PhD. (Environmental Management) / Climate change and variability has rapidly emerged as one of the most serious threats to sustainable development especially for developing African countries such as Rwanda. Since most of the agricultural activities in African countries are rain-fed, any adverse change in climate is likely to have a devastating effect on output and the livelihood of the majority of the population in the affected countries. Therefore, there should be continuous and regular preparedness to on-going climate variability. Climate change and variability derived information, are most likely to improve the agricultural outcomes when it is integrated into a framework for decision making to mitigate specific risks. It is in that regard, this research aims at analyzing climate change and variability and their impacts on the yields of major food crops in Rwanda. The raw climatic data (temperatures and precipitations) used in this study were obtained from the Rwandan Meteorological Center based in Kigali and Rwanda Environment Management Authority (REMA) while the agricultural records were collected from the National Institute of Statistics of Rwanda (NISR) and the Ministry of Agriculture and Animal Resources (MINAGRI). Length and completeness of records were the basic criteria used to select weather stations in order to have the most complete dataset. Five major crops, namely beans, cassava, Irish potatoes, maize, and sweet potatoes were selected for investigation because they are grown over large areas in most parts of the country during the two agricultural seasons i.e. season A (September-January) and season B (February-June). This research uses a number of statistical techniques in an attempt to quantify the magnitude and significance in temperature, rainfall, number of rainy days, aridity index and rainfall erosivity changes and variability taking place over Rwanda. The same techniques were applied in determining the magnitude and significance of inter-annual variations in food crop yields over Rwanda. A geographical information system (GIS) was used to present spatially the results on maps...

>Magister Scientiae - MSc / Aim: To compare osseous changes in the mandibular condyles in patients presenting to the Oral Health Center, Tygerburg Campus, with and without clicking of the temporomandibular joint. Background: Clicking of the temporomandibular joint (TMJ) is not a normal occurrence in its form or function. A chronic click may lead to the development of osteoarthritis. A clinical finding of clicking of the joint can reflect osseous changes of the bony structures and form part of the early signs of degenerative joint diseases. These osseous changes can be detected on Cone Beam Computed Tomography (CBCT) images. The purpose of this study is to confirm the presence osseous changes of the joint and institute the early management of these patients. Failure to intervene in the early stages could result in disease progression to possible osteoarthritis. CBCT imaging will be used to assess osseous changes in the temporomandibular joints with reference to erosions, flattening, lipping, sclerosis and osteophyte formation. Materials and methods: 25 patient records were selected for a control group and 25 patients that attended the Oral Health center were screened for asymptomatic clicking of the temporomandibular joints. Osseous changes of the 100 condyles were examined by the author and a senior member of the department. Changes were recorded when consensus was reached on the presence of any changes. Cone Beam Computed Tomography was used to assess the joints in both groups. Results: Age and gender showed no statistical significance between the 2 groups. The proportion of ‘yes’ for the variables showed that sclerosis (right) was statistically significant when comparing case versus control groups (P = 0.002). A chi-squared test applied to the data resulted in observed chi-square = 15.68, df = 1, p-value = 7.501e-05, (<0.0001) confirming that the discrimination is statistically significant. Conclusion: Osseous changes were found in both the control and case group. The case group exhibited equal or greater prevalence of osseous changes. Patients with asymptomatic click of the temporomandibular joints demonstrate osseous changes.

The main focus of my dissertation is on the conformational motion of DNA, studied by applying tools from the computational chemistry field. In addition, studies of relative α- and 310 helical stabilities in peptides/mini-proteins, and a molecular flooding study of the retinoid X-receptor as part of a continuing drug design effort are presented. In molecular biology, it has been well known that sequence determines structure, and structure controls function. For proteins or DNA to work properly, the correct configuration is required. Mutations may alter the structure, which can cause malfunction. Non-mutational effects, such as a change in environment may also cause a configurational change and in turn change the functionality of the protein or DNA. Many experimental technics have been developed to investigate the structural or configurational aspects of biological systems, and molecular dynamics simulation has been proven to be a useful complementary tool to gain insights into this problem due to its ability to explore the dynamics and energetics of biomolecular processes at high spatial and time resolution. Molecular dynamics simulations are constrained by the available computational power, but several computational techniques have been developed to reduce computational costs. Also, development of hardware has helped the issue. Years of hard work on force field parameter optimization built a solid foundation for molecular dynamics simulations, so that the computational model can satisfactory describe many biochemical systems in detail. Techniques such as umbrella ix sampling and reweighting methods have allowed researchers to construct free energy landscapes to reveal the relative stabilities of each major configurational state and the free energy barriers between configurations from relatively short simulations, a process which would otherwise require many microseconds of unbiased simulations. My dissertation applies multiple advanced simulation techniques to investigate several DNA conformational problems, including the coupling between DNA bending and base flipping, the anisotropy of DNA bending, and intercalation of the dye in a Cy3 labeled DNA system. The main part of this work addressed a long standing question about DNA bending: does DNA prefer to bend toward the major or minor groove. My simulations not only answered this question, but also identified the mechanism by which the one direction is favored. Another part describes peptide/mini-protein helical transitions and studies benefiting ligand design for the retinoid X-receptor.

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The study of landforms has, to a large extent been neglected by exploration geologists. This is surprising because field geology is intimately related with landforms of one type or another. An understanding of the geomorphological history of a particular area will assist in the appreciation of the surficial environment, the processes of weathering, soil formation and duricrust (calcrete , ferricrete silcrete) formation. This has direct application in planning and interpreting geochemical sampling programmes. In order to understand the evolution of landforms it is necessary to study slope development in some detail. Agents of erosion and denudation constantly at work, remove detritus from hillcrests down to the drainage lines which form the local base level from whence material is transported down to the sea. The system is one of dynamic equilibrium, and the concept of grade is important in understanding hillslope evolution. Thus Section (1) of this discussion deals with past and present theories of hillslope evolution. Very little work has been done recently on the geomorphology of Southern Africa and the presently accepted classification of land surfaces is based on the work of Prof. L.C. King (numerous publications). However, through the more recent work of De Swardt and Bennet (1974) on the geomorphology of Natal, it is apparent that the present system of landform classification in Southern Africa requires widespread revision. The relationship of erosion cycles in Southern Africa to the late Jurassic-early Cretaceous break-up of Gondwanaland has received insufficient attention in the past. Erosion cycles bear an intimate relationship to offshore Cretaceous and Tertiary-Recent sedimentation. Valuable information on these sediments has only recently become available as a result of offshore exploration for oil. The findings of De Swardt and Bennet (1974) are summarized in Section (2) and the present land surface classification of Southern Africa is reviewed. Finally, some suggestions on a new interpretation of land surfaces in Southern Africa are given.

Since the first period of the Kyoto Protocol, there has been a growing concern that the burden of reducing greenhouse gas emissions should not only be borne by developed countries, but developing countries as well. South Africa, as the 18th highest emitter of greenhouse gases in the world and highest in Africa, has a significant responsibility to reduce its emissions levels. The South African government is currently in the process of implementing a carbon tax for its short term response to climate change and considering the implementation of a carbon market as a medium to long term response to climate change. Both of these market based mechanisms are widely deemed effective in the mitigation of greenhouse gas emissions by economists, however are also known to have negative social and economic implications upon an economy. This study identifies these implications and attempts to provide considerations on how to alleviate the implications through the most appropriate process of revenue recycling. The negative effects of Implementing a carbon tax or carbon market could be severe as and not limited to: a significant decline in GDP, a reduction in the standard of living for certain households, a fall in a country's exports and even an increase in poverty. South Africa's environmental and development policies place a strict precedence on the protection of the poor and the prevention of economic hardship induced by such policies. This places significant importance on the prevention of these externalities from occurring. A primary means of doing so is through the process of revenue recycling, however, certain channels of revenue recycling are by no means helpful, hence the most appropriate channel needs to be identified. The study carried out a multiple case study analysis on Ireland, Mexico, New Zealand and Norway, to determine what effects a carbon tax had on their economies and how these effects were mitigated through carbon tax revenue recycling. An additional analysis of the EU ETS was carried out to determine how the EU ETS was implemented and the controversies and concerns that arose during its implementation. The findings of this analysis were then compared to a number of South African economist’s case studies, and the most appropriate method of revenue recycling identified and possible solutions to the EU ETS controversies found. The study concludes that a food subsidy has the potential to provide positive effects on welfare employment and GDP; therefore could be considered to be the most appropriate method of revenue recycling. However, these effects are limited to be experienced only at low levels of a carbon tax, hence, short term in nature. The study therefore provides a further consideration that the use of multiple channels for revenue recycling needs to be explored that could provide stable longer term effects. In addition, in the implementation of a carbon market, the study concludes that government should consider using an auction approach in the initial allocation phase of an ETS and the use of a centralized registry for monitoring and controlling of information and transactions.

Climate change continues to present a major challenge to food security around the world. The potential impact of climate change of rural livelihoods is especially significant as rural communities often rely heavily on natural resources to sustain their livelihoods and, hence, food security. This is applicable to the rural town of Hamburg, on the Eastern Cape coast of South Africa. The Sustainable Rural Livelihoods framework analyses livelihoods in terms of the context, available capitals and institutional framework that determines the livelihood strategies and outcomes for rural households. In terms of livelihood outcomes for Hamburg, it was found that the households have a heavy reliance on state grants in their livelihood portfolios. Natural resources, in the form of agriculture and harvesting of marine organisms, played only a supplementary role in livelihood strategies. Thus, given that climate change would impact negatively on the estuarine resources and the impact on agriculture is unknown as the climate becomes wetter and hotter, the impact on livelihoods and food security would not be significant. However, the sustainability of current livelihood strategies is questionable as grants, by their very nature, or unsustainable and therefore can result in vulnerability and food insecurity in the long-run for households. It is recommended that grants should be issued within the community, instead of in the distant town of Peddie, to help develop the local economy and reduce leakages. This would allow for diversification of livelihood strategies in Hamburg. In addition, government support through extension officers should be extended to Hamburg to assist in developing the local agriculture sector

Poor communities already face severe challenges in meeting their basic needs, whether because of poor income opportunities, inadequate service delivery, or degraded ecosystems that can no longer support the needs of people. Non profit organisations who provide support for development are also challenged by financial restrictions and social and political structures that prevent or limit project development. Climate change is understood to have the most severe impact on the most vulnerable communities and sectors of communities by reducing the availability and accessibility of basic resources such as water, food and energy, impacting severely on human health and wellbeing, and further reducing the capacity of ecosystems to support livelihoods. This will add a layer of significant new complications to the ability of poor communities to maintain or improve standards of living, and further challenge non profit organisations that support such communitiesAnticipatory adaptation to climate change can reduce some of the impacts of climate change, and also address some key development stresses. This thesis aims to provide a framework that is relevant for supporting adaptation to climate change within the context of resource poor communities in a developing country. Non profit organisations and donor agencies could support success and autonomy in adaptation processes by making provision for locally defined understanding of adaptation, and locally determined processes and programmes. This can be taken further into implementation of programming that addresses local short term development priorities alongside, or as part of long term adaptation work. The research followed a number of steps involving a multitude of techniques including literature review, interviews, a survey, consultation with an expert group, further consultation with stakeholders, and a final electronic review. Its outcome is a strategy that can be used to support climate change adaptation in resource poor communities. A definition for adaptation is proposed as an interpretation of adaptation that is relevant in this context. The intended end goal of adaptation as defined in this research is a better form of development that : supports a harmonious and respectful relationship between humans and their natural resource base; averts further destructive global change or at the very least prevents it from becoming unmanageable; and manages the impacts of past and ongoing destructive change so that there is lowest possible loss of natural, human, or cultural resources. The term transformative adaptation emerged from the research processes to describe adaptation to climate change that concurrently addresses development challenges, is grounded in community development aspirations, integrates programming work across multiple thematic areas and approaches, and addresses the causes of climate change within adaptation interventions. The following broad guidelines are used to inform programming within the framework of transformative adaptation : Human communities are faced with an enormous challenge resulting from global change and sociopolitical injustices; Well planned anticipatory adaptation can limit exposure and vulnerability to at least some of the projected impacts of climate change; Adaptation to climate change incorporates a reduction of vulnerability to underlying development stresses, alongside a reduction of vulnerability to specific climate change stresses; Existing development work forms the foundation for adaptation interventions, acknowledging the interdependence of social, natural and economic systems and the need to maintain their health; Adaptation decision making is community based, and acknowledges that resource poor communities are best placed to establish their own development needs, drive implementation of interventions in own spaces, and identify own limits to adaptation; Adaptation work incorporates mitigation objectives so that the causes of climate change are addressed as part of the strategy for coping with climate change; Adaptation programming acknowledges the strong interlinkages between, and integrates work across, the thematic areas of water security, food sovereignty, energy security, land security, human wellbeing and livelihood diversity; Adaptation uses a broad set of approaches that spans research, knowledge sharing, advocacy, and investment in technology and infrastructure; There is flexibility in project design and implementation to allow room for experimentation with new concepts, and also to change design as knowledge, understanding, and geophysical, biophysical and sociopolitical conditions change.

Mangrove forests are subjected to many environmental factors which influence species distribution, zonation patterns as well as succession. Important driving factors in these forests are salinity, water level fluctuations and available light. This study investigated the response of red mangrove (Rhizophora mucronata Lam.) seedlings to these factors in controlled laboratory experiments. Increase in salinity and prolonged inundation within estuaries are predicted impacts resulting from sea level rise due to climate change. The study investigated the effect of five salinity treatments (0, 8, 18, 35 and 45 ppt) with a semi-diurnal tidal cycle on seedling growth. In a separate experiment the effect of different inundation treatments: no inundation, 3, 6, 9 hour tidal cycles and continuous inundation (24 h) were investigated. Both morphological and physiological responses of R. mucronata seedlings were measured. There was a decrease in growth (plant height, biomass and leaf production) with increasing salinity. Seedlings in the seawater, hypersaline and no inundation treatments showed symptoms of stress, having increased leaf necrosis ("burn marks"). The highest growth occurred in the low salinity (8 ppt) treatment, but the highest photosynthetic performance and stomatal conductance occurred in the freshwater treatment (0 ppt). The typical response of stem elongation with increasing inundation was observed in the 24 hr inundation treatment. In the light and salinity combination study there were ten different treatments of five different light treatments (unshaded, 20 percent, 50 percent, 80 percent and 90 percent shade) combined with two salinity concentrations (18 and 35 ppt). In this study the seedling growth: plant height, biomass, leaf surface area and leaf production were higher in the moderate salinity (18 ppt) treatments compared to the seawater (35 ppt) treatments. Biomass in the 35 ppt experiment decreased with increasing shade as well as in the unshaded treatments. Photosynthetic performance and stomatal conductance were lower for the unshaded treatment in both 18 and 35 ppt salinity compared to all other treatments with the same salinity. This suggests that R. mucronata more shade than sun tolerant, but overall it can be concluded that the species has a broad tolerance range. The results may be relevant in mangrove rehabilitation and predicting responses to climate change. This is important as mangrove ecosystems may adapt to changing sea levels and in order to restore areas it will be necessary to choose the mangrove species which will grow best. The results may also help to increase the protection of existing mangrove habitats.

The total mangrove area cover in South Africa is 1631.7 ha, with the largest area cover in a few estuaries in the KwaZulu-Natal Province (1391.1 ha) and the remainder recorded in the Eastern Cape Province with 240.6 ha. This represents 0.05 percent of Africa‟s mangrove area cover and although small adds irreplaceable value to the biodiversity of South Africa. Mangroves are threatened by over-utilization through harvesting for firewood and building materials as well as excessive browsing and trampling by livestock. The objective of this study was to investigate the response of mangroves to different stressors from natural change as well as anthropogenic pressures. This was done by identifying pressures, measuring area cover, population structure and environmental parameters such as sediment characteristics. Mangroves in 17 estuaries along the east coast were investigated. Population structure and the area covered by mangroves in 2011/2012 were compared with data from the same area for 1999. Detailed studies were conducted in St. Lucia Estuary to investigate the response of mangroves to reduced tidal flooding; mangrove expansion at a latitudinal limit in a protected area at Nahoon Estuary was studied and the effect of cattle browsing on mangroves was measured at Nxaxo Estuary. The St. Lucia Estuary (28°S; 32°E) represented a unique study site as the mouth has been closed to the sea since 2002 and the mangrove habitats have been non-tidal. St. Lucia Estuary is both a Ramsar and World Heritage site and therefore understanding the response of mangroves to changes in the environment is important. In 2010 sediment characteristics and mangrove population structure were measured at four sites which were chosen to represent different salinity and water level conditions. The site fringing the main channel had the highest density of mangrove seedlings and saplings. The dry site had a lower density of mangroves with mostly only tall adult trees and few saplings. Mangrove tree height and density increased at sites with high sediment moisture and low surface sediment salinity. Few seedlings and saplings were found at sites with dry surface sediment and high salinity. Long term data are needed to assess the influence of mouth closure on recruitment and survival of the mangrove forest at St. Lucia Estuary; however this study has shown that sediment characteristics are unfavourable for mangrove growth at sites now characterized by a lack of tidal flooding. It is not known when exactly the mangroves were planted in Nahoon Estuary (32°S; 27° E), East London, but it is suspected that this was in the early 1970s. Avicennia marina (Forrsk.)Vierh. was planted first, followed a few years later by the planting of Bruguiera gymnorrhiza (L.) Lam. and Rhizophora mucronata (L.) among the larger A. marina trees. Surprisingly the mangrove population appears to be thriving and this study tested the hypothesis that mangroves have expanded and replaced salt marsh over a 33 year period. This study provides important information on mangroves growing at higher latitudes, where they were thought to not occur naturally due to lower annual average temperatures. It further provides insights on future scenarios of possible shifts in vegetation types due to climate change at one of the most southerly distribution sites worldwide. The expansion of mangroves was measured over a 33 year period (1978 - 2011) using past aerial photographs and Esri ArcGIS Desktop 10 software. In addition, field surveys were completed in 2011 to determine the population structure of the present mangrove forest and relate this to environmental conditions. The study showed that mangrove area cover increased linearly at a rate of 0.06 ha-1 expanding over a bare mudflat area, while the salt marsh area cover also increased (0.09 ha-1) but was found to be variable over time. The mangrove area is still small (< 2 ha) and at present no competition between mangroves and salt marsh can be deduced. Instead the area has the ability to maintain high biodiversity and biomass. Avicennia marina was the dominant mangrove species and had high recruitment (seedling density was 33 822 ± 16 364 ha-1) but only a few Bruguiera gymnorrhiza and Rhizophora mucronata individuals were found (< 10 adult trees). The site provides opportunities for studies on mangrove / salt marsh interactions in response to a changing climate at the most southern limit of mangrove distribution in Africa. This research has provided the baseline data, permanent quadrats and tagged trees to be used in future long-term monitoring of population growth and sediment characteristics. At Nxaxo Estuary (32°S; 28°E) the response of mangrove trees (Avicennia marina) to cattle browsing and trampling was investigated by using cattle exclusion plots. Exclusion plots were established by fencing in five 25 m2 quadrats and adjacent to each experimental quadrat a control quadrat (not fenced in, 25 m2) was set-up. Trees were tagged and measured annually from 2010 to 2012. Sediment salinity, pH, moisture, organic content, compaction as well as sediment particle size was also measured in each quadrat. Sediment characteristics did not vary between control and experimental plots but did show changes between the years. The mangrove trees in the cattle exclusion plots grew exponentially over a period of two years. There was a significant increase in mean plant height (5.41 ± 0.53 cm), crown volume (0.54 ± 0.01 m3) and crown diameter (7.09 ± 0.60 cm) from 2010 to 2012. Trees in the control plots had significantly lower growth (p < 0.05). There was a decrease in plant height (-0.07 ± 0.67cm1) and only small increases in crown volume (0.14 ± 0.1 m3) and crown diameter (2.03 ± 2.61 cm). The research showed that browsing on mangroves by cattle stunts growth and causes a shrubby appearance as a result of coppicing. The browsed trees were dwarfed with horizontal spreading of branches and intact foliage close to the ground while the plants in the cattle exclusion plots showed an increase in vertical growth and expansion. In the cattle exclusion plots there was a significantly higher percentage of flowering (67 percent) and fruiting (39 percent) trees in 2012 compared to the control sites where 34 percent of the plants were flowering and 5.4 percent of the plants carried immature propagules. Observations in the field also indicated that cattle had trampled a number of seedlings thus influencing mangrove survival. The study concluded that browsing changes the morphological structure of mangrove trees and reduces growth and seedling establishment. This is an additional stress that the mangroves are exposed to in rural areas where cattle are allowed to roam free. Seventeen permanently open estuaries provide habitat for mangrove forests along the former Transkei coast. This part of the Eastern Cape is mostly undeveloped and difficult to access. Mangrove area cover, species distribution, population structure and health of the mangrove habitat were compared with results from previous studies in 1982 and 1999. The mangrove Bruguiera gymnorrhiza had the densest stands and was widely distributed as it was present in 13 of the 17 estuaries. Avicennia marina was dominant in those estuaries which had the largest area cover of mangroves and was present in 10 estuaries, while Rhizophora mucronata was rare and only present in five estuaries. Anthropogenic and natural impacts were noted within the mangrove habitats in each of these estuaries. Harvesting of mangrove wood, livestock browsing and trampling and footpaths occurred in most of the estuaries (> 70 percent). It was observed that browsing on trees resulted in a clear browse-line and browsing on propagules mainly by goats resulted in reduced seedling establishment in most of the estuaries except those in protected areas. Mangroves had re-established in estuaries where they had been previously lost but mouth closure due to drought and sea storms resulted in the mass die back of mangroves in the Kobonqaba Estuary. There was a total loss of 31.5 ha in mangrove area cover in the last 30 years and this was a total reduction of 10.5 ha (11 percent) for every decade. This is high considering that the present total mangrove area cover is only 240.6 ha for all the Transkei estuaries. In this study it was concluded that the anthropogenic impacts such as livestock browsing and trampling as well as harvesting in these estuaries contributed most to the mangrove degradation as these are continuous pressures occurring over long periods and are expected to increase in future with increasing human population. Natural changes such as sea storms occur less frequently but could result in large scale destruction over shorter periods. Examples of these are mouth closure that result in mangrove mass mortality as well as strong floods which destroy forest by scouring of the banks.