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  • Key Find for Acid Mine Drainage on World Water Day

    Key Find for Acid Mine Drainage on World Water Day
    9th Apr 2013

    A newly developed membrane used to separate waste from water could become key in the treatment of pollutants ranging from acid mine drainage to oil-containing wastewater, as well as in processes ranging from desalination to kidney dialysis.

    The research was published in Scientific Reports (Nature Publishing Group) on Friday, 22 March, coinciding with World Water Day and falling within South Africa’s National Water Week.

    The technology – which was developed by a team of researchers from Wits University, in

    collaboration with NASA – will make it easier to filter pure water from waste produced during mining, oil and gas exploration and production, and nuclear exploration, to name a few. Even medical purification processes such as kidney dialysis could benefit.

    A commercial product will hopefully be developed soon, and there are plans to approach the US government regarding their problems with contaminants such as arsenic, mercury, and other heavy metals in their water. Closer to home, the technology could make huge inroads in dealing with the major issue of acid mine drainage.

    According to the Head of the School of Chemical and Metallurgical Engineering, Prof. Sunny Iyuke, who developed the product in collaboration with two PhD students, the membrane module (similar to a household water filter) could be used to catch water waste from mines before it entered drains or the water table. Water flow analytics could be used to track the direction and location of any escaped wastewater, where another membrane module (in the form of a borehole) could be stationed.

    The nanocomposite membrane gives two products: a smaller amount of concentrated waste and water so clean it could be drinkable. The waste can be reused, as in the case of arsenic, which is used in preservatives for wood and leather, ammunitions manufacturing, and pest control. Even the waste from acid mine drainage could be reused.

    “Water is critical to sustaining life, and water scarcity is becoming a huge problem not just in South Africa, but all over the world,” said Iyuke. “This technology produces a win win situation, for industry and the environment.”

    Source: Wits Newsroom, April 2013

  • CMEG researchers head for the Namib Desert

    9th Apr 2013

    In late April 2013, Don Cowan will lead the 20-strong Centre for Microbial Ecology and Genomics (CMEG) team, along with researchers from the University of the Western Cape (UWC), the University of Cape Town (UCT), Heriot-Watt University, Karlsruhe Institute of Technology and the Spanish National Research Council (Consejo Superior de Investigaciones Científicas – CSIC), on a week-long field research programme to the Gobabeb Research and Training Centre in the Namib Desert.
    Building on the work done during two previous visits, the team will undertake the first comprehensive survey of Namib Desert microbiology, using the latest molecular phylogenetic measurements.

    of Samples recovered during the week will be returned to the CMEG laboratory at the University Pretoria for chemical, physical and molecular analyses. These studies will rely heavily on genomic and metagenomic methods and will extensively employ next generation DNA sequencing.

    Individual research projects will focus on the gravel desert soils, the dune and inter-dune environments, the microbiology of different soil types and soil ages, and specialised niche environments such as spear-grass mounds, saline springs, ‘fairy circles’ and hypoliths. Macro and microclimatic effects, soil chemistry, carbon turnover and other factors are all expected to influence microbial community structures. These studies will include surveys of bacterial, fungal and bacteriophage diversity.

    Source: Prof Don Cowan, UP news April 2013

  • Faculty Launches WITS Research Institute For Malaria

    28th Mar 2013

    The Faculty is delighted to announce the Wits Research Institute for Malaria (WRIM) which was approved this month for a 5-year cycle. The formation of the WRIM will provide an environment to enhance the ground-breaking research already taking place at Wits into one of Africa’s deadliest diseases. The new Institute which will be situated jointly in the Schools of Pathology and Therapeutic Sciences, will fulfil not only the mission of Wits University (to be a leading research-intensive University), but also that of global players such as the World Bank and the Global Fund.
    Headed jointly by Professor Maureen Coetzee and Professor Thérèsa Coetzer in the Wits School of Pathology, the WRIM has been formed in an effort to strengthen malaria research in the existing fields as well as in the fields of epidemiology and clinical medicine. Professor Robyn van Zyl will form the third anchor in this remarkable group. The WRIM aims to produce top quality research and researchers that will benefit malaria control in Africa and place it amongst the leading malaria research groups in the world. Hearty congratulations!

    Story: Wits Health Sciences Research News  March 2013

  • ACGT and Inqaba biotec host Next Generation Sequencing Data Analysis Course

    ACGT and Inqaba biotec host Next Generation Sequencing Data Analysis Course
    28th Mar 2013

    The ACGT, in collaboration with Inqaba biotec and UP’s IRT for Genomics, recently hosted two next-generation sequencing NGS data analysis workshops at the University of Pretoria from the 11th-14th March 2013. Participants attended from all five ACGT partner institutions, as well the Universities of Limpopo and the North West. An overwhelming response was received both nationally, and from various African countries. A rigorous screening process saw 40 of the most deserving and suitable candidates attend the workshop free of charge at the University of Pretoria. Due to the overwhelming demand, two additional training courses were hosted at the ARC (18th-21st March 2013) by Prof Jasper Rees and his team from the ARC Biotechnology Platform. In excess of 60 researchers participated in the training event at Onderstepoort.

    Course presenter and field application specialist Dr Anne Arens from CLCbio headquarters in Denmark conducted the two day “hands-on” course. She was joined on the trip by Dr Reinhard Eckloff, Key Account Manager for Europe, Middle East and Africa. The course covered various topics including de novo assembly, RNA-Seq and miRNA analysis, sequencing tools and microbial finishing modules.

    Participant feedback indicated that the course was both highly beneficial and relevant to attendees.

    The workshops presented the first in a series of bioinformatics training courses hosted by ACGT and its partners to address specific needs in bioinformatics skills training. For more information on upcoming bioinformatics training events, visit the events page on the ACGT website or like us on Facebook.

    CLC Bio Workshop particpants 11th-12th March 2013, University of Pretoria
    CLCbio workshop participants, 11th-12th March 2013, University of Pretoria
  • Prestigious AU award for Prof Mike Wingfield

    5th Mar 2013

    Prof Mike Wingfield, Director of the Forestry and Agricultural Biotechnology Institute (FABI) in the Faculty of Natural and Agricultural Sciences, has been awarded the prestigious African Union (AU) Continental Scientific Award in the Life and Earth Sciences category.

    The AU Scientific Award Programme is a symbol of the commitment of AU heads of state and the government to raise community awareness and to engage African citizens in Africa’s science. It also seeks to improve technology programmes and to strengthen the continent’s research capacity.

    In 2012, Prof Wingfield was awarded the prestigious Johanna Westerdijk Award by the Centraalbureau voor Schimmelcultures (CBS) (Fungal Biodiversity Centre, the Netherlands), and in November he also received an honorary DSc degree from the University of British Columbia.

    He has published widely on the topic of tree health in more than 600 research papers and five books and as an invited speaker he has made numerous prestigious presentations globally. He has served in many distinguished positions and has received numerous awards and honours for contributions to education, research and industry in South Africa and elsewhere in the world. Based on these contributions, he has been elected as a fellow of scientific societies, including the Royal Society of South Africa, the Academy of Sciences of South Africa, the Southern African Society for Plant Pathology and the American Phytopathological Society. He is one of the few honorary members of the Mycological Society of America.

    The award will be presented to Prof Wingfield at the AU headquarters in Addis Ababa, Ethiopia on 25 May 2013.

    Story: UP newsroo, February 2013.

  • Ancient Remedies for Modern Diseases (SABINA)

    Ancient Remedies for Modern Diseases (SABINA)
    25th Feb 2013

    SABINA graduate Justin Omolo was the first RISE student to earn his PhD, which he completed in December 2011. In doing so he has traveled an original and creative path, exploring surprising links between the knowledge of traditional healers and the techniques of modern bioinformatics and synthetic chemistry. This journey may have brought him to the threshold of a treatment for HIV/AIDS that is both ancient and brand-new.

    Jusin Omolo

    His scientific education began at the bachelor’s level in the early 2000s, when he enrolled in a triple program of chemistry, biology, and education at the University of Dar es Salaam (UDSM) in Tanzania. After earning his B.S. in 2004, he won a DAAD-NAPRECA Regional Scholarship from Germany in 2005, which allowed him to continue his studies at the chemistry department of University of Botswana in Gaborone, Botswana. His main interest was in phytochemistry — analyzing plant extracts and looking for active compounds in medicines, especially those used by traditional healers. He began by focusing on a small tree called Ziziphus mucronata, or buffalo thorn, which commonly grows on termite mounds in Tanzania. Because of its thorns it is often used as a fence; it also bears nutritious, grape-sized fruits, Ziziphus genus, is used by traditional healers to reduce fever, kill pain, and treat various other symptoms.

    Traditional healers in Tanzania have been identifying, experimenting with, and using natural products to treat patients for millennia. While modern medicine came to regard the use of such crude extracts as unscientific a century or so ago, patients continued to trust their local healers, both because there were few medical doctors available and because they could not afford the cost of a modern clinic.

    In fact, the work of healers is based on a large and enduring truth: Virtually all plants have medicinal qualities because they must produce chemical defenses against pathogens. Plants lack legs, fangs, claws, or brains, and must remain rooted for a lifetime to the same spot from which they must face their attackers. Hence, they developed a sophisticated defense against invaders – a defense that early healers learned to “borrow” in order to treat viral, fungal, and bacterial infections of humans, often with great success. Many plant medicines are extracted from the roots, root bark, and stem bark — the zones where invading pathogens first attack and where attack – unlike a disease of the leaves or bark – can be fatal. In these vulnerable regions, a plant may have the ability to begin excreting as many as hundreds of unique chemicals within seconds of an attack. This sophisticated armamentarium now offers curious humans a vast selection of potential medicines we have only begun to analyze.

    While Justin was eager to get to the chemical core of Z. mucronata, he also had to do a year of coursework for his masters, leaving him only a year for lab research. During that year he succeeded in isolating the plant’s terpenoids, some of which showed moderate activity against HIV, and found them relatively easy to identify. He also demonstrated strong anti-microbial activity in a group of alkaloids, but when he began the complex task of identifying the specific alkaloid compounds responsible for the activity, progress slowed. “These alkaloids are much more complex than the terpenoids,” he said, “and I didn’t have the time to identify them. There were four alkaloids, but if you’re not experienced in that area, you can spend a year guessing which the active fractions are. At other times you may be lucky and get it right away.” Despite this difficulty, his work was judged favorably and he finished his MSc degree in December 2006.

    At that point Justin could not find support for further studies, and instead joined the staff of UDSM in June 2007 as an assistant lecturer. After supporting himself there for several years, in 2009 he heard about the RISE program and was able to secure a SABINA scholarship with the help of Quintino Mgani, a UDSM lecturer and RISE advisor.

    Together they developed a plan that would enhance Justin’s skills not only in phytochemistry, but also in synthetic chemistry. There were several reasons for pursuing both activities. First, phytochemistry is essential to identify pure compounds that have a desired medical activity. This begins with harvesting the plant itself, isolating the most active crude fractions, and, through repeated purification steps, isolating the single chemical responsible for the desired activity. This compound is then examined with an NMR instrument to identify the chemical properties of the molecules. Once the chemical structure is identified it can be produced synthetically and, in theory, developed into a drug that is sold commercially.

    Purifying a chemical from whole plants, however, is a burdensome process. The number of tons of raw plants required to obtain useful amounts of pure chemical can be so large as to jeopardize entire plant populations in the wild. Through the techniques of synthetic chemistry, however, producing an active compound can be done quickly and efficiently from commercially available raw materials.

    Fortunately, one of the SABINA faculty advisors, Prof. Charles de Koning of the University of the Witwatersrand in South Africa, is a synthetic chemist who agreed to help supervise Justin’s work. And Prof. de Koning, in turn, introduced him to a colleague, Dr. Vinesh Maharaj of South Africa’s Council on Scientific and Industrial Research (CSIR), who was already working closely with traditional healers. These healers lived in the region around Tanga, a city in northeastern Tanzania, where the humid coastal environment supports a treasure trove of biological diversity.

    An exciting aspect of Dr. Maharaj’s project was that he had found a willingness among both healers and modern doctors to pool their knowledge. This had already given rise to the Tanga AIDS Working Group (TAWG), formed at the height of the Tanzanian AIDS/HIV epidemic around 1990.

    The TAWG partnership had grown out of an observation made by a German physician, Dr. Elmar Ulrich of Pangani District Hospital, who had noticed that many of his surgery patients harbored clumps of what he thought were powders provided by healers. It is normal in Africa for patients to simultaneously visit hospitals and traditional healers in their search for help, but in this case, Ulrich decided to try to bring the two groups closer together and perhaps create a mutual referral network. The healers responded enthusiastically and soon began meeting with health professionals from Pangani Hospital on how they could collaborate.

    Dr. Ulrich succeeded in hosting a series of meetings where they shared knowledge and discussed how to treat various diseases and ailments. One of the participants was an 84-year-old healer named Waziri Mrisho. When discussing AIDS, Mrisho slowly stood up and said he would like to volunteer to treat HIV/AIDS patients with three traditional extracts — within the hospital. He said that his own grandfather had taught him the value and use of these plant extracts, and that they could alleviate many of the symptoms characteristic of AIDS. The group agreed, and Mrisho brought the extracts and administered them to various in-patients according to his family’s guidelines.

    At the time, the only medicines available for AIDS patients were aspirin, anti-fungals, and antibiotics, and even these basic medications were often unavailable. According to an American researcher and Tanga resident, David Scheinman, however, the use of traditional medicines brought to various patients improved appetites, weight gain, fewer and less severe opportunistic infections, and better health and well-being. Subsequently the plant remedies became the hospital’s standard HIV/AIDS treatment for patients who preferred herbal medicine. The success of the program brought support from OXFAM, the World Bank, and USAID.

    By the time Justin came into contact with the TAWG, Mrisho had died, a fourth extract had been added, and Scheinman and others had initiated an additional project, the Tanzania National Medical Group (TNMG). This group had the goals of identifying the active compounds in the four herbal remedies and then assessing the feasibility of synthesizing them and scaling up production to a commercial level.

    Justin began working with the plant extracts at the Council for Scientific and Industrial Research (CSIR) in Pretoria, with support from the Global Research Alliance, of which CSIR is a member. At first he worked on phytochemistry using dried plant samples purchased from the healers around Tanga. As his work became more specialized, he was able to prepare 17 separate fractions that showed antimicrobial activity. He took the most promising three of these to the University of Basel in Switzerland, where he tested them for activity against HIV/AIDS, and then to an institute in the Netherlands for further antimicrobial testing. He then concentrated on those fractions showing highest activity, and continued to purify them until he had isolated the chemical compounds.

    When scientists from the lab in Switzerland came to South Africa, they brought some encouraging news. It was already known that the HIV replication cycle begins with the fusion of the virus to the surface of the host cell, and continues with entry into the cell and multiplication of the viruses. They told Justin that the plant extract operated by inhibiting the HIV virus from fusing with the cell surface, and they promised him support in Basel to do a postdoc after completing his PhD studies.

    While Justin was doing the second part of his studies at the University of the Witwatersrand with Prof. de Koning, the Swiss emailed him again – but this time the news was disappointing. His fraction was indeed very active against HIV, they said, but it was also toxic to humans. Justin and his colleagues were puzzled to hear this — especially since TAWG had treated thousands of AIDS patients with good results since the early 1990’s. Justin and his advisors are determined to finalize their testing to resolve any such questions. Then they plan to take the results to the Gates Foundation and other funders to request support in synthesizing the compounds.

    He is also working with National Institute for Medical Research (NIMR) in Tanzania, attempting to isolate about five grams of each of the three compounds for further testing by a U.S. pharmaceutical firm. As of early 2013, the firm had not yet been identified. Justin estimates that the phytochemistry for that project alone will require half a ton of plant materials.

    He also continues to work with Mr. Scheinman, now residing in Houston, Texas, on all of the complex activities that make up a researcher’s life: writing proposals, editing papers, raising funds. “The hardest part,” he confesses, “is to wait for funding. We are ready to synthesize the compounds at the School of Chemistry, University of the Witwatersrand, which will allow production at larger scale than we can do by phytochemistry. But it is expensive, and we need more support.”

    Story by Alan Anderson, SIG,31 January 2013 

  • Exploring the Genotype of the Tea Plant (SABINA)

    Exploring the Genotype of the Tea Plant (SABINA)
    25th Feb 2013

    Raising and exporting black tea is an activity of major importance in Africa today; Africa  has become the world’s second largest tea exporting region after India. Tea has been grown in China for perhaps a millennium “by hand,” with farmers seeking out and hand-selecting the tea bushes producing the best yield and quality of tea. Since tea growing reached the West in the 19th century, however, tea cultivation has rapidly incorporated techniques of genetics and, most recently, of molecular biology. While tea breeders continue to walk the fields daily to monitor the health of crops and to seek out the most promising bushes, the real action today is in the laboratory, where the breeder’s skill is supplemented by work done at the molecular scale with instruments of enormous complexity and cost.

    Pelly Malebe, a doctoral student in the SABINA network, has been swept up in this genetic revolution and is eagerly helping to help push it along. She works under the supervision of Prof. Zeno Apostolides at the University of Pretoria’s Department of Biochemistry, riding the crest of an agro-technological revolution. The instruments of the present can not only analyze and compare the genes of the tea plants, but also allow biochemists to accomplish research feats undreamed of just a decade ago.

    Pelly Malebe

    Pelly is a member of a research partnership between the University of Pretoria and Malawi, where the Tea Research Foundation of Central Africa (TRFCA) is located. Another of her SABINA colleagues is Nicholas Mphangwe, a Malawian who is actively involved in the TRFCA’s breeding program. Their work carries considerable weight in Malawi, where the tea crop provides about nine percent of the country’s foreign exchange and about five percent of the world’s output.

    The primary focus of Pelly’s work is to locate and understand the sections of tea DNA that help the plant resist drought. Such a section is known as a marker, a gene or DNA sequence with a known location on a chromosome that can be used to identify the trait of interest in an individual or species. This is critical for tea, which prefers at least 50 inches of rain a year, and begins to drop its leaves when rainfall is not sufficient. Because Pelly is a native of the dry Limpopo province of South Africa, she is no stranger to drought, and her experience with dried-up crops and hungry farmers lends urgency to her work.

    As a master’s student at the University of Pretoria in 2009, Prof. Apostolides assigned her the task of searching for a genetic marker in tea plants that are relatively drought-hardy. She proved adept at picking up the complex techniques of tea genetics and was soon able to identify a putative marker for cultivars that show high resistance to drought. A cultivar is a plant selected by growers for certain traits and then vegetatively propagated by stem-cuttings so the next generation will have an identical genome. Virtually all food crops and ornamental plants sold today are cultivars that have been selected for certain traits; very few wild plants are used for commercial purposes.

    Such activities are by no means unique to tea; the analysis of genetic variation is an essential part of most plant genetics and crop improvement programs. Knowledge of DNA sequences has become indispensable for basic biological research and in numerous applied fields such as diagnostics, biotechnology, and forensic biology. The type of analysis depends on understanding the plant’s DNA and determining the precise order of the four bases (adenine, thymine, cytosine, and guanine) that function as the “letters” of the DNA alphabet (arranged in base pairs because of the double helix shape of DNA). The “words” that are formed by various arrangements of the letters determine the output, traits, and reproduction of the genome – for tea and every other organism, from virus to human. Any change in the spelling of these words is critical to DNA analysis as it might signify, for example, greater (or lesser) resistance to drought.

    Pelly spends much of her time analyzing the DNA sequences that determine the genetic makeup, or genome, of tea. The huge number of base pairs in the genome makes this analysis extremely complex. The tea genome, for example, is estimated to be about four billion base pairs long – even more than the 3.2 billion base pairs of the human genome. Such a “library” of genetic information is so daunting that it has taken many decades to decipher it. The structure of DNA was established as a double helix by James Watson and Francis Crick in 1953, but not until the early 1970s could scientists reliably interpret the sequence of even a few DNA fragments in the laboratory.

    Since the development of automated analysis, however, DNA sequencing has advanced rapidly. When Pelly first began to learn genotyping several years ago, she used a relatively slow technique known as RAPD PCR, or random amplified polymorphic DNA polymerase chain reaction. This technique limited her analyses as it is time consuming and has a low reproducibility rate. In the brief time since starting her PhD research in August 2011, she has moved to a more advanced genotyping technique that is orders of magnitude faster.

    “This technology is evolving so rapidly that there seems to be a new instrument every day,” she said.

    One reason Pelly and her colleagues depend on current generation technology is that the sequences of DNA that indicate various behaviors in tea involve many genes. She has found, for example, that about 40 percent of tea strains, or cultivars, which she has worked with have sequences of DNA that indicate some degree of drought tolerance. But for best results she needs to know exactly which base-pair combinations are generating the best drought tolerance. She also needs to recognize as many DNA markers as possible. She identified a 1,400-base-pair marker during her MSc work, but current technology will bring her far more information.

    Pelly and Nick are also looking for several kinds of selection methods for different traits, including the ability for better yield, disease resistance, and cold hardiness. From the breeding work done using conventional means over many years at the TRFCA, many desirable cultivars are already known.

    The trait of drought resistance is a particular concern for Africa, and many growers are concerned by the prospect of climate change. To refine her early work on drought resistance, Pelly relies on cultivars gathered by Nick and others from the Malawi fields, or from elite mother bushes gathered there in previous years. When a promising cultivar is recognized, it may be propagated at the TRFCA plant nursery. The DNA itself is extracted from a tea leaf with a special kit. Then the DNA is treated with anti-DNAase enzyme to prevent other enzymes from breaking up the DNA, and protease enzymes are added to clear away unneeded protein, producing a pure sample of DNA.

    “Then we run it through analysis looking for markers at the most likely DNA sequences,” said Pelly. “This technique is random, because we want to look everywhere. When we find possible sequences, then it’s up to me to identify which are most likely associated with the trait.”

    Once a cultivar that is thought to have genes involved in drought resistance has been identified, the next step is to test the plants in the field. Instead of waiting for a drought, however, this can be now done in real time. Thanks to a European Union grant to POL-SABINA (SABINA’s sister organization at the University of Pretoria) a rain shelter has now been erected at the TRFCA in Malawi. The tea is planted beneath the shelter, which can then simulate varying degrees of drought for the plants.

    “This will show whether the markers are there just by chance or whether they signal drought tolerance,” she said. “Then if you find the same marker in a second plant that is known to be drought-tolerant, you have a good clue. We got a head start using a small number of drought-tolerant plants identified in a previous experiment which are already available and perfectly valid for our testing. Eventually we hope to expand the numbers. This helps us with the breeding process – having a known trait and being able to use the plants with the trait as parents for the next generation.”

    Prof. Apostolides has been working with Kenyan and Chinese colleagues to plan cooperative sequencing research around the world that will be placed in the public domain. By promoting the sharing of knowledge with other countries, SABINA researchers are honoring the traditional scientific practice of openness.

    Story by Alan Anderson  SIG, 11 February 2013

  • African high-speed data network open to researchers

    12th Dec 2012

    A high-speed network that allows faster data transmission both among researchers in southern and eastern Africa and with scientists in Europe and other parts of the world has been launched.

    The UbuntuNet network, unveiled in Dar es Salaam, Tanzania, last month, builds on links initially established between Europe and five African countries by the UbuntuNet Alliance, the regional research and education network for eastern and southern Africa. The network provides a high-speed Internet connection between national research and education networks (NRENs) in the region and with the pan-European GÉANT network, giving access to 40 million users in 8,000 institutions.
    It was developed under the AfricaConnect programme, which aims to provide researchers across Africa with access to faster data transmission facilities to encourage global research collaboration. The European Commission provides 80 per cent of the programme’s funding, with the rest coming from African governments out of their support for the NRENs. European funding for AfricaConnect is due to last until 2015, after which the project is intended to be solely funded by its African partners.

    Speaking last week at the 2012 Africa-European Union Cooperation Forum on ICT, held in Lisbon, Portugal, UbuntuNet Alliance project officer Tiwonge Msulira Banda said that African scientists in fields such as agriculture, management of natural resources, climate change and earth observation, will benefit from access to a world-class data transmission network. “In all of these fields, UbuntuNet will open up opportunities for African researchers to get engaged in cutting-edge research at a global level,” he said. One research area that was already benefiting from high-speed access, he added, was genomics, where the high-speed links are being used to exchange data between researchers in Malawi and Kenya and the Wellcome Trust’s Sanger Institute in Cambridge, United Kingdom. Banda said that UbuntuNet could even allow more Africans to become involved in particle physics experiments at the Large Hadron Collider at CERN (the European Organization for Nuclear Research).

    Cathrin Stöver, chief international relations and communications manager of DANTE, the organisation that operates GÉANT and is coordinating AfricaConnect, emphasised that, although most of the initial funds were coming from Europe, “we will only do things that are agreed as beneficial by the African partners”.
    She added that AfricaConnect is also committed to establishing close ties with regional research networks in west and central Africa.

    Francis Tusubira, chief executive officer of the UbuntuNet Alliance, said that the organisation’s goal was to ensure that all countries in southern and eastern Africa had viable NRENs connected to the UbuntuNet network. But he added that it was a major challenge to build the capacity to run the national networks effectively, partly because of the lack of graduates with relevant computer skills being produced by universities.
    “We have thousands of engineering students coming out of universities, but put them in a working environment [involving computers] and they have no idea what to do,” he said.

    Therefore one priority for the UbuntuNet Alliance under the AfricaConnect project is to establish programmes to boost the teaching of computer engineering skills in African universities over the next four years. There was also a need to persuade African politicians of NRENs’ value so that they provide the funding required for their long-term operation, Tusubira said.

    Tusubira announced that he had already received commitments of 60 per cent of the total African contributions required by the AfricaConnect project up to 2015, and that 40 per cent of this money had already been received.

    Story by  David Dickson  SciDev.Net, 04 December 2012

  • Séralini et al. study conclusions not supported by data, says EU risk assessment community

    3rd Dec 2012

    Serious defects in the design and methodology of a paper by Séralini et al. mean it does not meet acceptable scientific standards and there is no need to re-examine previous safety evaluations of genetically modified maize NK603. These are the conclusions of separate and independent assessments carried out by the European Food Safety Authority (EFSA) and six EU Member States following publication of the paper in the journal Food and Chemical Toxicology on 19 September 2012.

    EFSA today delivered its final evaluation of the paper by Séralini et al. pharmacy rewards & more which raised concerns about the potential toxicity of genetically modified (GM) maize NK603 and of a herbicide containing glyphosate. In particular, it suggested a link between exposure to these substances and an increased incidence of tumours in rats.

    The Authority’s final review reaffirmed its initial assessment that the authors’ conclusions cannot be regarded as scientifically sound because of inadequacies in the design, reporting and analysis of the study as outlined in the paper. Consequently, it is not possible to draw valid conclusions about the occurrence of tumours in the rats tested. Based on the information published by Séralini et al., EFSA finds there is no need to re-examine its previous safety evaluations of NK603 or to consider these findings in the ongoing assessment of glyphosate.

    Per Bergman, who led EFSA’s work, said: “EFSA’s analysis has shown that deficiencies in the Séralini et al. paper mean it is of insufficient scientific quality for risk assessment. In addition, several national organisations were independently mandated by Member States to assess this study. These reviews have demonstrated a consensus among  a significant part of the EU risk assessment community that the conclusions of Séralini et al. are not supported by the data in the published paper. We believe the completion of this evaluation process has brought clarity to the issue.”

    Broad consensus

    EFSA’s final statement considered the independent assessments of the paper by organisations of six EU Member States: Belgium, Denmark, France, Germany, Italy and the Netherlands. Full copies of these evaluations can be found in the annex of EFSA’s statement.

    EFSA noted the emergence of a broad European consensus, with the reviewed Member State assessments finding the conclusions of Séralini et al. were not supported by the data presented in the study. Four of the national evaluations found the paper did not provide scientific information that would indicate the necessity to reopen the risk assessment of NK603 or glyphosate. The exceptions were France’s High Council of Biotechnology and  Italy, whose assessments did not examine this issue.

    Member States also identified many of the same weaknesses in the methodology and design of the paper as raised by EFSA. Unclear study objectives, the low number of rats used in each treatment group, a lack of detail on the feed and treatment formulation, key information missing on the statistical methods employed and incomplete endpoint reporting were all highlighted by Member State organisations.

    Inadequate sample size

    In the course of the review process, EFSA had requested Séralini et al.  to provide further information on their study documentation. No such material had reached the Authority before publication of this statement. However, on 9 November 2012, Séralini et al. published a general reply to the reactions from across the globe to their paper. After carefully examining the publication, EFSA concluded it provided only a limited amount of relevant information which failed to address the majority of the outstanding questions raised in the Authority’s first statement.

    In their ‘Answer to critics’ document, Séralini et al. stated the sample size of their treatment groups was too small to allow them to draw conclusions with regard to long-term carcinogenicity and mortality. EFSA noted this acknowledgement from the authors is inconsistent with the overall conclusions they made in the paper regarding the tumours and mortality.

    EFSA’s evaluation of the Séralini et al. article was in keeping with its mission to review all relevant scientific literature for GMO risk assessment. The Authority remains committed to monitoring relevant literature on an ongoing basis to ensure the advice it provides is up to date.

  • H 3-D Drug Discovery & Development Centre hosts its 1st Drug Discovery symposium

    20th Nov 2012

    Under the directorship of Prof Kelly Chibale, the H 3-D Drug Discovery  & Development Centre hosted its 1st drug discovery symposium at the beautiful Vineyard Hotel in Cape Town.  This symposium which took place between the 15th and 18th of October 2012, was attended by the ACGT intern, Mr Thabo Khoza.  The symposium kicked off with the newly appointed minister of Science and Technology, Mr  Derek Hanekom, opening the symposium. This was the minister’s first official address as the minister of Science and Technology.  The minister handed over to Prof Chibale to chair the symposium.

    The theme for the symposium was “New Paradigms in Drug Discovery”  and focused on drugs for malaria, TB, and cardiovascular diseases, diseases which are prevalent in Africa. The symposium had speakers from across the world with the Keynote Lecture on “Drug Discovery for Malaria: Results from the NITD Led NGBS Consortium”  being delivered by Prof Paul Herrling (Chair of the Novartis Institute for Tropical Diseases in Switzerland).  This four-day symposium was well attended by students and researchers from South African Universities and science councils. Few representatives from the ACGT partner institutions (UP, CSIR  and Wits) attended the symposium with some even presenting their posters at the event.

    On the 3rd night of the symposium, the delegates were treated with a celebration dinner in which Mrs Yvonne Chaka Chaka, who is also the UNICEF special ambassador on malaria in Eastern and Southern Africa , entertained the delegates with music.

    The symposium ended off with a series of lectures, some of which focused on the pharmacogenetics as well the state of research in South Africa, particularly capacity building in the field of drug discovery.

    To view the full programme  click here.