Natural and Agricultural Sciences Annual Report 2011 Natural and Agricultural Sciences Annual Report 2011 Contact Details Dean Prof Neil Heideman +27 (0)51 401 2322 [email protected] Vice-Dean Prof. Corli Witthuhn +27 (0) 51 4013855 [email protected] Faculty Manager Mr Johan Kruger +27 (0)51 401 2409 Issued by [email protected] Faculty of Natural and Agricultural Sciences Marketing Manager University of the Free State Ms Elfrieda Lotter Editorial Compilation +27 (0)51 4012531 [email protected] Betta van Huyssteen Physical Address Language Revision Room 9A, Biology Building, Main Campus, Bloemfontein Betta van Huyssteen Stella Mcgill Postal Address Revision of Bibliographical Data University of the Free State PO Box 339 Mercia Coetzee Bloemfontein Design, Layout South Africa 9300 Chrysalis Advertising & Publishing Fax: +27 (0)51 401 3728 Printing E-mail: [email protected] Oranje Drukkery • Printers Faculty website: www.ufs.ac.za/natagri Table of Contents Preface 5 Research Clusters 6 Agricultural Sciences 13 Agricultural Economics 14 Animal, Wildlife and Grassland Sciences 20 Plant Sciences 30 Soil, Crop and Climate Sciences 40 Building Sciences 49 Architecture 50 Quantity Surveying and Construction Management 56 Urban and Regional Planning 62 Natural Sciences 67 Chemistry 68 Computer Science and Informatics 86 Consumer Science 94 Genetics 100 Geography 108 Geology 116 Mathematical Statistics and Actuarial Science 126 Mathematics and Applied Mathematics 132 Microbial, Biochemical and Food Biotechnology 136 Physics 150 Zoology and Entomology 164 Centres 177 Disaster Management Training and Education Centre for Africa (DiMTEC) 178 Environmental Management 186 Lengau Agricultural Development Centre 196 Microscopy 202 Sustainable Agriculture, Rural Development and Extension 208 Experimental Farm 215 Paradys 216 Institute 223 Groundwater Studies 224 Workshops 231 Electronics 232 Instrumentation 238 Statistical Data 243 Students 244 Research 246 Glossary 249 4 Message from the Dean Faculty of Natural and Agricultural Sciences Preface Message from the Dean Cutting edge research culminating in exciting prospects for new technologies, scholarly leadership in compelling national issues, exciting discoveries, prestigious international research awards and highly sophisticated new state-of-the-art equipment again characterized the achievements of our faculty in 2011. The uncovering of new insights for drug development using nanotechnology made world headlines and opened up an exciting new area for scientific exploration while the discovery of a multi-cellular organism (a nematode worm) at the greatest depth below the earth’s surface ever recorded was greeted with much excitement by the research community. The studying of seasonal movements, migration routes and behavioural patterns in giraffes using GPS equipped collars was also a world first. Significant new discoveries were made with regard to the identification of wheat and barley genotypes having genetic resistance to leaf and stem rust. And work on a model eukaryote showed that its epigenome was adjusted to reflect a general state of transcriptional repression during quiescence, a fundamentally important finding. While numerous Annual Report 2011 prestigious awards were once again conferred on several staff members, a particularly special one was the African 5 Union Kwame Nkrumah Scientific Award for research advancing socio-economic development on the continent which was won by one of our leading female researchers. We also have to extend a word of gratitude to our numerous Prof. NJL Heideman collaborators, both nationally and internationally, whose involvement in our work makes it possible for staff and students to achieve more and also helps us to continually rand Time of Flight Secondary Ion Mass Spectrometer as deepen our academic rigor. Our students also again excelled an addition to our highly sophisticated nanotechnological in various ways, winning awards for architectural creativity, research equipment, a further significant stride forward in being recognized for presenting outstanding papers on this area of research. their research at international conferences, and winning It is therefore once again my pleasure to present to you prestigious bursaries to continue with their higher degrees. our 2011 Annual Report and extending my sincere gratitude Special mention also has to be made of the outstanding to the staff and students for their selfless commitment to successes achieved by our foundation programmes academic excellence and further raising the stature of our which offer students with potential the opportunity to faculty and the university. perform themselves into our degree programmes. Finally, without state-of-the-art equipment research leadership is Prof. NJL Heideman impossible which makes the acquisition of a multi-million Dean, Faculty of Natural and Agricultural Sciences StrategicStrategic AcademicAcademic ClustersClusters Faculty of Natural and Agricultural Sciences 6 Strategic Academic Clusters Strategic Academic Strategic Academic Cluster: Advanced Biomolecular Research The Advanced Biomolecular Research Cluster had a full and spectrometers and 2DGE apparatus in the Facility for successful year in 2011. There was a significant increase Genomics and Proteomics were also heavily used by research in activity in all focus areas, with the High Throughput groups from the campus and from other universities Biology and Bioinformatics focus areas experiencing a large and industry for protein identification and quantitative growth in the number of projects. The inter-faculty multi- proteomics. This included a project with the Water Research disciplinary philosophy was also expanded with the cluster Commission making use of the MS instruments for a participating in the annual Research Day of the Faculty of national reconnaissance study on the presence of emerging Health Sciences, with the identification of many possible contaminants such as pesticides and pharmaceuticals in collaborative activities. drinking water in South Africa. The major achievements of the ABR cluster within the The Bioinformatics focus area was also very active, with a Faculty of Natural and Agricultural Sciences include the project simulating the effect of post-translation modifications investigation of the post-translational modification of the of the core histone N-terminal extensions on the secondary Annual Report 2011 structures of these extensions being completed, which made core histones in the model eukaryote, Saccharomyces 7 cerevisiae, where entry into stationary phase, mimicking use of the High Performance Computing centre at the UFS. a state of senescence of multi-cellular eukaryotes, was Results from this study was presented by Prof. Patterton shown to be accompanied by quantitative deacetylation of at the bi-annual FASEB conference on Epigenetics and histones H3 and H4. This finding showed that the epigenome Chromatin Structure in Colorado, US. This study provided a of this eukaryote was adjusted to reflect a general state of theoretical basis for further experiments on the location of transcriptional repression during quiescence. This study was the N-terminal tails in condensed chromatin, making use of published in BMC Biochemistry (Ngubo et al., 2011). chemical cross-linking and mass spectrometry. The use of mass spectrometry (MS) in the structural In another major achievement, Prof. Derek Litthauer com- elucidation of mega-Dalton multi-unit protein complexes pleted the sequencing of the Thermus scotoductus SA-01 genome, and showed that this species acquired many genes was further expanded with the development of software from other thermophilic micro-organisms. This study was for the analysis of MS/MS spectra for the identification published in the impact 4 BMC Genomics (Gounder et al., 2011). of cross-linked amino acid residues in di-peptides. This approach allows identification of regions of proteins that are In the Advanced Cloning System focus area, Profs J. Albertyn in close spatial proximity, and facilitates questions regarding and M. Smit registered two provisional patents related complex structures at a resolution that lies between that to novel plasmids that can be used for the expression of of X-ray crystallography and cryo-electronmicroscopy. A genes in a number of different yeasts. Profs A. Marston review on this topic was published in the impact 7 Briefing and J. van der Westhuizen were also very active in the Novel in Bioinformatics (Mayne and Patterton, 2011). The mass Drug Discovery focus area and published several papers on pharmacologically active compounds isolated from South Participating staff African plants. Prof. Marston also published a review on the isolation of protein kinase inhibitors and activators from Prof. Hugh Patterton natural products in Current Topics in Medicinal Chemistry Dr Gabré Kemp (Marston, 2011). Protein kinases are involved in many signal Dr Dirk Opperman Prof. Koos Albertyn transduction pathways, systems that allow cells to react to Prof. Martie Smit the environment, and which are involved in many cellular Prof. Derek Litthauer responses associated with diseased states in humans. Dr Charlene Boucher Cluster seed funding allowed several new projects to start, Prof. Paul Grobler many of which generated preliminary data that was used Dr Linda Spies in major funding applications. The ABR cluster continues Dr Botma Visser to support multi-disciplinary projects in its focus areas, Prof. Felicity Burt and facilitates the development