22nd May 2007
The BioPAD funded Microarray Platform Project was started in June 2005, with the aim of increasing capacity in microarray science in the BioPAD region. Led by Professor Dave Berger, its activities are centered at the ACGT microarray facility at the University of Pretoria, with additional input coming from inqaba biotec, and the University of the Witwatersrand.
In its first two years of operation, the project has achieved many of its aims, by providing a unique and much needed resource to researchers from all over South Africa and by facilitating the training of several young scientists in all aspects of microarray techniques including experimental design, technical lab skills and data analysis.
Activities at the project are divided into three major work packages, namely standard operating procedures (SOPs), training, and support of external users:
Standard operating procedures covering all aspects of microarray experiments have been developed and tested in the labs of the project members. These SOPs are regularly updated and are freely available, along with plenty of other useful information on the facilities website.
In-house training at the project has focused on an experiment comparing the oligonucleotide and cDNA microarray platforms. Individuals within the platform have contributed their particular skills to the group, resulting in a core of well-trained scientists capable of performing all aspects of microarray experiments and using these skills to provide assistance to external users. Trainees from inqaba biotec have provided sequencing and oligonucleotide synthesis services for the project, and have also learned how to complete microarray experiments on their own.
One of the biggest achievements in the first phase of the project has been the hosting of two major microarray workshops, where scientists from several institutes and South African universities converged on Pretoria for a full week of lab work and lectures. In all, over 40 attendees have been given the experience of completing a simple microarray experiment from RNA extraction to image analysis, and enjoyed lectures on experimental design, data analysis and the lab experiences of visiting experts.
A promising outcome of the project is that several of the course participants have since gone on to successfully perform microarray experiments in their own research, many of them making use of the facilities at the ACGT lab, and producing results that have been incorporated in theses, published articles in peer-reviewed journals, and presentations at national and international conferences.
Development has not been restricted to Pretoria, as an exciting aspect of the project has been the involvement of researchers from Wits. A new node of expertise is developing in Johannesburg, and a microarray users group that meets to discuss technical and experimental issues has been formed to support users there.
With the solid foundations developed during the last two years, the BioPAD supported microarray platform project at the ACGT microarray facility is ready to maintain its track record of excellence and provide increasing in depth support to greater than ever numbers of researchers in the years ahead.
By Luke Solomon, Microarray Scientist-in-Training, University of Pretoria
22nd Apr 2007
Prof. Dmitrij Frishman, Professor of Bioinformatics at the Technical University of Munich, visited the ACGT Bioinformatics and Computational Biology Unit at the University of Pretoria from 10-12 April 2007.
Prof. Frischman is also the Associated Editor of the Bioinformatics journal and a co-founder of the Biomax Informatics AG.
During his visit, he held seminars and presented his work at the University of Pretoria, the University of the Witwatersrand in Johannesburg and at the Central Node of the National Bioinformatics Network (NBN) in Cape Town.
In his talk, Prof. Frischman focused on modern procedures used for manual genome annotation and their current status, as well as computational methods and software infrastructure for analysing protein function at genomic scale.
He also described the new version of the PEDANT genome analysis system and its integration with SIMAP, a pre-computed similarity matrix for six million amino acid sequences. Possible ways to reduce the error level of automatically generated annotation by using machine intelligence was also discussed.
During his visit, opportunities for collaboration between Germany and South Africa in the development of services for genome annotation and metagenomic data processing were discussed.
South African bioinformaticists are challenged by the recent acquisition of a modern Roche 454 Genome Sequencer System that was installed at the Inqaba Biotec company (Pretoria). Genomic sequences are being deciphered at an unprecedented pace, and the demand in sequence data is also continuously growing, fuelled by the potential applications which range from personalised genome-based medicine and targeted cancer therapies, to microbial strain optimisation and bioterrorism prevention. New services and bioinformatics tools for fast and reliable data mining in DNA sequences are in great demand.
A fruitful discussion on highlighting how collaboration with leading European bioinformatics institutions may facilitate the services provided by the NBN was also held with Prof. Frischman.
21st Apr 2007
The Department of Science and Technology kindly provided funding for Jane Morris’s visit to France to attend the EU-SA dialogue on Knowledge Based Bio-Economy Partnerships for Sustainable Development and the BioVision World Life Sciences Forum, from 11-15th March 2007.
BioVision and the Millennium Development Goals
The theme of the BioVision meeting was “The Contribution of Life Sciences to the Millennium Development Goals”. Accordingly the meeting was attended by a number of prominent international players with a role to play in addressing these important goals, namely:
Goal 1: Eradicate extreme poverty and hunger
Goal 2: Achieve universal primary education
Goal 3: Promote gender equality and empower women
Goal 4: Reduce child mortality
Goal 5: Improve maternal health
Goal 6: Combat HIV/AIDS, malaria and other diseases
Goal 7: Ensure environmental sustainability
Goal 8: Develop a global partnership for development
Jeffrey Sachs, Director of the UN Millennium Development Goal programme, stressed that these goals are quantitative, time-bound commitments to be achieved by the year 2015, but so far there have been major delays in progress. The adoption and diffusion of science based technology is at the core of the goals, but technologies do not generally reach the poor because at least a sixth of humanity is too poor to get a foothold in the global economic system. There is a backlog in adoption and diffusion of existing technologies, let alone R&D for new and improved technologies.
Margaret Chan, Director of the World Health Organization, followed this topic by stressing that health system weaknesses are the major constraint to delivery of treatments for malaria, TB and HIV. Public-Private Partnerships are seen as essential for the delivery of existing and new medicines to those in need.
The organization of the meeting provided significant opportunities for discussion forums as well as actual lectures. There was considerable debate on a variety of key issues for the developing world, including
- the appropriateness of biofuels for the developing world
- the role of GM technology in agriculture in the developing world
- strategies to address malnutrition in developing countries
- health system weaknesses in developing countries
- IP protection and its relevance or otherwise for the developing world
- the need for society to drive the research agenda
Nobel Prize laureates
A feature of the BioVision meeting has been presentations by a number of Nobel prize winners. It was not possible to attend all these presentations, but some highlights included a description by Kurt Wüthrich (2002 Chemistry prize) of the analysis of 3D protein structures in solution using NMR; a presentation by Edmund Fischer (1992 Medicine prize) on the role of protein phosphorylation in cell regulation and signalling; and a talk by Bengt Samuelsson (1982 Medicine prize) on the role of prostaglandins and the arachidonic acid cascade in the inflammatory response, leading to the development of anti-inflammatory drugs.
EU-SA dialogue meeting
This meeting was organized as a side event of the BioVision meeting, and was well attended by most South Africans present at the meeting, as well as by some key figures from the European Commission. The meeting was co-chaired by Dr Christian Patermann, Director of Biotechnology Agriculture and Food Research in the European Commission, and Mr Daan du Toit from DST.
At the request of DST Jane Morris gave a presentation on South Africa’s National Biotechnology Strategy, focusing primarily on the Food, Agriculture and Biotechnology domain. She also highlighted South Africa’s successful participation in a number of EU 6th Framework projects with relevance to this area. Dr Antonio Llobell of Plantbio gave a presentation on the implementation of the National Biotechnology Strategy, and explained the various instruments such as the BRICs, National Bioinformatics Network etc.
Following the presentations, Jane acted as a panellist in a round table discussion. During this session, it was agreed that there was an excellent opportunity for South Africa and Europe to build closer ties.
Prior to the dialogue meeting, Daan du Toit kindly hosted a dinner with Line Matthiesson-Guyader, of the Biotechnology, Agriculture and Food Directorate in the European Commission DG Research. This provided an ideal opportunity to further our acquaintance following her attendance of the Bio2Biz meeting in South Africa in 2006.
It is likely that this meeting will open up significant opportunities for future collaboration with Europe in the area of Food, Agriculture and Biotechnology through the EU 7th Framework Programme.
19th Apr 2007
Dr Jane Morris has recently been appointed as the assistant national contact point for Theme 2 (Food, Agriculture and Biotechnology) of the European Union’s Seventh Framework Programme. This appointment will run from March 2007 till the end of FP7 in 2013. She will be working with the South African Food, Agriculture and Biotechnology National Contact point, Dr Geoff Meese to fulfil the following responsibilities:
- Information and awareness raising on the FP7 in SA
- Advising, assisting and training FP7 participants
- Providing feedback to DST on any problem or difficulties experienced by SA FP7 participants
- Informing overseas counterparts of developments and initiatives in SA
In this role, Jane Morris recently attended a European Union – South Africa dialogue on the “Knowledge Based Bio-Economy, Partnerships for Sustainable Development”. This was organized as a side event at the 2007 BioVision meeting in Lyon, France. The event was co-hosted by the South African Department of Science and Technology and The European Commission, Directorate of Biotechnology, Agriculture and Food Research.
The meeting was extremely positive, and further significant collaboration is envisaged between the European Union and South Africa, particularly in the area of food, agriculture and biotechnology.
22nd Jun 2006
The Eucalyptus research community may in the near future benefit from a second eucalypt genome sequencing effort (the first effort is being undertaken by Japan). At the last business meeting of the International Eucalyptus Genome Consortium (see meeting report at www.ieugc.up.ac.za) the Consortium was invited to submit a proposal to the Joint Genome Institute (JGI), the sequencing powerhouse of the US Department of Energy, to generate a draft sequence of the genome of Eucalyptus grandis, one of the most widely planted Eucalyptus tree species.
At the same meeting, Dr. Takashi Hibino of Oji Paper reported on the ongoing E. camaldulensis genome sequencing effort at KAZUSA DNA Research Institute in Japan. These are certainly exciting times for eucalypt researchers! The detailed genome sequencing proposal to be submitted by June 2006 is now being finalized by a group of scientists from several countries world-wide, led by ACGT contributor Dr. Zander Myburg from the University of Pretoria, the coordinator of the International Eucalyptus Genome Consortium.
The formation of an international collaborative network around the Eucalyptus genome started some three years ago at an IUFRO Tree Biotechnology conference in Umea, Sweden in 2003. After a series of meetings in Australia and Japan in the last two years, DOE scientist, Dr. Jerry Tuskan, announced at the Tree Biotechnology conference held in Nov 2005 in Pretoria, South Africa, that JGI would consider a proposal for a Eucalyptus genome sequencing project in the context of the “Genomes to Energy” focus area of the recently launched Laboratory Science Program at JGI.
The availability of a draft sequence of the Eucalyptus grandis genome will generate extraordinary opportunities for reaching a much higher level of understanding of the unique biology of forest trees and will have obvious implications for eucalypt-based production forestry as well as environmentally relevant issues such as carbon sequestration and water use efficiency of eucalypt plantations.
ACGT contributors will take active roles in the genome sequencing initiative and generation of eucalypt genomics resources after the completion of the draft genome sequence. Dr. Fourie Joubert of the Pretoria Node of the National Bioinformatics Network (NBN) will contribute towards the generation of a bioinformatics resource for the eucalypt research community. Dr. Zander Myburg will contribute towards the high-density genetic mapping of the E. grandis genome.
21st Jun 2006
The Director of the CGIAR Generation Challenge Program (GCP), Jean-Marcel Ribaut, visited the ACGT on 30 and 31 June 2006, together with Carmen de Vicente who is responsible for capacity building activities in the GCP.
The visit provided an opportunity for discussion about the future role of the ACGT partner institutions in the GCP, both from the perspective of capacity building and involvement in research activities. The visitors also had an opportunity to gain a better understanding of the interests and activities in the ACGT institutions, during the course of a number of meetings with senior management and researchers from the University of Pretoria, the CSIR and Wits University.
19th Jun 2006
General food safety management issues; mycotoxins as emerging risks; approaches to food safety communication and environmental issues regarding genetically modified organisms (GMOs) – these were some of the issues discussed during a SAFE FOODS workshop, held near Pretoria recently. This CSIR-organised workshop preceded the project’s bi-annual meeting, held at the same venue. (more…)
17th Jun 2006
Under the auspices of the Novel Drug Discovery Platform project, the MRC organized a visit to South Africa by scientists from Newcastle in England. The aim of the visit was to allow the UK researchers to meet with researchers in SA in order to explore opportunities for collaborative research in novel drug development from medicinal plants.
The delegation visited various centres in South Africa, including visits to the CSIR and the University of Pretoria on 8 June 2006. Researchers from both sides were keen to learn about the latest research technologies and methodologies.
Discussions at the University of Pretoria focused on the opportunities to assess the effects of potential anti-malarial drug leads. An additional common interest was identified as health promoting compounds in foodstuffs.
The visit allowed researchers to identify possible opportunities for collaboration under the EU FP7 programme.
22nd Dec 2005
African scientists and postgraduates working in biotechnology are set to benefit from a partnership between the African Centre for Gene Technology (ACGT), a South African network of excellence in modern biotechnology, and the University of the Witwatersrand (Wits), announced in Pretoria this week.
22nd Oct 2005
Malaria is the world’s most important parasitic disease. Clearly a disease of poverty, commonly referred to as a “neglected disease”, it rates amongst one of the major health and development challenges facing many of the poorest countries in the world.
At the end of 2004, 107 countries and territories had areas at risk of malaria transmission, with about 40% of the world’s population living in these areas. Up to 500 million clinical cases and 2 million deaths are reported annually, of which 57% occur in Africa, 30% in Asia and around 5% in the Americas.
Although millions of patients are affected by parasitic diseases every year, their inability to pay for market-financed products has resulted in a lack of innovative products and only 10% of global R&D resources directed at such diseases, including malaria, that account for 90% of the global disease burden.
The South African Malaria Initiative (SAMI) contracted Dr Lorraine Thiel to gather information about the scale of the malaria problem, the international funding streams and the local role players in malaria research. Two reports, funded by the Department of Science and Technology, were submitted to DST in October this year.
These reports, from which the above extracts have been taken, are made available here as downloadable pdf files. They remain the property of the Department of Science and Technology.
Report Section 1 – PDF file size 612 KB
Gathering of Data on the Global Epidemiology of the Malaria Threat, Applied Interventions and Socio-economic Impact
Report Section 2 – PDF file size 913 KB
Gathering of Data on the Funding Mechanisms for Malaria Research and the Status of Malaria Research in South Africa