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  • ACGT Represented on NEPAD SANBio Plant Genetic Resource Task Force

    21st Jun 2008

    NEPAD Southern African Network forBiosciences (SANBio) has established a Task Force on the Enhancement of Capabilities of Conservation and Utilization of Plant Genetic Resources in Southern Africa. The first meeting of this task force was held at the University of KwaZulu-Natal, Durban, on 2-3 June 2008.

    The objective of the task force is to assist in the development of a five year regional project to “enhance the capabilities of conservation and utilization of plant genetic resources in southern Africa”. This is one of the priority projects identified by the region aimed at ensuring sustainable food security and socioeconomic development of the people of the region.

    The ACGT was represented at the meeting by Dr Jane Morris (ACGT Director) and Dr Ereck Chakauya (CSIR). Representatives were also present from gene banks in the SADC region.

    The meeting participants noted that Conservation of plant genetic resources was a fast expanding field, especially with the advent of climate change, biotechnology and HIV/AIDS.· In order to fully safeguard our plant genetic resources it was recognized that there is a strong need to adopt new and robust technologies, including biotechnology, micropropagation, GIS, non destructive ways of determining moisture, cryostorage, molecular diagnostics, DNA Banking, bioinformatics, etc.

    The meeting offered opportunities for presentations on the possible role of the ACGT and the CSIR in a gene banking initiative, with particular focus on DNA banking and bioinformatics, and the link between these and plant biotechnology research.

    It was agreed that the Task Force should adopt a tight timetable for the development of a detailed project proposal. This process would be led by the SADC Plant Genetic Resource Centre (Ms. T Lupupa) and UKZN (Prof. Pat Berjak) as Project Coordinator and Deputy Coordinator respectively.

    At the end of the meeting, participants were taken on a tour of the laboratory facilities at the University of Kwa-Zulu Natal.

  • ACGT Travel Awards 2008

    20th Jun 2008

    A number of travel awards were granted to young scientists in the ACGT partner institutions to enable them to travel to learn new techniques and upgrade their skills in the gene technologies.

    The recipients of these awards are as follows:

    Dr Tina Kresfelder, post-doc in the Dept of Medical Virology, UP. Visit to the Netherlands to learn techniques for the study of identify genetic polymorphisms that may be associated with severe respiratory disease in South African children.

    Dr Amadi Ihunwo, School of Anatomical Sciences, Wits University. Partial funding for visit to Germany to learn stereology techniques in brain research for adult neural stem cell transplantation.

    Riann Naguran, PhD student at Wits, based at NICD. Receive training in microarray data analysis from the ACGT microarray facility at UP, for analysis of molecular mechanisms of insecticide resistance in malaria mosquitoes.

    Charlotte Mashaba, MSc student, CSIR Biosciences. Attendance of the 2nd annual proteomics and genomics conference on 3-5 March 2008 at University of Western Cape.

    Jacqueline Brown, Department of Molecular Medicine and Haematology, Wits University. Visit to Dana Farber Cancer Institute, Broad Institute of Harvard and MIT to learn techniques for the analysis of copy number data from Affymetrix microarrays for oesophageal cancer.

  • ACGT represented at Biovision Alexandria 2008

    18th Jun 2008

    The ACGT was represented at the recent Biovision meeting in Alexandria, Egypt, by Dr Jane Morris and Dr Oleg Reva (ACGT Bioinformatics and Computational Biology Unit at the University of Pretoria). Both were invited speakers at the meeting. Prof Norman Casey, from the Department of Animal and Wildlife Sciences at the University of Pretoria, also attended and acted as a rapporteur.

    The meeting was held in the modern Library of Alexandria, and was the 4th international biennial conference to be held at the venue. The theme of the meeting was “From promises to practice” and focused on why the immense advances that are taking place in science do not adequately translate noticeable improvements in the lives of the poorest 20% of the human race.

    The meeting was attended by over 1000 participants from all corners of the globe, including three Nobel Laureates. Some key issues addressed were the challenges of climate change, food production, health and neglected diseases, science in society, globalization and the need for societal responsibility. The impact of these factors on the developing world was a particular concern.

    Dr Reva’s talk was entitled “Oligonucleotide Signatures of Pathogenic Microorganisms for Diagnostic Genetic Chips and Metagenomics”. His work focused on development of computer-based algorithms to address the problems of clustering and identification of environmental sequences generated by modern high-throughput sequencers. Discovery of unique oligos and patterns of infrequent oligos allowed for development of a tool to search the most appropriate DNA probes for use in diagnostic chips.

    The talk by Jane Morris was given on behalf of the South African Malaria Initiative and addressed “Functional Genomics and Heterologous Expression of Plasmodial proteins as Tools Towards New Drugs Against Malaria”. She outlined the utility of new tools in functional genomics and gene expression to speed up the drug discovery process. Functional genomics has applications in drug discovery to determine the response of an organism to drug challenge and to validate new drug targets. At the same time, novel approaches are being developed to increase the number of putative Plasmodial drug targets that can be solubly expressed in heterologous systems.

  • Eucalyptus Tapped as the Next Tree Genome to be Sequenced, Characterized & Harnessed for Bioenergy, Carbon Sequestration, and other Industrial Applications

    22nd Jul 2007

    An ambitious international effort has been launched to decode the genome of Eucalyptus, one of the world’s most valuable fibre and paper-producing trees-with the goal to maximize its potential in the burgeoning bioenergy market and for capturing excess atmospheric carbon.

    The scientific effort to characterize the Eucalyptus genome, uniting some two dozen institutions world-wide, is led by Alexander Myburg of the University of Pretoria (South Africa), with co-leads Dario Grattapaglia, of EMBRAPA and Catholic University of Brasília (Brazil) and Gerald Tuskan of Oak Ridge National Laboratory (United States). The DNA sequence of the 600-million-nucleotide tree genome will be generated under the auspices of the U.S. Department of Energy Joint Genome Institute (DOE-JGI) Community Sequencing Program (CSP) and the information will be made freely available over the Worldwide Web.

    “Sequencing the Eucalyptus genome will help us overcome many of the major obstacles toward achieving a sustainable energy future,” said Myburg. “Embedded in this information is the molecular circuit map for superior growth and adaptation in woody plants that can be optimized for biomass production. Its unique evolutionary history, keystone ecological status, and adaptation to marginal environments make Eucalyptus the focus of choice for expanding our knowledge of the evolution and adaptive biology of all perennial plants.”

    The genus Eucalyptus, comprised of over 700 different species, include some of the fastest growing woody plants in the world and, at approximately 18 million hectares in 90 countries, it is one of the most widely planted genus of plantation forest trees in the world. These trees evolved in the Southern Hemisphere quite separately from Northern Hemisphere tree species. Only the second tree to be sequenced, Eucalyptus offers extraordinary opportunities for comparative genomic analysis with Populus, the first tree sequenced and published in the journal Science by DOE JGI and collaborators in 2006.

    “The Eucalyptus genome will provide a window into the tree’s metabolic pathways, shedding light on such traits as cold tolerance, osmotic potential, membrane integrity, and other agronomic features,” said co-lead Tuskan. “As the genus is amenable to genetic transformation, it can serve as a validation platform for candidate gene expression studies-helping us to expand Eucalyptus’ range and exploit its potential as a bioenergy plantation crop,”

    “This monumental project will enable improved breeding strategies for cellulosic ethanol feedstocks and contribute to environmentally sound improvements in productivity for the global forestry industry,” said project collaborator Barbara Wells, President and CEO of ArborGen, LLC, a U.S.-based forestry biotechnology company. “This effort will help us advance our goals of producing renewable high-value biomass from a smaller environmental footprint.” Wells added that ArborGen brings a wealth of experience with Eucalyptus and its enormous potential as a dedicated bioenergy crop, noting that “this fast growing, high yield tree offers a new source of hardwood in the Southern U.S. that can play a key role in national energy security and economic development in the region, in addition to providing numerous environmental benefits.”

    Already, a considerable amount of carbon is tied up in Eucalyptus biomass. Coupled with the emerging economic incentives for carbon sequestration, Eucalyptus is a prime candidate for increased efforts to remove carbon from the atmosphere. “In countries such as Brazil, Eucalyptus is used as a source of renewable energy for high quality steel production in a way that reduces the net production of greenhouse gases. Eucalyptus is capable of sequestering carbon at rate of 10 tons of carbon/hectare/year and has a positive net carbon balance even when it is used to generate energy from charcoal or for pulp and paper production. Furthermore plantation forestry of Eucalyptus plays a crucial role to reduce the pressure on tropical forests and associated biodiversity” said project co-lead Grattapaglia.

    “From a phylogenetic standpoint,” said project collaborator Brad Potts, University of Tasmania, “Eucalyptus sits at a pivotal position in the tree of life at the base where the Eurosids split occurred.” This event is estimated to have happened some 100 million year ago, leading to a completely independent evolutionary trajectory from poplar and Arabidopsis, the Eurosids that have been sequenced to date. The Eucalyptus genome would be the first representative of the Myrtales order of flowering plants contributed to the public databases.

    The project will be coordinated and the information disseminated by the Eucalyptus Genome Network, EUCAGEN. EUCAGEN was established in 2004 with the aim to promote the generation of public resources for Eucalyptus genomic research. More than 130 scientists from 18 countries are currently involved in EUCAGEN. This number is expected to grow as the Eucalyptus genome sequence, and the genomic research tools that will result from it, becomes a reality.

    The South African project leader of this ambitious effort, Alexander Myburg, is a key contributor to the African Centre for Gene Technologies (ACGT), a joint initiative of the University of Pretoria, CSIR and University of the Witwatersrand. “We are very excited to be embarking on this initiative, and proud of the leading role of Prof Myburg and the University of Pretoria”, said Jane Morris, director of the ACGT.

  • "From basic genomics to systems biology"

    22nd Jun 2007

    Bridget Crampton of CSIR Biosciences recently attended an EMBO plant science conference in Ghent, Belgium entitled “From basic genomics to systems biology“.

    The conference took place from 2 – 4 May 2007, and was dedicated to the memory of Jozef Schell, who was instrumental in the discovery of the Ti plasmid Agrobacterium tumefaciens, and that a segment of this plasmid, the T-DNA, is transferred to plant cells. This discovery formed the basis of plant transformation studies today.

    The conference covered a broad range of topics including control of plant development; photosynthesis and chloroplast and mitochondrial function; plant-microbe and virus interactions; plant reproduction, genetic variation and comparative genomics; metabolism and metabolic signalling; and RNA processing, gene silencing and recombination.

    The conference featured many talks by prominent plant scientists including Marc Van Montagu (The future of Plant Science), Dirk Inze (Endoreduplication: a matter of efficiency), Jeff Dangl (The Plant-Immune System), Barbara Hohn (Transgeneration memory of stress in plants), Dianna Bowles (The role of glycosylation in cellular homeostasis), Csaba Koncz (Signalling roles of plant AMP-activated protein kinases), Thomas Hohn (Plant viruses and siRNA) and David Baulcombe (Short silencing RNA networks).

    Bridget Crampton presented a poster entitled “The salicyclic acid signalling pathway confers tolerance to a biotrophic rust pathogen in pearl millet” which was received well and attracted a number of questions.

  • The BioPAD Microarray Platform Project

    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

  • Prof. Dmitrij Frishman visits the ACGT

    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.

  • Jane Morris attends BioVision meeting in Lyon, France

    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.

  • Assistant national contact point for Food, Agriculture and Biotechnology appointed

    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.

  • Eucalyptus tree genome to be sequenced

    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.