Faculty of Natural and Agricultural Sciences
School of Biological Sciences
Department of Biochemistry
Selected Highlights from Research Findings
The SWB (Soil Water Balance) irrigation-scheduling model has been adapted to generate simplified irrigation calendars to help resource-poor, emerging commercial barley farmers in the Taung area of the North West Province. The calendars are simple site-specific seasonal recommendations, based on long-term evaporative demand of the area. Calendars are used as a guide of expected crop water usage, but can be updated using actual rainfall data and feedback from soil measurements, such as Wetting Front Detectors (WFD’s). Promising results have been obtained with the use of these calendars. This project was mutually funded by the Water Research Commission and South African Breweries.
Contact person: Dr F Joubert.
The Bioinformatics and Computational Biology Unit was formally inaugurated by the Vice-Chancellor Prof C Pistorius following the presentation of invited lectures by leading experts in the field including Dr D Landsman of the National Institutes of Health, USA. Genome annotation was performed for the Ehrlichia ruminatium genome that was recently completed by the group of Prof Basil Allsopp. The identification of all the genes from this organism will have immediate implications in the design of vaccines against heartwater (see article on Animal Vaccines elsewhere in this volume). Development was done on an analysis module for the BASE microarray system as well as on a new general system for data archiving that include microarray data. A programme for the automated modification of ligands is currently being developed. A database initiated for the structural annotation of the malaria proteomes will be developed further.
Die Bioinformatika en Berekeningsbiologie Eenheid is formeel geopen deur die Vise-Kanselier Prof C Pistorius na die aanbieding van genooide lesings deur voorste kundiges op dié gebied insluitende Dr D Landsman van die National Institutes of Health, VSA. Genoomannotasie is gedoen vir die Ehrlichia ruminantium genoom wat onlangs deur die groep van Prof Basil Allsopp voltooi is. Die identifikasie van al die gene van die organisme sal onmiddellike implikasies in die ontwerp van entstowwe teen hartwater hê (sien artikel oor Dierentstowwe elders in hierdie publikasie). Ontwikkeling is gedoen op 'n analise module vir die BASE-mikroskyf datasisteem asook op 'n nuwe algemene sisteem vir databerging wat mikroskyfdata insluit. 'n Program vir die outomatiese modifikasie van ligande word tans ontwikkel. 'n Databasis wat begin is vir die strukturele annotasie van die malaria proteoom sal verder ontwikkel word.
Contact person: Dr F Joubert.
The malaria research programme investigates the biochemical properties of several enzymes in the polyamine and folate metabolic pathways of the human malaria parasite, P. falciparum, with a view to ultimately discover parasite-specific features that can be exploited for therapeutic intervention strategies. Cutting edge technologies such as bioinformatics, microsatellite typing, structural modelling, DNA microarray and molecular biology are applied in these studies. Specific highlights from the findings include the description of three-dimensional structures for two enzymes in the folate metabolic pathway, which occur in a unique bifunctional arrangement, and explanations of the drug resistance mechanism of the malaria parasite to anti-folates; the description of the three-dimensional structures of a further two enzymes of the polyamine pathway of the parasite and the identification of parasite-specific features worthy of further investigations; experimental confirmation of parasite-specific properties and, thus, drug target sites located in a unique bifunctional enzyme regulating the polyamine pathway, which were previously identified by bioinformatic analysis and molecular modelling investigations; the first-time production in Africa of the DNA microarray gene expression profile of the malaria parasite under selective drug pressure and the identification of a new potential anti-malaria drug target; and the near-completion of a web interface named MicroArray Data Interface for Biological Annotation (MADIBA) as an integrated approach for functional annotation (explanation) of large datasets such as those produced by DNA microarray, to assist the drug discovery process.
Die malaria navorsingsprogram ondersoek die biochemiese eienskappe van verskeie ensieme in die poli-amien- en folaatbane van die menslike malaria parasiet, P. falciparum, met die doel om uiteindelike parasiet-spesifieke eienskappe te ontdek wat in terapeutiese ingypingstrategieë gebruik kan word. Die voorste tegnologiese metodes soos bioinformatika, mikrosatelliet tipering, struktuurmodelering, DNA mikroreekse en molekulêre biologie word in hierdie studies aangewend. Spesifieke hoogtepunt-bevindinge sluit in die beskrywing van die drie-dimensionele strukture van twee ensieme in die folaatbaan wat in 'n unieke bifunksionele kompleks voorkom, en verklarings vir die weerstandigheid van die parasiet teenoor anti-folaat medikamente; die beskrywing van die drie-dimensionele strukture van twee ander ensieme van die poli-amienbaan van die parasiet en die identifikasie van parasiet-spesifieke eienskappe vir verdere ondersoeke; eksperimentele bevestiging van parasiet-spesifieke eienskappe en dus terapeutiese teikenareas, wat gelokaliseer is in 'n unieke bifunksionele ensiem wat die poli-amienbaan reguleer en voorheen deur bioinformatika en modeleringsmetodes geïdentifiseer is; die eerste voorstelling in Afrika van die DNA mikroreeks geenuitdrukkingsprofiel van die malaria parasiet onder druk van selektiewe medikamente en die identifikasie van 'n nuwe potensiële anti-malaria terapeutiese teiken; en die byna-voltooide web-gebaseerde koppelvlak genaamd MicroArray Data Interface for Biological Annotation (MADIBA) as 'n geïntegreerde benadering vir die funksionele annotasie (verduideliking) van groot databasisse soos die wat deur DNA mikroreekse opgestel word, om die ontdekking van medikamente te bevorder.
Contact person: Prof AI Louw.
In current studies blood coagulation and platelet aggregation inhibitors of the tick Ornithodoros savignyi are under investigation. The nucleotide sequence of the latter has been identified. Recombinant expression of these proteins are under investigation. This can eventually lead to the development of anti-tick feeding strategies. By using molecular biological techniques, numerous tick proteins involved in exocytosis were identified. The studies are aimed at enhancing the understanding of the molecular basis underlying tick feeding and disease transmission. It is envisaged that targets may be identified for the design of a vaccine directed against tick infestation.
In huidige studies word bloedstolling- en bloedplaatjie-aggregasie inhibitore van die bosluis Ornithodoros savignyi ondersoek. Die nukleotied volgordes van laasgenoemde is geïdentifiseer. Rekombinante uitdrukking van hierdie proteïene word tans ondersoek. Dit kan uiteindelik lei tot die ontwikkeling van anti-bosluisvoeding strategieë. Deur gebruik te maak van molekulêre biologiese tegnieke is verskeie proteïene van bosluise wat betrokke is in eksositose geïdentifiseer. Dié studies het die opklaring van die molekulêre basis wat bosluisvoeding en siekte-oordraging onderlê, ten doel. Die vooruitsigte is dat teikens geïdentifiseer sal word wat bruikbaar sal wees vir die ontwerp van 'n entstof gerig teen bosluisinfestasie.
Contact person: Prof AWH Neitz.
The Biomolecular Interaction Analysis Programme focuses on the interaction of patient antibodies with antigens of lipid, carbohydrate and protein nature. A new collaboration with Prof C Kenyon of CSIR created the opportunity to become involved in research on the prevention and treatment of AIDS, by identifying critical viral antigenic peptides. The progress made with the development of a biosensor based serodiagnostic assay for tuberculosis based on the detection of anti-TB antibodies in patients against TB lipid antigens, matured into a South African provisional patent application.
Die Biomolekulêre Interaksie-analise navorsingsprogram fokus op die interaksie van pasiënte-teenliggame met antigene van lipied-, koolhidraat- en proteïenaard. 'n Nuwe samewerking met Prof C Kenyon van die WNNR het die geleentheid geskep om betrokke te raak by navorsing oor die voorkoming en behandeling van VIGS, deur die identifikasie van kritiese virale antigeniese peptiede. Die vordering met die ontwikkeling van biosensor-gebaseerde serodiagnostiek van tuberkulose, gebaseer op die aantoon van anti-TB teenliggaampies in pasiënte teen TB lipiedantigene, het ontwikkel in 'n Suid-Afrikaanse voorlopige patentaansoek.
Contact person: Prof JA Verschoor.
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