5th May 2014
A new study by scientists at the University of the Witwatersrand and the University of Arizona has found that in single-celled algae, suicide benefits the organism’s relatives.
“Death can be altruistic – we showed that before – but now we know that programmed cell death benefits the organism’s relatives and not just anybody,” says Dr Pierre Durand from the Department of Molecular Medicine and Haematology and the Sydney Brenner Institute for Molecular Bioscience (SBIMB) at Wits University.
When Durand and his colleagues from the University of Arizona released the results of their first study on suicide in single-celled algae in 2011, they showed that when an organism commits suicide by digesting up its own body, it releases nutrients into the environment that can be used by other organisms.
In a new study, they have proven that these nutrients can only be used by relatives. In fact, the nutrients inhibit the growth of non-relatives, so not only does suicide benefit relatives, it can also harm competitors. This is remarkable. Even after death, an organism can continue to exert species-specific fitness effects on its neighbours.
“If one focuses purely on the individual organism, programmed death doesn’t fit with the paradigm of survival of the fittest. Why should something like suicide exist at all? This has been an evolutionary mystery and we have discovered one of the clues,” says Durand.
The team used Chlamydomonas reinhardtii (a type of alga) as a model organism, but they suspect that this phenomenon is happening in all unicellular organisms.
The trigger is a stressful environment. “When the environment becomes difficult for everybody, some individuals sacrifice themselves for the benefit of kin. We suspect that it is the older and more damaged who are more likely to commit suicide,” says Durand. For example, during algal blooms in freshwater or marine environments the nutrients eventually run out causing some algae to commit suicide to sustain the others.
The increased environmental stresses of climate change could also impact the dynamics of programmed death. “The planet won’t be able to sustain everyone at the current rate of exploitation. Whether we’re talking about humans or microbes, it is becoming a crowded place and this is impacting the way microbes respond,” says Durand.
Story by: Wits Health Sciences Research News
5th May 2014
A future HIV vaccine is widely assumed to require broadly neutralizing antibodies, which are able to recognize and neutralize diverse viruses from across the world. No vaccine so far has managed to elicit these kinds of antibodies, but some HIV infected people are able to naturally develop broadly neutralizing antibodies. Understanding how and why these rare people are able to make these antibodies may therefore provide a roadmap for HIV vaccine design.
In a paper published this month in Nature, WITS/NICD researchers Dr Penny Moore, Jinal Bhiman (a PhD student at the NICD, pictured) and Professor Lynn Morris, along with a consortium of researchers in South Africa and the USA describe the developmental pathway of one such antibody.
Antibodies which target a conserved epitope in the V2 region of the HIV envelope develop fairly frequently during infection. These are characterized by long CDRH3 “arms”, which are required to penetrate through the glycan shield that protects the HIV envelope. Until now it was not clear how these long CDRH3s developed. In this study, the team isolated a family of V2-directed antibodies with long CDRH3s from an infected donor, CAP256. Using deep sequencing of the antibody genes over 3 years of infection, they showed that the unmutated common ancestor (UCA) of the antibody family emerged 30-38 weeks after infection. Interestingly, the UCA contained a fully formed long CDRH3, which arose entirely as a result of VDJ recombination, and in contrast to the idea that this might take many years to develop.
A second part of the study defined exactly how breadth developed in CAP256. The UCA was initially able only to neutralize the virus that superinfected CAP256 at 15 weeks post-infection. However in response to extensive viral diversification, there was rapid somatic hypermutation resulting in these antibodies becoming broadly reactive for HIV within 4 months.
This study shows that a future vaccine targeting this region will rely on immunogens that are able to engage the rare subgroup of naïve B cells expressing B cell receptors with pre-formed long CDRH3. However this work also suggests that sequential immunogens that mirror viral evolution may be needed to drive the development of breadth. Overall, the precise delineation of the developmental pathway for the CAP256 antibody lineage should provide a basis for attempts to elicit broad V1V2-directed HIV-1-neutralizing antibodies through vaccination.
Story by: Wits Health Science Research News
30th Apr 2014
“Malaria is a very complex disease. Trying to stop it is like trying to hit thousands of tennis balls with a teaspoon.” Using this analogy, Lyn-Marie Birkholtz, an associate professor in the Department of Biochemistry and a member of the Centre for Sustainable Malaria Control at the University of Pretoria (UPCSMC) reiterates the importance of on-going, trans-disciplinary research in an effort to eliminate the disease that remains one of Africa’s greatest killers.
Prof Birkholtz, a leader in the discipline of antimalarial target discovery, will be heading the South African Research Chair (SARChl Chair) in Sustainable Malaria Control with a budget of R1.5 million per year, funded by the DST through the NRF.
The chair will be officially launched on 24 April 2014, on the eve of World Malaria Day, and will enhance UP’s recognised and unique integrated focus on malaria parasite biology, functional genomics, drug discovery efforts, innovative mosquito control strategies as well as public health and community engagement. As holder of the chair, Prof Birkholtz will use her expertise on the parasite to investigate sustainable mechanisms to control not only the parasite itself, but also its mosquito vector.
“When it comes to the Big Five of most dangerous organisms on our planet, three are mosquitoes. What’s more, these three species – Anopheles gambiae, Anopheles arabiensis, and Anopheles funestus – are the most efficient carriers of the fourth of the Big Five killers: the malaria parasite itself,” explains Prof Leo Braack, a specialist in mosquito ecology. His newly established Research Initiative in Integrated Vector Management (IVM) will also be launched on 24 April at UP.
“The parasite is a microscopically small blood borne parasite that annually kills more than 500 000 people in Africa,” he explains.
According to Prof Braack, the battle to control malaria is largely based on two strategies: control the mosquitoes and control the parasite.
“There is another strategy quietly being pursued that holds great hope, the development of an effective vaccine, but that remains an elusive trophy – tantalizingly close but never quite reached,” he says.
The greatest effort in malaria control goes towards the control of mosquitoes, mostly through insecticide-treated bed nets (ITN’s) or long lasting insecticide-treated nets (LLINs) as well as spraying the inside walls of homes with insecticides (indoor residual spraying or IRS).
“Although major successes have been achieved over the past decade in reducing the number of malaria cases in Africa by way of mainly mosquito control, challenges are emerging in the form of new genetic strains of mosquitoes that are resistant to traditional insecticides being used, and even adaptive shifts in the feeding behaviour of at least one of the main malaria mosquitoes,” Prof Braack says.
“So, if globally the two main strategies for malaria control depend on mosquito control and parasite control (and the first is the most effective), then we better start thinking about new tools to supplement existing strategies. This is exactly what the UPCSMC is working towards.”
Malaria is a complex parasitic disease confined mostly to tropical areas and transmitted by female Anopheles mosquitoes. There are an estimated 250 million clinical cases of malaria yearly, which cause more than half a million deaths, mostly of children under 5 years of age and mostly in sub-Saharan Africa. Malaria-endemic countries are faced with the high cost of prevention and treatment of the disease.
About the Centre for Sustainable Malaria Control at the University of Pretoria
The vision of the UPCSMC is to make a substantial contribution towards the creation of a malaria-free Africa.
The Centre is the only one of its kind due its unique approach to malaria by addressing all aspects of malaria, including the parasite, the mosquito carrier, and the human host, and doing so in integrated, trans-disciplinary strategies. Collaborative teams in different departments, faculties and even institutions form clusters to bring together skills and resources from different sources to address all aspects of the disease, including:
Malaria case management is an important focus within this cluster. Sustainable but safe methods to control malaria must be developed while at the same time focusing on the health of the public and the environment. Research projects on safe alternatives for DDT, as well as educational projects like the new Sibo book form part of this cluster.
This research group focuses on anything related to the malaria parasite from the parasite biology and surveillance (epidemiology) to the transmission blocking strategies and anti-malarial discovery and development as well as other methods to prevent the transfer of the disease-causing parasite. Another important focus within this group is the study of related malaria-like infections where the differences and similarities between the malaria parasite and similar disease-causing parasites (eg babesiosis in dogs) can be used to better understand this devastating disease in humans. The SARChI Chair falls under this cluster.
This research group focuses on anything related to the mosquito (vector) and the variety of current and new methods to prevent them from transmitting the parasite and therefore the disease. Here physical methods of control are looked at along with monitoring and evaluation. Important factors such as biting behaviour, the behaviour of mosquitoes in their natural habitat as well as research on what attracts or repels them is done, bionomics and semiochemistry of the vectors are studied in order to better understand the vector’s preferences and methods when searching for targets to feed on. This aids to find better methods to control the vector from reaching or biting their targets.
Some of the research currently being done in the UPCSMC includes the following:
- The use of insecticide-impregnated wall linings
- Cross-border malaria surveillance between South Africa and its neighbours, in close collaboration with the National Department of Health.
- Discovering and using various plant extracts to repel malaria-transmitting mosquitoes.
- A project to isolate and use key molecules as attractants in inexpensive mosquito traps to reduce populations in rural villages.
- Vector Control policy development and support in East Africa.
- The biting behaviour of the main malaria vector mosquitoes: a research collaboration between UP, the Wits Malaria Research Institute and Uganda.
- The use of an innovative low-cost cell-phone technology, mSpray, by spray-workers to record IRS applications of pesticides in homesteads for malaria control is being tested.
- A project looking at a new series of chemical derivatives of naturally occurring anticancer compounds that showed potent activity against malaria parasites at very low concentrations.
- Prof Birkholtz, in collaboration with scientists from Wits and the CSIR, constitute the Gauteng Malaria Transmission Blocking Platform. The platform focuses particularly on the identification, validation and characterisation of chemical entities with potential transmission blocking ability. The effect of potential antimalarial drugs on the complete life cycle of the P. falciparum.
- The use of a book (Sibo fights malaria) as a tool to educate young children about malaria, its symptoms and how to avoid getting it. This could potentially alter attitudes towards the disease (in children and hopefully their parents) and lead to lifestyle patterns that could help lessen the burden of malaria in endemic areas
Please visit our website, www.malaria.up.ac.za, for further information.
Story by: Department of University Relations, University of Pretoria
25th Apr 2014
Genomics Research Institute member Prof Dave Berger from the Plant Science Department of the Forestry and Agricultural Biotechnology Institute (FABI) at the University of Pretoria, South Africa was awarded a 2013 US Department of Agriculture (USDA) Norman E Borlaug International Agricultural Science and Technology Fellowship.
These fellowships were established in honour of Norman Borlaug, recipient of the Nobel Peace Prize in 1972, for his role in breeding improved varieties of wheat, which led to the Green Revolution. The fellowships provide opportunities for agricultural researchers around the world to work with US scientists for periods up to three months.
Prof Berger spent three months of his sabbatical, hosted by Dr Burt Bluhm, in the Department of Plant Pathology at the University of Arkansas, Fayetteville. Dr Bluhm is a leading international researcher in the genetics of fungal pathogens of crops. The topic that Prof Berger researched during his visit was grey leaf spot disease of maize, a limiting factor in maize production globally and also in sub-Saharan Africa. The project that Prof Berger’s Molecular Plant-Pathogen Interactions research group focused on was the fungus Cercospora zeina, the causal agent of this disease in Africa. Genome sequencing of an African isolate of the fungus is underway, partially funded by the Genomics Research Institute at UP with additional funds leveraged from an NRF Bio-informatics and Functional Genomics grant. Prof Berger visited the Genomics Facility at Purdue University, USA, as well as the Yale Centre for Genome Analysis, New Haven, Connecticut which has a state-of-the-art PacBio single molecule sequencer. This technology has the advantage over current next-generation sequencing methods of direct sequencing of the fungal DNA and produces longer DNA sequence runs.
An outcome of the visit was the resolution to improve the C.zeina genome sequence using PacBio. Genome assembly and annotation are being carried out in collaboration with Prof Yves van der Peer, Professor in Bio-informatics and Genome Biology, Group Leader of Bio-informatics and Systems Biology, Ghent University, Belgium who also holds a joint appointment at the University of Pretoria. Prof Van der Peer hosted UP PhD student Nicky Olivier during 2013, and the C. zeina genome assembly was subsequently improved. This visit was funded by the NRF, the Department of Plant Science, the Faculty of Natural and Agricultural Sciences, the GRI and the NRF. The Ghent group will be visiting UP in April 2014, and a follow-up visit by Prof Berger to Ghent is planned for later in the year.
Further outcomes of the USDA Borlaug Fellowship are the planned visit of a student from Dr Bluhm’s laboratory to UP in May 2014 and a USDA-funded follow-up visit by Dr Bluhm to Prof Berger’s laboratory in mid-2014. This collaborative research, in which Dr Bridget Crampton of the Department of Plant Science and FABI is also involved, investigates the pathogenicity mechanisms and population genetics of C. zeina and has the long-term aim of finding weaknesses in the armoury of the fungus which can be exploited to develop novel control strategies.
Story by: D. Berger, UP News, University of Pretoria
2nd Apr 2014
ACGT support scientist, Jessika Samuels, recently attended the Physiologically Relevant Cellular Models for Drug-Discovery and High Content Analysis Conference. Held in La Jolla, California. The conferences were held concurrently and were preceded by informative user sessions. With the growing need to develop predictive in vitro models to aid in drug discovery and support high content approaches, the conferences were complimentary and attracted much attention from the ~200 delegates in attendance.
Topics included: high content analysis for 3D cell models, 3D cell culture for drug discovery, high content analysis of live cells and tissues, and stem cell-derived models amongst a myriad of topics.
Ms Samuels presented a poster on the work undertaken by staff and researchers in the African Centre for Gene Technologies (ACGT) partnership, which attracted much attention and possibilities for building future collaborations in the Health Sector. Researchers were especially interested and impressed by the existing infrastructure in SA. Moreover, developers of supporting platforms were eager to form partnerships with local consortia, to test the efficacy of their platforms across continents an in the South African research environment. International researchers were also pleasantly surprised at what SA researchers were focusing on, judging by the feedback on a research poster presented by the local contingent.
During her stay, she also visited the laboratory of a Witsie, now based at the Scripps Institute, Prof Marco Weinberg. The visit in its entirety highlighted the intensity and competitive nature of research in and around Silicon Valley and in the USA as a whole. It also emphasized current developments and pitfalls that globally leading laboratories are facing in drug discovery and the development of relevant in vitro cellular models.
Contact Jessika for a discussion on the two conferences:
27th Feb 2014
A new study by a Wits University scientist has overturned a long-standing hypothesis about plant speciation (the formation of new and distinct species in the course of evolution), suggesting that agricultural crops could be more vulnerable to climate change than was previously thought.
Unlike humans and most other animals, plants can tolerate multiple copies of their genes – in fact some plants, called polyploids, can have more than 50 duplicates of their genomes in every cell. Scientists used to think that these extra genomes helped polyploids survive in new and extreme environments, like the tropics or the Arctic, promoting the establishment of new species.
However, when Dr Kelsey Glennon of the Wits School of Animal, Plant and Environmental Sciences and a team of international collaborators tested this long-standing hypothesis, they found that, more often than not, polyploids shared the same habitats as their close relatives with normal genome sizes.
“This means that environmental factors do not play a large role in the establishment of new plant species and that maybe other factors, like the ability to spread your seeds to new locations with similar habitats, are more important,” said Glennon.
“This study has implications for agriculture and climate change because all of our important crops are polyploids and they might not be much better at adapting to changing climate than their wild relatives if they live in similar climates.”
Glennon’s study also provides an alternative explanation for why plants are so diverse in places like the Cape where the climate has been stable for hundreds of thousands of years. Although her study examined plant species from North America and Europe only, she is looking forward to testing her hypotheses using South African plants.
Glennon’s paper has been published in Ecology Letters, a flagship journal for broad-scale ecology research.
Image: Output for Larrea tridentata (creosote bush) diploid and polyploid populations that shows that both ploidies share similar climate habitats, but differ in how they share that climate.
About Dr Kelsey Glennon
Dr Kelsey Glennon is a Carnegie Postdoctoral Fellow in Climate Change Research in the School of Animal, Plant and Environmental Sciences and the Global Change and Sustainability Research Institute at the University of the Witwatersrand, Johannesburg. She became interested in plant genetics while volunteering in the Hunter Lab at Salisbury University in her second year of college. She pursued a PhD at George Washington University in Washington, DC, studying plant hybridisation, its effects on species boundaries, and resulting conservation issues. Dr Glennon came to Wits University from a prestigious NSF Bioinformatics Fellowship at Syracuse University in New York. She is currently doing active field research on baobab trees in Limpopo Province and the medicinally important plant imphepho (Helichrysum odoratissimum purchase discount medication! generic versus name brand zoloft .
26th Feb 2014
Prof Jolanda Roux from the University of Pretoria’s Forestry and Agricultural Biotechnology Institute (FABI) in the Faculty of Natural and Agricultural Sciences, was awarded the International Union of Forest Research Organizations (IUFRO) Scientific Award.
This prestigious award, which is the highest that is given to forestry researchers, will be bestowed on her at the next IUFRO World Congress in October this year. One award is given every five years in each of nine categories and Prof Roux will receive the award for research accomplishment in the field of Tree Health.
In 2012 Prof Roux also won the NSTF-BHP-Billiton Award (sponsored by Eskom) in the category Female Researcher who made an outstanding contribution to SETI through Research Capacity Development over the last five to ten years. In 2011 she was awarded the Queen’s Award for Forestry, by the Commonwealth Forestry Association, when she met Queen Elizabeth II. Prof Roux has received many other forms of recognition for her work, notably the DSTs Distinguished Young Women in Science Award, also in 2011.
Prof Roux is a professor in the Department of Microbiology and Plant Pathology, a member of the management committee of FABI and the manager of the Tree Protection Cooperative Programme’s field and extension services.
Her research focuses on tree diseases and she is particularly passionate about tree health in general and more specifically, fungi that cause diseases of trees on the African continent. She collaborates with researchers in many other parts of the world and has travelled widely to undertake her research.
Prof Roux has published over 120 papers in her research area and has successfully supervised numerous PhD and MSc students. She serves on a number of international committees and is currently the coordinator for the Division Research Group on Forest Pathology of the International Union of Forestry Research Organisation.
She is currently the Vice-President of the Southern African Society for Plant Pathology, serves on the editorial boards of the South African Journal of Science, Forestry and Forest Pathology, and is an honorary professor in the Chinese Academy of Forestry.
Story by: Martie Meyer, UP News and Events, University of Pretoria
24th Jan 2014
Tinotenda Shoko is one of many young Zimbabweans who have managed to find opportunities both outside and inside their country during times of limited resources. He joins other RISE students and faculty from Zimbabwe who have brought high levels of energy, talent, and optimism to their fields – often as true leaders in their scientific activities.
Tinotenda began with the benefit of family models: His father taught primary school in Mutawatawa, and he is still teaching there today. On the basis of his strong performance in grades 1 through 7, Tinotenda was admitted to a mission boarding school for a four-year ordinary-level education. He was powerfully drawn to science, scoring high marks in calculus, physics, biology and chemistry. He was then admitted to advanced-level coursework for two additional years, and did well enough on his exams to gain admittance to the University of Zimbabwe in 2002.
Despite his facility at basic science, he began to feel a tug toward the “real world” of industry. “Why?” he asked. “I thought it was more interesting, practical, and linked to the benefits that science brings to society. I saw so many people around who didn’t have enough food or money. I didn’t want to live like that, and I didn’t want other people to live like that. To me, education was a way out.”
Even with his strong educational background and encouragement, he faced powerful competition when it came time to enter the university. “Despite the stiff competition from others who were sometimes better prepared,” he said, “I did come in at the top of my class; I had to work hard and I’m still working harder.”
This appears to be an understatement. During his first year, Tinotenda tackled a daunting menu of pure science coursework that included genetics and molecular biology, mathematics, physical, general, organic and analytical chemistry, and cell biology and immunology. In addition, he also took agricultural economics, because of its links to practical areas, and statistics because of its central role in applied sciences. “I took 13 courses that year, 7 of which I passed with distinctions. I loved chemistry the best, and I got distinctions in physical and general chemistry.”
In the second year he continued at this ambitious pace, but he moved farther in the direction of applied subjects, especially food engineering, food microbiology, food toxicology, food analysis, sensory evaluation of food, food chemistry, and biochemistry. In the third year his courses were still more applied, and included meat technology, fruits and vegetables, cereals, fats and oils, quality assurance and experimental design, product development, marketing, and industrial methods. By the time he had completed his BSc in food science and technology in 2005, he had taken 35 courses in sciences related to his major and passed 16 of them with distinction.
After graduation, he immediately went to work for Blue Ribbon Industries, a milling company in Harare, as a quality control technician and research and development assistant. He helped develop a gluten-free flour blend that enabled individuals allergic to gluten to enjoy flour products. He did this by replacing wheat flour with a mixture of millet flour, sorghum flour, rice flour, and potato starch and determining the most appropriate ratio. The resulting flour, he said, baked and tasted just like wheat flour, although it required additional ingredients for successful bread making. He worked until 2008 at Blue Ribbon, which has since closed.
His interest in food science and technology was already growing beyond the content of his traditional coursework. He sought out a program at the Zimbabwe Institute of Management (ZIM) where he could learn more about the business side of the food industry, and from the ZIM he earned a diploma in business administration in 2007.
In 2008 Tinotenda continued his experience with the food industry when he took a job in Cape Town, South Africa, at a food processing company called Mexicorn that manufactures tortillas, tacos, and corn chips. As a Food Technologist, he was responsible for new product development and improving tortilla quality, including process and shelf life testing.
With this practical experience under his belt, he was ready for more science when a new opportunity presented itself. A former lecturer, keeping track of events at RISE, heard about the SABINA network and urged him to apply for a fellowship being offered at the University of Malawi. He sent his application to Jane Morris in Pretoria and was accepted.
“I knew my work had to be something in natural products,” he said. “I already had my objectives for the next opportunity to study.” He started working with local fruits and vegetables, with the objective of identifying their volatile flavor constituents.
“A problem for fruits and vegetables is seasonality,” he said, “which limits when people can find them in the markets. If you’re able to identify the compounds which constitute the flavor of a food, you can take that to industrial level and synthesize the flavor in the lab, making it available to everyone all year round.” Among the fruits he studied were Mobola plum and monkey orange, using solid-phase micro-extraction. He used gas chromatography and gas chromatography coupled to mass spectrometry to identify the volatile constituents. He also worked with some vegetables, including cassava leaves, and a herbal tea, using hydro distillation methods to heat the plant material, drive out the essential oils, and collect the oils for identification by gas chromatography and gas chromatography coupled to mass spectrometry.
Although Tinotenda has learned a great deal from his early work with foods, including his MSc research in applied chemistry, he is now aiming higher in his study of natural products. His dream is to complete a PhD on neutraceuticals, which are plant extracts that have not only flavor but potentially powerful nutritional and medicinal efficacy. The term, a conjugate of “nutritional” and “pharmaceutical,” is applied to products that range from isolated nutrients and herbal products to specific diets and processed foods. “There are so many diseases in Africa,” he said, “and medical costs are very high. There is also enormous biodiversity, and we want to tap into that to cure diseases.”
He has written a more formal personal statement about his dream to help people who cannot afford the cost of medicines, offering them instead cheaper but still effective alternatives. “In Africa, it is known that certain plants have medicinal properties or health benefits, but the knowledge has not been harnessed. There is not much scientific evidence to establish the link between a particular biological function and the identification of the specific compounds in those plants. In fact, most knowledge about the usage of these plants has remained traditional and undocumented.”
He put together his current educational strategy while in a short-term academic appointment at Chinhoyi University of Technology (CUT) in Zimbabwe as a part-time lecturer in food science. His responsibilities included teaching at the undergraduate level, developing learning materials, and participating in faculty seminars.
As he was completing this appointment in his home country, he learned of the next exciting stage of his career – the opportunity to continue his research under a second RISE scholarship. Tinotenda is now entering a PhD program under SABINA, this time at the University of Pretoria in South Africa, where he can anticipate strong mentoring and cutting-edge instrumentation. He has also applied for a Washington Fellowship for Young African Leaders, with the strong endorsement of SIG.
Once Tinotenda has earned his PhD, he looks forward to returning to Zimbabwe to apply the fruits of his research. He is confident that he will have an academic appointment and also work with Zimbabwe’s Scientific and Industrial Research & Development related organisations, focusing on product development and commercialization.
Story: Alan Anderson, Science Initiative Group, Blog posts, January 2014
15th Jan 2014
The Minister of Science and Technology, Derek Hanekom, launched South Africa’s Bio-economy Strategy on 14 January 2014.
The bio-economy refers to an entire innovation chain (from research and development to commercialisation) based on biological sources, materials and processes, and aimed at sustainable economic, social and environmental development.
The science-based Bio-economy Strategy, approved by Cabinet in November last year, positions bio-innovation as essential to the achievement of government’s industrial and social development goals. The strategy calls for industry, science councils, government departments and academia to cooperate closely to ensure that biotechnology and bio-innovations are market relevant and find easier application in South Africa.
At the launch, Minister Hanekom said that the Bio-economy Strategy would take the National Biotechnology Strategy from 2001 to the next level, creating an enabling environment that will allow government departments, industry, venture capital and other stakeholders to move forward with initiatives that will be able to meet the challenges and embrace the opportunities of the future.
“We are confident that the strategy we are launching today will address the full value chain, going beyond the mere generation of new technologies to ensuring that technology development is informed by the needs of the country and people, and that social and economic value is generated. If we look at the sustainable utilisation of resources and encourage role players to work together to achieve common goals, we will be helping to close the innovation chasm,” Mr Hanekom said.
“Our aim is to grow the bio-economy through strengthened partnerships with industry, and to extract the full potential of our living systems through the application of our collective competencies and capabilities. The benefits to society will include the more sustainable use of resources, the development of new products, and improved job prospects,” he added.
The Bio-economy Strategy is aligned to the National Development Plan, which considers science, technology and innovation key to the South African developmental agenda, as advances in these fields underpin advances in the economy and in society. It is expected that by 2030 biotechnology and bio-innovation will be making a significant contribution to South Africa’s gross domestic product through the creation of bio-based services, products and innovations, intellectual property management and support for bio-entrepreneurs.
In addition, the strategy recognises and builds on the important contributions that indigenous knowledge can and should play in the development of our bio-economy, and the important developmental contributions of this interface.
South Africa has a comparative advantage because it is the third most biologically diverse country in the world, with almost 10% of the world’s known plant species and 15% of all known coastal marine species, as well as nine unique vegetation types, of which three have been declared global biodiversity hotspots. It is also home to one of the world’s six floral kingdoms, the Cape Floristic Region. Combined with the country’s wealth of indigenous knowledge and its established biotechnology capacity, South Africa’s biodiversity is one of the country’s greatest assets.
The Bio-economy Strategy builds on the Department of Science and Technology’s National Biotechnology Strategy and Ten-Year Innovation Plan for South Africa, driving the development of a bio-economy in which the biotechnology sector, the information and communication technologies sector, environmental agencies and the social sciences create holistic solutions for the agriculture, health and industry.
Source: The Department of Science and Technology, January 2014
8th Jan 2014
The more we learn about living things, the more complex they seem. New discover to have gained speed with the unfolding of molecular genetics and the understanding that most biological functions are determined by the order of chemicals that make up our DNA. Many features of this complexity continue to baffle us: Why should we clever humans have around three million pairs of these DNA chemicals when the “simple” tea plant we cultivate for our pleasure has about a million more?
Pelly Malebe’s curiosity as a young child inclined her toward questions like this, and she realized early that the answers to many of those questions about how life “works” could be found in her school books, especially those explaining biology, and, when she was a little older, genetics. She was drawn to the challenge of understanding the most intricate structures of living systems, and then of how they worked.
Today as a young adult and member of RISE-SABINA, she is even more deeply involved in such questions. Under the guidance of Professors Zeno Apostolides and Zander Myburg, she is pursuing her PhD in the University of Pretoria’s biochemistry department, where she has become adept at the advanced technologies used to identify, quantify, and replicate the DNA-based genes of organisms. One of her most useful tools is a biochemical technology called the polymerase chain reaction (PCR), by which she has learned to amplify copies of particular DNA sequences, each of which may include one or more fragments of genes.
Because of the department’s longstanding work on the biochemistry of the tea plant, Camellia sinensis, Pelly has joined in the same pursuit – specifically in exploring the genetic makeup of tea in hopes of identifying new drought-resistant varieties, which are urgently needed in dry southern Africa. Whether or not the African climate changes in the direction of lower rainfall, as many scientists have predicted, drought has long been a barrier to the production of tea crops. In fact, there is a strong correlation between some of the most popular strains, or cultivars, of tea and a low tolerance for even moderate degrees of drought.
When tea plants are faced with a period of light rainfall, they use a number of tactics to survive:
• Dropping leaves
• Closing the stomata of the leaves, which slows or blocks photosynthesis
• Constricting the main stem, which reduces plant function
• Accumulating starch in the roots, a survival measure stimulated by harsh conditions
• Superoxide dismutase (detoxifying)
Virtually all of these tactics reduce the tea plant’s value as a commercial crop. These tactics, like virtually every aspect of the plant’s life, are determined by the complex tea genome, or genetic makeup, which is the frontier Pelly is exploring. In particular, she is seeking techniques to protect tea plants against drought that do not also reduce its ability to produce tasty tea. Even more desirable are drought-resistant, desirable cultivars that also have genes that can resist multiple pests and respond to cultivation in other positive ways.
Knowing that DNA composition varies among different cultivars, and that these molecular differences can now be detected by laboratory technologies, she has painstakingly learned modern techniques for searching out the distinctive patterns or molecular “markers” for such behaviors, beginning with drought tolerance. She is also alert for markers that indicate other desirable traits and that may be molecular neighbors of the drought tolerance markers. In this way, she hopes that the tea plant will offer signals that allow the tea grower to take advantage of any number of plant behaviors that bring advantages to the grower – and sipper.
Like other plant research, Pelly’s study of tea relies on a close partnership between researchers in the lab and those in the field. One advantage of RISE is that such partnerships are often easy to arrange. In the case of tea, Pelly has been collaborating for several years with Nick Mphangwe of Malawi, who has already earned his PhD at the University of Pretoria and now spends most of his time at the Tea Research Foundation of Central Africa’s center in Malawi. At TRFCA, cultivars that show good drought resistance are identified in the field. DNA samples are then harvested from those particular plants and transported to the Pretoria lab for genetic analysis. In addition to Nick’s field work in Malawi, Pelly also makes use of the university’s own smaller tea fields at the University of Pretoria, where the traits of these and other cultivars are studied.
Since beginning her master’s work in the RISE program, Pelly has pinpointed a section of tea DNA that is associated with drought tolerance. This section, which is 1200 base pairs long, is identified in the lab with the help of a process called electrophoresis (electro plus migration). The process begins with the preparation of agarose, one of the components of agar, a valuable component of algae that is harvested along the beaches in Tanzania, Kenya, and elsewhere (and studied in the WIO-RISE network). To make this gel, the agarose is extracted from the agar, dried to a powder, mixed with hot water, and cooled. When the agarose gel is cut into slabs, mixtures of DNA, RNA, and other large molecules can be placed on it and made to move, or “migrate,” through the gel matrix by application of an electrical field. Because small fragments move faster than large ones, the fragments can be identified according to their size, with those of the same length gathering as distinct visible “bands” in the gel. The formation of a band of fragments matching the length of the marker for drought resistance tells the geneticist that this plant is drought-resistant; the marker does not appear in drought-susceptible cultivars.
For her work in developing a method for screening tea cultivars for drought tolerance, completed during her MSc studies, Pelly and Prof. Apostolides were awarded a provisional patent. The potential outputs of their work are robust molecular markers that can be used in a selection process to improve tea yields throughout the global tea industry. Pelly’s focus is on increasing the understanding of the genetic basis of drought tolerance in plants, which may lead to other drought-tolerant crop varieties and thus to improved food and job security.
The final filing of the patent is underway with the African Regional Intellectual Property Organization, and also in India, Sri Lanka, China and South Africa, other leading tea producers. According to the wording of the patent application, the techniques developed at Pretoria include “the steps for providing plant material to be screened; extracting genomic DNA from the plant materials; and selectively amplifying the portion of the genomic DNA coding for drought tolerance.”
In the future, Pelly has several objectives. The first is developing the use of genetic markers for decision making and for conserving the crop plant germ plasm. Another is to develop marker-assisted selection for drought tolerance, yield, and quality, all of which have great potential value for the tea breeding industry. Finally, she hopes to use marker data to find associations with other traits of economic importance, which “may be useful to tea breeders world-wide.”
Pelly has already received much recognition for her work. As a bachelor’s student in human genetics and a master’s student in biotechnology, she was employed by the University of Pretoria as a teaching assistant, and elected to membership in the Golden Key International Honor Society. After she began her PhD work at Pretoria, she was funded not only by RISE through SABINA, but also by the South African National Research Foundation’s Innovation Doctoral Scholarship.
In addition, she was given a South African Women in Science Award (WISA) by the Department of Science and Technology. This award was created to recognize and reward the achievements of women scientists and researchers in South Africa, and also to dispel the myth that science is for men only. The DST hopes that the achievements of the award winners will encourage other women to persevere in overcoming gender discrimination to contribute to research and knowledge generation.
Story: Alan Anderson, Science Initiative Group, Blog posts, December 2013