2012 Natural and Agricultural Sciences Annual Report International Water Cooperation In December 2010, the United Nations General Assembly declared 2013 as the United Nations International Year of Water Cooperation (Resolution A/RES/65/154). In reflection of this declaration, the 2013 World Water Day, which will take place on 22 March 2013, also will be dedicated to water cooperation. Source: www.unwater.org Contact Details Dean Prof Neil Heideman +27 (0)51 401 2322 [email protected] Faculty Manager Mr Johan Kruger +27 (0)51 401 2409 [email protected] Issued by Faculty of Natural and Agricultural Sciences Marketing Manager University of the Free State Ms Elfrieda Lotter +27 (0)51 4012531 Editorial Compilation [email protected] Mercia Coetzee Physical Address Language Revision Room 9A, Biology Building, Main Campus, Grammar Guardians Bloemfontein Wordsmith 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] Colour Planet Faculty website: www.ufs.ac.za/natagr Table of Contents Preface 4 Research Clusters 5 Advanced Biomolecular Research 5 Materials and Nanosciences 8 Technologies for Sustainable Crop Industries in Semi-arid Regions 14 Water Management in Water-scarce Areas 18 Agricultural Sciences 22 Agricultural Economics 22 Animal, Wildlife and Grassland Sciences 26 Plant Sciences 32 Soil, Crop and Climate Sciences 38 Building Sciences 44 Architecture 44 Quantity Surveying and Construction Management 49 Urban and Regional Planning 52 Natural Sciences 56 Chemistry 56 Computer Science and Informatics 71 Consumer Science 75 Genetics 78 Geography 82 Geology 86 Mathematical Statistics and Actuarial Science 93 Mathematics and Applied Mathematics 97 Microbial, Biochemical and Food Biotechnology 99 Physics 109 Zoology and Entomology 116 Centres 125 Disaster Management Training and Education Centre for Africa 125 Environmental Management 129 Lengau Agricultural Development Centre 136 Microscopy 140 Sustainable Agriculture, Rural Development and Extension 143 Experimental Farm 147 Paradys Experimental Farm 147 Institute 152 Institute for Groundwater Studies (IGS) 152 Annual Report 2012 Workshops 158 Electronics 158 Instrumentation Division 162 Statistical Data 165 Students 165 Research 167 Glossary 169 Natural and Argricultural Sciences Preface: Message from the Dean Research Clusters The past year once again saw the Faculty do justice to the academic and human projects of the university which lie at the heart of its vision and mission. Our growth in fulltime equivalents continued its upward trajectory for a third successive year as did out outputs in research units, and masters and doctoral graduates. Prof. N.J.L. Heideman The top ten publishers of accredited journal articles Food biotechnology) in its list of 200 young South for 2012 had numbers ranging from 4 to 10 units each Africans (35 years and younger) who were the most and also included some of our emerging scholars, influential achievers in various fields, in his case in which is gratifying. Several scholarly books saw the the Health category. light and included ones in physics, the biological In the Dean’s Office Ms Elzmarie Oosthuizen received sciences, grassland science and geography. Progress the Patricia K. Elder Award for Extraordinary was also made with respect to diversifying the Commitment and Dedication to the Advancement of academic cadre of the faculty with the appointment International Economic Education from the National of several black staff members. Association of Economic Educators together with Both emerging and experienced scholars excelled in The Council for Economic Education in the USA. various ways elevating the stature of the university Profs. Lodewyk Kock (Microbial, Biochemical and in the national and international academic arenas. Food biotechnology), Hugh Patterton (Advanced Dr Marieka Gryzenhout (Plant Sciences) was elected Biomolecular Strategic Cluster) and Martin to the South African Young Academy of Science Ntwaeaborwa were elected members of the South and was also the first recipient of the International African Academy of Science. A yeast genus was named Mycological Association Young Mycologist Award Kockiozyma in honour of Prof. Lodewyk Kock for his for Africa in the form of the Ethel Mary Doidge contributions to yeast systematics while Prof. James Medal. Prof. Maryke Labuschagne (Plant Sciences) du Preez from the same department was elected was Grain SA’s Scientist of the Year. Prof. Liezel joint Editor-in-Chief for the journal Biotechnology Herselman was re-elected President of the South for Biofuels. Prof. André Roodt (Chemistry) became African Plant Breeders’ Association with Dr Adré the first person from outside Europe to be elected Minnaar-Ontong as a member of its executive, both President of the European Crystallographic Society. Annual Report 2012 also being from Plant Sciences. Dr. Jana Vermaas The awarding of two research chairs to the faculty (Consumer Science) received a certificate as one under the SARCHi initiative of the DST and NRF was of the five best presenters during their conference also a notable highlight. in Melbourne, Australia. Prof. Martin Ntwaeaborwa These are but some of the outstanding achievements (Physics) was elected the new Chairperson of by staff of the faculty in 2012 for which I gratefully the South African Nano Initiative while Dr Johan acknowledge them. I also thank our support staff van Niekerk (Sustainable Agriculture, Rural and general workers for their commitment and Development & Extension) was elected to the South contributions to the success of the faculty. African Society for Agricultural Extension’s National Natural and Argricultural Sciences Executive Committee. The Mail & Guardian included Prof. Neil Heideman 4 Dr Olihile Sebolai (Microbial, Biochemical and Dean, Faculty of Natural and Agricultural Sciences Research Clusters Strategic Academic Cluster: Advanced Biomolecular Research Overview Focus Areas The Advanced Biomolecular Research Cluster brings High Throughput Biology: In this focus area all aspects together expertise from various disciplines to synergise of genomes and proteomes, including genome func- in the study of biological systems in a high throughput tion, regulation, and evolution are addressed. Ac- manner, often at the level of the whole genome tivities include genome sequencing, transcriptomics or proteome. Disciplines that are directly involved and other genome-related microarray endeavours in the research activities include biochemistry, such as chip-on-chip. The focus area also involves molecular biology, microbiology, virology, statistics, the high-throughput analysis of proteins, including mathematics and computer science. The Cluster directed evolution, proteome analysis, and high- Annual Report 2012 does not limit the scope of research questions that throughput enzyme assays, including the screening can be asked within the Cluster, but rather provides of archae for activities of biotechnological value, and an opportunity to address biological questions in a the screening of plant extracts for inhibitory/activat- manner that provides a far more definitive answer ing activities for specific enzymes. than that of a classic biological approach. Although the Cluster incorporates several focus areas, these areas Bioinformatics/Computational Biology: Activities in are interdependent, and activities in the one focus this focus area include all bioinformatics related re- area will require support from one or more of the other search, bioinformatics collaborations with projects in focus areas. the other focus areas that require bioinformatics sup- Natural and Argricultural Sciences 5 port such as genome annotation, gene identification, Isolation and characterisation of compounds from database design and the development of specialised plants that are pharmacologically active against the analysis software. A significant degree of molecular HIV virus. The AIDS endemic has stimulated research modeling and molecular dynamics research is also into anti-HIV drugs. This includes phytochemical undertaken in this Focus Area. investigations into pharmacognostically interesting plant material that has, according to anecdotal Novel Drug Discovery: The novel drug discovery evidence, the potential to treat AIDS. The Chemistry programme focuses on activity guided isolation and Department has initiated a project to identify the structure elucidation of bioactive compounds from active ingredients in some of these plant materials natural sources with high throughput screening. and to determine the toxicity, bioavailability and The programme includes synthesis of bioactive in vivo efficacy of these molecules against HIV and Research Clusters compounds, analogues and internal standards other commercially-important viral infections. The for further drug development and bioavailability project involves advanced chromatography and studies. The team collaborates with national and structure elucidation. international experts. Old Yellow Enzymes (OYEs) and cytochrome P450 Advanced Cloning Systems: In this focus area the (CYP450s) enzymes from Crytococcus neoformans. cloning and/or characterisation and/or expression Eicosanoid production is seen as an important of any product is the central theme. A major focus is virulence factor in the pathogenic yeasts Cryptococcus the development and/or improvement