 43526 (American Type Culture Collection, Manassas, VA, USA) and 48 pure cultures obtained from clinical isolates cultured from gastric corpus biopsy specimen of patients with gastric morbidities who were ix visiting the endoscopy unit in Livingstone Hospital, Port Elizabeth between June 2008 to December 2008 were initially used as source of urease enzyme as per extraction method done by Amin et al. (2013), but with modifications. Prior to urease extraction, H. pylori strains were identified by biochemical tests (urease, catalase, oxidase, Gram stain), confirmed by PCR targeting the glmM gene (140 bp) and drug resistance profiling was done on all the 48 strains according to Seanego et al. (2012). The screening for anti-urease active compounds was done according to Kaltwasser et al. (1966), a method relying on the reduction of NADH in a coupled urease dehydrogenase (GDH) system. Acetohydroxamic acid was used as a standard inhibitor. Prevalence of cytotoxin-associated gene A (cagA) gene and vacuolating cytotoxin gene A (vacA) gene was determined among all 48 clinical samples. The standard strains of H. pylori, X47 (cagA positive), J99 (vacA s1m1) and Tx30a (s2m2) were used as positive controls. H. pylori’s growth was then monitored under acidic pH in a cocktail spiked with anti-urease compounds (test samples) and in a cocktail without anti-urease compounds (negative control). Acetohydroxamic acid was used as a standard urease inhibitor. H. pylori multiplication was monitored in Brain Heart Infusion Broth (BHIB) adjusted to pH of 2, 3, 4, 5, 6 and 7. The strain MP01 was used as a standard urease negative strain while X47 and J99 were used as positive standards for cagA and vacA s1m1 respectively. The compounds that had anti-urease activity and were successful towards suppressing the multiplication of H. pylori under acidic environment, all other factors optimised, were subjected to gas chromatograph mass spectrometry (GC-MS) and liquid chromatograph spectrometry (LCMS) to determine volatile compounds and drugs in honey extracts respectively. The findings of this study revealed that at a concentration of 50 mg/mL, urease inhibition by petroleum ether extracts of Gold Crest and Fleures honey, hexane extracts of Little Bee and Manuka honey, and chloroform extracts of Bush honey and Q Bee honey had a range above or equal to 50 percent and there was no significance difference in urease inhibition percentage (I percent) of urease from different sources including that extracted from drug resistant H. pylori (p >0.05). Virulence factors are important for the pathogenesis of H. pylori. All the 48 clinical isolates were glmM (140 bp) positive and cagA was detected in 97.9 percent of the test isolates. The vacA gene was detected in all isolates but with different subtypes. The vacA allelic combination s1m1 was detected in 75 percent of the test isolates and s1m2 allelic combination was detected in 16.7 percent of the test isolates while the combination s2m2 was detected in 8.3 percent of the test isolates. None of the test isolates possessed the allelic combination s2m1. When H. pylori multiplication was monitored under acidic conditions in the presence of anti-urease active compounds, it was revealed that anti-urease active compounds in honey are capable of inhibiting the normal multiplication of H. pylori strains that are cagA positive, vacA positive and drug resistant. The GC-MS analysis showed that Fleures honey (urease I percent = 67.8 – 68.5 percent) and Gold Crest honey (urease I percent = 50.9 percent – 53.3 percent), all petroleum ether extracts had 27 and 26 volatile compounds. The hexane extract of Manuka honey (urease I percent = 50.0 – 53.2) had 43 compounds detected. The chloroform extract of Q Bee (urease I percent = 64.2 – 66.2 percent) had 13 volatile compounds detected. All the volatile compounds considered as representative samples of GC-MS analysis had a spectral matching ≥ 90 percent with the NIST11 library. However, the majority of compounds that were detected by LC-MS in representative honey extracts include vardenafil, urapidil, hydrocortisone, e.t.c which are drugs commonly used in the treatment of different ailments or infections that affect human beings. In addition, two xi drugs, sulfaquinoxaline and hydroxyquinoline which are used in veterinary medicine and antiseptic, disinfectant and pesticide applications in agricultural activities were detected in Little Bee honey. We therefore conclude that inhibition of urease has a bactericidal effect on drug resistant, cagA positive and vacA positive H. pylori strains growing under acidic environment.
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- Date Issued: 2017
Assessment of antibacterial potentials of Garcinia Kola seed extracts and their interactions with antibiotics
- Authors: Sibanda, Thulani https://orcid.org/0000-0002-6422-2871
- Date: 2007
- Subjects: Drug resistance in microorganisms http://id.loc.gov/authorities/subjects/sh85039709 , Garcinia http://id.loc.gov/authorities/subjects/sh85053063 , Antibiotics http://id.loc.gov/authorities/subjects/sh85005638
- Language: English
- Type: Master's theses , text
- Identifier: http://hdl.handle.net/10353/19236 , vital:43038
- Description: The antibacterial potency of the extracts of the seed of Garcinia kola (bitter kola) was investigated in this study against a panel of referenced, environmental and clinical bacterial strains. The killing rates of the active extract as well as their potential for combination antibacterial therapy with standard antibiotics were also elucidated using standard procedures. The aqueous and acetone extracts of the seed were screened for activity against 27 bacterial isolates. The aqueous extract exhibited activity mainly against Gram positive organisms with Minimum inhibitory concentration (MIC) values ranging from 5 mgml-1 – 20 mgml-1, while the acetone extract showed activity against both Gram negative and Gram positive organisms with MIC values ranging from 10 mgml-1 - 0.156 mgml-1. The acetone extract also showed rapid bactericidal activity against Staphylococcus aureus ATCC 6538 with a 3.097 Log10 reduction in counts within 4 hours at 0.3125 mgml-1 and a 1.582 Log10 reduction against Proteus vulgaris CSIR 0030 at 5 mgml-1 after 1 hour. In addition, the aqueous, methanol and acetone extracts of the seeds also exhibited activity against four clinical strains of Staphylococcus isolated from wound sepsis specimens. The MIC values for the aqueous extract were 10 mgml-1 for all the isolates while the acetone and methanol extracts had lower values ranging from 0.3125 - 0.625 mgml-1. The acetone extract was strongly bactericidal against Staphylococcus aureus OKOH3 resulting in a 2.70 Log10 reduction in counts at 1.25 mgml-1 within 4 hours of exposure and a complete elimination of the organism after 8 hours. The bactericidal activity of the same extract against Staphylococcus aureus OKOH1 was weak, achieving only a 2.92 Log10 reduction in counts at 1.25 mgml-1 (4× MIC) in 24 hours. In the test for interactions between the acetone extract of the seeds and antibiotics, synergistic interactions were observed largely against Gram positive organisms using the FIC indices, (indices of 0.52 - 0.875) with combinations against Gram negatives yielding largely antagonistic interactions (indices of 2.0 to 5.0). Synergy (≥ 1000 times or ≥ 3 Log10 potentiation of the bactericidal activity) against both Gram negative and Gram positive organisms was detected by time kill assays mainly involving the antibiotics tetracycline, chloramphenicol, amoxycillin and penicillin G. Combinations involving erythromycin and ciprofloxacin consistently gave antagonistic or indifferent interactions. We conclude that the acetone extract of Garcinia kola seeds possess strong bactericidal activities against both Gram positive and Gram negative organisms and can be therapeutically useful in the treatment of bacterial infections including the problematic staphylococcal wound infections. In addition, the acetone extract can be a potential source of broad spectrum resistance modifying compounds that can potentially improve the performance of antibiotics in the treatment of drug resistant infections. , Thesis (MSc)-- Microbiology, University of Fort Hare, 2007
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- Date Issued: 2007
Assessment of antibiotic production by some marine actinomycetes belonging to the genera norcadia, saccharopolyspora and kibdellosporangium.
- Authors: Koba, Siziwe (https://orcid.org/0000-0002-6761-6403)
- Date: 2010
- Subjects: Actinobacteria , Bacteria , Actinomycetales
- Language: English
- Type: Master's theses , text
- Identifier: http://hdl.handle.net/10353/25811 , vital:64488
- Description: Antibacterial potency of the extracts of the three marine actinomycetes strains which were isolated in the Nahoon Beach and tentatively identified as the genera Norcadia, Kibdellosporingium and Saccharopolyspora were investigated in this study against a panel of referenced, environmental and clinical bacterial strains. The ethyl acetate extracts of these marine actinomycetes were screened for activity against 32 bacterial isolates. Out of the 32 organisms, 10 were susceptible to one or all the extracts used. Antibacterial activity was mainly observed against Gram-negative organisms with Minimum inhibitory concentration (MIC) values ranging from 0.078 mg/ml to >10mg/ml. The killing rates of the active extracts were also elucidated using standard procedures. The two extracts NO64 and NO53 showed rapid bactericidal activity against B. pumilus ATCC 14884 and Serratia marcens with a 3Log10 reduction in counts within 6 hours at 3.75 mg/ml and 5 mg/ml respectively. In conclusion, the ethyl acetate extract of these marine actinomycetes strains possess strong bactericidal and bacteriostatic activities against Gram negative organisms and can be therapeutically useful in the treatment of bacterial infections which are mainly caused by Gram negative bacteria. , Thesis (MA) -- Faculty of Science and Agriculture, 2010
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- Date Issued: 2010
Assessment of phytochemical constituents, antioxidant properties and cytotoxicity potentials of Leonutis leonurus and Boophone disticha extracts used in the management of Alzheimer’s disease in Hogsback, Eastern Cape, South Africa
- Authors: Tonisi, Sipho
- Date: 2019
- Subjects: Medicinal plants Alzheimer's disease
- Language: English
- Type: Thesis , Masters , MSc (Microbiology)
- Identifier: http://hdl.handle.net/10353/14726 , vital:40067
- Description: In this present study, the phytochemical compounds, antioxidant activities, and cytotoxicity potentials of solvent extracts (polar solvents) of Leonotis leonurus (L. leonurus) and Boophone disitcha (B. disticha) commonly used in the management of Alzheimer’s diseases in Hogsback, in the Eastern Cape, South Africa were investigated. The phytochemical compounds were determined by standard protocols of Folin–Ciocalteu method, aluminium chloride colorimetric method as well as Mayer’s and Wagner’s method. The antioxidant capabilities were assessed using 2,2-diphenyl-1-picrylhydrazyl (DPPH), hydrogen peroxide, 2,2'-azino-bis(3-ethylbenzothiazoline-6-sulphonic acid) (ABTS) and nitric oxide radical scavenging assays. The majority of extracts from both plant species exhibited free radical scavenging potential for oxidants they were tested against viz; DPPH, hydrogen peroxide, ABTS and nitric oxide. They further displayed good reducing potential against ferric iron. The results have shown a concentration-dependent dose of inhibition/scavenging activity (in DPPH, hydrogen peroxide, ABTS and nitric oxide assays) and reducing ability (in ferric reducing assay). However, leaf extracts of L. leonurus displayed ineffective scavenging activity against nitric oxide whereas extracts from L. leonurus flower and B. disticha bulb had higher scavenging potential against the production of nitric oxide radical. The GC-MS profiles of the plants extracts revealed the presence of numerous bioactive compounds that are known to possess excellent anti-inflammatory and most importantly antioxidant properties. Another interesting observation of GC-MS analysis data was the presence of compounds reported to inhibit Acetycholinesterase (AChE), which is a key enzyme targeted in the treatment of Alzheimers’ Disease (AD). The cytotoxicy tests for these extracts were carried out in order to assess the potentential detrimental effects on human health using Alamar Blue assay. It was noted that an increase in the extract concentration of both plant species resulted in a noticeable decline in cell population. These extracts were then declared xix to be quite toxic against HeLa (human cervix adenocarcinoma cells) cells as the cell viability in some extracts was quite low. Hence, toxicity testing of the studied plants’ extracts against normal cells is highly imperative in the future study. The results from this present study scientifically validated the use of the studied plants in folkoric medicine for the management of Alzheimer’s diseases.
- Full Text:
- Date Issued: 2019
Assessment of rangeland condition and evaluation of farmers' perception in Njwaxa and Mbizana communal rangelands of the Eastern Cape, South Africa
- Authors: Ngcofe, Odwa Armstrong
- Date: 2016
- Subjects: Rangelands -- South Africa -- Eastern Cape Land tenure -- South Africa -- Eastern Cape
- Language: English
- Type: Thesis , Masters , MSc
- Identifier: http://hdl.handle.net/10353/13259 , vital:39627
- Description: This study was conducted to determine of rangeland condition in terms of botanical composition, soil nutrient composition, and also to evaluate farmers’ perception on rangeland condition and degradation in two communal villages Njwaxa and Mbizana in the Eastern Cape Province of South Africa in 2014. A Structured questionnaire consisting of close and open-ended questions was used to investigate farmers’ perceptions on range condition, land degradation, and their causes. Fifty households with livestock were randomly selected in two communal areas of Middledrift (i.e. Njwaxa and Mbizana). Respondents of 21 years and above were selected. For assessment of range condition three homogeneous vegetation units (HVU) were demarcated in all study sites, namely slope; valley and toplands were demarcated and sub-divided into four 100m x 50m replicates. In each replicate, four 100m transects were laid parallel to each other 25m apart 1m2 quadrant was systematically located four times along each transect for herbaceous vegetation and soil sampling. The step point method was employed to determine herbaceous species composition and basal cover. A 400m2 belt transect was used to determine woody vegetation composition, density and tree equivalents in each HVU. The germination method was employed for soil seed bank composition and plant density. The soil micro and macro nutrients (N, P, K OC, Ca, Mg, Zn, Cu and Mn) and pH were also analyzed The majority of the respondents were between the ages of 51-60 years. Most of the farmers had more cattle (38percent) than goats (32percent) and sheep (30percent). Livestock numbers were perceived to have declined over the previous 20 years by the majority of respondents (96percent). The respondents indicated that their rangelands were mainly used for browsing (1.37), fire wood (2.01), building and fencing (2.63) and medical purposes (3.66). All the respondents indicated that their rangelands were highly degraded. Sheet erosion (50percent) was perceived to be the major type of soil erosion indicator mentioned by the farmers, followed by gully erosion (29percent) and rill erosion (21percent). The rangeland was dominated by Increaser II (pioneer) (63.2 percent) grass species followed by Decreaser (mesophytes) species (26.3percent). Digitaria eriantha in the valley (53.5 percent) was significantly higher (p<0.05) than both in the top (10.5percent) and sloppy areas (33.5percent) at Njwaxa communal rangeland, the abundance of D. eriantha was significantly higher (p<0.05) than top and valley in Mbizana communal rangeland. The results showed that soil seed banks were dominated by perennials, followed by annuals and biennial species being least abundant. The dominant forb Jamebrittenia c.f. albanesis was significantly higher (p<0.05) in both slopes (6.65percent) and toplands (7.34percent) than in the valley (3.15). The second most dominant species Puesdognaphalium undulata was significantly higher (p<0.05) in topland areas (6percent) than in valley bottom (3.8percent) and sloppy areas (4.3percent). The results of soil nutrients revealed no significant differences (p>0.05) in the concentration of OC, Ca, and Mg between the communities and seasons. Phosphorus (P) was significantly higher (p<0.05) in winter (concentrations) in most of the sites, except the top sites of Mbizana where summer concentration of P was significantly higher than winter. Potassium (K) was significantly higher (p<0.05) in summer than in winter in most of the HVUs, except the topland areas of Njwaxa and Mbizana sloppy areas where there were no significant differences (p>0.05) in the concentration of K. Soil pH did not display any significant differences (p>0.05) between communities and sites. The mean soil pH recorded in this study was 5.4 implying the soils of Njwaxa and Mbizana communities were acidic. It is evident that communal farmers are well aware of their rangeland condition, changes occurring in their rangelands, their causes and are capable of suggesting some solutions in controlling the declining condition of the rangelands. This study has shown the importance of engaging farmers’ inputs in range assessment since those are people bearing the consequences of rangeland degradation.
- Full Text:
- Date Issued: 2016
Assessment of soil erosion based on clustered geoinformatics approaches: a case study of Tyume River Catchment, Eastern Cape, South Africa
- Authors: Mbatyoti, Siyanda https://orcid.org/0000-0002-9736-5684
- Date: 2022-03
- Subjects: Soil erosion , Geoinformatics
- Language: English
- Type: Master's theses , text
- Identifier: http://hdl.handle.net/10353/22852 , vital:52969
- Description: This research centres on the holistic assessments of spatial and temporal dimensions of soil erosion zones based on the parameters of geomorphometry, hydro-statistics, and land use/cover dynamics. The study used a case study approach based on a clustered framework model of soil erosion parameters in the Tyume River basin in Eastern Cape, South Africa. The methods adopted for the investigation are, namely; non-parametric time-series assessment of streamflow dataset, semidecadal assessment of land use/cover (LU/C) dynamics, geospatial analysis of geomorphometric variables, vulnerability analysis of soil erosion zones, regression analysis of determination coefficient, and Receiver Operating Characteristic Curve (ROC). The delineation of soil erosion zones was based on the integrated analysis of the parameters of geomorphometry, geology, hydrology, and land use/ cover. The result of the hydro-statistical analysis of the Tyume River reports a major decline in the inter-annual regime frequency of storm flow based on the Mann- Kendall (MK) test and Sen’s slope assessment in 1992 (p-value = 0.031), 1997 (p-value = 0.045), 2003 (p-value = 0.021), 2008 (p-value = 0.003), and 2016 (p-value = 0.002). The MK test depicted a recurrence of peak streamflow acceleration in every three years based on low-flow and highflow transition. The sensitivity of LU/C to temporal dynamics of streamflow trends shown by the coefficient of correlation of trends of the LU/C water bodies with streamflow semi-decadal acceleration indicates a moderately relevant relationship, R = 0.76. The temporal analysis of LU/C and hydro-statistical analysis shows that the Tyume basin was highly vulnerable to soil erosion by water in 1999, 2009, and 2019. The vulnerability of the Tyume River basin in 2019 is exceptional and this is due to the conversion of forested area (woodland) into a built-up environment and farmland, with a high vulnerability in 2019 due to the slump in the rate of change of woodland and precipitation, and the increase in the rate of built-up and agricultural activities. The soil erosion vulnerability mapping divides the river basin into the critical high, high, moderate, low, nonvulnerable zones that cover 40 km2, 135 km2, 209 km2, and 186 km2 respectively. Regression analysis shows that the areas of soil erosion in the Tyume basin are moderately represented by the model (R2 = 56) while the model performance assessment based on success rate and prediction rate estimation from the area under the ROC curve shows that the model is good, Area Under Curve of the ROC = 0.899, and 0.897. The analysis suggests that soil erosion is driven by the impact of land use/land cover change, particularly in areas of high drainage density. Significantly, high vegetation density played a vital role in lowering high-flow on the hill-slope and low topographic wetness area as well as in areas with erodible geologic properties. The study, therefore, recommends the advocacy of crop rotation method of agricultural practice in the highly critical areas of soil erosion and recommends the development of riparian forests around the Tyume River. The study provides important information for environmental stakeholders on degradable areas which may require the urgent implementation of sustainable development measures. , Thesis (MPhil) -- Faculty of Science and Agriculture, 2022
- Full Text:
- Date Issued: 2022-03
Assessment of some bacteria species isolated from woodlands of Raymond Mhlaba Local Municipality for high activity laccase production
- Authors: Gogotya, Asemahle
- Date: 2019
- Subjects: Laccase
- Language: English
- Type: Thesis , Masters , MSc (Microbiology)
- Identifier: http://hdl.handle.net/10353/19098 , vital:39879
- Description: The function of enzymes in keeping the earth clean is enormous; being executed in the biodegradation of different natural pollutants and biocatalysis of different responses by substituting the ecologically risky and harmful concoction impetuses offering a situation inviting option, laccases is an example of an enzyme described as it doesn’t produce harmful byproducts. Laccases are employed in several industrial processes that play a key responsibility in transformation of life and making the environment a better place. Bacteria have been described as best producers of laccases with a potential in the industrial scale processes. Laccase was produced from different bacterial isolates identified and named as Bacillus sp. strain GFN1 isolated from soil sample, Bacillus sp. strain GLN and Streptomyces sp. strain LAO both isolated from decaying wood samples in Raymond Mhlaba local municipality with accession numbers MK290988 to MK290990 respectively, as identified by partial sequencing, these were the best producers some of which were positive for Napthol and guaiacol; even upon quantitative screening they were better laccase producers. For quantitative laccase screening, 2,2'-azino-bis(3-ethylbenzothiazoline-6- sulphonic acid) was utilised as the substrate for laccase assays. These laccase producing bacteria were subjected to optimization of growth conditions using submerged fermentation which increased the activity of the produced laccase in great amounts. In optimizing basal medium growth conditions where laccase was harvested after every 72 hours where optimal activity was 16 obtained, studying several factors such as pH which turned out to be pH 5 for all isolates, effect of supplemented carbon and nitrogen sources with the be best being lactose and urea respectively with their effective concentrations using lignin as the main carbon and nitrogen source. Copper sulfate was used as the main inducer and the species preferred guaiacol and ferullic acid and the Fe2+ asthe best supplemented metal ion. The time course was done investigating parameters such as cell growth which was determined by observing the optical density, laccase activity, protein concentration and pH and the presented results suggested that when there was an increase in cell growth, enzyme activity decreased pH had no much effect on the enzyme production as it was almost stable all the time with protein concentration exhibiting no direct effect on enzyme activity also. Characterization of the crude enzyme was done to check the stability of the enzyme produced in various parameters. The enzymes produced by the different strains were thermophilic as they were able to withstand elevated temperatures between 90 and 100 C, with pH stability within an extensive variety of alkaline pH, typical of most bacterial laccases. Various metal ions affected the stability of the enzyme with CuSO4 increasing the stability of two of the bacterial enzyme and appeared to slightly decrease the stability of one enzyme. The studied inhibitors only decreased the stability on the enzyme and couldn’t completely inhibit the enzyme, and the enzymes showed specificity towards varying substrates. The studied bacterial laccases exhibit tremendous characteristics which are of great significance in the industries and will add to the novelty of bacterial laccases and their stability amongst the most studied fungal laccases.
- Full Text:
- Date Issued: 2019
Assessment of the Department of Rural Development and Agrarian Reform's maize cropping programme in the Eastern Cape
- Authors: Mqamelo, Luvolwethu
- Date: 2017
- Subjects: Cropping systems Crops and climate Crop yields
- Language: English
- Type: Thesis , Masters , MSc
- Identifier: http://hdl.handle.net/10353/9165 , vital:34288
- Description: The Department of Rural Development and Agrarian Reform maize cropping programme is one of the flagship projects that has been entrusted by the provincial government to tackle the social ills faced by the rural communities of the Eastern Cape Province. The programme is in line with a number of policies that strive to unlock the agricultural potential in inducing the much talked about radical economic transformation. This study was aimed at establishing if the outlay of the implementation processes and the outcomes of the maize cropping programme in Eastern Cape are sufficient to achieve the stated objectives. The study adopted a triangulation method to get comprehensive understanding of the programme and for accuracy and verification of the data collected. A pre-tested semistructured questionnaire was used to collect the demographics and socio-economic status of the respondents; technical skills and capabilities; implementation processes of the programme and the perceptions of the participants and key strategic role players in the maize cropping programme. A total of 120 respondents from DRDAR’s 2016/2017 financial year supported list and 9 key informants were sampled for the study. Furthermore, a gross margin analysis was used to establish the viability and the sustainability of the programme with and without DRDAR’s subsidies. For purposes of determining if there was any relation between the maize enterprise income and 13 independent variables, a multiple regression model was employed. The results of the study show that the programme is dominated by old and uneducated individuals with an average age of 60 years. The implementation processes are proving to be fairly progressed however, at a very limited scale. This includes provision of production inputs and mechanization services on time, formation of self-serving legal entities and unlocking the private sector investment. The gross margins generated from the programme have been observed to be non-viable and unsustainable. As a result, only 31% of the respondents were able to attain a gross margin equal or greater than the allocable costs of producing maize both under irrigation and dry land. The results of the regression model indicated that, only 5 of the 13 independent variables (household gender, marital status, years of participation, area planted and yield) were found to have a significant effect to the maize enterprise income. Overall, the DRDAR’s maize cropping programme has failed to meet its intended objectives. In addition, more than 70 percent of the programme participants produced for subsistence purposes and showed no desire to fully commercialise their operations.
- Full Text:
- Date Issued: 2017
Assessment of the human health implications of climate variability in East London, Eastern Cape, South Africa
- Authors: Orimoloye, Israel Ropo https://orcid.org/0000-0001-5058-2799
- Date: 2018
- Subjects: Climatic changes http://id.loc.gov/authorities/subjects/sh85027037
- Language: English
- Type: Doctoral theses , text
- Identifier: http://hdl.handle.net/10353/19715 , vital:43171
- Description: Impacts associated with climate variability and extreme heat are already obvious in varying degrees and expected to be disruptive in the near future across the globe especially in the urban regions. Urban areas have distinctive features that leave their residents and properties vulnerable to extreme climate events. Global temperatures continue to change, reaching new levels almost every year for the past two decades. However, even though the causes are debated it is evident that climate variability is real. Climate variability and disaster risk are threats to human health that adversely reinforce each other. Better knowledge on the association between climate change, variability and extreme weather-related illness is needed and can aid strategies to reduce vulnerabilities. The impacts of climate variability on the health of residents in East London (EL) area in the Eastern Cape Province, South Africa were explored through four interdependent research segments. The first section examined the climate variability and urban surface thermal characteristics implication on human health using Remote Sensing (RS) and Geographic Information System (GIS) techniques. Remote sensing was used to assess the Land Surface Temperature (LST) and estimated Radiation (R) of East London area from Landsat Thematic Mapper (TM) images for 1986, 1996, 2006 as well as from Operational Land Imager (OLI) and Thermal Infrared Sensor (TIRS) for 2016 spanning a period of 30 years. Rapid urbanization and land cover changes in this area have contributed significantly to this drastic change in the natural land surface characteristics (increased land surface temperature and surface solar radiation). For instance, vegetation cover declined by about 358.812km2 while built-up areas increased by 175.473km2 during this period which correlates with the area thermal characteristics changes. Radiation levels also increased over the years with values exceeding the global solar radiation index. Exposure to increased surface radiation poses risks of heat stroke, skin cancer and heart disease to the local population. Consequently, this study provides pertinent information on human health sustainability and epidemiological case management. The second part explored past temperature and humidity trends (1986-2016) and projects future trends (2017-2030). The historical data of meteorological variables were obtained from the archives of the South African Weather Service and analyzed using the ordinary least square regression model in GRETL (GNU Regression Econometric and Time-series Library) statistical software. This study discovered a local consistency between models and the observations add to existing knowledge and this is crucial in knowing the shifts in climatic change as well as recognizing variability and its conflicting effects on human health, environment, agriculture, ecological sustainability and socioeconomic status in the region. The third segment assessed the potential impacts of climate variability on health using existing heat indices during the study period. The results demonstrated that in East London from 1986 to 2016 during summer and autumn (December to May) of various years exceeded high heat index values. It is obvious that summer and autumn months are more vulnerable to heat extreme and humidex. The humidex and Heat Index (HI) increased annually by 0.03 percent and 0.9 percent respectively throughout the study period. The increment in the various indices showed highly significant ill-health and environmental impacts on humans especially with prolonged exposure. The last segment appraised the association between climatic elements and epidemiological incidences of the study area between 2012 and 2016. The epidemiology incidences data were obtained from the archives of the Cecilia Makiwane Hospital in East London area and National Tertiary Service Grant (NTSG) database for the period. The results have showed that there exists significant effects of climate variability on the health of East London residents and these have been identified to have negative impacts on health of the people in the area. This study also revealed noticeable impacts of extreme heat on human health and a positive correlation between meteorological components (HI and temperature) and epidemiological cases (cardiovascular, skin cancer and diarrhea) during the study period. , Thesis (PhD) (Geography) -- University of Fort Hare, 2018
- Full Text:
- Date Issued: 2018
Assessment of the human health implications of climate variability in East London, Eastern Cape, South Africa
- Authors: Orimoloye, Israel Ropo
- Date: 2018
- Subjects: Climatic changes -- South Africa -- Eastern Cape
- Language: English
- Type: Thesis , Doctoral , Geography
- Identifier: http://hdl.handle.net/10353/10113 , vital:35346
- Description: Impacts associated with climate variability and extreme heat are already obvious in varying degrees and expected to be disruptive in the near future across the globe especially in the urban regions. Urban areas have distinctive features that leave their residents and properties vulnerable to extreme climate events. Global temperatures continue to change, reaching new levels almost every year for the past two decades. However, even though the causes are debated it is evident that climate variability is real. Climate variability and disaster risk are threats to human health that adversely reinforce each other. Better knowledge on the association between climate change, variability and extreme weather-related illness is needed and can aid strategies to reduce vulnerabilities. The impacts of climate variability on the health of residents in East London (EL) area in the Eastern Cape Province, South Africa were explored through four interdependent research segments. The first section examined the climate variability and urban surface thermal characteristics implication on human health using Remote Sensing (RS) and Geographic Information System (GIS) techniques. Remote sensing was used to assess the Land Surface Temperature (LST) and estimated Radiation (R) of East London area from Landsat Thematic Mapper (TM) images for 1986, 1996, 2006 as well as from Operational Land Imager (OLI) and Thermal Infrared Sensor (TIRS) for 2016 spanning a period of 30 years. Rapid urbanization and land cover changes in this area have contributed significantly to this drastic change in the natural land surface characteristics (increased land surface temperature and surface solar radiation). For instance, vegetation cover declined by about 358.812km2 while built-up areas increased by 175.473km2 during this period which correlates with the area thermal characteristics changes. Radiation levels also increased over the years with values exceeding the global solar radiation index. Exposure to increased surface radiation poses risks of heat stroke, skin cancer and heart disease to the local population. Consequently, this study provides pertinent information on human health sustainability and epidemiological case management. The second part explored past temperature and humidity trends (1986-2016) and projects future trends (2017-2030). The historical data of meteorological variables were obtained from the archives of the South African Weather Service and analyzed using the ordinary least square regression model in GRETL (GNU Regression Econometric and Time-series Library) statistical software. This study discovered a local consistency between models and the observations add to existing knowledge and this is crucial in knowing the shifts in climatic change as well as recognizing variability and its conflicting effects on human health, environment, agriculture, ecological sustainability and socioeconomic status in the region. The third segment assessed the potential impacts of climate variability on health using existing heat indices during the study period. The results demonstrated that in East London from 1986 to 2016 during summer and autumn (December to May) of various years exceeded high heat index values. It is obvious that summer and autumn months are more vulnerable to heat extreme and humidex. The humidex and Heat Index (HI) increased annually by 0.03percent and 0.9percent respectively throughout the study period. The increment in the various indices showed highly significant ill-health and environmental impacts on humans especially with prolonged exposure. The last segment appraised the association between climatic elements and epidemiological incidences of the study area between 2012 and 2016. The epidemiology incidences data were obtained from the archives of the Cecilia Makiwane Hospital in East London area and National Tertiary Service Grant (NTSG) database for the period. The results have showed that there exists significant effects of climate variability on the health of East London residents and these have been identified to have negative impacts on health of the people in the area. This study also revealed noticeable impacts of extreme heat on human health and a positive correlation between meteorological components (HI and temperature) and epidemiological cases (cardiovascular, skin cancer and diarrhea) during the study period.
- Full Text:
- Date Issued: 2018
Assessment of the human health implications of climate variability in East London, Eastern Cape, South Africa
- Authors: Orimoloye, Israel Ropo https://orcid.org/0000-0001-5058-2799
- Date: 2018-05
- Subjects: Climatic changes , Global temperature changes
- Language: English
- Type: Doctoral theses , text
- Identifier: http://hdl.handle.net/10353/25360 , vital:64224
- Description: Impacts associated with climate variability and extreme heat are already obvious in varying degrees and expected to be disruptive in the near future across the globe especially in the urban regions. Urban areas have distinctive features that leave their residents and properties vulnerable to extreme climate events. Global temperatures continue to change, reaching new levels almost every year for the past two decades. However, even though the causes are debated it is evident that climate variability is real. Climate variability and disaster risk are threats to human health that adversely reinforce each other. Better knowledge on the association between climate change, variability and extreme weather-related illness is needed and can aid strategies to reduce vulnerabilities. The impacts of climate variability on the health of residents in East London (EL) area in the Eastern Cape Province, South Africa were explored through four interdependent research segments. The first section examined the climate variability and urban surface thermal characteristics implication on human health using Remote Sensing (RS) and Geographic Information System (GIS) techniques. Remote sensing was used to assess the Land Surface Temperature (LST) and estimated Radiation (R) of East London area from Landsat Thematic Mapper (TM) images for 1986, 1996, 2006 as well as from Operational Land Imager (OLI) and Thermal Infrared Sensor (TIRS) for 2016 spanning a period of 30 years. Rapid urbanization and land cover changes in this area have contributed significantly to this drastic change in the natural land surface characteristics (increased land surface temperature and surface solar radiation). For instance, vegetation cover declined by about 358.812km2 while built-up areas increased by 175.473km2 during this period which correlates with the area thermal characteristics changes. Radiation levels also increased over the years with values exceeding the global solar radiation index. Exposure to increased surface radiation poses risks of heat stroke, skin cancer and heart disease to the local population. Consequently, this study provides pertinent information on human health sustainability and epidemiological case management. The second part explored past temperature and humidity trends (1986-2016) and projects future trends (2017-2030). The historical data of meteorological variables were obtained from the archives of the South African Weather Service and analyzed using the ordinary least square regression model in GRETL (GNU Regression Econometric and Time-series Library) statistical software. This study discovered a local consistency between models and the observations add to existing knowledge and this is crucial in knowing the shifts in climatic change as well as recognizing variability and its conflicting effects on human health, environment, agriculture, ecological sustainability and socioeconomic status in the region. The third segment assessed the potential impacts of climate variability on health using existing heat indices during the study period. The results demonstrated that in East London from 1986 to 2016 during summer and autumn (December to May) of various years exceeded high heat index values. It is obvious that summer and autumn months are more vulnerable to heat extreme and humidex. The humidex and Heat Index (HI) increased annually by 0.03percent and 0.9percent respectively throughout the study period. The increment in the various indices showed highly significant ill-health and environmental impacts on humans especially with prolonged exposure. The last segment appraised the association between climatic elements and epidemiological incidences of the study area between 2012 and 2016. The epidemiology incidences data were obtained from the archives of the Cecilia Makiwane Hospital in East London area and National Tertiary Service Grant (NTSG) database for the period. The results have showed that there exists significant effects of climate variability on the health of East London residents and these have been identified to have negative impacts on health of the people in the area. This study also revealed noticeable impacts of extreme heat on human health and a positive correlation between meteorological components (HI and temperature) and epidemiological cases (cardiovascular, skin cancer and diarrhea) during the study period. , Thesis (PhD) -- Faculty of Science and Agriculture, 2018
- Full Text:
- Date Issued: 2018-05
Assessment of the impact of land use practices on vegetation , soil and carbon-nitrogen sequestration potential in Mopane rangelands of Central Northern Namibia
- Authors: Kahumba, Absalom
- Date: 2018
- Subjects: Rural development Land use Land tenure
- Language: English
- Type: Thesis , Doctoral , Pasture Science
- Identifier: http://hdl.handle.net/10353/11718 , vital:39100
- Description: This study was conducted in Ogongo district, situated in Omusati Region of the central northern Namibia. The objectives of this study were to assess the impact of land use practices on 1) vegetation distribution and status; 2) soil properties; 3) carbon-nitrogen sequestration potential, and 4) investigate the indigenous pastoralists’ knowledge and perceptions on livestock production, rangeland degradation and its indicators in three villages (Omaandi, Epukunoyana and Oshitutuma) in Mopane savannah rangelands of central northern Namibia. For vegetation and soil assessment, three grazing land management systems (communal, game reserve and cattle ranch) were identified adjacent to each other. In each grazing system, three sites (for game reserve and cattle ranch, these were camps) were selected. In each site, three belt transects of 50 m x 5 m2 were marked to record vegetation and soil data as well as to collect vegetation samples for analysis. Grass species composition was recorded using step point methods from 250 points per belt transect. A total of five 0.25 m2 quadrats were randomly laid within each 250 m2 belt transect to record the herbaceous plant density, tuft diameter, tuft distance and biomass. All woody plants in the belt transect (250 m2) were measured and recorded for species plant height and canopy diameters. Three soil samples per belt transect were collected at the time of forage sampling down to a depth of 20 cm using a soil auger. Soil and plant samples were analysed for macro and micro minerals, total organic carbon, total nitrogen, carbon-nitrogen ratios, and carbon and nitrogen isotopes. For bulk density, soil samples were collected using soil core samplers. In the social study, a total of 90 households were randomly selected from three villages and a total of 48 elders were purposefully selected based on the age, time spent in the village and livestock ownership. A combination of structured and semi-structured questionnaires were used to gather household information, while a structured questionnaire and open ended discussion were used to interview elders on the constraints of livestock production, rangeland degradation related issues and their consequences on livelihood. Field vegetation and soil data were analyzed using a General Linear Model (GLM) in SAS (2007), whereas the social data were analyzed using SPSS version 21 (2014). A total of 23 grass species were identified in all three land management systems, of which 48% were perennials and the remaining 52% were annuals. Aristida meridionalis dominated the game reserve and the ranch, whereas Eragrostis trichophora was dominant in all land management systems. Forbs occurred commonly in the game reserve and the ranch, but were dominant in the communal areas. The abundance of A. meridionalis responded significantly (P < 0.001) to land management systems with the game reserve showing remarkably greater abundance than the ranch. In summer, the abundance of E. trichophora was high (P < 0.001) in the game reserve followed by the communal and ranch sites, whereas in winter, the species had still greater abundance in the game reserve followed by the ranch. In summer, the mean grass density was greatest (P < 0.001) in the game reserve and least in the communal lands, but vice versa for the tuft distance. In summer, the average distance between tufts showed great variations (P < 0.001) with the communal areas having greater values than the ranch and game reserve. In winter, both the game reserve and the ranch showed records of similar grass tuft density and distance between tufts, whereas these values were nil for communal areas, because, there were no grasses recorded. Herbaceous plant dry matter was significantly greater (P < 0.05) in the game reserve followed by the ranch and the least in the communal areas. Results on biomass showed remarkably higher values (P < 0.001) in summer than winter in all land management systems. The total woody plant density was significantly higher (P < 0.001) in the ranch (542 TE ha-1) than the game reserve (449 TE ha-1) and communal area (324 TE ha-1). However, percentage of canopy cover did not differ significantly (P > 0.05) between the three land management systems. Woody plant density of height classes were significantly different (P < 0.05) between three land management systems. The abundance of seedlings, saplings and young shrubs were significantly greater (P < 0.05) in the ranch than the game reserve and communal area. The mature trees had a significantly greater density (P < 0.05) in the game reserve than the ranch and communal area. Soil analysis results showed that Magnesium (Mg), Potassium (K), Manganese (Mn) and Copper (Cu) had similar (P > 0.05) concentrations in soils obtained from all land management systems in both seasons. Soil Calcium (Ca) levels showed differences between land management systems in winter only being greater (P < 0.001) in the game reserve than the ranch and the communal lands. Soil Phosphorus (P) and Iron (Fe) also showed variations between land management systems in winter being significantly greater (P < 0.001) in the ranch than the other land management systems. The concentration of soil K differed between the two seasons in soils collected from the ranch and the communal lands, being greater (P < 0.001) in winter than summer seasons. Soil Zinc (Zn) also showed differences between land management systems in summer being greater (P < 0.001) in the game reserve than in the ranch and communal land. Seasonal variations were observed in soil P level of samples collected from the ranch being greater (P < 0.001) in winter than summer season. The concentration of soil Zn was higher (P < 0.001) in the soil collected from the game reserve and the ranch in summer than winter season. Woody forage analysis results showed that browse samples harvested from the ranch had greater (P < 0.001) Nitrogen (N) level than the other land management systems in both seasons. The browse samples harvested from the game reserve had greater (P < 0.001) Ca level than the other land management systems in winter season only. The level of P showed variations (P < 0.05) between land management systems in samples harvested during winter only being greater (P < 0.001) in samples from the ranch than the other land management systems. Similarly, browse harvested during winter showed significant differences (P < 0.05) in K levels being lowest in samples collected from game reserves, where the Ca level was greatest. Browse samples collected from the communal land and the ranch had the lowest Mg levels in summer and winter seasons, respectively. In all management systems, browse harvested during summer had greater (P < 0.001) N and P levels than those harvested in winter, and the reverse holds true for K and Ca levels. Browse samples harvested during winter had greater (P < 0.001) Mn levels in samples from the communal area and game reserve than the ranch, but in summer, the game reserve had higher Mn level than the other two sites. Browse samples harvested during winter only showed differences (P < 0.05) in Cu and Zn levels being greatest (P < 0.001) in samples collected from ranch and game reserves. In all management systems, browse samples harvested during winter had greater (P < 0.001) Fe, Mn, Zn and Cu (except for the game reserve and communal land) levels than those harvested in summer. Herbaceous analysis results showed that samples harvested in summer from the game reserve and ranch had greater (P < 0.001) TOC levels than the communal area, but in winter, samples from the game reserve and ranch had similar TOC levels, except for communal areas that had no herbaceous vegetation. Herbaceous samples harvested in winter from the ranch had greater (P < 0.001) TN levels than the game reserve, and that made the C:N ratio higher (P < 0.001) in the game reserve. Woody foliar samples harvested in winter from the game reserve and communal lands had greater (P < 0.001) TOC than the ranch. Values on C:N ratio showed that in winter, the communal and ranch had greater (P < 0.001) C:N than the game reserve, but in summer, the ranch had higher (P < 0.001) C:N than the game reserve and communal area. The vegetation TOC (kg ha-1) showed the order of the game reserve > ranch > communal area and the trend was similar in both seasons. In summer, the game reserve had the greatest (P < 0.001) TN (kg ha-1) followed by the ranch and the lowest in the communal area, but in winter the game reserve and ranch had similar and higher (P < 0.001) TN (kg ha-1) than the communal areas. In summer, both the game reserve and ranch recorded greater (P < 0.001) herbaceous δ13C and lowest δ15N than the communal area, but in winter, the game reserve had higher (P < 0.001) δ13C than the ranch, though both the game reserve and ranch had similar (P > 0.001) δ15N values. In summer, both the communal and ranch had slightly higher (P < 0.001) woody foliar δ13C than the game reserve, but in winter the ranch had greater (P < 0.001) δ13C than game reserve and communal areas. Woody foliar samples harvested from the ranch showed variations (P < 0.05) in δ15N between seasons being higher (P < 0.001) in summer than winter. The TOC was greatest in summer, in soils collected from the game reserve followed by the ranch and least in the communal land, but in winter, the lowest TOC was recorded in soils collected from the ranch. The soil C:N ratio varied between land management systems in soils collected during summer only being greater (P < 0.001) in the game and ranch than the communal area. The soil TOC (kg ha-1) and TN (kg ha-1) did not show (P > 0.05) differences between land management systems. Soil δ13C level was remarkably (P < 0.05) affected by land management systems, but did not interact with seasons. In both seasons, the communal land had slightly higher (P < 0.001) δ13C level than the other two land management systems. In both seasons, δ15N levels showed great differences (P < 0.001) between land management systems, with highest soil δ15N levels observed in the communal area than the ranch and game reserve. Results on social survey showed that the majority of the interviewed households in Omaandi (63percent), Oshitutuma (53percent) and Epukunoyana (50percent) were female headed families and the remaining were male headed. The mean population of goats and cattle were significantly higher (P < 0.05) in Omaandi and Epukunoyana than in Oshitutuma village, respectively. In this study, household respondents in all villages indicated that all livestock species were primarily kept for wealth status and provision of meat for consumption. Respondents in all villages also indicated that lack of grazing lands and shortage of feed were the primary constraints of livestock production followed by water scarcity and recurring droughts. Elder respondents in all villages perceived overgrazing and climate change as the primary cause of rangeland degradation. Elder interviewees in Omaandi and Oshitutuma villages regarded low grass cover and dominance of poor quality grass (Epukunoyana only) as the primary vegetation indicators of rangeland degradation. The animal related indicators such as stunted animal body as a result of mineral deficiency, high livestock mortality, emaciated body and animals traveling long distance for grazing and water (Oshitutuma only) were regarded in all villages as the primary livestock related indicators of rangeland degradation. Elders from Epukunoyana village ranked low rainfall, high soil and atmospheric temperatures as the primary climate related indicators of rangeland degradation, although in Omaandi and Oshitutuma, high soil and atmospheric temperatures were considered as the primary climate related indicators of rangeland degradation. Based on the findings, this study concludes that land management systems had great influences on the distribution and production of herbaceous and woody vegetation in summer and winter seasons. This study also observed that land management systems interacted strongly with season to influence most vegetation and soil variables. Lastly, based on the study findings, the study concludes that all three communal rangelands are degraded and degradation led to a gradual declining trend in the livestock population over the past 10 to 20 years in the communal areas as a result of feed shortage.
- Full Text:
- Date Issued: 2018
Assessment of the physicochemical and microbiological qualities of Tyume River in Amathole District in the Eastern Cape Province, South Africa
- Authors: Sibanda, Timothy https://orcid.org/0000-0002-6864-3796
- Date: 2013-05
- Subjects: Water -- Purification , Sewage -- Purification
- Language: English
- Type: Doctoral theses , text
- Identifier: http://hdl.handle.net/10353/24465 , vital:62812
- Description: The bioflocculant-producing potentials of three marine bacteria isolated from the sediment samples of Algoa Bay in the Eastern Cape Province of South Africa were assessed. Analysis of the partial nucleotide sequence of the 16S rDNA of the bacteria revealed 99 percent, 99 percent, and 98 percent similarity to Cobetia sp. L222, Bacillus sp. A-5A, and Bacillus sp. HXG-C1 respectively and the sequence was deposited in GenBank as Cobetia sp. OAUIFE, Bacillus sp. MAYA and Bacillus sp. Gilbert (accession number JF799092, JF799093, and HQ537128 respectively). Cultivation condition studies for Cobetia sp. OAUIFE revealed that bioflocculant production was optimal with an inoculum size of 2 percent (v/v), initial pH of 6.0, Mn2+ as the metal ion, and glucose as the carbon source. Metal ions, including Na+, K+, Li+, Ca2+and Mg2+ stimulated bioflocculant production resulting in flocculating activity of above 90 percent. This crude bioflocculant is thermally stable, with about 78 percent of its flocculating activity remaining after heating at 100 oC for 25 min. Analysis of the purified bioflocculant revealed it to be an acidic extracellular polysaccharide. FTIR analysis revealed the presence of methoxyl, hydroxyl, and carboxyl - groups in the compound bioflocculant and SEM micrograph of the bioflocculant revealed a crystal-linear structure. On the other hand, bioflocculant production by Bacillus sp. MAYA was optimal when glucose (95.6 percent flocculating activity) and ammonium nitrate (83.3 percent flocculating activity) were used as carbon and nitrogen sources respectively; inoculum size was 2 percent (v/v); initial pH 6; and Ca2+ as coagulant aid. Chemical analysis of the purified bioflocculant shows that it is composed of uronic acid, neutral sugar and protein. FTIR analysis also revealed the presence of methoxyl, hydroxyl, carboxyl and amino- groups in this bioflocculant. The bioflocculant is thermostable with about 65.6 percent residual flocculating activity retained after heating the bioflocculant at 100 oC for 25 min. However bioflocculant production by Bacillus sp. Gilbert was optimal when sodium carbonate (95.2 percent flocculating activity) and potassium nitrate (76.6 percent flocculating activity) were used as carbon and nitrogen sources respectively; inoculum size was 3 percent (v/v); initial pH 9; and Al3+ as cation. The crude bioflocculant retained 44.2 percent residual flocculating activity after heating at 100 oC for 15 min. FTIR analysis reveals the presence of hydroxyl, carboxyl and methylene - groups in the compound bioflocculant. SEM micrograph of the bioflocculant revealed an amorphous compound. The consortia of these bacteria strains also produced bioflocculants with high flocculating activities which were highly efficient in removing turbidity and chemical oxygen demand (COD) from brewery wastewater, diary wastewater and river water. The bioflocculants from the consortia seemed better than traditional flocculants such as alum . The characteristics of the bioflocculant produced by the consortium of Cobetia sp. OAUIFE and Bacillus sp. MAYA showed that this extracellular bioflocculant, composed of 66percent uronic acid and 31percent protein and an optimum flocculation (90 percent) of kaolin suspension, when the dosage concentration was 0.8 mg/ml, under weak alkaline pH of 8, and Ca2+ as a coagulant aid. The bioflocculant is thermally stable, with a high residual flocculating activity of 86.7 percent, 89.3 percent and 87.0 percent after heating at 50 oC, 80 oC and 100 oC for 25 min respectively. The FTIR analysis of the bioflocculant indicated the presence of hydroxyl, amino, carbonyl and carboxyl functional groups. Scanning electron microscopy (SEM) image revealed a crystal-linear spongy-like bioflocculant structure and EDX analysis of the purified bioflocculant showed that the elemental composition in mass proportion of C,N,O,S and P was 6.67:6.23:37.55:0.38:4.42 (percent w/w). However, the characteristics of the bioflocculant produced by the consortium of Cobetia sp OAUIFE and Bacillus sp. Gilbert showed an optimum flocculation (90 percent) of kaolin suspension when the dosage concentration was 0.2 mg/ml, under neutral pH of 7, and Ca2+ as a coagulant aid. The FTIR analysis of the bioflocculant Tyume River water samples were collected monthly, over a 12-month period starting from August 2010 and ending in July 2011, and transported on ice to the Applied and Environmental Microbiology Research Group (AEMREG) Laboratory at the University of Fort Hare, Alice for analyses within 6 h of collection. Electrical conductivity (EC), total dissolved solids (TDS), temperature, pH and dissolved oxygen (DO) of water samples were determined in situ using a multi-parameter ion-specific meter. Concentrations of orthophosphate and total nitrogen (nitrate + nitrite) were determined by standard photometric methods. Total coliforms (TC), faecal coliforms (FC) and enterococci were determined by the membrane filtration method. Viruses in water samples were concentrated using the adsorption-elution method, followed by extraction of viral nucleic acids and purification done using commercially available kits. The concentrations of human enteric viruses in the river-water samples were estimated using quantitative PCR. RNA viruses were quantified in a two-step protocol where RNA was first transcribed into cDNA in a separate reverse-transcription step. Adenovirus species and serotypes were simultaneously detected using serotype-specific multiplex PCR. Norovirus genogroups GI and GII were detected by semi-nested PCR. The risk of infection associated with recreational and domestic use of the water was also estimated. Biochemical oxygen demand (BOD) levels fell within the stipulated BOD guideline of 10 mg/ℓ for surface waters where full contact use is allowed and ≤ 30 mg/ℓ where public access is prohibited, restricted, or infrequent. DO concentrations generally ranged between 7.47 mg/ℓ and 10.42 mg/ℓ, well within the target water quality requirements. The temperature regime ranged between 6°C and 28°C and for most sampling sites, the temperature regimes were within the acceptable limit of no risk (≤ 25°C) for domestic water uses in South Africa. EC ranged between 47 μS/cm and 408 μS/cm well within the South African target water quality EC guideline of 700 μS/cm though it was observed to increase as the river flowed through settlements. The pH in the period beginning September 2010 through to January 2011 was consistently below pH 9, but from February 2011 to June 2011 the pH significantly increased to between pH 10 and pH 11 at most sampling sites. Unpolluted waters normally show a pH of between 6.5 and 8.5. Most of the pH values observed in this study lie between pH 8.5 and pH 10.8 levels which are not far off from the upper level guideline of pH 9.0 for domestic use. Turbidity ranged between 6 NTU and 281 and fell short of the target water quality range (0 NTU to 1 NTU) of no risk for domestic water uses in South Africa. Monthly TDS values and EC values showed direct proportionality. TDS concentrations at all sites fell within the acceptable guideline of 0 mg/ℓ to 450 mg/ℓ of TDS for domestic use. Nutrient profiles were as follows: nitrate (0.18 mg/ℓ to 4.21 mg/ℓ); nitrite (0.02 mg/ℓ to 2.35 mg/ℓ); and orthophosphate (0.06 mg/ℓ to 2.72 mg/ℓ). The bacteriological qualities of the water were poor, exceeding the guideline of 200 CFU/100 mℓ and 33 CFU/100 mℓ for FC and enterococci respectively, for recreational water. FC counts also exceeded the 1 000 CFU/100 mℓ guideline for water used in fresh produce irrigation. Generally, higher counts of TC, FC and enterococci were recorded at the sampling sites located at the lower reaches of the river compared to the upper reaches. Adenovirus was detected in 31percent of the river samples in concentrations ranging between 1.0×100 genome copies/ℓ and 8.49×104 genome copies/ℓ. Serotyping showed the presence of species C adenovirus serotypes 1, 2, 6 and 7, and species F adenovirus serotype 41. The prevalence of norovirus was 4percent while rotavirus was detected in 4percent of river samples in concentrations ranging between 9×100 genome copies/ℓ and 5.64×103 genome copies/ℓ. Hepatitis A virus was detected in 13percent of river samples in concentrations ranging between1.67×103 and 1.64×104 genome copies/ℓ while enteroviruses were not detected. Detection of enteric viruses was inversely correlated to temperature. Risk analysis showed that both hepatitis A virus and adenovirus presented significantly higher risk of infection values compared to rotavirus in the case of ingestion of 10 mℓ or 100 mℓ of water from Tyume River while enteroviruses did not present any significant risk of infection. Tyume River water samples also did not conform to the US Environmental Protection Agency (US EPA) bacterial criteria of 200 CFU/100 mℓ faecal coliforms and 33 CFU/100 mℓ enterococci for bathing waters. Whereas the physicochemical parameters showed that Tyume River water was relatively clean, the bacteriological water quality was poor. Most of the microbiological contamination observed in this study (especially FIBs) can be blamed on inadequate sanitary infrastructure as we observed that open defecation is commonplace in this catchment, which also serves as a conduit for effluent discharges from wastewater-treatment facilities. Enteric viruses were detected along the course of the river in a sporadic pattern, generally not related to natural hydrological cycles and so we conclude that the presence of enteric viruses in the river is suggestive of the dynamics of the same in the host population. Even though the proportion of infective viruses was estimated in this study, fact remains that there is considerable risk of infection posed by the use of raw surface water for either domestic or recreational use. This study further confirmed the lack of correlation between faecal indicator bacteria and enteric virus occurrence in environmental waters, showing that assaying for enteric viruses in environmental waters remains the best method for determining the health risks associated with the use of faecally contaminated water. , Thesis (PhD) -- Faculty of Science and Agriculture, 2013
- Full Text:
- Date Issued: 2013-05
Assessment of the water quality, incidence of enteric viruses and microbial risk in the Buffalo River in the Eastern Cape Province of South Africa
- Authors: Chigor, Vincent Nnamdigadi https://orcid.org/0000-0002-0811-4526
- Date: 2013-03
- Subjects: Water quality , Water -- Microbiology
- Language: English
- Type: Doctoral theses , text
- Identifier: http://hdl.handle.net/10353/24272 , vital:62596
- Description: Buffalo River is an important water resource in the Eastern Cape Province of South Africa. Over a 1-year period (August 2010–July 2011), the water quality and incidence of human enteric viruses (HEntVs) was assessed, using standard methods and molecular techniques and a total 72 composite water samples collected monthly from a total of 6 sites located on the river and three dams along its course. The sites were selected based on a number of factors including geographical location, anthropogenic activity/major water use, rural/urban status and access. A total of 13 physicochemical parameters were determined using the standard methods. The counts of faecal indicator bacteria (FIB) including total coliforms (TC), faecal coliforms (FC) and enterococci (ENT) were determined by the membrane filtration technique. HEntVs were concentrated using an adsorption-elution method based on cation (Al3+)-coated membrane filter. Real-time quantitative polymerase chain reaction (qPCR) was used for the detection and quantification of human adenoviruses (HAdV), and real-time reverse transcriptase-PCR (RT-qPCR) was used for the quantitative detection of hepatitis A virus (HAV), human rotaviruses (RoV) and enteroviruses (EnV). The detected HAdV were characterized by multiplex conventional/semi-nested PCR methods. The risks for human health constituted by exposure to the detected HEntVs at the six sites were evaluated by a static quantitative microbial risk assessment (QMRA) using both the exponential and beta-Poisson models. Water temperature ranged from 11 to 28oC, while pH varied from 6.6 to 10.7, and turbidity from 1.7 to 133 NTU. Electrical conductivity (EC), total dissolved solids (TDS) and salinity showed drastic variations (42.3-46693 μS/cm, 20.3–23350 mg/L and 0.02–33.8 PSU respectively). The concentrations of other parameters ranged as follows: chloride (3.7–168 mg/L); DO (6.9–11.1); BOD (0.6–9.4); COD (3.7–45.9); nitrite-nitrogen (0.02–0.21); nitrate-nitrogen (1–4.47); and orthophosphate (0.01–1.72). TC, FC and ENT counts were high and ranged from 1.9 × 102–3.8 × 107 cfu/100 mL, 0–3.0×105 cfu/100 mL and 0–5.3 × 105 cfu/100 mL for TC, FC and ENT respectively. Significantly (P<0.05) higher concentrations of FC and ENT were observed at the sampling sites located at the lower reaches of the river compared to the upper reaches. The FIB counts mostly exceeded the maximum limits recommended by national and international guidelines for safe fresh produce irrigation, domestic applications, full-contact recreation and livestock watering. Significant (P<0.01) positive correlations existed between TDS and salinity (r=0.921), between turbidity and each of TC (r=0.552) and FC (r=0.425), as well as between BOD and each of TC (r=0.282), FC (r=0.472) and ENT (r=0.552). Phosphate correlated positively with FC (r=0.424), and nitrate also with the same, FC (r=0.460). A strong positive correlation existed between FC and ENT (r=0.915). There existed a significant (P˂0.01) inverse correlation between enteric viruses and each of water temperature (r=-0.191) and pH (r=-0.234). No correlation could be deduced between enteric viruses and all the tested chemical and bacteriological parameters. HAV, HAdV, RoV and EnV were detected in 43.1percent, 34.7percent, 13.9percent and 9.7percent respectively of the total 72 water samples tested. Two or more viruses were detected in 22.2 percent of the samples. HAdV were detected at 5 of the 6 sampling sites with concentrations ranging from 1.2×101 genome copies (GC)/litre to 4.71×103 GC/litre. Epidemiologically important serotypes, Ad40/41 constituted 83.3percent, while Ad21 made up 16.7percent of all the HAdV detected. HAV was detected at all the sites in significantly (p < 0.05) varying concentrations that ranged from 1.5 × 101–1.9 × 105 GC/litre compared to RoV and EnV. Neither of RoV nor EnV was detected at any of the dams. The detected concentrations at the non-dam sites ranged from 2.5 × 101–2.1 × 103 GC/litre and 1.3 × 101–8.6 × 101 GC/litre for RoV and EnV respectively. The values for the estimated daily risks of enteric virus infection varied with sites and exposure scenario, and ranged from 7.31×10-3–1 (for HAdV), 4.23×10-2–6.54×10-1 (RoV), 2.32×10-4–1.73×10-1 (HAV) and 1.32×10-4–5.70×10-2 (EnV). The yearly risks of infection in individuals exposed to the river/dam water via drinking, recreational, domestic or irrigational activities were unacceptably high, exceeding the acceptable yearly risk of 0.01percent (10-4 infection/person/year) recommended by the USEPA for drinking water. The risks of illness and of death from infection ranged from 6.58×10-5–5.0×10-1 and 6.58×10-9–5.0×10-5 respectively. Data on the physicochemical and bacteriological parameters showed that the Buffalo River water quality was poor, and deteriorated in the plains compared to the upper reaches. These water quality data, the presence of enteric viruses and the QMRA data, that revealed unacceptably high risks of enteric virus infections, and of illness and mortality from the infections, show that the Buffalo River and its dams are contaminated waters that constitute significant public health hazards. Provision of adequate sanitary infrastructure will help prevent source water contamination, and public health education aimed at improving personal, household and community hygiene is imperative. Monitoring enteric viruses in rivers and source water dams is necessary and useful as a risk assessment tool for the exposed population. Future research should consider a comprehensive characterization of the detected viruses. This work is both a significant contribution to the molecular epidemiology of enteric viruses and the first report on molecular detection and quantification of enteric viruses in surface waters in the Eastern Cape. , Thesis (PhD) -- Faculty of Science and Agriculture, 2013
- Full Text:
- Date Issued: 2013-03
Assessment of the willingness-to-pay for indigenous animal products in Ngxakaxa households in Mbashe local municipality in Eastern Cape province of South Africa
- Authors: Lusawana, Nangamso
- Date: 2015-06
- Subjects: Willingness to pay , Animal products
- Language: English
- Type: Master's theses , text
- Identifier: http://hdl.handle.net/10353/24879 , vital:63667
- Description: The demand for animal products is projected to increase progressively due to extensive urbanization, rapid growth of the human population and income dynamics. The demand for indigenous animal products will increase due to increasing income levels and this will be happening at the time when the supply of indigenous product is reducing as a result urbanization. The purpose of the current study was to assess consumption and willingness to pay for indigenous animal products looking at chicken and pork. The study intended to determine the socio- economic determinants influencing consumer willingness and consumption. Multistage sampling was used to derive a sample of 120 consumers at households. Primary data were collected using a structured interview schedule. Data collected was on household consumer characteristics, responses to different bid levels for indigenous meat and socio-economic determinants. The study used a Contingent Valuation Method to assess consumers‟ mean WTP for indigenous meat and logit model to determine socio-economic determinants influencing consumers‟ WTP. Results indicated that consumers were willing to pay an average premium of 33percent above the current prevailing price of convectional meat. They also showed that about 87percent of consumers who were willing to pay for indigenous meat and about 12.8percent who are willing to pay if the price increases. Of those who were willing a greater proportions were females. About 64percent of those who are willing and aware of indigenous meat most of them obtained information from neighbours and friends, Age, level of education, consumer awareness and monthly household income had a positive and significant effect on WTP. Most of the consumers indicated that indigenous meats are affordable, healthier when compared conventionally-produced meat. The main significant barrier to the purchase of indigenous meat was identified as its limited availability at convenient locations. The study recommends policy intervention aimed at facilitating development of marketing infrastructure, creation of awareness of important nutritional and health benefits of indigenous meat, and boosting the development of animal production systems that can add value to indigenous meat, so as to capture existing market opportunities. This would enhance food security and income generation of the small-scale resource-constrained farmers. , Thesis (MSc) -- Faculty of Science and Agriculture, 2015
- Full Text:
- Date Issued: 2015-06
Barriers and reasons for exercise of rural and urban overweight and obese populations in Buffalo City Metropolitan Municipality, Eastern Cape
- Authors: Mrwebi, Thembani
- Date: 2021-04
- Subjects: Obesity--Prevention , Public health--Exercise
- Language: English
- Type: Master's theses , text
- Identifier: http://hdl.handle.net/10353/22522 , vital:52388
- Description: It is documented that obesity is highly prevalent across rural and urban groups in industrialised and underdeveloped countries. This problem is an alarming issue as community members remain unsure about avoiding risking their health. Various health surveys reveal that obesity has increased among communities in the Buffalo City Metro Municipality in the Eastern Cape, and it has consequently made communities vulnerable to non-communicable diseases. The researcher explored factors and barriers of exercise for rural and urban obese populations in Buffalo City Metropolitan Municipality, Eastern Cape. This study was descriptive and explorative, utilising a questionnaire for gathering information. A purposive sample of 80 members from the two selected communities completed the questionnaire. A factor analysis was performed to identify factors that motivate physical activity and barriers to physical activity. It was discovered that all evaluated members were fully aware of the harmful repercussions of being overweight or obese. Nevertheless, only a tiny percentage of those who took part in the study decided to live a healthier lifestyle because of their obesity. Constructive motivating factors included increasing their self-image, enhancing their wellbeing, and getting highly involved in active and regular exercise. Negative motivators included finding it challenging to fit into old clothes and the worry of developing obesity-related diseases. Respondents noted the following impediments in regular exercises and physical activities; African cultural values, limited operational hours of physical activity facilities, insufficient time, and a lack of enthusiasm. , Thesis (MPhil) -- Faculty of Science and Agriculture, 2021
- Full Text:
- Date Issued: 2021-04
Bayesian spatial modelling of tuberculosis and its effects on socio-economic and demographic factors in South Africa : a case study of the Eastern Cape Province
- Authors: Obaromi, Abiodun Davies
- Date: 2018
- Subjects: Tuberculosis -- South Africa -- Eastern Cape Tuberculosis -- Epidemiology -- Statistics
- Language: English
- Type: Thesis , Doctoral , PhD
- Identifier: http://hdl.handle.net/10353/9648 , vital:34813
- Description: This dissertation is concerned with evolving and extending statistical models in the area of Bayesian spatial modelling, an increasingly important field of spatial epidemiology with particular interest towards application to Tuberculosis data in the Eastern Cape province of South Africa. In spatial epidemiology, the diseases to be examined usually occur within a map that needs spatial statistical methods that are appropriate, to model the observed data in the presence of some covariates and also cater for the variation of the disease. In this thesis, the Bayesian models were developed in such a way that they allowed several factors classified as fixed and random effects, to be included in the models and using the Bayesian approach. The basic model used in disease mapping is the Besag, York and Mollie model, which incorporates two random effects; one which is spatially structured and the other random effect which is spatially unstructured. The effects (fixed and random) were the covariate effects, socio-economic and demographic variability and the spatial variability respectively, which were all investigated in seven different hierarchical/multilevel Bayesian models. These factors showed varying and substantial effects in the posterior relative risk estimation of the disease. We assumed a negative binomial and generalized Poisson distributions to the response variable or relative risk estimate, 𝑦𝑖 ,to capture the over-dispersion phenomenon that is common and inherent with Poisson density for counts data. Spatial and non-spatial models were developed to model over-dispersion with all the distributions; Poisson, negative binomial and generalized Poisson. Negative binomial and generalized Poisson showed varying properties from comparisons with DIC values and parameter estimates to standard errors, which made either of them fit depending on the choice of model selection. It was found that a lower DIC value could be insufficient to determine a best fit model, if other models present estimates with lower variances even at higher DIC values. The generalized Poisson, a two parameter distribution like the negative binomial, which also has the ability to capture both under-dispersion and over-dispersion, was found to perform better in the results than the negative binomial on the basis of a lower variance and with more exact parameter estimates. A new weighted prior distribution, the “Besag2” ICAR model for the structured spatial random effects, which is an extension of the traditional ICAR prior model with two hyperparameters, was also developed and compared with some existing prior models; BYM and ICAR, to measure for spatial dependency in the regions. This new prior distribution was found to show a better fit, when compared to the basic ICAR prior usually assumed for the spatial random effect in the BYM model. This newly parameterized prior distribution in the Besag, York and Mollie model also led to improved parameter control, as the hyperparameters can be seen independently from each other. The result also showed that the new model performed well, both presenting good learning abilities and good shrinkage behaviour. In terms of model choice criteria, the proposed model performed at least equally well and better than the existing models, and the new formulation also gave parameters that are interpretable and have a clearer meaning. To interpolate scattered or regularly distributed data, there are imprecise or exact methods, but there are some of these methods that could be used for interpolating data in a regular grid and others in an irregular grid. Linear and biharmonic spline methods were implemented in MATLAB, to compare for smoothing in the distribution patterns of tuberculosis in the province. This smoothing spline is a method of fitting a smooth curve to a set of noisy observations using a spline function. This new method is rarely used in disease mapping applications, but it has a superior advantage to be assessed at subjective locations rather than only on a rectangular grid as seen in most traditional GIS methods of geospatial analyses. The proposed new models and methods in this thesis were found to be flexible and robust, since they can be reduced or extended according to the nature of the data. Nevertheless, great care must be considered in the choice of prior densities. The approaches developed in this dissertation helped to broaden the scope for spatial analysis and disease mapping applications in epidemiology and public health studies.
- Full Text:
- Date Issued: 2018
Bayesian spatio-temporal zero-inflated mixed models for overdispersion on chronic disease mapping
- Authors: Osuji, Georgeleen O https://orcid.org/0000-0002-8408-3928
- Date: 2021-12
- Subjects: Medical mapping , Bayesian statistical decision theory
- Language: English
- Type: Doctoral theses , text
- Identifier: http://hdl.handle.net/10353/23644 , vital:58230
- Description: Background: Life expectancy in most developing countries has remarkably increased and decreased in mortality, but under 5 years old mortality has increased due to HIV and Tuberculosis incidence. Many factors have been established to influence the mortality rate among HIV patients and understanding the factors contribution to the risk of under 5-year-old mortality is important for designing appropriate health interventions. Excess zeros usually occur in such HIV mortality count data. Mixed models consisting of count part and zero part are often used to describe the observed excess zero in the data. Poisson models are popular modeling inference, but Negative-Binomial models are more flexible in analyzing count data and dealing with overdispersion. Method: This research proposed to develop two-part hurdle models in analyzing areal zero count data. A spatial Bayesian lognormal-logit hurdle model (BLLHM) with random effects characterizes and cross-spatial dependencies were introduced. The parameter inferences and predictions were evaluated using the Markov Chain Monte Carlo algorithm. The model proposed was applied to HIV-positive under 5-year-old mortality collected from the Eastern Cape Department of Health. Results: Bayesian lognormal-logit hurdle model is selected as the best model fit. It is observed that the total number of HIV patients not on ART-HIVnotTB (0.000612, p <0.000) was positively and statistically significantly associated with the HIV-positive mortality of under 5 years patients. Both CD4 counts were done on newly diagnosed HIV rate (CD4count) and HIV-positive new patients screened for TB rate (HIVTBrate) were negatively and statistically significantly associated with the HIV-positive mortality of under 5 years patients (-0.6294, p = 0.000 and -0.00056, p = 0.0052). However, the covariate HIV positive Tuberculosis Preventive therapy (TPT) uptake rate (HIVandTB) was not statistically significantly associated with the HIV-positive mortality of under 5 years patients (-0.00155, p = 0.5392). Conclusion: The model is flexible to deal with zero-inflated and over-dispersed count data. There is a need to consider the risk of cause-specific under-5-year-old mortality in terms of spatial effects. , Thesis (PhD) -- Faculty of Science and Agriculture, 2021
- Full Text:
- Date Issued: 2021-12