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Professor Jill Farrant

Head of Department; desiccation tolerance; resurrection plants; seeds; plant physiology; molecular biology
Professor Edward Rybicki

Plant- and tissue culture-derived vaccines; Human papillomavirus (HPV); Human immunodeficiency virus (HIV); Beak and feather disease virus; geminivirus; Maize streak virus; molecular virology; molecular biotechnology

Professor Jennifer Thomson

Transgenic maize for resistance to the African Maize streak virus and tolerance to drought

Associate Professor Val Abratt

Bacteroides fragilis; nitrogen metabolism; virulence; metronidazole; DNA damage and repair; Bifidobacterium; probiotics

Associate Professor Wolf Brandt

Protein chemistry; proteomics; MALDI-TOF mass-spectrometry; desiccation tolerance; polyphenols
Associate Professor Vernon Coyne

Marine biotechnology; marine microbiology; mariculture; abalone; macroalgae

Associate Professor Nicola Illing

Microarray analysis; regulation of gene expression; cell signalling

Associate Professor George Lindsey

Protein chemistry; yeast and plant seed stress tolerance

Associate Professor Sagadevan Mundree

Environmental stress tolerance; regulation of plant gene expression; genetic engineering for drought tolerance; resurrection plant Xerophyta viscosa; Arabidopsis thaliana
Associate Professor Sharon Reid

Gram-positive and anaerobic bacteria; Corynebacterium; Clostridium; Bifidobacterium; gene regulation of nitrogen- and carbon-substrate utilisation; probiotics; molecular systematics; fibre-degrading bacteria

Dr Katherine Denby

Senior Lecturer; plant molecular biology; plant-pathogen interactions; plant disease resistance; signal transduction; Arabidopsis molecular genetics

Dr Colleen O'Ryan

Senior Lecturer; evolution; population genetics; conservation genetics; neutral DNA markers (microsatellite and mitochondrial DNA) and MHC loci

Dr Paul Meyers

Lecturer; actinomycetes; Streptomyces; bacterial taxonomy; “bioprospecting”; novel antibacterial antibiotics; Mycobacterium tuberculosis; bacterial metabolism

Dr Suhail Rafudeen

Lecturer; abiotic stress tolerance in plants; signalling and regulation of plant gene expression during stress; protein expression profiling; protein mining; Xerophyta viscosa

Dr Laura Roden

Lecturer; flowering time; plant growth substances; circadian rhythms and photoperiodism; regulation of plant gene and transgene expression; plant molecular biology; Arabidopsis genetics

Dr Jerry Rodrigues

Lecturer; protein chemistry; plant desiccation tolerance; chromatin remodelling

Dr Arvind Varsani

Lecturer; virus structure, structure-based vaccine design, virus diversity and evolution through recombination

HONORARY STAFF

Professor Jonathan Blackburn

Protein function microarrays; enzymology; in vitro selection of new protein activities; cancer biomarker discovery; effect of polymorphic variation on drug metabolism; protein-DNA interactions; protein-drug interactions; protein-carbohydrate interactions; proteomics; biotechnology

Professor Horst Klump

Physical biochemistry; uncommon DNA structures; self-assembly nanostructures; non equilibrium DNA structures

CONTRACT RESEARCH STAFF

Dr Inga Becker-Hitzeroth

Senior Scientist; plant-derived vaccines; human papillomaviruses
Dr Jacqueline Bishop

Post-doctoral fellow; population and conservation genetics; molecular evolution of the Major Histocompatibility Complex (MHC); mate choice and the evolution of mating systems

Dr Anne Brill

Post-doctoral fellow; protein microarrays; heparin/heparan sulphate binding proteins; differential binding to heparan sulfate structures

Dr Ereck Chakauya

Post doctoral fellow; plant biotechnology; plant-based vaccines; Human immunodeficiency virus

Dr Amirtha Ganesh

Post-doctoral fellow; identification of novel cancer biomarkers; colorectal cancer; microarrays; design and development of high throughput screening strategies

Dr Robert Ingle

Post-doctoral fellow; plant stress biology; analysis of novel defence-related proteins in Arabidopsis

Dr Revel Iyer

Post-doctoral scientist; agricultural biotechnology; plant molecular biology; plant transgenics

Dr Arnaud Lehner

Post-doctoral fellow; plant stress biology; antioxidant systems; sugar and HSP regulation in response to stress; biochemistry and molecular biology

Dr Ann Meyers

Senior scientist; plant-derived vaccines; human immunodeficiency virus; Gracilaria gracilis transformation studies; recombinant protein expression in Gracilaria gracilis

Dr Martin Mills

Post-doctoral fellow; physical biochemistry; diversity of nucleic acid structures; triplexes, quadruplexes, trinucleotide-repeats, networks and strand-displacement cycles

Dr Monique Morse

Post-doctoral fellow; plant stress tolerance; GC characterisation; cGMP signalling in plants

Dr Shane Murray

Post-doctoral fellow; disease-resistance signal transduction in plants; transcript profiling using microarrays; Arabidopsis genomics

Dr Lynthia Paul

Post-doctoral fellow; Bacteroides fragilis metronidazole resistance; mutational analysis; DNA recombination and repair genes

Dr Siddharth Sharma

Post-doctoral fellow; protein microarrays; drug-metabolizing enzymes; effect of SNPs on cancer risk assessment and drug metabolism

Dr Dionne Shepherd

Post-doctoral fellow; virology and plant biotechnology; development of maize streak virus resistant maize; maize streak virus diversity; plant-virus interactions

Dr Aubrey Shoko

Post-doctoral fellow; functional protein microarrays; human kinase activity; selectivity of kinase inhibitors; p53 DNA binding activity

Dr Fiona Tanzer

Senior scientist; DNA vaccines; plant-derived vaccines; insect cell transgenesis; Human Immunodeficiency Virus

Contact Details

Postal address: Department of Molecular and Cell Biology, University of Cape Town, Private Bag X3, Rondebosch, 7701, South Africa

Telephone: [phone]

Fax: [phone]

E-mail: [e-mail]

Web: http://www.mcb.uct.ac.za

Research Output
ARTICLES IN PEER-REVIEWED JOURNALS
Balsamo, R., Vander Willigen, C., Bauer, A.M. and Farrant, J.M. 2006. Drought tolerance of selected eragrostis species correlates with leaf tensile properties. Annals of Botany, 97(6): 985-991.
Chakauya, E., Chikwamba, R. and Rybicki, E.P. 2006. Riding the tide of biopharming in Africa: Considerations for risk assessment. South African Journal of Science, 102(7/8): 284-288.
Chakauya, E., Coxon, K.M., Whitney, H.M., Ashurst, J.L., Abell, C. and Smith, A.G. 2006. Pantothenate biosynthesis in higher plants: Advances and challenges. Physiologia Plantarum, 126(3): 319-329.
Chakauya, E., Tongoona, P., Matibiri, E.A. and Grum, M. 2006. Genetic diversity assessment of sorghum landraces in Zimbabwe using microsatellites and indigenous local names. International Journal of Botany, 2(1): 29-35.
Garwe, D., Thomson, J.A. and Mundree, S.G. 2006. XVSAP1 from Xerophyta viscosa improves osmotic-, salinity- and high-temperature-stress tolerance in Arabidopsis. Biotechnology Journal, 1(10): 1137-1146.
Glenn, I.E. and Rybicki, E.P. 2006. Douglas Livingstone’s two cultures. Current Writing, 18(1): 78-89.
Heath, L.E., Williamson, A.-L. and Rybicki, E.P. 2006. The capsid protein of beak and feather disease virus binds to the viral DNA and is responsible for transporting the replication-associated protein into the nucleus. Journal of Virology, 80(14): 7219-7225.
Ingle, R.A., Carstens, M. and Denby, K.J. 2006. PAMP recognition and the plant-pathogen arms race. Bioessays, 28(9): 880-889.
Johnson, S.A., Jackson, S., Abratt, V.R., Wolfaardt, G.M., Cordero-Otero, R. and Nicolson, S.W. 2006. Xylose utilisation and short-chain fatty acid production by selected components of the intestinal microflora of a rodent pollinator (Aethomys namaquensis). Journal of Comparative Physiology, 176(7): 631-641.
Kirby, B.M., Le Roes, M. and Meyers, P. 2006. Kribbella karoonensis sp. nov. and Kribbella swartbergensis sp. nov., isolated from soil from the Western Cape, South Africa. International Journal of Systematic and Evolutionary Microbiology, 56(5): 1097-1101.
Klump, H. 2006. Exploring the energy landscape of the genetic code. Archives of Biochemistry and Biophysics, 453(1): 85-90.
Klump, H. 2006. Students overcome impossible odds and professors sometimes too. Bunsen Magazin. German Bunsen Society for Physical Chemistry, May 2006(3): 72.
Klump, H., Chauhan, M., Mills, M. and Lin, C. 2006. Progress in designing nucleic acid structures and fine-tuning their interactions. Archives of Biochemistry and Biophysics, 453(1): 91-98.
Klump, H., Koch, K. and Lin, C. 2006. DNA-mediated biomineralization of a new planar Pt-complex. South African Journal of Science, 102(May/June): 264-266.
Kohl, T.O., Hitzeroth, I.I., Stewart, D., Varsani, A., Govan, V.A., Christensen, N.D., Williamson, A.-L. and Rybicki, E.P. 2006. Plant-produced cottontail rabbit papillomavirus L1 protein protects against tumor challenge: A proof-of-concept study. Clinical and Vaccine Immunology, 13(8): 845-853.
Kullin, B.R., Abratt, V.R. and Reid, S.J. 2006. A functional analysis of the Bifidobacterium longum cscA and scrP genes in sucrose utilization. Applied Microbiology and Biotechnology, 72(5): 975 - 981.
Le Roes, M. and Meyers, P. 2006. Nocardia gamkensis sp. nov. Antonie van Leeuwenhoek International Journal of General and Molecular Microbiology, 90(3): 291-298.
Legg, J.P., Owor, B., Sseruwagi, P. and Ndunguru, J. 2006. Cassava Mosaic Virus Disease in East and Central Africa: Epidemiology and management of a regional pandemic. Advances in Virus Research, 67: 355-418.
Macey, B.M. and Coyne, V.E. 2006. Colonization of the gastrointestinal tract of the farmed South African Abalone Haliotis midae by the Probionts Vibrio midae SY9, Cryptococcus sp. SS1, and Debaryomyces hansenii AY1. Marine Biotechnology, 8(3): 246-259.
Marais, D.J., Sampson, C., Jeftha, A., Dhaya, D., Passmore, J.S., Denny, L.A., Rybicki, E.P., Van der Walt, E., Stephen, L.X.G. and Williamson, A.-L. 2006. More men than women make mucosal IgA antibodies to Human papillomavirus type 16 (HPV-16) and HPV-18: A study of oral HPV and oral HPV antibodies in a normal healthy population. BMC Infectious Diseases. [Online]. http://www.biomedcentral.com/1471-2334/6/95.
Maree, H.J., Van der Walt, E., Tiedt, F.A.C., Hanzlik, T.A. and Appel, M. 2006. Surface display of an internal His-tag on virus-like particles of Nudaurelia capensis omega virus (NomegaV) produced in a baculovirus expression system. Journal of Virological Methods, 136: 283-288.
Moore, J.P., Nguema-Ona, E., Chevalier, L.M., Lindsey, G.G., Brandt, W.F., Lerouge, P., Farrant, J.M. and Driouich, A. 2006. Response of the leaf cell wall to desiccation in the resurrection plant Myrothamnus flabellifolius. Plant Physiology, 141(2): 651-662.
Mowla, S.B., Cuypers, A., Driscoll, S.P., Kiddle, G., Thomson, J.A., Foyer, C.H. and Theodoulou, F.L. 2006. Yeast complementation reveals a role for an Arabidopsis thaliana late embryogenesis abundant (LEA)-like protein in oxidative stress tolerance. Plant Cell, 48(5): 743-756.
Newton, R., Bond, W.J. and Farrant, J.M. 2006. Effects of seed storage and fire on germination in the nut-fruited Restionaceae species, Cannomois virgata. South African Journal of Botany, 72(1): 177-180.
Passmore, J.S., Milner, M., Denny, L.A., Sampson, C., Marais, D.J., Allan, B.R., Gumbi, P.P., Hitzeroth, I.I., Rybicki, E.P. and Williamson, A.-L. 2006. Comparison of cervical and blood T-cell responses to human papillomavirus-16 in women with human papillomavirus-associated cervical intraepithelial neoplasia. Immunology, 4(119): 507-514.
Price, C.E., Reid, S.J., Driessen, A.J.M. and Abratt, V.R. 2006. The Bifidobacterium longum NCIMB 702259T ctr gene codes for a novel cholate transporter. Applied and Environmental Microbiology, 72(1): 923-926.
Scheffler, K., Martin, D. and Seoighe, C. 2006. Robust inference of positive selection from recombining coding sequences. Bioinformatics, 22(20): 2493-2499.
Seoighe, C., Nembaware, V. and Scheffler, K. 2006. Maximum likelihood inference of imprinting and allele-specific expression from EST data. Bioinformatics, 22(24): 3032-3039.
Shepherd, D.N., Martin, D., Varsani, A., Thomson, J.A., Rybicki, E.P. and Klump, H. 2006. Restoration of native folding of single-stranded DNA sequences through reverse mutations: An indication of a new epigenetic mechanism. Archives of Biochemistry and Biophysics, 453(1): 108-122.
Stein, D.J., Daniels, W., Emsley, R., Harvey, B., Blackburn, J., Carey, P., Ellis, G.F.R., Illing, N., Flisher, A.J., Moolman-Smook, H., Mwaba, K., Ramesar, R., Russell, V.A., Seedat, S., Tredoux, C.G., Vaughan, C.L., Vythilingum, B.V. and Warwick, J. 2006. A brain-behaviour initiative for South Africa: The time is right. Metabolic Brain Disease, 21(2-3): 266-271.
Van Rooyen, J., Abratt, V.R. and Sewell, B.T. 2006. Three-dimensional structure of a Type III glutamine synthetase by single particle reconstruction. Journal of Molecular Biology, 361(4): 796-810.
Varsani, A., Van der Walt, E., Heath, L.E., Rybicki, E.P., Williamson, A.-L. and Martin, D. 2006. Evidence of ancient papillomavirus recombination. Journal of General Virology, 87(9): 2527-2531.
Varsani, A., Williamson, A.-L., Jaffer, M.A. and Rybicki, E.P. 2006. A deletion and point mutation study of the human papillomavirus type 16 major capsid gene. Virus Research, 122(1-2): 154 - 163.
Varsani, A., Williamson, A.-L., Stewart, D. and Rybicki, E.P. 2006. Transient expression of Human papillomavirus type 16 L1 protein in Nicotiana benthamiana using an infectious tobamovirus vector. Virus Research, 120(1-2): 91-96.
Whitlock, K.E., Illing, N., Brideau, N.J., Smith, K.M. and Twomey, S. 2006. Development of GnRH cells: Setting the stage for puberty. Molecular and Cellular Endocrinology, 254-255: 39-50.

BOOKS
Thomson, J.A. 2006. GM Crops: The impact and the potential: i-xviii, 1-158. Collingwood VIC Australia: CSIRO Publishing.

CHAPTERS IN BOOKS
Mergny, J., Gros, J., De Cian, A., Bourdoncle, A., Rosu, F., Saccà, B., Guittat, L., Amrane, S., Mills, M., Alberti, P., Takasugi, M. and Lacroix, L. 2006. Energetics, kinetics and dynamics of quadruplex folding. In S. Neidle and S. Balasubramanian (eds), Quadruplex nucleic acids: 31-80. Cambridge: RCS (Royal Society of Chemistry).
Mtwisha, L., Farrant, J.M., Brandt, W.F. and Lindsey, G.G. 2006. Protection mechanisms against water deficit stress: desiccation tolerance in seeds as a study case. In J.-M. Ribaut (ed.), Drought adaptation in cereals: 531-550. New York: Food Products Press. An imprint of Haworth Press.
Mundree, S.G., Iyer, R., Baker, B., Conrad, N., Davis, E.J., Govender, K., Maredza, A.T. and Thomson, J.A. 2006. Prospects of using genetic modification to engineer drought tolerance in crops. In N.G. Halford (ed.), Plant biotechnology: Current and future applications of genetically modified crops: 193-205. Chichester: John Wiley & Sons.

THESES AND DISSERTATIONS PASSED FOR HIGHER DEGREES
Bajic, J. 2006. Exploring the longevity of dry Craterostigma wilmsii (homoiochlorophyllous) and Xerophyta humilis (poikilochlorophyllous) under simulated field conditions: 174. PhD.
Bamuamba, K. 2006. Pharmacognostic study of 5 medicinal plant species from Western Cape Province (South Africa) for anti-tubercular activity: 142. PhD.
Bredenkamp, N. 2006. Evolutionary analysis and functional characterization of the Forkhead transcription factor FoxG1: 111. MSc (Research), University of Cape Town.
Chang, C. 2006. Compaction of chromatin in Saccharomyces cerevisiae: 89. MSc (Research).
Chopera, D.R. 2006. Molecular characterization of XvNI01, a myo-inositol 1-phosphate synthase gene from Xerophyta viscosa: 74. MSc (Research).
Cook, A.E. 2006. Development of methods in Actinomycete taxonomy to enhance the search for novel anti-tubercular antibiotics: 156. PhD.
Dzobo, K. 2006. Characterization of polyphenols in leaves of four desiccation tolerant plant families: 172. MSc (Dissertation).
Govender, K. 2006. Characterisation of XvPrx2, a type II peroxiredoxin isolated from the resurrection plant Xerophyta viscosa (Baker): 178. PhD.
Heath, L.E. 2006. Molecular studies on Beak and feather disease virus: 79. PhD.
Joubert, N. 2006. The classroom transferability of a university-based INSET program of workshops in practical work for senior high school biology educators: 139. PhD.
Karreman, R.J. 2006. The localization, function and applications of the stress response protein HSP12P in the yeast Saccharomyces cerevisiae: 144. PhD.
Kohl, T.O. 2006. An investigation into the development of plant-derived vaccines against human papillomaviruses type 11 and Cottontail Rabbit papillomavirus: 247. PhD.
Moore, J.P. 2006. The role of polyphenols and the cell wall in relation to the desiccation tolerance of the resurrection plant Myrothamnus flabellifolia (Welw.): 198. PhD.
Munian, A.C. 2006. Pineapple dietary fibre and the effects of processing on its functional properties: 181. MSc.
Naidoo, R.K. 2006. Characterisation of the population genetics of farm-bred Haliotis midae using microsatellite DNA markers: 94. MSc.
Patel, E. 2006. Rhamnose metabolism and metronidazole resistance in B. thetaiotaomicron VPI-5482: 132. PhD.
Paul, L.V. 2006. Melanin production by V. Cholerae 569B: its role as a mechanism of protection against oxidative and other environmental stresses: 165. PhD.
Pillay, R. 2006. Strain differentiation and screening for resistance against isolates of soybean mosaic virus: 108. MSc.

Newspaper Articles
Thomson, J.A. 2006. Genetically modified foods. Business Day 07/02/2006.
Department of Oceanography

Research Report 2006
(Including the Research Diving Unit)
Head of Department: Professor Frank Shillington
Departmental Profile
The Department of Oceanography is the only such Department in sub-Saharan Africa, and is the major focus for research in physical oceanography, atmospheric science and ocean climatology in South Africa and elsewhere in Africa. The Department has research groupings in sea-going observations, satellite marine remote sensing, coastal oceanography, numerical modelling, marine and coastal meteorology, and climate variability. Future research is expected to pave the way to the science underpinning operational oceanography. Five scientists in the Department have been favourably evaluated in the review process of the National Research Foundation. Active international associations are maintained by collaborative projects with the Netherlands, France, Germany, USA and the European Union. The Department maintains close contact with marine science activities in the governmental, private and academic sectors in South Africa and into Africa. The UCT Research Diving Unit (RDU) is housed within the Department and is fully equipped with a decompression chamber and compressor. Most scientific diving at UCT is carried out in conjunction with the RDU.

Departmental Statistics
Permanent and Long-term Contract Staff

Professors	3
Senior Lecturer	1
Lecturer	1
Research Staff	5
Technical Support Staff	2
Administrative and Clerical Staff	2
Total	14

Honorary Staff

Emeritus Professor	1
Honorary Professor	1
Honorary Research Associates	15
Total	17

Students

Postdoctoral Fellows	4
Doctoral	15
Masters	31
Honours	6
Undergraduate	98
Total	154