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Department of Biotechnology - Research Interests and Current Projects

A biotechnologist is a scientist who studies all aspects of life. Biotechnologists create or improve products and processes involving biologically based materials.  Every day, biotechnologist’s findings are critical to research and application in health, industrial, agricultural and environmental sciences. They contribute significantly to the quality of life. To conduct their studies, biotechnologists combine the techniques of microbiology, genetics, chemistry, biochemistry, physiology, physics, ecology and pathology. The many accomplishments of biotechnologists have significantly affected our lives


Prof W-D Schubert

Structural Biology of Infectious Diseases

We are investigating the molecular mechanisms used by pathogens to invade and infect humans and other organisms. We do this by producing proteins specifically involved in the infection process and their molecular targets, crystallizing them, and solving their three-dimensional structures by X-ray crystallography. We then interpret the structures in terms of their known function and analyze the binding affinities as well as other biophysical parameters so as to understand their specific modes of action and to then ideally develop strategies to counter the infection.

Current Projects.

  • InlA of Listeria monocytogenes in complex with human E-cadherin

  • InlC of Listeria monocytogenes in complex with human Tuba

  • Phospholipase PatA of Legionella pnemophila

  • Inactivation of mammalian TLR2 by an inhibiting antibody

  • A number of proteins from Mycobacterium tuberculosis

 

Prof Ndiko Ludidi

Plant Biotechnology Research Group

The main research thrust of the PBRG is to investigate genetic determinants of plant responses to drought and salinity because of the impact that these two abiotic stresses have of crop yield and food security. Current research uses a suite of molecular biology tools and plant physiology studies to determine how signaling molecules contribute to the way plants respond to drought and salinity, together with technologies aimed at enhancing the tolerance of crop plants to drought and salinity in order to improve their yield under unfavorable climate conditions.

Current Projects:

  • Identification and characterization of genes determining plant responses to drought and salinity.

  • Role of small signaling molecules in plant responses to drought and salinity.

  • Genetic improvement of plant tolerance to drought and salinity.

 

Prof. Mongi Benjeddou

Pharmacogenetics Laboratory

The main research project of our laboratory seeks to identify genetic factors that are responsible for individual differences in drug efficacy and susceptibility to adverse drug reactions. Emerging pharmacogenetic evidence strongly suggests that drug transporters are subject to both genotypic and phenotypic polymorphism, and that these variations may be the reason for inter-individual variability in pharmacokinetic disposition, efficacy, and toxicity of drug transporter substrates. The aim of this project is therefore to investigate the genetic diversity of the solute carrier transporter genes and its pharmaco-genetics/genomics implications within the South African and Sub-Saharan African populations. This includes establishing baseline frequency distribution of previously reported alleles for the SLC22A1, SLC22A2, SLC22A3, SLC47A1, SLC47A2, SLCO1B1 genes, as well as the discovery of new genetic variants within the investigated populations for these members of the family of solute carrier transporters.

Current Projects:

  •     Pharmacogenomics of Drug Transporters

  •     Pharmacogenomics of Metformin response in type II diabetes mellitus

  •     Pharmacogenomics of anti-hypertensive drugs

  •     Pharmacogenomics of anti-cancer Drugs

 

 

Prof Eugenia D’Amato

Forensic DNA Laboratory

My main research interest in the study of human genetic diversity for its application in forensics. We are currently conducting research on mitochondrial DNA, Y-chromosome and diploid markers applied to individual identification. Along with the Biolabels lab, we are applying nanotechnology methods for DNA detection in a forensic context.

Current Projects:

  • Y-chromosome forensic kit, development of a commercial prototype.

  • Indels genotyping of African populations.

  • Y-chromosome genotyping of African populations.

  • Maternal and paternal ancestry study of admixed communities in South Africa.

  • International collaborations: study of local genetic diversity with Highly Mutating Y-STRs and indels.

  • South African Innocence Project: Profiling DNA isolated from historical crime scenes.

  • Nanotechnology applications to DNA genotyping.

  • Nanotechnology methods for DNA isolation.


 Prof Sean Davison

Forensic DNA Laboratory

The Forensic DNA Labs (FDL) specialises in the profiling of highly degraded DNA. The lab first applied this technology to identifying anti-apartheid activists exhumed from mass graves, and currently assists the police in identifying human remains from crime scenes. We recently founded an Innocence Project in South Africa which seeks to exonerate wrongfully imprisoned people by profiling degraded DNA from old crime scenes that was not tested at the time of the person’s conviction.

Current Projects:

  • Y-chromosome forensic kit, development of a commercial prototype.

  • Indels genotyping of African populations.

  • Y-chromosome genotyping of African populations.

  • Maternal and paternal ancestry study of admixed communities in South Africa.

  • International collaborations: study of local genetic diversity with Highly Mutating Y-STRs and indels.

  • South African Innocence Project: Profiling DNA isolated from historical crime scenes


Prof Pieter Gouws

Food Microbiology Research Group

It is our aim at the Food Microbiology Research Group, UWC, to develop novel methods and processes for the food and water industry.  Research in food microbiology centres on food safety, food borne pathogens, diagnostics and preservation.

Current Projects:

  • Molecular based technology for the rapid detection and identification of food borne pathogens in complex food systems.

  • The influence of traditional and new processing technologies on the bacteria associated with Aspalathus linearis.

  • DNA authentication of animal species present in commercial raw meat products.

  • PCR and phage assay for the detection and control of pathogens in foods.

  • Survival and elimination of pathogenic, heat resistant and other relevant microorganisms treated with UV-C.


 Marlene du Preez

My research focus is the analysis of expressed genes involved with colour development in pome (apple and pear) fruit skin using high throughput transcriptome analysis on next generation sequencing platforms.  This research underpins my work in the Marker Assisted Breeding (MAB) programme whose members include researchers from UWC and the ARC.  The main focus of the MAB group is the generation of new pome cultivars by combining aspects of classical plant breeding with molecular Marker Assisted Selection (MAS).  This non-GMO strategy aims to generate new pome cultivars with desirable traits for the local and export markets.  Results of this research have been published Acta Horticulturae and the African Journal of Biotechnology.

Current research project: (for Postgraduate student participation)

  • Analysis of an F1 generation of the cross Bon Rouge x Packham’s Triumph by Simple Sequence Repeat (SSR/microsatellite).


Dr. Marshall Keyster

Our research aims to understand how soil contaminants mostly heavy metals specific to South Africa impacts important food and animal feed crops. Specific aims would be the deciphering of molecular pathways involved in plant responses to heavy metal stress especially the reactive oxygen species (ROS)-antioxidant enzyme system which is an important mechanism for coping under heavy metal stress. Other goals would be the identification of novel growth promoting bacteria that can be applied to crops (plant roots) in order to assist these crops during heavy metal stress, and identifying proteins and molecules involved in metal binding and changing the metals to less toxic forms will also be one of the research aims. Identifying various lipid signalling molecules which increase plant tolerance to heavy metal stress and deciphering the pathways by which these lipid signalling molecules play a role in mitigating the effects of heavy metals on plants is also an important part of our research. 

 
Current Projects:
  • Identifying heavy metal tolerant and sensitive genotypes

  • Characterization of genes involve in heavy metal tolerance

  • Isolation of novel growth promoting bacteria to assist crops during heavy metal stress Identifying lipid signalling molecules for increasing plant tolerance to heavy metal stress   


Prof Bongani Ndimba

 Proteomics Research & Services Group

The Proteomics Research & Services Group was established in 2006. In 2011, through a Joint Venture between UWC and the Agricultural Research Council’s (ARC), a National Agricultural Proteomics Research & Services Unit was formed. This was made possible through Prof. Bongani Ndimba’s ARC/UWC joint-appointment MOA, signed in March 2011 between the ARC & UWC. The group was recently awarded a National Equipment Programme Grant plus ARC/UWC support for a Tandem Mass Spectrometry workstation worth over R9M.      Proteomics, which is generally defined as the simultaneous and high throughput study of protein expression profiles. This technology is normally used to monitor proteome profiles towards the understanding of molecular mechanisms associated certain biological cues.  

Current Projects

  • Identification and profiling of abiotic stress-responsive proteins in Arabidopsis thaliana and Sorghum bicolor.

  • Analysis of sugar biosynthesis-related proteins of sorghum bicolor and investigation of their role in drought-stress tolerance

  • Evaluation of the suitability and sustainability of Sweet Sorghum for bioethanol (and other by-products) production in South Africa

  • Guayule Proteome Analysis: Towards development of a sustainable low tech-hypoallergenic latex (and byproducts) agroprocessing system designed for South African small-holder farmers.

  • A number of fee-for-service and cost sharing projects are ongoing. In 2013 these will be expanded through employment of full-time Services Manager &  Contract Technicians.


 Dr. Ashley Pretorius

The Bioinformatics Research Group (BRG)

The Bioinformatics Group in the Department of Biotechnology at the University of the Western Cape research mainly focuses on combining computational biology (Bioinformatics) and Biotechnology. BRG looks at the identification of new therapeutic and diagnostic tools in the fight against Cancer (breast cancer, ovarian cancer, prostate cancer) and HIV. Through the use of bioinformatics several genes/proteins are identified and their roles explored in the onset and development of several cancers. These identified potential biomarkers are confirmed to play a role in these respective cancers by using Molecular Biology, Cell Biology and Proteomics technologies. BRG as a member of the Nanotechnology Innovation Centre, employ nanotechnology to create point of care devices for the early diagnosis of several cancers. The same approach is used in the identification of anti-HIV-1 therapeutic agents.

Current Projects:

  • Prediction of anticancer antimicrobial peptides using HIMMER and support vector machine

  • Identification and validation of novel therapeutic antimicrobial peptides against Human Immunodeficiency Virus: An in silico and molecular approach

  • Identification of biomarkers associated with ovarian cancer: A combined in silico and molecular approach

  • Identification of biomarkers in breast cancer as potential diagnostic and therapeutic agents using a combined in silico and molecular approach

  • Identification of MiRNA’s as potential biomarkers for the early detection of prostate cancer: an in silico and molecular approach

  • Validation of putative identified genes in breast cancer tissue as biomarkers for the early detection of ductal and lobular breast cancers


Prof David Pugh

My research group focuses on the identification and characterisation of protein-protein interactions involved in the regulation of cancer. Research is carried out both in vitro using bacterially expressed proteins and mutants as well as in healthy and tumourous mammalian cell lines. Most of my students are currently investigating the regulation of cancer-associated proteins by the E3 ubiquitin ligase Retinoblostoma Binding Protein 6 (RBBP6).

Current Projects

  • Assessing the importance of Retinoblastoma Binding Protein 6 (RBBP6) in the regulation of the cancer-associated protein Y-Box Binding Protein 1 (YB-1)

  • Investigating the role played by Retinoblastoma Binding Protein 6 (RBBP6) in the regulation of the tumour suppressor p53 by Mouse Double Minute 2 (MDM2)

  • Structural characterisation of the anti-oxidant activity of the 1-Cys peroxiredoxin Prx2 from the resurrection plant Xerophyta viscosa


Dr Mervin Meyer

Nanotechnology

The DST/Mintek Nanotechnology Innovation Centre (Biolabels Unit) focus on the development of nanotechnology-based diagnostic and therapeutic systems to address some of the major health concerns in South Africa (www.nic.ac.za). The Biolabels Unit use proteomic and transcriptomic approaches to identify disease biomarkers that can be used for the development of point-of-care diagnostic systems or to improve current diagnostic methods. The Unit is also developing nanoparticle/drug conjugates with the aim of producing targeted drug delivery systems for the treatment of diabetes, HIV and cancer.

Apoptosis and Cancer

The activation of apoptosis in cancer cells is a target for mechanism-based anti-cancer drug development. In order to assess the possible anti-cancer properties of indigenous medicinal plants, we screen extracts of these plants for the presence of pro-apoptotic agents. Mechanism-based apoptosis bioassays are used to evaluate the ability of the extracts to induce apoptosis in human cancer cell cultures. We also investigate the anti-cancer properties of novel quinone containing and metallo-organic compounds.

Selected research project titles:


  • Evaluating cancer specific peptides for applications in the diagnosis of cancer.

  • The development of quantum dot-based detection system for the diagnosis of breast cancer.

  • Fabrication of target specific nano-constructs for in vivo imaging and treatment of cancer.

  • Evaluating novel quinone compounds as anti-cancer agents.

  • Targeted delivery of embelin to cancer cells.

  • Biochemical investigation of the anti-cancer activity of Tulbaghia violacea extracts.

  • Screening the anti-cancer activity of novel organo-metallic compounds.

  • Development of nanotechnology-based therapeutic approaches to treat HIV.

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