22nd May 2009
By Prof Zander Myburg
The Department of Science and Technology (DST) has awarded a strategic grant of R1.5 million to a team of UP researchers in support of a project to decipher the complete transcriptome (DNA sequence of all expressed genes) of a Eucalyptus tree and to produce a high-density molecular marker map of the genome of this tree. Fast-growing eucalypt trees are viewed as future bioenergy crops due to their ability to produce vast amounts of energy-rich lignocellulosic materials. They are already utilized as fibre crops for pulp, paper and cellulose in South Africa. The UP research team led by Prof. Zander Myburg in the Department of Genetics and Forestry and Agricultural Biotechnology Institute (FABI) in collaboration with the Bioinformatics and Computational Biology Unit at UP (directed by Prof. Fourie Joubert) is generating a complete catalogue of expressed genes for a South African bred eucalypt tree.
In addition to expanding their understanding of the molecular basis of wood and fibre formation in trees, this project will allow Prof. Myburg’s team to discover thousands of DNA markers that can be used for the genetic improvement of eucalypt trees in South Africa. This work is further supported by Sappi, Mondi, the Technology and Human Resources for Industry Program (THRIP) and the National Research Foundation (NRF) through the Wood and Fibre Molecular Genetics (WFMG) programme at UP.
The DST funding also provides support for the leadership role of UP in an international project to sequence the complete genome of a Eucalyptus tree. The United States Department of Energy (US-DOE) announced in 2007 that it will fund a project to sequence the genome of Eucalyptus grandis, a fast-growing forest plantation tree species which it considers a potential bioenergy crop. This will only be the second forest tree genome to be sequenced after that of the poplar tree. Prof. Myburg is the principal investigator and UP the lead partner organization for this international project.
20th May 2009
Jane Morris participated in a meeting of the International Organization for Standards (ISO) Council Task Force on Biotechnology in Geneva on 29th and 30th April, on behalf of SABS (South African Bureau of Standards). The Task Force is made up of representatives from 9 different countries, and was tasked with identifying areas of biotechnology where standardization is needed. Previously there has been no major focus on biotechnology standards in ISO. The recommendations from the meeting will be forwarded to the ISO Council for follow-up action.
22nd Jul 2008
The ACGT was recently represented by its Director, Prof Jane Morris, at the launch of the Innovation for Sustainable Development and Poverty Reduction towards an Enabling Environment for Systems of Innovation of Southern Africa (ISP-TEESA) in Windhoek, Namibia from 22 to 25 June.
ISP-TEESA is a programme of the Regional Agricultural and Environmental Initiatives Network – Africa (RAEIN-AFRICA) and aims to develop, promote and harmonise science, technology and innovation polices in the region, build a pool of human capacity resources for scientific research and technological development and also promote public understanding in the areas of science, technology and innovation.
Prof Morris’ keynote address, titled ‘Innovation Systems in Biotechnology – Addressing Africa’s challenges’, spoke to the development of innovation systems and how to use biotechnology to sustainably address the needs of the poor. Central to her presentation was the description of what she has termed as ‘Africa’s dilemma’. According to Prof Morris, biotechnology innovation so far has not occurred in Africa to any major extent. Among the factors contributing to this are a lack of sufficient long-term investment by governments in R&D; a relatively underdeveloped private sector; limited purchasing power and access to markets; and some reluctance to adapt and adopt technologies developed elsewhere in the world.
She says that in an increasingly internationalised and competitive world, the needs of the poor have to be addressed in the context of major global trends. The major social, environmental and economic challenges in Africa will require radical, rather than incremental, innovation. “If we are going to make biotechnology work in Africa, we have to develop completely new innovation systems. If we don’t do that, we will basically be left sitting on the sidelines”.
According to her, 5th and 6th generation innovation – the space in which the ACGT plays – require the creation of collaborative networks, partnerships and social relations in order to stimulate knowledge innovation. The ACGT itself is an example of the use of collaboration to build innovation, she says. Activities such as participation in the Southern African Biochemistry and Informatics for Natural Products (SABINA) network programme and the current capacity audit being undertaken within ACGT partner and affiliate organisations demonstrate the importance of partnerships and cross-boundary collaboration.
The SABINA network includes the three ACGT partner institutions as well as the University of Malawi, University of Namibia and University of Dar es Salaam, while the capacity audit covers the CSIR, University of Pretoria, Wits University, and ACGT affiliate institutions – the Universities of Johannesburg and Limpopo. The latter initiative is being undertaken with the aim of identifying potential areas for collaboration and the availability of equipment within each institution to the other institutions. In addition, the capacity audit will be a key input to a needs analysis process that will identify whether there are common issues that exist and that the five institutions can work together to address.
“While the core focus of the audit has been on advanced biotechnology, we have now spread into the broader area of biosciences and life sciences in general, as very often we apply advanced technologies in other areas. If we can harness and bring together this varied expertise, we greatly increase the potential to create more innovative solutions”, says Prof Morris.
21st Jul 2008
The Carnegie-IAS Regional Initiative in Science and Education (RISE aims to develop human capacity through science and technology training and research in a regional context in sub-Saharan Africa, enabling individuals to use Science and Technology to contribute to national and regional economic development. This will be done by preparing PhD- and MSc-level scientists and engineers in sub-Saharan Africa through university-based research and training networks in selected disciplines. Its primary emphases are on training new faculty to teach in African universities and on upgrading current faculty.
In an intense competition that attracted 48 proposals from 29 African countries, the proposal “Southern African Biochemistry and Informatics for Natural Products” (SABINA), was among the three networks selected by an international panel of distinguished scientists.
SABINA was selected because of its competence to combine the strongest science with the greatest potential to have a positive impact on faculty development across the region.
The SABINA network aims to train both PhD and MSc scientists from 2009 onwards, through research in the biochemistry and chemistry of natural products, including bioinformatics as an essential tool for data management and the elucidation of structure and function.
In 2009, SABINA will recruit and support three PhD and three MSc students. In the subsequent years, it is anticipated that three new PhD and three new MSc students will enter the programme each year.
Research will focus on increasing the understanding of useful plants or fungi (such as mushrooms, and tea crops) through the study of screening assays, biosynthetic pathways, gene expression, modes of action, synthetic production, and genetic diversity. Nonetheless, the specific research projects selected for the MSc and PhD students will be determined based on ongoing research in the partner institutions, and will be tailored to the previous scientific background of those students.
The institutions participating in the SABINA network program are:
- University of Malawi
- University of Namibia
- University of Dar es Salaam
- University of Pretoria
- University of the Witwatersrand
- CSIR (Council for Scientific and Industrial Research)
- Tea Research Foundation of Central Africa, Malawi
The involvement of the South African institutions will be coordinated through the office of the ACGT.
The Academic Director of the SABINA network is Professor John DK Saka, of the Department of Chemistry in india.
22nd Jun 2008
The ACGT has been mentioned under authors’ affiliation in a variety of publications over the last 12 months. These include the following articles:
- Berger, D.K., Crampton, B.G., Hein, I. and Vos, W Screening of cDNA Libraries on Glass Slide Microarrays. Methods in Molecular Biology 382 177-203 (2007).
- Birkholtz, L,. van Brummelen A.C,. Clark K, Niemand J, Maréchal E, Llinás M and Louw A.I. Exploring functional genomics for drug target and therapeutics discovery in Plasmodia Acta Tropica 105 (2), 113-123 (2008).
- Clark, K., Dhoogra, M., Birkholtz, L. and Louw, A.I. Transcriptional responses of Plasmodium falciparum to a-difluoromethylornithine-induced polyamine depletion. Biological Chemistry. 389(2), 111-125 (2008).
- Crampton, B.G., Law, P., Coetzer, N.,Vos W. and Berger, D. K. Can genomics and bioinformatics be applied to studies of non-model plants such as pearl millet? South African Journal of Botany, 73 (2),279 (2007).
- Law, P.J., Claudel-Renard C., Joubert, F., Louw,A.I. and Berger. D.K. MADIBA: A web server toolkit for biological interpretation of Plasmodium and plant gene clusters. BMC Genomics 9:105 (2008)
- Morris, E.J. The Cartagena Protocol: Implications for regional trade, research and technology development in Africa. Development Policy Review, 26(1), 29-57 (2008).
- Virgin, I., Bhagavan, M., Komen, J., Kullaya, A., Louwaars, N., Morris, E.J., Okori, P. and Persley, G. Agricultural Biotechnology and Small-scale Farmers in Eastern and Southern Africa. Stockholm Environment Institute Working Paper. ISBN 978-91-976022-1-1 (2007).
Many more publications from the CSIR, University of Pretoria and University of the Witwatersrand reflect the application of gene technologies in the partner institutions.
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.
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.
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.
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.
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.