Hicd.nrf.ac.za

Ana Casanueva
University of the Western Cape
Mentor: Prof D Cowan
Contact: acasaneuva@uwc.ac.za
Broad research area: gene discovery and
Specific research field: Identification of
Ayesha Parker
Cape Peninsula University of Technology
Mentor: Prof S Burton
Broad research area: Biocatalysis
Purpose of study:
Specific research area: Antioxidants
The majority of the world’s energy supply is dependent on fossil fuels, such as coal, natural Purpose of study:
gasses and oil. All of these sources are non- Antioxidants are smal molecular weight compounds renewable, finite and at the current rate will be useful in the prevention of oxidative damage due consumed in only a few decades. An alternative to the free radicals generated by reactive oxygen species (ROS). ROS play a role in some deleterious Such an alternative would be the production physiological processes, such as aging and damage of bioethanol from cheap and renewable biomass such as lignocellulose. This is a complex structure The laccase enzyme produced by the white rot composed of cellulose, hemicellulose and lignin. fungus, Trametes pubescens has been successfully Enzymes such as laccases and peroxidases are used in our research group for the biocatalytic needed to break down the different components production of novel antioxidant polymers with of lignocellulosics into simple sugars that can higher antioxidant properties than the monomeric then be fermented to bioethanol. Actinomycetes The aim of this research is therefore to assay In this study mesophilic and thermophilic novel antioxidants produced through biocatalysis actinomycetes were identified containing laccase reactions, for their antioxidant capacities in vitro and peroxidase activities. Large-insert fosmid and ex vivo by standard antioxidant assays, and libraries of the 41 mesophilic actinomycetes to assess their protective properties against the were constructed and screened on solid media. damaging effects of UV radiation on cultured skin No activities were identified, possibly due to the poor expression of actinomycete genes in E. coli. For the production of laccase, T. pubescens Laccase-specific primers were designed. Out of was grown in airlift reactors. The enzyme was the 41 mesophilic strains, 7 amplified using the purified from T. pubescens culture medium by 80 above primers. The PCR product was used as % ammonium sulphate precipitation and analysed a probe for screening the library by colony blot. by Sodium dodecyl sulphate polyacrylamide gel Several putative clones have been identified and electrophoresis (SDS-PAgE) for the confirmation Large-insert libraries were also constructed Non-immobilized laccase was used to synthesise in an E. coli-Streptomyces shuttle vector, polymeric species of ferrulic acid, and the to screen in Streptomyces for the enzyme products were analysed by gas Chromatography- activities, circumventing the E. coli expression problem. Transformation into the Streptomyces Chromatography-MS (LC-MS). Purified enzyme will host is being optimized. Construction of E. be immobilized for the use in the biotransformation coli-Streptomyces libraries of the thermophilic of antioxidant monomers in organic media. Our research focuses on the double mutant of transgenic grapevine plants and to allow the osterix (for osteoblasts) and PPARgamma2 of the purified enzyme for the use in the NHase properties and its potential in new suitable screening of more candidates in a short period (for adipocytes) is also measured. Our current biotransformation of antioxidant monomers in applications. We started studying the nitrile- of time, the grapevine infecting plant virus was work focuses on differences in osteoblastic and organic media, the identification and purification degrading reaction with a range of substrates to modified to allow the expression of foreign adipocytic differentiation potential between ADSCs IO of the reaction products as well as assessing define its chemio-, regio- and stereo- specificity. proteins. This will give the possibility to pre-screen harvested from subcutaneous (scADSCs) and B the antioxidant properties of the various reaction A second step has been to investigate its AMPs for their efficiency against several grapevine perirenal visceral adipose tissue (vADSCs). O products in vitro and assessing the protective feasibility as an industrial biocatalyst reporting pathogens before the selection of an AMP We also study ADSCs harvested from rats that the characterisation of the enzyme kinetics, expressing transgenic plant line is started. This will have been fed on a high-caloric diet. These rats respectively, in the production of amides fine be the first attempt to express AMPs in plants by become hyperphagic (over-eating), and as a result Contact: ayesha.parker.ay@gmail.com
chemicals or in the degradation of polluting nitrile a viral vector. First results of the use of gVA as develop visceral obesity, hyperinsulinaemia and compounds. The results we obtained add new a protein expression vector and VIgS system for hyperlipidaemia, which are hallmarks of Western- information to develop further understanding of the grapevine will be presented and discussed.
type life-style diseases. Our results demonstrate Carlo Bressa
active site mechanism of the nitrile hydratase.
that scADSCs have in vitro osteogenic potential, LO Cape Peninsula University of Technology
Contact: dstephan@sun.ac.za
while vADSCs do not. scADCS from hyperphagic O Mentor: Prof S Burton
Contact: bressac@cput.ac.za
animals have reduced osteogenic potential, Broad research area: Biotechnology
compared to scADSCs from lean animals. In Specific research field: Biocatalysis
Hanel Sadie-van Gijsen
addition, we have also found that vADSCs have Dirk Stephan
Stellenbosch University
greater adipogenic potential than scADSCs.
Purpose of study:
Stellenbosch University
Mentor: Dr W Ferris
The answer scientific researchers gave to the Mentor: Prof J Burger
Broad research area: Biochemistry
Contact: Hsadie@sun.ac.za
question on how to improve industrial production Broad research area: Plant virology, molecular
Specific research field: Cell biology
in terms of quality and quantity and, at the same time, how to become environmental friendly, is Specific research field: Virus induced gene
Purpose of study:
Hussaini Makun
Our group utilises a system of cultured rat adipose- University of Johannesburg
In the past 30 years the high availability of derived stromal cells (ADSCs). These cells can Mentor: Prof M F Dutton
microorganisms in the environment associated with Purpose of study:
differentiate (develop) into several other cell-types, Broad research area: Biochemistry (toxicology)
the possibility to make great scientific discovers In the presented work a grapevine (Vitis vinifera) including osteoblasts (bone-forming cells) and Specific research field: Mycototoxicology
drove researchers in biotechnology field to develop infecting plant virus wil be evaluated for its use adipocytes (fat cells), and can therefore be used as fast and safe selection and screening methods. as molecular tool for grapevine gene function a model system in which to study osteoblast and Purpose of study:
On the other hand during these years investigation studies by virus-induced gene silencing (VIgS) adipocyte differentiation, as well as the balance In a previous study [PhD project] Fusarium shifted progressively from the immediate and delivery tool for antimicrobial peptides verticillioides (Sacc.) Nirenberg was demonstrated (AMPs). For these two different approaches, the In culture, osteoblastic differentiation can be to be the novel, most toxic metabolites producing nowadays the emphasis is placed on attempting to grapevine infecting virus, grapevine virus A (gVA, induced by supplementing the standard culture fungi contaminating rice in Niger State, Nigeria. redesign enzymes in order to tailor their properties. family Flexiviridae, genus Vitivirus) was modified in media with ascorbic acid, glycerol-2-phosphate Mice and chicks were susceptible to the crude Although, in the scientific literature, there are the laboratory to al ow the integration of non-viral and 10 nM of the glucocorticoid dexamethasone extract of the fungus and the organs injured were reports of many promising biocatalysts, making (OM). Adipocytic differentiation can be induced the liver, kidney and intestinal tracts of the animals. them suitable for industrial application takes time: For the gVA-based VIgS system the partial by supplementing the standard culture media Total fumonisins quantified in the culture material certain industrial parameters must be met in order sequence of the grapevine phytoene desaturase with insulin, indomethacin, isobutylmethylxanthine of the fungus was 8.233 ppm, this quantity of to implement the biocatalytic steps in production (PDS) gene was integrated into the viral genome. toxin is not known to be acutely toxic to rodents as After optimisation of the grapevine agro-inoculation shown in the above studies which is indicative of Our project, started from a successful genetic procedure, the recombinant virus successfully osteoblastic and adipocytic differentiation are engineering modification of a thermostable nitrile silenced the PDS gene, visible by a photobleaching extracellular matrix mineralisation (Alizarin Red This therefore necessitates the cytotoxicity hydratase from geobacillus pallidus. The double phenotype. The photobleaching was restricted to S staining) for osteoblasts and intracellular lipid evaluation and complete elucidation of the mutant βF52gβF55L g. pallidus RAPc8 NHase leaf veins, which reflects the movement limitation accumulation (Oil Red O staining) for adipocytes. mycotoxins elaborated by this strain of fungus. showed activity towards both aliphatic and aromatic In addition, the expression of phenotype-specific Another comprehensive mycotoxins survey of rice nitriles, while the “wild type” is aliphatic specific.
In a similar attempt to avoid the generation transcription factors, including Cbfa1, Mx2 and from same state using PCR and DNA sequencing and high performance liquid chromatography will considerably depending on the environmental The industry is hampered by the severe loss of Margaretha van der Merwe
be more informative than the previous studies that conditions and the period during the cell cycle.
young, newly shorn Angora goats, which occur Stellenbosch University
employed basic techniques of macroscopic and This work investigates the effect of the during cold spells. Investigations into cold-stress Mentor: J Kossmann
microscopic methods for fungi identification and population age on the mechanical properties of the related deaths at first implicated the adrenal cortex Broad research area: Natural sciences
IO thin layer chromatography for mycotoxin detection. yeast cell. Saccharomyces cerevisiae reproduces and subsequently a single steroidogenic enzyme, Specific research field:
This Postdoctoral Fellowship project will asexually by budding that leads to a chitinous ring cytochrome P450 17β-hydroxylase/17,20 lyase O therefore be of two parts. The first is the structure being formed at the point of cytokinesis Purpose of study:
cytotoxicity and elucidation of mycotoxins in the in both the mother and daughter cells. In the In mammals, CyP17, which is encoded by a Small molecule regulation of plant growth and IC crude extract of Fusarium verticillioides while the mother cell this ring is a persistent bud-scar single gene, plays a critical role in the production of development results in a great deal of phenotype second is the fungal and mycotoxin survey of rice structure and the number of scars on a cells mineralocorticoids, glucocorticoids and androgens plasticity and metabolic redundancy. My work, surface is indicative of the cell age. The birth scar by the adrenal cortex. Two CyP17 isoforms with concerned with the regulation of metabolism, will The extract of the isolated F. verticillioides has is a much weaker structure appearing to increase unique catalytic properties have been identified in focus here on the role of primary metabolites and been shown to have stimulatory effects on human in size with cell age and eventually becoming this study. A real-time-based genotyping assay was phytohormones, and how they attenuate growth LO lymphocytes and contains fumonisins B1, B2 indistinguishable from the surrounding cell wall. used to identify the distribution of the two CyP17 responses. As an example, I will firstly discuss O and B3. In the second survey, various toxigenic Age synchronised cell populations of the alleles in the South African Angora population. Acacia longifolia gall formation as a result of the fungal species and major mycotoxins (aflatoxins, budding yeast S. cerevisiae were prepared using encapsulation of the pteromalid wasp Trichilogaster ochratoxin A, deoxynivalenol, T-2 toxin zearalenone cell separation by rate zonal sedimentation in isoforms were not the product of two alleles of acaciaelongifoliae. These galls result in carbon and fumonisins) were found in Nigerian grown rice. sucrose density gradients. Using this procedure the same gene, but two separate CyP17 genes nitrogen constraints in plant growth, reducing plant The projects will generate incidence data and it is possible to produce high yield populations encoding the two unique CyP17 isoforms. This fitness and results in premature senescence. profile of fungi and mycotoxins of rice grown in up to the eighth generation with high purity. novel finding was subsequently confirmed by This work will highlight the progress made Nigeria, with a view to demonstrating the types Fluorescence and confocal microscopy techniques quantitative real-time PCR. goats were divided into to understand how this occurs. Secondly, novel of animal and human diseases expected from our have been used to accurately determine the yeast three unique genotypes which differed not only plant growth promoting substances and/or diets and the extent of risk to these mycotoxicoses.
cell generation as well as providing information on in the genes encoding CyP17, but also in copy phytohormones are constantly discovered. Here number. Furthermore, in vivo assays revealed that I will report on one such novel player in plant Contact: hussainimakun@yahoo.com
Cell breakage studies will be conducted on these the identified genotypes differed in their ability to growth promotion and the molecular network that it separated populations using sonication and high- produce cortisol in response to intravenous insulin pressure homogenisation. The resultant protein and John Stenson
enzyme release profiles will be used to determine This study clearly demonstrates the presence Contact: mvdm@sun.ac.za
University of Cape Town
the influence of the generation age on the cell of two CyP17 genes in the South African Angora Mentor: Prof S Harrison
goat, and further implicates CyP17 as the primary Broad research area: yeast cell wall structure
cause of the observed hypocortisolism in this Nuraan Khan
Specific research field: Understanding yeast
Contact: johnstenson@gmail.com
Cape Peninsula University of Technology
cell wall structure to inform structure – function Mentor: Prof S g Burton
relationships in biological response of yeast Contact: storbeck@sun.ac.za
Broad research area: Biotechnology
to processes stresses and for manipulating Kark-Heinz Storbeck
Specific research field: Oxidative enzyme
Stellenbosch University
Mentor: Prof P Swart
Purpose of study:
Broad research area: Biochemistry
Purpose of study:
The yeast cell envelope is of critical importance Specific research field: Cytochromes P450
Peroxidases catalyse the peroxide-dependent in bioprocesses, affecting the impact of process oxidation of a wide range of organic and inorganic stresses on yeast physiology, defining yeast Purpose of study:
compounds. They are ubiquitous in nature, and are resilience and controlling the release of intracellular South Africa is the world leader in mohair widely distributed intracellularly in plants, animals products on altered cell permeability and cell production, supplying approximately 55% of the and microorganisms. Extracellular peroxidases, breakage. The construction of the cell wall is a global demand. South African Angora goats (Capra however, have only been identified in a few specific tightly regulated process where the polysaccharide hircus) are the most efficient fibre producing, but microorganisms including ligninolytic fungi and composition, structure and wall thickness can vary least hardy small stock breed in Southern Africa. associated molecular pattern (PAMP) molecules Samantha Gildenhuys
substructures within proteins that can play a role heterogenous group of bacteria that are widely can occur through pattern recognition receptors University of the Witwatersrand
during folding of a protein to its native structure, distributed in natural environments. These Mentor: Prof H W Dirr
once folded the interface between domains organisms secrete a range of extracellular Lipopolysaccharides (LPS) embedded in the cell Broad research area: Protein biochemistry.
can produce active sites of enzymes. Folding of IO enzymes, including peroxidases that are believed wall of gram-negative bacteria can trigger defence Specific research field:
monomeric gST members such as glutaredoxin-2 B to play a role in the degradation of complex responses or prime the plant in order to respond where potential domain-domain interaction O organic compounds such as lignin. Unlike fungal more rapidly, following perception of bacterial disrupting mutations have been created will provide peroxidases, extracellular peroxidases produced by pathogens. A receptor-like kinase was identified Purpose of study:
information on key residues involved in folding. IC actinobacteria are not as widely described in terms as a putative receptor for LPS. This RLK was has Functional three-dimensional proteins are now been further characterized as an S-domain, produced during a process of folding form the Contact: Samantha.gildenjuys@wits.ac.za
In this study, actinobacteria have been isolated one-dimensional amino acid sequence. Key amino from a wide variety of environments including the Extensive analyses are required in order to acids direct folding while others play pivotal roles in Antarctic Dry Val eys, alkaline lakes in Ethiopia, determine the exact role NS-RLK plays within structure and function. The role of these residues Sharath Govind
LO hotsprings in Zambia, Namibian desert soils, termite an interactive signal transduction pathway, via is assessed by site directed mutagenesis, following Stellenbosch University
O guts, sea sponges and sea squirts from Algoa the innate immunity or basal resistance models identification of the residues as conserved within Mentor: Prof M Vivier
Bay and Marion Island, geothermal areas in New expressed in literature. Current studies include the sequences of structurally and functionally Broad research area: grapevine biotechnology.
Zealand and a wide variety of other environments expression analyses using other PAMPs (e.g. Specific research field: grape berry suspension
in South Africa. These isolates have been screened flagellin or peptidoglycan) as inducers of NS-RLK. glutathione transferases (gST’s) are one cultured cells – a model to study grape berry for peroxidase activity and the top peroxidase In addition, the effects that these other PAMPs such group of proteins, consisting of monomeric ripening changes – a protemic approach producers have been identified. The current focus have on the S-domain RLKs already reported to be members as well as dimeric detoxification enzymes. of this project is to induce and optimize extracel ular associated with defence responses in other plant The dimeric enzymes conjugate the addition Purpose of study:
peroxidase production in the organisms identified. of glutathione to xenobiotic compounds within In addition to their economic importance, the The next step in the project is the purification Orthologues of NS-RLK in crop plants have also an active site composed of two binding sites a consumption of grapes has numerous nutritional and and characterisation of these enzymes, which will been identified and are currently being investigated g- (glutathione) and H- (hydrophobic) site, each health benefits for humans. There are more than be optimal y produced under bioreactor conditions. for crop-protection strategies. The identification of subunit possess one such active site. Arg15 a key 200 polyphenolic compounds that are anti-oxidants. Purified peroxidases will also be used in studies genes whose transcription is altered locally by LPS residue situated at the interface of the g- and Therefore, for a variety of reasons there is a involving the degradation of lignin in agricultural treatment, will allow the development of screens to H- sites impacts on catalysis of the conjugation great scientific interest in manipulating grape feedstocks for biofuel production and in biocatalytic identify plant mutants that are insensitive to LPS. reaction through transition state stabilization and berry development. The grape berry has a double reactions for the production of useful antioxidants.
Resistance may then be achieved, either by genetic the binding of substrates (predominantly a the sigmoid pattern of growth. Surge in genomic data modification or, by using breeding programmes led to a large scale tissue specific proteomic Contact: nkhun@cput.ac.za
with a direct selection for these specific genes. Mutation of Arg15 to Leu results in substantially studies on berries sampled at single time point Additional analyses to determine the sub-cellular localisation of NS-RLK protein (using a fusion dinitrobenzene to glutathione) conjugating activity However, these studies mentioned above were Natasha Sanabria
protein), and to determine whether or not LPS of the enzyme, 3-fold decrease in affinity at the limited to berries collected during the growing University of Johannesburg
directly binds to the NS-RLK protein (using ELISA) H-site for anionic non-substrate ligand 8-anilino-1- season. Thus, a more simplified model system Mentor: Prof I A Dubery
naphthalene sulphonate (ANS) and reduced affinity which be used for the study of ripening related Broad research area: Biological sciences,
for anionic β-complex formed between gSH and changes and also for large scale production of Contact: nmsanabria@yahoo.com
1,3,5-trinitrobenzene (an analogue of the anionic favorable compounds needs to be established. Specific research field: Plant defense responses
transition state of the SNAr reaction between Use of suspension cultured cells established from grape berries is therefore a viable alternative. Purpose of study:
This mutation however has little effect on The results we have obtained in terms of proteins This study investigates the profiling of plant glutathione binding and protein structure and identified and their expression profiles in part receptor-like kinase (RLK) genes up-regulated stability. Domain-domain interactions between confirm proteomic studies carried out on whole the thioredoxin like N-terminal domain and alpha Current models regarding plant: pathogen helical C-terminal of monomeric gST’s produces These studies have also observed that most interactions assume that recognition of pathogen- cooperative folding. Domains are compact dramatic changes in terms of relative expression occur at Veraison. The data presented here from chlorinated hydrocarbon contaminated site as well industrial processes. In the past 20 years there has from various areas in South Africa, copper- three different ripening stages and two growth as a metagenomic analysis of the site. Samples been an increased interest in the oxidative enzymes contaminated soil in the Zambian copperbelt stages suggests that berry cell cultures actually obtained from this site are batch cultured in minimal produced by actinobacteria. Oxidative enzymes region, the Bwanda and gwisho hot springs in encompass a vast group of enzymes with varied Zambia, from the dry Miers Valley, Antarctica medium containing various chlorinated hydrocarbons These studies have also observed that most present in this site and repeatedly enriched. catalytic abilities. Among them, the enzymes laccase, and from the Namib Desert, Namibia. Symbiotic B dramatic changes in terms of relative expression A halogen release assay is performed in order peroxidase and tyrosinase are known for their actinobacteria were also isolated from marine O occur at Veraison. Several other studies using to determine whether individual isolates possess ability to catalyze oligomerisation, depolymerisation sponges and sea squirts collected from Algoa and hydroxylation reactions. These enzymes have Bay and Marion Island. 16S rRNA analyses have iTRAQ labelling coupled with nanoLC/MS has the ability to cleave carbon-halogen bonds. Enzyme IC proved to be more sensitive than gel–based activities are confirmed with cell free extracts using successful y been used in our research group in revealed that laccase producers are ubiquitous in electrophoresis with regards to quantitation but all of the intermediates in proposed chlorinated various biotransformation reactions, notably using nature and are mostly represented by members there was limited replicable detection of proteins hydrocarbon degradative pathways and compared of the genus Streptomyces and members of “rare” to known chlorinated hydrocarbon degrading The aim of this study was to devise a screening actinobacteria genera including Actinomadura, However, to get a tissue specific understanding program to isolate actinobacteria from unique Micromonospora and Verrucosispora. Peroxidase of ripening processes in the berry cell cultures Total DNA was isolated from contaminated environments and to screen them for potential y producers (mostly Streptomyces spp.) were O it is important to delve deeper by sub celular borehole water and primers based on genes novel oxidative enzymes suitable for industrial identified amongst the isolates from termite guts application. A multi-faceted screening program was and the copper-contaminated soil, while the fractionation including cel wal and the secretome. involved in both hydrolytic and reductive designed involving the use of direct assays, solid Antarctic strains were the predominant tyrosinase Detailed proteomic analysis with berry suspension degradation of chlorinated hydrocarbons were cel s and their sub fractions at different stages synthesized. PCR analysis indicated the presence media assays and liquid media assays. The existing producers. Optimisation studies for enzyme of ripening is the next step towards a complete of both hydrolytic and reductive dehalogenases. culture col ections screened included actinobacteria production by the top enzyme producers are understanding of protein expression related to berry Future work involves the use of denaturing isolated from deep-sea environments and those ripening processes in model cel suspension culture. gradient gel electrophoresis (DggE) of the isolated from the intestinal tracts of an indigenous 16SrRNA regions to determine the identity of lower-order termite, Microhodotermes viator. Contact: mleroes@gmail.com
Contact: sharath@sun.ac.za
the bacterial isolates. The metagenome will be Others were isolated from soil samples collected sequenced and analyzed in order to identify novel gene sequences involved in degradation Algasan Govender
of chlorinated hydrocarbons. This overall aim of University of KwaZulu-Natal
this study is to identify novel genes and bacteria Mentor: Prof B Pillay
involved in the degradation of chlorinated Broad research area: Microbiology
hydrocarbons as well as to provide insight into Specific research field: Microbial
the overall strategy to be used to bio-remediate chlorinated hydrocarbon contaminated sites.
Purpose of study:
Contact: govenderal@ukzn.ac.za
Chlorinated hydrocarbons are some of the most widely used and produced chemicals of the modern Marilize Le Roes-Hill
world. These carcinogenic compounds are used Cape Peninsula University of Technology
as solvents, chemical intermediates as well as Mentor: Prof S Burton
fuel additives and are toxic to both terrestrial and Broad research area: Microbiology and
Accidental spills, poor handling and illegal Specific research field: Oxidative enzymes in
dumping have resulted in contamination of the environment. Thus far several bacteria have been identified that are capable of utilising these Purpose of study:
compounds as a sole carbon and energy source. Unique environments and their microbial populations are constantly being exploited for novel secondary characterisation of bacterial isolates from a metabolites or enzymes with potential application in

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