The in vitro detection and measurement of the unfolded protein response in Saccharomyces cerevisiae

>Magister Scientiae - MScBioethanol is currently the most widely used biofuel and can be used as a direct replacement for current fossil fuel based transportation fuels. Consolidated bioprocessing (CBP), in which bioethanol is produced in a single reactor by a single microorganism, is a cost-effective way of producing bioethanol in a second generation process using lignocellulosic biomass as feedstock. The yeast Saccharomyces cerevisiae possesses industrially desirable traits for ethanol production and is able to produce heterologous cellulases, which are required for CBP. However, S. cerevisiae produces low titres of cellulases and one suspected reason for this is the stress caused by the heterologous proteins that induce the unfolded protein response (UPR). The UPR is a stress response pathway that will either lead to increased folding capacity within the ER or to degradation of these proteins and possibly apoptosis of the cell. It is thus beneficial to be able to determine when and to what extent the UPR is active during CBP organism development. Current methods of measuring the UPR include RNA and reverse transcriptase qPCR (r.t.qPCR) measurements, which can be cumbersome and expensive. The purpose of this study was to develop a vector based biosensor that will detect and quantify UPR activation. The vector consisted of either the T.r.xyn2 or eGFP reporter genes under the control of the S. cerevisiae HAC1p or KAR2p promoters. HAC1 and KAR2 are important regulators of UPR as their activation allows the UPR to achieve its function. The eGFP reporter under the transcriptional control of KAR2p was shown to be the superior combination due to the improved dynamic range when the UPR was induced in transformed S. cerevisiae strains by the stress inducer, tunicamycin. This UPR biosensor also proved to be more sensitive when measuring UPR induction in cellulase producing strains, depicting significant differences, compared to previous r.t.qPCR based tests which were unable to detect these differences. We thus developed a UPR biosensor that has greater sensitivity for changes in UPR induction compared to RNA based methods and the first KAR2p based UPR biosensor plasmid that allowed for more accurate detection and measurement of the UPR in cellulase secreting S. cerevisiae strains. The ability to quantify UPR induction will assist in identifying candidate cellulase genes that do not greatly induce the UPR, making them ideal to use in developing CBP yeasts

In the halls of history: the making and unmaking of the life-casts at the ethnography galleries of the Iziko South African Museum

This mini-dissertation is a study of the phenomenon of life-casting and the display of these in the museum space. It looks specifically at the practice as it came into use at the turn of the twentieth century at the South African Museum in the Western Cape. The research aims to place the practice in context with the historical triggers and larger perspectives of the subject of indigenous races. A focus on particular life-casts and its display in designed productions allows the reader insight into knowledge production. I point to this to unpack a loaded history informing deeply seated identity constructs and prejudices. A trajectory of the use of the life-casts is supported by visual records included in this text. The museum's archive also affords a plethora of correspondence and research giving context and insight. A close analysis of the archive exposes the museum's processes and the exchange in consumption and production by museum visitors and related institutions both private and state supported. The making and unmaking of the life-casts acts as proxy for peoples brutally subjugated

Patterns in diversity, abundance, distribution and community structure of epi-pelagic copepods in the south-western Indian Ocean

Philosophiae Doctor - PhD (Biodiversity and Conservation Biology)The primary objective of this study was to investigate patterns in diversity, abundance, distribution and community structure of epi-pelagic copepods across the South West Indian Ocean Ridge (SWIOR). A survey was conducted across the SWIOR at two off-ridge and five seamount stations between 26.94 oS to 41.48 oS in November and December 2009. Copepod species richness and abundance was compared at vertical and horizontal scales day and night, at irregular time intervals across the Agulhas Return Current (ARC), Subtropical Front (STF) and Sub-Antarctic Front (SAF). A total of 49 genera and 135 epi-pelagic copepod species were identified along the SWIOR transect, and the Order Calanoida had the most genera. Species richness was highest in the ARC and lowest at the stations associated with the frontal areas of the STF and the SAF. The total number of copepod species was higher during the night than day. Total copepod abundance along the transect was highest towards the frontal area of the STF, and the genus Oithona spp. comprised almost 50% of the total number in all copepod samples. Three distinctive copepod assemblages were identified by multivariate analysis, and communities were associated with the STF, ARC and SAF. Clausocalanus laticeps, Metridia lucens and Calanus simillimus were only recorded in the southern part of the survey area and their absence in the north may demonstrate the strong stratification of the STF, and more likely to be the physiological properties, adaptation to their environment and life histories

Policy targeting as a strategy to increase access to higher education

In an era of reconstruction of the educational landscape, South African higher education’s contribution to social and economic development has been concretised through policy targeting and reforms in four cardinal planks and mission. These include Teaching, as this contributes to the development of human capital, Learning which invigorates the order for human capital to develop through knowledge, Research which builds the foundation for the development of sound knowledge bases and Social Responsiveness which becomes the cornerstone for the dissemination and application of knowledge across the educational and social platform. The article proposes that South Africa must address the quagmires experienced by the poor and the marginalised. The political re-draw of intentions that is emerging under the new administration presents the country with an opportunity to issues pertaining to higher education as a people-centred activity rather than a marketcentred commodity. The article further contends that as a necessary pre-condition for policy targeting to become a channel for deliberative discourse, it is apparent that higher education authorities must have the requisite capacity for these strategic policy initiatives in a synchronised policy-targeted manner.am201

The registration of professional designations on the NQF : a South African policy predicament?

South African Qualifi cations Authority (SAQA) completed the development of and is implementing the Policy and Criteria for Recognising a Professional Body and Registering a Professional Designation for the Purposes of the National Qualifi cations Framework Act, Act 67 of 2008. The entity has recognised 85 professional bodies and registered 290 professional designations since July 2012. However, this article argues that there is a legal and subsequent policy error related to the registration of professional designations on the NQF. This must be rectifi ed in law and in policy. While professional designations do have a relationship to the NQF by virtue of underlying qualifi cations, designations in itself cannot be registered on the NQF. However, through another mechanism, the National Learners’ Records Database, a separate register for professional designations must be established in order to measure the real impact of professionalisation in contributing to the continuing transformation in South Africa. Addressing unfair exclusionary practices within the professions will require political will and consistency in ensuring meaningful stakeholder participation, academic rigour and investment in ensuring sustainable capacity in regard to systems, people and money.no websitehb2016School of Public Management and Administration (SPMA

The impact of tripartite politics on the leadership function in public administration : dialogue between the ANC, COSATU and the SACP in South Africa

Since 1994 the South African state has been governed through an Alliance of the African National Congress (ANC), South African Communist Party (SACP) and Congress of South African Trade Unions (COSATU). Whilst each of these organisations claims autonomy and independence, it shares a common history and core ideological persuasions which has been articulated as the National Democratic Revolution (NDR). Whilst ANC members may not necessarily be members of the SACP or COSATU, any member of the SACP or COSATU who desires to enter politics is required to be a member of the ANC. The SACP and COSATU do not contest elections. As part of the agreement, only the ANC contests elections and as such leads the Alliance. This has led to a number of challenges, specifi cally related to public administration. This article describes the nature of the tripartite alliance by considering the historical roots of the alliance itself and its performance in government; and by concluding that there is an understanding of the leadership role of the ANC within the Alliance. The ANC itself is a refl ection of the broad church nature of such an Alliance. Irrespective of this convergence of ideology, there is periodic divergence on the leadership role of the ANC viz a viz that of the Alliance as the strategic centre for policy and governance issues. However, the ANC has, over the years, successfully challenged this assertion and, through practice, has led the Alliance in a politically driven manner that is predicated on consultation, due diligence and functional purpose. However, any member of the SACP or COSATU who desires to be part of Parliament or the executive is required to be a member of the ANC. While COSATU and the SACP provide advice, through Alliance structures, on the deployment of cadres in the public service, the deployment committee is an ANC structure and the fi nal decisions with regard to deployment, resides with the ANC.am201

Dialogue between the ANC, COSATU and the SACP : the impact on leadership, governance and public policy in South Africa

Since 1994 the South African state has been governed through an Alliance of the African National Congress (ANC), South African Communist Party (SACP) and Congress of South African Trade Unions (COSATU). Whilst each of these organisations claims autonomy and independence, it shares a common history and core ideological persuasions which has been articulated as the National Democratic Revolution (NDR). Whilst ANC members may not necessarily have membership of the SACP or COSATU, any member of the SACP or COSATU who desires to enter politics are required to be a member of the ANC. The SACP and COSATU do not contest elections. As part of the agreement, only the ANC contests elections and as such leads the Alliance. This has led to a number of challenges, specifically related to public administration. This article describes the nature of the tripartite alliance by considering the historical roots of the alliance itself and its performance in government; and by concluding that there is an understanding of the leadership role of the ANC within the Alliance. The ANC itself is a reflection of the “broad church” nature of such an Alliance.nf201

Metabarcoding of marine zooplankton in South Africa

Metabarcoding is an emerging method in which DNA barcoding is combined with next-generation sequencing to determine the biodiversity of taxonomically complex samples. We assessed the current state of DNA barcode reference databases for marine zooplankton in South Africa and undertook a metabarcoding analysis to determine the species composition of samples collected with plankton tow nets. Analysis of DNA sequences mined from the literature and in online barcode reference databases revealed incomplete records for all taxa examined. Barcode records were dominated by meroplanktonic species with commercially important life-history phases (fishes and decapod crustaceans) and by species occurring in easily accessible nearshore habitats. Holoplanktonic species were underrepresented, despite making up the bulk of zooplankton biodiversity, including most potential indicator species. Metabarcoding analysis of plankton samples could identify 45% of amplicon sequence variants to species level based on BOLD databases (123 species) and similar numbers using GenBank and the MIDORI COI classifier. Morphological analysis of samples could not achieve comparable resolution at species level, but with some exceptions it recovered similar classes of organisms to those found by metabarcoding. The need for integrative molecular/morphological studies to increase and validate barcode reference databases of key zooplankton taxa is recognised. Metabarcoding of marine zooplankton in South Africa has now been successfully undertaken and the methodology is expected to facilitate high-resolution monitoring of zooplankton biodiversity in pelagic ecosystems and accelerate the discovery of new species

Metabarcoding of zooplankton to derive indicators of pelagic ecosystem status

Zooplankton play a key role in marine food webs and carbon cycling and are useful indicators of climate-related changes and ocean health in pelagic ecosystems. Zooplankton are traditionally identified to species through microscopy, but new molecular techniques have enabled the identification of individual specimens (DNA barcoding) or multiple species in the same sample (DNA metabarcoding). Metabarcoding has been tested and refined using zooplankton collected in South African waters for the first time. Challenges to the implementation of DNA-based methods to measure zooplankton biodiversity easily and routinely include an incomplete DNA barcode reference library, logistical complexity and uptake of the new technology by environmental management agencies. These challenges call for a national effort to intensify zooplankton barcoding initiatives and to effectively engage stakeholders in developing a roadmap towards application of DNA-based methods in marine environmental management

Metabarcoding of zooplankton to derive indicators of pelagic ecosystem status

Zooplankton play a key role in marine food webs and carbon cycling and are useful indicators of climate-related changes and ocean health in pelagic ecosystems. Zooplankton are traditionally identified to species through microscopy, but new molecular techniques have enabled the identification of individual specimens (DNA barcoding) or multiple species in the same sample (DNA metabarcoding). Metabarcoding has been tested and refined using zooplankton collected in South African waters for the first time. Challenges to the implementation of DNA-based methods to measure zooplankton biodiversity easily and routinely include an incomplete DNA barcode reference library, logistical complexity and uptake of the new technology by environmental management agencies. These challenges call for a national effort to intensify zooplankton barcoding initiatives and to effectively engage stakeholders in developing a roadmap towards application of DNA-based methods in marine environmental management. Significance: Metabarcoding has been successfully applied to marine zooplankton for the first time in South Africa, demonstrating its potential as a tool to generate ecosystem indicators during routine ocean observations. National barcoding efforts must be intensified to provide a comprehensive reference library of zooplankton DNA. Effective engagement with stakeholders is required to overcome logistical and policy challenges, and to provide a roadmap towards application of DNA-based methods in marine environmental management