Biogeographic patterns of endolithic cyanobacteria and their negative impacts on mussels along the South African coast
- Authors: Ndhlovu, Aldwin
- Date: 2020
- Subjects: Cyanobacteria -- South Africa , Cyanobacteria -- Geographical distribution , Prokaryotes -- South Africa , Mexilhao mussel -- South Africa , Mytilus galloprovincialis -- South Africa , Coastal biology -- South Africa , Coastal ecology -- South Africa , Mussels -- Geographical distribution , Mussels -- Predators of , Mussels -- Mortality -- South Africa , Mussels -- Ecology -- South Africa , Mussels -- Growth -- South Africa , Mussels -- Fertility -- South Africa
- Language: English
- Type: Thesis , Doctoral , PhD
- Identifier: http://hdl.handle.net/10962/144656 , vital:38367
- Description: Endolithic cyanobacterial species occur in a wide range of environments including cold and hot deserts as well as marine systems where they attack biological material such as corals and the shells of molluscs including limpets, mussels and abalone. Endoliths live as parasites in mussel shells, where they erode and extract calcium carbonate leading to shell weakening, creating fracture holes that lead to shell collapse and death, but they also have positive effects when they lead to discolouration of mussel shells hence giving them the ability to reduce stressful heat gain during periods of extreme heat stress. Mussels are ecological engineers on which the abundance and diversity of associated species assemblages depend. Understanding how endolithic cyanobacteria affect mussels will not only help in predicting future patterns of mussel abundances, but also future patterns of the infauna that depend on them. Firstly, I identified endolithic species infesting mussels and assessed the prevalence of endolithic parasitism in two intertidal mussel species in South Africa, the native Perna perna and the invasive Mytilus galloprovincialis. Large-scale surveys of endolithic infestation of mussels were conducted along 2500 km of the South African coast, covering three biogeographic regions: the subtropical east coast, dominated by P. perna, the warm temperate south coast where the indigenous species coexists with M. galloprovincialis, and the cool temperate west coast which is dominated by M. galloprovincialis. The prevalence of endolithic infestation was higher in the cool temperate bioregion than in the warm temperate and subtropical bioregions which did not differ and for P. perna endolithic species assemblages revealed clear groupings by bioregion. Results for endolithic induced mortality followed the same trend, with no significant difference between the two mussel species where they coexist and these results attribute biogeography of endoliths to environmental factors rather than host identity. Secondly, I assessed energy budgets of infested and clean mussels, to evaluate the energetic cost of infestation. This involved measuring energy acquisition, expenditure, calculating scope for growth and lethal temperatures (LT50s). The results revealed that endolithic cyanobacteria have a negative effect on scope for growth due to increased metabolic rates for infested mussels, with no effect of endoliths on the rates or efficiency of energy acquisition through filtration and no effect on lethal temperatures. The effects of infestation were then examined in more detail through a qualitative and quantitative analysis of mussel gonads and byssal attachment strength to the substratum. Endolithic infestation was found to affect reproduction by affecting the size (mass) of gonads, but not the density of eggs within them. Attachment strength was affected by endolithic infestation with very infested mussels requiring much less force to detach them from the substratum compared to mussels with low or no infestation. These results show that endolithic infestation affects mussel fitness by directly affecting attachment strength and by reducing their reproductive output. Thirdly, endolithic succession within mussel shells was examined by assessing endolithic species composition in different regions of the shell and as a function of time. The results on the spatial distribution of endolith species within a shell supported those for temporal succession in shells deployed in the field. Endolithic species that were early colonists of clean shells were similar to those that were found in the distal edge, the new and growing region of the shell and species that arrived late in succession were similar to endolithic species found near the umbo, the oldest region of the shell. Overall, the study shows that endolithic cyanobacteria show the effects of biogeography on species distribution and clear patterns of succession within mussel shells. Cyanobacteria affect mussels negatively; they lead to low scope for growth and hence low growth rates, low reproductive output and reduced attachment strength for infested mussels. This, in turn is expected to have indirect consequences for other species that rely on mussels as ecological engineers for their survival.
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- Date Issued: 2020
BODIPY dyes for application in the photo-oxidation of pollutants, photodynamic antimicrobial chemotherapy, and nonlinear optics
- Authors: Kelechi, Lebechi Augustus
- Date: 2020
- Subjects: Dyes and dyeing -- Chemistry , Fluorescent probes , Fluorescence spectroscopy
- Language: English
- Type: text , Thesis , Masters , MSc
- Identifier: http://hdl.handle.net/10962/140298 , vital:37859
- Description: The synthesis and structural characterization of a series of BODIPY dyes to analyze both the effects of halogenations at the 2,6-positions and the introduction of styryl groups at the 3,5-positions. The photophysical properties of these dyes were investigated to determine their suitability as singlet oxygen-generating photosensitiser dyes for application in photocatalytic degradation of azo dyes and in photodynamic antimicrobial chemotherapy (PACT). Upon halogenation, the dyes showed high to moderate singlet oxygen quantum yields. The potential utility of electrospun polystyrene (PS) nanofibres embedded with halogenated BODIPY dyes for the photocatalytic degradation of Orange G and Methyl Orange from textile industry effluents were investigated. A comparison of the singlet oxygen quantum yield of the BODIPY dyes in solution and when embedded in the PS nanofibres support demonstrates that its photosensitiser properties are maintained in the nanofibre mats. The photocatalytic degradation properties of the PS nanofibres for Orange G and Methyl Orange were determined by using a 530 nm and 660 nm light-emitting diodes. The rate of photodegradation increases with both the Orange G and Methyl Orange concentrations and follows pseudo-first-order kinetics. The PACT activities of brominated BODIPYs on Escherichia coli and Staphylococcus aureus were investigated. Log reduction values of over 9 were obtained during the photoinactivation of Staphylococcus aureus. To be able to red-shift the main spectral band of the BODIPY dyes into the therapeutic window, styryl groups were introduced at the 3,5-positions through a modified Knoevenagel condensation reaction. Because the red-shifted spectral band lies above 532 nm, the second harmonic of the Nd:YAG laser, there is very minute absorption at this wavelength. One of the novel brominated BODIPY dyes was investigated for its potential utility as optical limiting materials in nonlinear optics (NLO), and the dyes demonstrated typical nonlinear absorption behaviour characterised by reverse saturable absorption (RSA) in Z-scan measurements. Excellent optical limiting parameters were obtained for third-order susceptibility and hyperpolarisability.
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- Date Issued: 2020
Building a flexible and inexpensive multi-layer switch for software-defined networks
- Authors: Magwenzi, Tinashe
- Date: 2020
- Subjects: Software-defined networking (Computer network technology) , Telecommunication -- Switching systems , OpenFlow (Computer network protocol) , Local area networks (Computer networks)
- Language: English
- Type: text , Thesis , Masters , MSc
- Identifier: http://hdl.handle.net/10962/142841 , vital:38122
- Description: Software-Defined Networking (SDN) is a paradigm which enables the realisation of programmable network through the separation of the control logic from the forwarding functions. This separation is a departure from the traditional architecture. Much of the work done in SDN enabled devices has concentrated on higher end, high speed networks (10s GBit/s 100s GBit/s), rather than the relatively low bandwidth links (10s MBit/s to a few GBit/s) which are seen, for example, in South Africa. As SDN is increasingly becoming more accepted, due to its advantages over the traditional networks, it has been adopted for industrial purposes such as networking in data centres and network providers. The demand for programmable networks is increasing but is limited by the ability of providers to upgrade their infrastructure. In addition, as access to the Internet has become less expensive, the use of Internet is increasing in academic institutions, NGOs, and small to medium enterprises. This thesis details a means of building and managing a small scale Software-Defined Network using commodity hardware and open source tools. Core to the SDN Network illustrated in this thesis is the prototype of a multi-layer SDN switch. The proposed device is targeted to serve lower bandwidth communication (in relation to commercially produced high speed SDN-enabled devices). The performance of the prototype multilayer switch had shown to achieve: data-rates of up to 99.998%, average latencies that are under 40µs during forwarding/switching and under 100µs during routing while using packet sizes between 64 bytes and 1518 bytes, and a jitter of less than 15µs during all tests. This research explores in detail the design, development, and management of a multi-layer switch and its placement and integration in small scale SDN network. This includes testing of Layer 2 forwarding and Layer 3 routing, OpenFlow compliance testing, the management of the switch using created SDN applications, and real life network functionality such as forwarding, routing and VLAN networking to demonstrate its real world applicability.
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- Date Issued: 2020
Carnivore intra-guild competition in Selati Game Reserve, Limpopo Province, South Africa
- Authors: Comley, Jessica
- Date: 2020
- Subjects: Hyenas -- Behavior -- South Africa , Hyenas -- South Africa , Hyenas -- Ecology -- South Africa , Top predators -- South Africa , Top predators -- Ecology -- South Africa , Animal communities -- South Africa , Animal behavior -- South Africa , Mutualism (Biology) -- South Africa , Coexistence of species -- South Africa , Game farms -- South Africa , Selati Game Reserve (South Africa)
- Language: English
- Type: text , Thesis , Doctoral , PhD
- Identifier: http://hdl.handle.net/10962/115558 , vital:34163
- Description: Carnivore intra-guild interactions can be important drivers of carnivore community composition and ecosystem functioning. Large carnivores are particularly important since they occupy the highest trophic levels and can exert extensive influences on subordinate carnivores and prey species. Given Africa’s rapidly expanding human population, enclosed reserves such as those found in South Africa, may become increasingly important for carnivore conservation. A major concern, however, is that the interactions and co-existence of multiple carnivores in these systems is poorly understood. Additionally, the majority of reserves in South Africa are small ( 400km²), potentially increasing the likelihood of competition. My research aimed to provide insight into the interactions and co-existence of a multi-carnivore community within a small, enclosed reserve in South Africa (Selati Game Reserve). I tackled this task by using a combination of field techniques including camera trap surveys, ungulate transect surveys, aerial count surveys, location data collected from collared large carnivores and scat and kill site analyses. I found that carnivore-carnivore interactions, and their associated impacts, varied within the carnivore guild and that co-existence may be due to trade-offs between various risks (i.e. interference and exploitative competition) and benefits (i.e. resources such as food and space). My findings also revealed that large carnivores, such as lions (Panthera leo), spotted hyaenas (Crocuta crocuta) and leopards (Panthera pardus) do not have homogenous effects and that site-specific research on multiple-carnivores is integral for conserving biodiversity and ecosystem dynamics. Lions were the dominant large carnivore (in terms of intra-guild predation, space use and resource use) despite being outnumbered seven to one by spotted hyaenas. Leopard occupancy was negatively influenced by lions and leopard diet overlapped almost completely (91%) with spotted hyaenas, suggesting increased kleptoparasitism of leopard kills by spotted hyaenas. While my study provides valuable insight into the complexity of carnivore intra-guild competition in a small, enclosed reserve it also highlights major research gaps and emphasises the need for ecosystem-based research throughout southern Africa to fully understand how multiple sympatric carnivores co-exist in these systems.
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- Date Issued: 2020
Chasing Eden: Margaret Atwood’s MaddAddam trilogy and the value of reading in a technological age
- Authors: Bosman, Zoë June
- Date: 2020
- Subjects: Atwood, Margaret, 1939- MaddAddam trilogy , Speculative fiction -- History and criticism , Capitalism in literature , Dystopias in literature , Science fiction -- History and criticism , Technology in literature
- Language: English
- Type: Thesis , Masters , MA
- Identifier: http://hdl.handle.net/10962/145796 , vital:38467
- Description: This thesis is focussed on Margaret Atwood’s MaddAddam trilogy: Oryx and Crake (2003) The Year of the Flood (2009) and MaddAddam (2013). Detailing Atwood’s own specifications as to why these texts should be categorised as works of speculative fiction, the thesis examines how this literary genre, and Atwood’s MaddAddam trilogy in particular, is uniquely capable of encouraging readers to interrogate critically the socio-economic, environmental, and ethical problems to which she, and the contemporary reader, bear witness in the present technological age. With reference to Atwood’s essays and critical writings, Darko Suvin’s Metamorphoses of Science Fiction, and Wolfgang Iser’s The Act of Reading, this project explores the value of reading speculative fiction and details how Atwood has constructed the fictional, yet plausible, possible future world of her trilogy by extrapolating our current scientific capabilities, environmental challenges, and political configurations to their logical conclusions. It explores the close relationship that exists between the near-future world of Atwood’s texts and the contemporary context from which she has drawn her subject matter, and argues that the trilogy demonstrates graphically the long-term consequences of capitalism, sustainability, and the doctrine of human exceptionalism, which this project, following Yuval Harari, defines as orthodox guiding narratives: fictions that humanity has created, and which structure our perception of reality and guide our behaviour. The project maintains that Atwood’s trilogy presents the reader with a hypothetical future that looks towards and beyond the end of contemporary technological society in order to urge her reader to imagine, and actualize, alternatives to the scenarios that these texts depict. The most significant question Atwood’s texts ask is whether contemporary technological society is willing and able to transform in order to avert the ecological apocalypse that is the logical conclusion to the Anthropocene?
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- Date Issued: 2020
Chirema Chine Mazano Chinotamba Chakazendama Madziro
- Authors: Mapondera, Wallen
- Date: 2020
- Subjects: Art, Zimbabwean , Art -- Economic aspects -- Zimbabwe , Artists -- Zimbabwe , Takadiwa, Moffet , Nyandoro, Gareth , Clottey, Serge Attiku , Mapondera, Wallen -- Exhibitions
- Language: English
- Type: text , Thesis , Masters , MFA
- Identifier: http://hdl.handle.net/10962/147457 , vital:38638
- Description: This mini-thesis has developed as a practice-based supporting document to the exhibition Chirema Chine Mazano Chinotamba Chakazendama Madziro. The exhibition responds to how people become innovative in finding alternative means of survival and staying relevant in an economically depressed country. Zimbabwe is often the first country that comes to mind when people talk about hyperinflation; the situation was and still is intolerable, but somehow its citizens find means to pull through. Unemployment and poverty are the main causes of physical and mental problems for an individual. With this thesis, I highlight the innovations employed by Zimbabweans as a way of keeping themselves busy. I approach this through analysing the Zimbabwean general public’s creative reactions, and by tracing Zimbabwean visual artists’ use of found objects as a reaction to the country’s economic hardships. As people have been pushed to find alternative ways of survival, Zimbabwean artists in particular also shifted from using conventional art materials due to their unavailability. They began to redefine what art material is by employing objects in their artworks that previously had a non-art function. As such, there is a growing need to recognise, classify and document the shifts and establish platforms to generate growth of these innovations. In this minithesis I discuss my own practice, and I analyse the works of Moffat Takadiwa, Gareth Nyandoro and Serge Attiku Clottey.
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- Date Issued: 2020
Choreographies of protest performance as recruitment to activism and the movement of perception during the 2015 re-emergence of student activism at Rhodes University
- Authors: Qoza, Phiwokazi
- Date: 2020
- Subjects: College students -- Political activity -- South Africa , Student protesters -- South Africa , Student movements -- South Africa , Higher education and state -- South Africa , Performance art -- Political aspects -- South Africa , Protest songs -- South Africa
- Language: English
- Type: text , Thesis , Masters , MA
- Identifier: http://hdl.handle.net/10962/141692 , vital:37997
- Description: It has been argued that individuals participate in activism due to an identification with the preferences and interests of an emerging group of actors or in solidarity with a pre-existing network that has resorted to a number of protest repertoires in order to make claims or demands. Additionally, an emerging instance of protest is often linked to an image of previous protest events through the employment of a combination of master frames which function as discursive articulation of the encounter in familiar terms, creating a frame resonance which recruits adherents and constituents. To understand why some bystanders to protest transcended to actors in protest and the development of frames within a protest cycle, a performance ethnography is employed to observe and analyse choreographies of protest which took place at an institution of higher education in South Africa during the 2015 re-emergence of wide-spread student activism. It is found that in encountering an atmosphere of protest there emerged a relation of feeling, referred to as “feeling the vibe or atmosphere”, which those who became protest performers resolved in ways which increased their capacity to act in favour of co-constituting that atmosphere. During the encounter between the bystander body and the atmosphere of protest, non-linear somatic communication, characterised by active and passive gestures and postures, occurred through which protest performers developed contact and connection with other bodies as a result of the displacement of space. This thesis suggests that participation in activism can be about going with the flow of movement in an uncertain and ambiguous moment and is not limited to an identification with the pre-existing organization of preferences and interests as a frame of resonance emerges to signify somatic communication which differentiated bodies in the duration of protest performance. Therefore, this thesis uses the theory of affect to situate student activism in-between the politics of performance and the performance of politics whereupon the rhythm of song creates an opening for the kinaesthetic to create form from spontaneous movement of the body as an event of the movement of perception and the perception of movement.
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- Date Issued: 2020
Combination ecosystem green engineering and early life history processes to enhance the intertidal biodiversity in the Port of East London
- Authors: Mafanya, Sandisiwer
- Date: 2020
- Subjects: Biotic communities -- South Africa -- East London , Perna -- Ecology --South Africa -- South Africa-- East London , Mexilhao mussel -- Ecology -- South Africa -- East London , Habitat (Ecology) -- Modification -- South Africa -- East London , Benthic animals -- Effect of habitat modification on -- South Africa -- East London , Harbors -- Environmental aspects -- South Africa -- East London
- Language: English
- Type: text , Thesis , Masters , MSc
- Identifier: http://hdl.handle.net/10962/166376 , vital:41357
- Description: Marine coastal ecosystems are highly impacted by anthropogenic activities, including the development of, and practices within, harbours and/or ports. Artificial structures associated with harbours have a different chemical composition, texture and orientation than that of the natural benthic habitats they have replaced, and are therefore not generally favourable for the settlement and occurrence of indigenous species. Attempts are being made to identify what structures and materials can be used to aid in the rehabilitation of native species within harbours. The aim of this study was to investigate the effects of utilising environmentally-friendly artificial structures (tiles) with varying complexity (crevices and ridges with different depths) with ecological engineers (the indigenous bivalve Perna perna), on the associated benthic biodiversity within an international port in South Africa (Port of East London). The objectives of the study were to test the effects of artificial habitat complexity and the presence of bivalves on 1) the growth, mortality and biomass of a selected model species of ecosystem engineer (P. perna), and 2) the associated intertidal biodiversity. Tiles seeded with bivalves (P. perna) were deployed at two sites in the Port of East London and monitored monthly over a period of 12 months (November 2016-October 2017) to assess survival, growth and associated biodiversity. Environmental variables were also measured every month. The results of the three-way repeated measures ANOVAs indicated that tile treatment (especially high complexity of 2.5 and 5 cm) had an effect on the diversity of mobile species, length, height and biomass of the bivalves used as model ecosystem engineer, indicating the potentials for protection from wave dislodgement and refuge provision. Treatment (especially flat tiles) also had an effect on sessile/sedentary species diversity, indicating the greater proportion of space provided by these non-complex tiles. In addition, month had an effect on the mortality, height and biomass of the bivalves. Mortality was highest in October 2017, while the growth in height and biomass of P. perna were largest in January and October 2017 respectively. The use of artificial tiles also had a positive effect on the survival, growth, and biomass of bivalves (especially the length, weight and dry weight in 2.5 cm and 5 cm complexity). Additionally, this research investigated patterns of settlement and recruitment of the local bivalve population (P. perna) in the Port of East London and adjacent natural coastline to understand the early life history temporal and spatial dynamics of this model ecosystem engineer species. Settlement and recruitment were assessed every month by deploying and replacing artificial collectors for a total period of 19 months (November 2016-May 2018). The results of the two-way ANOVAs indicated that month and site (port vs natural) had an effect on settlement and recruitment of bivalves. Settlement and recruitment of bivalves were highest in July 2017 (port) and March 2018 (natural rocky shore). This study has highlighted that the use of artificial concrete tiles with increased complexity, as well as the investigation of the early stages of mussel populations could be important to consider in a framework of rehabilitation of urban coastal environments such as the Port of East London. Ecological engineering (in terms of increased complexity and heterogeneity) has indeed the potentials to be incorporated in South African programmes aiming at improving natural biodiversity in coastal urban environments. Nonetheless, the spatio-temporal variability of early driver of mussel populations (settlement and recruitment) is also an important feature to be closely monitored if biodiversity in South African coastal armouring is to be enhanced effectively and in the long term.
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- Date Issued: 2020
Combining DNA barcoding and morphology to identify larval fishes from the nearshore environment off the south-east coast of South Africa
- Authors: Somana, Zinzi Sinazo
- Date: 2020
- Subjects: Fishes -- Larvae -- South Africa -- Identification , Fishes -- Genetics -- Research -- Technique , Fishes -- South Africa -- Classification , Genetic markers
- Language: English
- Type: text , Thesis , Masters , MSc
- Identifier: http://hdl.handle.net/10962/144605 , vital:38362
- Description: The early life history stages of most marine fish species are undescribed. The problem is, most of these fishes have pelagic larvae which are minute, delicate forms. Linking the larval stage to an adult counterpart is extremely challenging as larvae are morphologically different from the adults. Historically, larval fish identification relied solely on distinguishing morphological characteristics and meristic measurements, which has resulted in taxonomic confusion and misidentification. The introduction of the deoxyribonucleic acid (DNA) barcoding technique as an alternative approach has been successful in positively identifying larval fishes. The correct identification of larval specimens is the key to a better understanding of larval ecology, which underpins the success of any adult fish population. This study aimed to positively identify larval fishes of the south-east coast of South Africa using morphological characteristics and DNA barcoding. Larval and eggs specimens for this study were collected from the shallow nearshore waters of the south-east coast of South Africa. A total of 177 larval specimens were used for morphological analysis. Body shape, gut shape, pigmentation and morphometric measurements (such as body depth, preanal length and total body length) were used to identify each specimen to the family level. In addition, a fragment of mitochondrial cytochrome c oxidase subunit 1 gene (COI) was adopted for sequencing to identify larval fish specimens and fish eggs. Sequences generated from this study were compared to those in the Barcode of Life Database (BOLD). When there were no close matches to a sequence, the GenBank nucleic acid sequence database, maintained by the National Center for Biotechnology Information (NCBI), was used as an alternative. A total of 18 different families were identified through morphology. Seventy-seven of the 177 larval specimens were not subjected to morphological identification due to physical damage. The majority of larvae identified using morphological characteristics belonged to either the Sparidae, Tripterygiidae or Gobiesocidae fish families. Through DNA barcoding, 12 fish families, 16 genera and 18 different species were identified. Ten DNA barcodes (categorised as ‘no match’) from 10 different larval specimens were not identified through any of the online databases. Therefore, the 2% threshold value was used to identify members of the same species. The K2P genetic distance relationships were calculated among the no match sequences and downloaded probability matches from NCBI. This resulted in two unknown specimens assigned to the Blenniidae and Gobiidae. All other taxa were identified to species level, except specimens representing the Gobiidae and Tripterygiidae families. Based on the K2P genetic distances Gobiidae representatives were categorised as members of the Caffrogobius genus. Twenty-eight barcodes represented specimens from the Tripterygiidae. DNA barcode data from COI was analysed using the standard phylogenetic procedures in MEGA6 to examine relationships and differentiation among sequences. These could not be identified to the lowest taxonomic rank due to limited sequence data to compare them with. The sequence data from these specimens gave different results in the two online databases. BOLD results were to family level (Tripterygiidae) and NCBI to the species level (Clinidae: Pavoclinus profundus). Results in this study confirmed the efficiency of the DNA barcoding technique in species level identification of fish larvae. The evidence from genetic barcodes of the Tripterygiidae specimens, supported by morphological characteristics, suggests the need for thorough research to identify the individuals to the species level. The fact that this study identified taxonomically problematic Gobiidae and Tripterygiidae specimens suggests that studies similar to this may highlight additional diversity and help to resolve the taxonomy of other species in these families. However, the lack of reference sequence data from the adult specimens, and especially those with cryptic diversity, were both shortcomings for the positive identification of larvae. With that being said, it shows the necessity for more research to be conducted on barcoding of larvae in general as to accommodate all kinds of species from biodiversity to economic perspectives.
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- Date Issued: 2020
Come listen quickly
- Authors: Gouws, Leigh-Anne
- Date: 2020
- Subjects: South African fiction (English) -- 21st century
- Language: English
- Type: text , Thesis , Masters , MA
- Identifier: http://hdl.handle.net/10962/141559 , vital:37985
- Description: Creative work portfolio.
- Full Text:
- Date Issued: 2020
Commonplaces
- Authors: Orsmond, Joseph Granger
- Date: 2020
- Subjects: South African fiction (English) -- 21st century
- Language: English
- Type: text , Thesis , Masters , MA
- Identifier: http://hdl.handle.net/10962/144061 , vital:38307
- Description: My thesis is a collection of short to medium length poems. All of the subject matter is sustained by reflections, anecdotes or stories. The pieces in the collection are concerned with experiences linked to the seemingly ordinary and mundane. In this regard, I am inspired by how Alan Ziegler (in “Tales of Teaching” and Love at First Sight) and Raymond Carver (All of Us: The collected Poems) find stories in subject matter which is so commonplace, that it is often ignored creatively. Likewise, the lyricism and modes of expression of William Carlos Williams, Federico García Lorca and Luis Cernuda have informed how I write and structure my poetry.
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- Date Issued: 2020
Computer aided approaches against Human African Trypanosomiasis
- Authors: Kimuda, Magambo Phillip
- Date: 2020
- Subjects: African trypanosomiasis , African trypanosomiasis -- Chemotherapy , Genomics , Macrophage migration inhibitory factor , Trypanosoma brucei , Pteridines , Tetrahydrofolate dehydrogenase , Adenylic acid , Molecular dynamics , Principal components analysis , Bioinformatics , Single nucleotide polymorphisms , Single Nucleotide Variants , Candidate Gene Association Study (CGAS)
- Language: English
- Type: Thesis , Doctoral , PhD
- Identifier: http://hdl.handle.net/10962/142542 , vital:38089
- Description: The thesis presented here is divided into two parts under a common theme that is the use of computer based tools, genomics, and in vitro experiments to develop innovative ways of tackling Human African Trypanosomiasis (HAT). Part I of this thesis focused on the human host genetic determinants while Part II focused on the discovery of novel chemotherapeutics against the parasite. Part I is further sub-divided into two parts: The first involves a Candidate Gene Association Study (CGAS) on an African population to identify genetic determinants associated with disease and/or susceptibility to HAT. The second involves studying the effects of missense Single Nucleotide Variants (SNVs) on protein structure, dynamics, and function using Macrophage Migration Inhibitory Factor (MIF) as a case study. Part II is also sub-divided into two parts: The first involves a computer based rational drug discovery of potential inhibitors against the Trypanosoma the folate pathway; particularly by targeting Trypanosoma brucei Pteridine Reductase (TbPTR1) which is an enzyme used by trypanosomes to overcome T. brucei Dihydrofolate Reductase (TbDHFR) inhibition. Lastly the derivation of CHARMM force-field parameters that can be used to accurately model the geometry and dynamics of the T. brucei Phosphodiesterase B1 enzyme (TbrPDEB1) bimetallic active site center. The derived parameters were then used in MD simulations to characterise protein-ligand residue interactions that are important in TbrPDEB1 inhibition with the goal of targeting the cyclic Adenosine Monophosphate (cAMP) signalling pathway. In the CGAS we were unable to detect any genetic associations in the Ugandan cohort analysed that passed correction for multiple testing in spite of the study being sufficiently powered. Additionally, our study found no association of the Apo lipoprotein 1 (APOL1) G2 allele association with protection against acute HAT that has been previously reported. Future investigations for example, Genome Wide Association Studies using larger samples sizes (>3000 cases and controls) are required. Macrophage migration inhibitory factor (MIF) is a cytokine that is important in both innate and adaptive immunity that has been shown to play a role in T. brucei pathogenicity using murine models. A total of 27 missense SNVs were modelled using homology modelling to create MIF protein mutants that were investigated using in silico effect prediction tools, molecular dynamics (MD), Principal Component Analysis (PCA), and Dynamic Residue Network (DRN) analysis. Our results demonstrate that mutations P2Q, I5M, P16Q, L23F, T24S, T31I, Y37H, H41P, M48V, P44L, G52C, S54R, I65M, I68T, S75F, N106S, and T113S caused significant conformational changes. Further, DRN analysis showed that residues P2, T31, Y37, G52, I65, I68, S75, N106, and T113S are part of a similar local residue interaction network with functional significance. These results show how polymorphisms such as missense SNVs can affect protein conformation, dynamics, and function. Trypanosomes are auxotrophic for folates and pterins but require them for survival. They scavenge them from their hosts. PTR1 is a multifunctional enzyme that is unique to trypanosomatids that reduces both pterins and folates. In the presence of DHFR inhibitors, PTR1 is over-expressed thus providing an escape from the effects of DHFR inhibition. Both TbPTR1 and TbDHFR are pharmacologically and genetically validated drug targets. In this study 5742 compounds were screened using molecular docking, and 13 promising binding modes were further analysed using MD simulations. The trajectories were analysed using RMSD, Rg, RMSF, PCA, Essential Dynamics Analysis (EDA), Molecular Mechanics Poisson–Boltzmann surface area (MM-PBSA) binding free energy calculations, and DRN analysis. The computational screening approach allowed us to identify five of the compounds, named RUBi004, RUBi007, RUBi014, RUBi016 and RUBi018 that exhibited antitrypanosomal growth activities against trypanosomes in culture with IC50 values of 12.5 ± 4.8 μM, 32.4 ± 4.2 μM, 5.9 ± 1.4 μM, 28.2 ± 3.3 μM, and 9.7 ± 2.1 μM, respectively. Further when used in combination with WR99210 a known TbDHFR inhibitor RUBi004, RUBi007, RUBi014 and RUBi018 showed antagonism while RUBi016 showed an additive effect. These results indicate that the four compounds might be competing with TbDHFR while RUBi016 might be more specific for TbPTR1. These compounds provide scaffolds that can be further optimised to improve their potency and specificity. Lastly, using a systematic approach we derived CHARMM force-field parameters to accurately describe the TbrPDEB1 bi-metal catalytic center. For dynamics, we employed mixed bonded and non-bonded approach. We optimised the structure using a two-layer QM/MM ONIOM (B3LYP/6-31(g): UFF). The TbrPDEB1 bi-metallic center bonds, angles, and dihedrals were parameterized by fitting the energy profiles from Potential Energy Surface (PES) scans to the CHARMM potential energy function. The parameters were validated by means of MD simulations and analysed using RMSD, Rg, RMSF, hydrogen bonding, bond/angle/dihedral evaluations, EDA, PCA, and DRN analysis. The force-field parameters were able to accurately reproduce the geometry and dynamics of the TbrPDEB1 bi-metal catalytic center during MD simulations. Molecular docking was used to identify 6 potential hits, that inhibited trypanosome growth in vitro. The derived force-field parameters were used to simulate the 6 protein-ligand complexes with the aim of elucidating crucial protein-ligand residue interactions. Using the most potent ligand RUBi022 that had an IC50 of 14.96 μM we were able to identify key residue interactions that can be of use in in silico prediction of potential TbrPDEB1 inhibitors. Overall we demonstrate how bioinformatics tools can complement current disease eradication strategies. Future work will focus on identifying variants identified in Genome Wide Association Studies and partnering with wet labs to carry out further enzyme-ligand activity relationship studies, structure determination or characterisation of appropriate protein-ligand complexes by crystallography, and site specific mutation studies
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- Date Issued: 2020
Conceptualisations of and responses to plagiarism in the South African higher education system
- Authors: Mphahlele, Martha Matee (Amanda)
- Date: 2020
- Subjects: Plagiarism , Plagiarism -- Prevention -- South Africa , Education, Higher -- Moral and ethical aspects , Education, Higher -- South Africa , Cheating (Education) -- South Africa , College students -- Legal status, laws, etc. -- South Africa , College discipline -- South Africa
- Language: English
- Type: text , Thesis , Doctoral , PhD
- Identifier: http://hdl.handle.net/10962/162642 , vital:40963
- Description: Violations of academic integrity are a cause for concern in universities around the world and plagiarism is one of the most significant examples of these academic integrity issues with which universities are grappling . The approach taken to managing plagiarism depends to a large extent on the understanding of the phenomenon within institutions. This study investigated how plagiarism is conceptualised and responded to in the South African Higher Education system and how this impacts on teaching and learning. Data was collected from 25 out of the 26 South African public universities; the missing university had just been established and did not yet have policies or processes in place. The data was primarily in the form of documents known in these institutions as ‘plagiarism policies’, along with a wealth of other related policies and reports. This was supplemented by interviews as a means of verifying the document analysis with seven plagiarism committee members from across the three institutional types in South Africa, namely: traditional universities, comprehensive universities, and universities of technology. Using Bhaskar’s (2008) critical realism as a metatheory and Archer’s (1995) social realism as both a substantive theory and analytical framework, the experiences and events of plagiarism management were critically examined. Critical realism consider s these experiences and events at the level of the e mpirical and the actual , in order to identify the mechanisms at the l evel of the r eal from which these emerge. Social realism argues that when undertaking such an analysis in the social world, this entails identifying the emergent properties of both the parts (structure and culture) and people (agents). Therefore, the data was analysed using Archer’s analytical dualism to identify structural, cultural and agential mechanisms shaping the understanding of plagiarism and the practices associated with managing the phenomenon. The study found that dominant in the sector was an un derstanding of plagiarism as always being an intentional act, with implications for teaching and learning practices, which then focused on identifying and punishing incidents of plagiarism in student writing. A legal discourse was found to permeate the universities’ plagiarism management systems, such that most procedures replicated the legal framework. This was seen to undermine the identity of universities as teaching and learning spaces and of students as novice members of the disciplinary fields. The study further highlighted that due to plagiarism being perceived as an intentional act, punishment in almost all universities is prioritised as the key means of attending to plagiarism in the se institutions. This emerged as a structural constraint to students’ acquisition of academic writing norms. Such understandings and approaches were seen to be complementary to the risk-aversion of many institutions in a globalised era of university rankings. As increased bureaucracy has been put in place to attend to incidents of plagiarism, including obligatory reporting thereof, an unintentional consequence emerged, where it was at times simpler for academics to ignore incidences of plagiarism than to act on them. Turnitin was frequently referred to across the data as the preferred text - matching tool, but Turnitin together with other text-matching tools , was often used in a way that complemented the understanding of plagiarism as always being an intentional act. The stu dy found that text - matching software was largely misunderstood to be plagiarism software, where the similarity index was perceived to be a measure of plagiarism. This led to an understanding that students needed to paraphrase texts in order to avoid detect ion by the program me, and this may inadvertently encourage plagiarism , as students are taught to write towards the software. The research found that in those instances where educational responses to plagiarism were in place, they often demonstrated a lack of understanding of academic literacies development and the extent to which norms of knowledge production are disciplinary specific. Most (but not all) of the data about educational responses focused on add-on workshops and the signing of a declaration form, indicating that the student has not plagiarised. The workshops were seen to emphasise technical skills, such as the punctuation norms of referencing, and were often offered in a generic format by people outside of the target disciplines. These workshops were found to ignore the connection between the technical skills of referencing and the norms of knowledge construction, with a potential deleterious effect on the development of authorial identity. Finally, the data showed a few instances where particular institutions acknowledged that plagiarism occurs along a continuum, where on one side is intentional plagiarism associated with cheating and requiring punishment, and on the other side is unintentional plagiarism, which is understood to require an educational response , and was seen to emerge from either a lack of understanding of academic literacy norms , or from negligence. Literacy development with regard to taking on the norms of knowledge-making in the academy was seen to be a complex and lengthy process that was fundamental to educational endeavours of facilitating epistemological access, while cases of negligence were seen to be mainly caused by technical oversight rather than a lack of access to the relevant knowledge production norms. The study concludes by arguing that cases of intentional plagiarism require quick and appropriate punishment, but that there also needs to be an institution-wide understanding that unintentional plagiarism often emerges from students failing to access the specific knowledge-making norms of the discipline. There is thus a need for academics to be aware of the complexities related to taking on literacy practices, and who also understand the role of feedback in this process. But it ought not to be assumed that academics would have such insights simply by virtue of their expertise in the discipline. These academics need to have carefully constructed staff development support, as they take on such pedagogical approaches. The study argues that the dominant conceptualisation of plagiarism in the domain of culture as an intentional act and the complementary policies and processes in the domain of structure as focusing on detecting and punishing incidents of plagiarism, fail to address plagiarism in appropriate educational ways.
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- Date Issued: 2020
Conceptualising community radio: from global histories to the Kenyan example
- Authors: Korir, Geoffrey Kiplimo
- Date: 2020
- Subjects: Community radio , Community radio -- Kenya , Community development -- Kenya , Social change -- Kenya , Radio broadcasting -- Kenya
- Language: English
- Type: Thesis , Doctoral , PhD
- Identifier: http://hdl.handle.net/10962/165766 , vital:41279
- Description: This study sets out to gain insight into the way that the establishment of community radio in Kenya is located within the global history of ideas about such radio. The first four chapters in this study provide terms of reference for this examination through a series of literature reviews. It sets out, firstly, to locate the internationally shared conceptualisaiton of community radio within an existing spectrum of approaches to social analysis. It proposes that community radio can be located at the critical, emancipatory end of this spectrum. It then maps out the global circulation of ideas about community radio and proposes that such circulation was informed by the broader history of critical, emancipatory social analysis. The final literature review then deals with community radio in Kenya and examines the way in which the establishment of this sector was shaped by the social and political history of this country. It is argued that the establishment of a community radio sector became possible only when support for emancipatory approaches to media became acceptable in Kenya, in context of the establishment of multiparty democracy. It is proposed, further, that the articulation of a vision for community radio in Kenya depended in part on the existence of international support for such radio and in part on the efforts of local actors in civil society. The empirical component then focuses on the way global ideas about community radio have become realised in Kenya. The study achieves this purpose by drawing on qualitative interviews with individuals from within civil society who have participated in the history of the establishment and growth of community radio in Kenya. These individuals demonstrate consciousness of the internationally shared set of principles that can facilitate a successful establishment of community radio. However, they are also sceptical of the assumption that guidelines for community radio are universally applicable. They point, in particular, to the challenges involved in the realisation of these guidelines in an environment in which economic resources are limited, and which is characterised by extreme social inequality and conflict. The study concludes that it is individuals such as these participants, who are embedded within the local context, who are best placed to articulate locally appropriate alternatives to these guidelines.
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- Date Issued: 2020
Conserving land for people: transformative adaptive co-management of sustainable protected areas in the eastern Democratic Republic of Congo
- Authors: Kalyongo, Kujirakwinja Deo
- Date: 2020
- Subjects: Protected areas -- Congo (Democratic Republic) , Protected areas -- Government policy -- Congo (Democratic Republic) , Protected areas -- Management -- Congo (Democratic Republic) , Conservation of natural resources -- Congo (Democratic Republic)
- Language: English
- Type: text , Thesis , Doctoral , PhD
- Identifier: http://hdl.handle.net/10962/165912 , vital:41296
- Description: Conservation practices and approaches in the Democratic Republic of Congo (DRC), as in other parts of the world, have evolved from traditional to fortress and collaborative contemporary approaches such as adaptive co-management. These approaches aim to include multiple decision-makers using diversified resources and, existing formal and informal governance structures. Collaborative approaches also consider conflict resolution and external factors that can influence conservation outputs and outcomes. In the DRC context, conflicts over resources are related not only to resource access and power but also to the ineffectiveness of collaborative approaches that exclude stakeholders such as local communities. These conflicts have negatively affected protected areas and weakened the management and governance of protected areas. Therefore, evolving approaches such as adaptive co-management that consider power relations, the multi-scaled involvement of actors and learning loops to adjust strategies are seen as better options to improve the governance of protected areas and minimise the degradation of key ecosystems. My research explored the gazettement processes of three protected areas in the eastern DRC (Itombwe, Kabobo and Okapi Reserves). I focused on the influence of social-political, historical and psychological factors on the management and governance of protected areas in the DRC. In addition, the research reveals the inclusive gazettement processes of protected areas is the foundation of successful co-management approaches. I found that values and good governance practices play a key role in influencing local perceptions and support to conservation interventions. Whilst some conservation practitioners believe that economic benefits to communities are the most predominant motivating factor, I found that good conservation management practices can motivate communities to support protected area management. Bad management practices were related not only to inadequate conservation approaches and practices but also to factors such as corruption, inadequate law enforcement and the inappropriate equipment of rangers. Therefore, I suggest that long term protected area management in DRC should consider how the value of resources for communities and protected areas have been changing throughout the history of conservation, and how to best share power and responsibilities with local resource users and stakeholders. This is only possible if conservation practices and approaches, governance process and institutions are transformed at multiple levels.
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- Date Issued: 2020
Constructions of United States government development funding in response to the global gag rule
- Authors: Molobela, Reabetswe Lee-Anne
- Date: 2020
- Subjects: Pro-choice movement -- South Africa , Abortion -- Law and legislation -- South Africa , Abortion -- Moral and ethical aspects -- South Africa , Abortion -- Psychological aspects , Reproductive rights -- South Africa , Economic assistance, American -- South Africa , Non-governmental organizations -- South Africa , Discourse analysis , Social constructionism , Global Gag Rule
- Language: English
- Type: Thesis , Masters , MA
- Identifier: http://hdl.handle.net/10962/148295 , vital:38727
- Description: Despite South Africa’s progressive abortion law, barriers to safe abortion are numerous and exist at both the macro and micro level. Barriers include abortion stigma, discrimination, strong moral judgements against abortion within society and conscientious objection among health care workers. Furthermore, women’s lack of knowledge regarding the legal status of abortion and the voluminous illegal advertisements of back street abortions undermines the legislation and promotes unsafe abortions. Sexual and reproductive health rights (SRHR) non-governmental organizations (NGOs) have served as a link between service and people by providing information about safe abortion to women, especially in rural areas and have received funding from various platforms including United States government. However, the United States government has established the global gag rule which forbids foreign non-governmental organizations receiving United States government funding from using United States government and non-United States funds for abortion related activities. The global gag rule has been reinstated and extended by the current United States president. As such the global gag rule is expected to have an adverse effect on sexual and reproductive health rights in South Africa and on Sexual and reproductive health rights non-governmental organizations. The aim of the study is to highlight the constructions and responses to the global gag rule by sexual and reproductive health rights non-government organization workers in the South African context. This study used semi-structured individual interviews to collect data through purposive and snowball sampling of 10 South African Sexual and reproductive health rights non-governmental organizations workers. The study is situated within the social constructionist framework with emphasis on Fairclough’s three aspects of the constructive effects of discourse as an analytic tool in conjunction with Braun and Clarke’s social constructionist thematic analysis. The results of the study reflect on participants’ construction of United States government as imposing conservative agendas and taking regressive steps towards Sexual and reproductive health rights, which have in turn invoked indirect and direct resistance from non-governmental organizations. Additionally, NGO workers have constructed subject positions that highlight the vulnerability of non-governmental organizations dependency on United States government 1funding as it destabilizes and fragments civil society organization while it compromises the effectiveness of non-governmental organizations in serving the needs of intended communities. United States government is also constructed as strengthening abortion stigma and strengthening barriers to safe abortion that already exist in the country.
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- Date Issued: 2020
Creative production and existential thought: a feminist existential analysis of South African visual artist Berni Searle’s artwork
- Authors: Mokwena, Palesa
- Date: 2020
- Subjects: Women artists -- South Africa , Women artists, Black -- South Africa , Existentialism and art , Feminism and art -- South Africa , Searle, Berni
- Language: English
- Type: text , Thesis , Masters , MFA
- Identifier: http://hdl.handle.net/10962/148005 , vital:38701
- Description: Through an analysis of the work of South African artist Berni Searle, my study will investigate feminist existential ideas and concepts that have been explored by various creative producers in and outside of Europe/South Africa through different forms of creative productions and under different epistemological categories. ‘Canons’ of European existentialist/feminist thought often exclude the existence of feminist existential knowledge productions and producers outside of Europe. In conducting this study, I am responding to the past and present separatist and identitarian categorisations of creative productions from black/African creative producers, particularly women creative producers in South Africa, creating an alternative canonisation around their selected works. Although canons have been and can be used to drive separatist and identitarian categorisations, it is my hope to elucidate a discourse around the preservations and acknowledgements of South African creative and knowledge productions through a feminist existential framework that canonises important black feminist existentialist works and thereby brings to light their intellectual contributions over and above their identities. My development of a South African feminist existentialism is an attempt to graft a more intersectional, holistic framework to introduce in the feminist and existential discourses, and to proffer a new intersectional holistic paradigm of discussing categories that do not limit creative productions. To frame this research, I will reflect on the politics of historical and contemporary South African society as it is reflected in the works of the chosen creative producers and theorists and to question how we respond as creative feminist existentialists to contemporary South African struggles and how such a lens can be activated as a creative-theoretical tool of investigation.
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- Date Issued: 2020
Critical success factors in implementing projects on restituted land parcels in South Africa
- Authors: Whiting, Christoper Whiting
- Date: 2020
- Subjects: Community development -- Management -- South Africa , Community development -- Management -- South Africa -- Case studies , Economic development projects -- Management -- South Africa , Economic development projects -- Management -- South Africa -- Case studies , Land reform -- South Africa -- Economic aspects , Land reform beneficiaries -- South Africa -- Case studies , Restitution -- South Africa -- Case studies
- Language: English
- Type: text , Thesis , Masters , MBA
- Identifier: http://hdl.handle.net/10962/167697 , vital:41504
- Description: Currently there is a perception in South Africa that projects undertaken on parcels of restituted land are experiencing a much higher failure than success rate. There are, however, a few projects that are reaping the rewards and uplifting their communities, as intended by the land redistribution program. One community in particular, located in Mpumalanga, called community A, is presently undertaking a development project. This development project is one of the most successful restituted land parcel projects ever in South Africa. The purpose of the study is to determine the critical success factors in this community development project that have allowed it to enjoy such high levels of success. Are these critical success factors different from the generic industry critical success factors and, if so, what are they? As informed through literature, the critical success factors focused on in this study are as follows: the influence of management, project communication, knowledge management, the role of senior management, business strategy, project success measurements, and training and development. For the empirical study, a physical questionnaire was handed to 35 management members currently employed in the community development project. The questionnaire requested the demographics of all participants and asked them to rate, using a five-point Likert scale, their perceptions of the present project activities and of the importance of the project activities mentioned in making the project successful. Participants had to indicate the extent to which they agreed with each statement in the questionnaire. The responses obtained from the survey were presented and analysed. The study found that the critical success factor “role of senior management” was the largest problem area in the restituted land development project. “Training and development opportunities” came in second, with both factor areas showing large variances. Recommendations have been given on how to address both these problematic areas in the development project and how future restituted land parcel projects can better utilize these factors to ensure successful project implementation and long-term project success.
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- Date Issued: 2020
Crossing shades
- Authors: Singh, Shareen
- Date: 2020
- Subjects: South African fiction (English) -- 21st century
- Language: English
- Type: text , Thesis , Masters , MA
- Identifier: http://hdl.handle.net/10962/145049 , vital:38404
- Description: This collection of stories draw on culture, history, memory, musings and imagination. The stories are set primarily in South Africa but includes travels to other countries. I explore journeys to different worlds and minds. I challenge the reader to see how place and time influence our ways of seeing, living and evolving. I use different forms and tones that resonate with the subjective nature of each creative piece. My writing includes formal prose as well as works that experiment with fragments, vignettes and flash fiction.
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- Date Issued: 2020
Cyclooxygenase-1 as an anti-stroke target: potential inhibitor identification and non-synonymous single nucleotide polymorphism analysis
- Authors: Muronzi, Tendai
- Date: 2020
- Subjects: Cerebrovascular disease , Cerebrovascular disease -- Treatment , Cerebrovascular disease -- Chemotherapy , Cyclooxygenases , High throughput screening (Drug development) , Drug development , Molecular dynamics , South African Natural Compounds Database , ZINC database
- Language: English
- Type: Thesis , Masters , MSc
- Identifier: http://hdl.handle.net/10962/143404 , vital:38243
- Description: Stroke is the third leading cause of death worldwide, with 87% of cases being ischemic stroke. The two primary therapeutic strategies to reduce post-ischemic brain damage are cellular and vascular approaches. The vascular strategy aims to rapidly re-open obstructed blood vessels, while the cellular approach aims to interfere with the signalling pathways that facilitate neuron damage and death. Unfortunately, popular vascular treatments have adverse side effects, necessitating the need for alternative chemotherapeutics. In this study, cyclooxygenase-1 (COX-1), which plays a significant role in the post- ischemic neuroinflammation and neuronal death, was targeted for identification of novel drug compounds and to assess the effect of nsSNPs on its structure and function. In a drug discovery part, ligands from the South African Natural Compounds Database (SANCDB-https://sancdb.rubi.ru.ac.za/) and ZINC database (http://zinc15.docking.org/) were used for high-throughput virtual screening (HVTS) against COX-1. Additionally, five nsSNPs were being investigated to assess their impact on protein structure and function. Three of these SNPs were in the COX-1 dimer interface. Molecular docking and molecular dynamics simulations revealed asymmetric nature of the protein. Several ligands, peculiar to each monomer, exhibited favourable binding energies in the respective active sites. SNP analysis indicated effects on inter-monomer interactions and protein stability.
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- Date Issued: 2020