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  • ACGT, BSP and UP's GRI, team up to host the Genome Analysis ToolKit (GATK) workshop

    ACGT, BSP and UP's GRI, team up to host the Genome Analysis ToolKit (GATK) workshop
    25th Aug 2015

    The African Centre for Gene Technologies (ACGT) in conjunction with the Bioinformatics Service Platform (BSP) and UP’s Genomics Research Institute (GRI)  hosted a 5-day Genome Analysis ToolKit (GATK) Workshop between the 22-26 June 2015 at the  Centre for Bioinformatics and Computational Biology at UP .  The Toolkit was developed at the Broad Institute and was designed to analyse next-generation sequencing (NGS) data. Although it was initially developed for the analysis of human genomes, it has since been modified to handle and analyse data of non-model organisms by simply adapting and changing various parameters in the software.

    A total of 23 delegates were trained at the workshop and this group was representative of three of the ACGT partner institutions (UP, ARC and WITS). Furthermore, attendees representing UNISA, Vaal University of Technology and North West University were also present.  The five day hands-on workshop was presented by Drs. Geraldine Van der Auwera, Laura Gauthier and Yossi Farjoun from The Broad Institute. The workshop focused on analysing human data, but also covered various strategies for adapting the Best Practices to the study of non-human and non-model organisms. Each day consisted of a lecture session in the morning and a hands-on session in the afternoon. In the afternoon session, the attendees had the opportunity to apply what they had learnt in the morning to real data through a variety of exercises as well as explore various useful tips and tricks to improve efficiency and deal with common problems. The topics were covered in the following order: (1) Introduction to high-throughput sequencing, experimental designs, QC, (2) Processing of sequence alignment data (i.e BAM files, incl. RNAseq), (3) Germline variant discovery + recalibration/filtering, (4) Somatic variant discovery + filtering and (5) Genotype refinement, variant manipulation & evaluation.

    Overall, the workshop was well received and participants found it to be well presented and extremely useful and relevant to their research.

    This workshop forms part of a series of open-source bioinformatics training workshops planned for 2015 that is being sponsored by the Bioinformatics Service Platform (BSP) and the ACGT. For further information on upcoming bioinformatics training events or to be added to our mailing list, visit the events page on the ACGT website or email Farhahna Allie (az.ca1569109315.ju@e1569109315illaf1569109315)

    IMG_20150626_142456 IMG_20150623_152606  IMG_20150623_090338IMG_20150623_100104 IMG_20150623_152553  IMG_20150623_152553

  • Scientist's early success required passion, commitment and difficult choices

    13th Aug 2015

    The early success of Dr Stephanie Fanucchi leaves most people astounded. This young biologist had already completed her PhD when she joined the CSIR in 2011, her first job. Hardly three years later and a few months before her 29th birthday, she was part of a team of South African researchers who published a ground-breaking study about gene regulation in Cell, one of the world’s most prestigious research publications.


    The group showed that gene activity is a consequence of genes engaging in physical contact in three dimensions, also known as ‘gene kissing’.
    “This was a fundamental observation and has broad implications for how scientists understand gene regulation. Many diseases are caused by aberrant gene regulation and activity. It is ultimately our genes that dictate how cells in our bodies grow, so understanding how genes work will help scientists to find medical cures,” Fanucchi explains.

    State-of-the-art microscopes, custom-built in South Africa by the CSIR’s gene expression and biophysics group under the leadership of Dr Musa Mhlanga, were an important tool for imaging the ‘gene kissing’ interactions. As these microscopes are able to achieve single-molecule resolution, they are able to detect the activity of a single gene. Then using genome-editing tools – nicknamed ‘molecular scissors’ – the team was able to cut DNA at precise locations to prevent genes from making contact. This led to the registration of a new patent.

    Being part of this work required immense commitment and Fanucchi needed to make some difficult decisions about her personal life, which may resonate with women scientists globally.

    “I have not felt that being a woman has limited my career, but nor has it helped. There is a perception that some of the old-school scientists don’t really believe that men and women are intellectual equals, but I have not encountered that in our research group.

    “When we worked on the Cell paper, the hours were crazy. This is not an eight-to-five job. We were trying to answer a difficult question and there was no formula for how to do it. We had to process an enormous amount of information and therefore we often worked through the night.”

    “Perhaps herein lies the challenge women still face pursuing their academic and then scientific careers: One has to make difficult decisions relating to your personal life, for example to postpone starting a family, like I did.”

    Fanucchi almost considered a career in dancing, another passion, when she was in high school. Coming from an academic family, she was encouraged to go to university. After completing matric in 2003, she enrolled for a BSc degree at the University of the Witwatersrand, followed by an honours degree in biochemistry and cell biology. Thereafter she enrolled for a Master’s degree.

    She soon upgraded this to a PhD and as she was completing her studies, was recruited by Dr Mhlanga, who had joined the CSIR in 2008, after completing a post-doctoral fellowship at the Institut Pasteur in Paris in the laboratory of nuclear cell biology. “I was thrown into this entirely new field. Those who think that biology is a narrow field are mistaken. It is incredibly broad. It was a steep learning curve for me.
    “We were focusing on several projects in parallel. The work was cutting edge and high risk, meaning that we had to put in a lot of work that may not have paid off. This often happens in high-risk science, but in our case led to the Cell publication.”

    According to Fanucchi the fact that she had completed her PhD by then was an advantage. “PhD projects can require a very structured research environment. Having completed mine, I was free to do more high-risk science.”

    Fanucchi’s advice to other young scientists is to be very committed early in their careers.
    “I put my head down for ten years to get where I am now. Also, it is extremely competitive at this level with not that many positions available, so you have to excel, you cannot do anything half-heartedly. Our research group leader (Mhlanga) is a world-class scientist, one of the best to work with, but he does not believe in mediocrity. He always says that we use tax payers’ money to do research and have to be very serious about what we do.”

    Story by Antoinette Oosthuizen, CSIR

  • Online bioinformatics tools for sequence analysis

    29th Jul 2015

    Bioinformatics is a field of study concerned with computational analysis and storage of biological data. The field is broad, ranging from the study of DNA and proteins, to structural biology, drug design and comparative genomics. Dr Trevor Bell and Professor Anna Kramvis, from the Hepatitis Virus Diversity Unit (HVDRU) in the Department of Internal Medicine, have developed a number of free, online bioinformatic tools, described in several Open Access papers (1-4).

    The standard workflow in the HVDRU includes DNA extraction, PCR amplification, direct DNA sequencing, viewing and checking of chromatograms, preparation of curated sequences, multiple sequence alignment, sequence analysis, serotyping, genotyping, phylogenetic analysis and preparation of sequences for submission to public databases such as GenBank. The tools developed in the HVDRU are used at several of the steps in this process, with a particular focus on processing of chromatograms and DNA sequence data. Although developed and tested with sequence data from hepatitis B virus (HBV), sequences from other organisms can be submitted to most of the tools.

    The suite includes the following tools too: plot and visualize chromatogram quality scores; generate contigs directly from forward and reverse chromatograms; conservatively clean or curate sequence data; extract HBV protein sequences; calculate 2-by-2 contingency tables; determine HBV serotype; merge long overlapping sequence fragments; summarize and graph nucleotide or mutation distribution; automate phylogenetic analysis and prepare fragments for GenBank submission. Two tools have been developed to assist with processing and analysis of ultra-deep re-sequencing (pyrosequencing) data.

    These stand-alone, web-based tools allow users on any operating system platform to access the tools they require from any location with an internet connection, without needing to learn a new bioinformatics software suite or a new programme and without having to install any software on to their computer. The appropriate tool is simply used as and when required. They are available online at no cost and do not require extensive computer skills or training to use. Data can easily be processed by a mixture of online tools and other software packages, as standard file formats are used. Using specific tools designed to perform a single task, means that workflows can be partitioned into logical units and that processes or analyses can be easily repeated.

    The tools are available online on the HVDRU server at the following addresses:
    http://hvdr.bioinf.wits.ac.za/tools
    http://hvdr.bioinf.wits.ac.za/SmallGenomeTools.
    The source code for some of the tools is released under the GPL version 2 and is available online via GitHub, at the following address:
    https://github.com/DrTrevorBell/SmallGenomeTools.

    The tools are described in the following papers:
    1. Bell T.G, Kramvis A (2015). Bioinformatics tools for small genomes, such as hepatitis B virus. Viruses, 7, 2:781-97.
    2. Bell T.G, Kramvis A (2013). Fragment merger: an online tool to merge overlapping long sequence fragments. Viruses, 5, 3:824-33.
    3. Bell T.G, Kramvis A (2013). Mutation Reporter Tool: an online tool to interrogate loci of interest, with its utility demonstrated using hepatitis B virus. Virology Journal, 10:62.
    4. Yousif M, Bell T.G, Mudawi H, Glebe D, Kramvis A (2014). Analysis of ultra-deep pyrosequencing and cloning based sequencing of the basic core promoter/precore/core region of hepatitis B virus using newly developed bioinformatics tools. PLOS ONE, 9, 4:e95377.

    Story by: Dr Trevor Bell, Wits Health Science Research News July 2015

  • The University of Johannesburg hosts the 11th Regional Plant Biotechnology Forum

    The University of Johannesburg hosts the 11th Regional Plant Biotechnology Forum
    17th Jul 2015

    The University of Johannesburg (UJ) hosted the 11th Regional Plant Biotechnology Forum on the 13th of April 2015 at the UJ’s Council Chambers. Prof Ian Dubery and Dr Lizelle Piater worked closely with the ACGT in organising the forum that was attended by 56 scientists and students represented by all the ACGT partner institutions.

    The forum programme had six speakers, with Dr Paul Hills from the Stellenbosch University (SUN) being the keynote speaker for the day. Dr Paul Hills has been lecturing at SUN since 2008 within the Institute for Plant Biotechnology and his research interests relates to “how plant growth is regulated by myriad of small signalling molecules present in the environment, whether from biotic (e.g. bacterial, fungal, plant) or abiotic (e.g. fire) source.” Dr Hills gave a fascinating talk at the forum on “Overexpression of fungal volatile biosynthetic genes for enhanced growth in Arabidopsis”.

    Dr Khayalethu Ntushelo followed with another interesting talk on “Metagenomic analysis of spoiled potato and tomato and the use of the dominant bacterial species in plant growth studies”. Dr Ntushelo is a senior lecturer from the University of South Africa with research interests in plant-microbe interactions. Ms Nikita Da Camara, Dr Arnaud Djami-Tchatchou and Ms Sherrie-Ann New from UJ; as well as Prof Dave Berger from the University of Pretoria, gave captivating talks on their current research.

    A “Poster Session” at this forum was replaced by a “Short-Presentation Session”. The following researchers gave 10 minute presentations at the forum:

    – Ms Natrisha Devnarain (CSIR/UP) – Unravelling genetic mechanisms of drought tolerance in sorghum

    – Dr Pierre Durand (Wits) – Genome sequencing projects in microalgae

    – Prof Oleg Reva (UP) – Distribution and alternative strategies of root colonization in plant growth promoting Bacillus

    – Ms Stephanie Cornelissen (ARC) – Characterisation of the QTL associated with chill requirement during endodormancy in Malus x domestica Borkh

    The attendees were afforded an opportunity to network over lunch after all the presentations were completed.

     

    To access the main presentations, please click on the title below:

    • Dr Paul Hills (SUN) – Overexpression of fungal volatile biosynthetic genes for enhanced
    growth in Arabidopsis

    • Dr Khayalethu Ntushelo (UNISA) – Metagenomic analysis of spoiled potato and tomato and the use of the dominant bacterial species in plant growth studies

    • Ms Nikita Da Camara (UJ) – Proteome analysis of isonitrosoacetophenone-treated plant systems

    • Prof Dave Berger (UP) – Genomics of grey leaf spot disease of maize: from the field to
    the lab

    • Dr Arnaud Djami-Tchatchou (UJ) – LPS perception leads to dynamic changes in miRNA profiles of Arabidopsis thaliana cells and leaf tissues

    • Ms Sherrie-Ann New (UJ) – Investigation of the “Brassica-stunting disorder” affecting various Brassica crops in South Africa

    Visit the ACGT Facebook page for photos.

    Story by: The ACGT team

  • Ebola Sequencing Data Released Online

    25th Jun 2015

    A team of British scientists representing an international, multi-organisational effort to curb the further spread of Ebola in Sierra Leone have released their first dataset of the virus’ genetic structure online on virological.org

    The information is intended for the global scientific community to monitor the pathogen’s evolution in real-time and conduct research that can lead to more effective strategies against further outbreaks.

    The team of scientists, funded by the Wellcome Trust, is using semi-conductor next-generation sequencing (NGS) technology developed by Thermo Fisher Scientific to generate data in a lab facilitated by Public Health England and International Medical Corps.

    Head of Virology at the University of Cambridge, Professor Ian Goodfellow, travelled to Sierra Leone in December 2014 and then again in March 2015 to help set up a new diagnostics centre attached to an Ebola Treatment Centre in one of the country’s worst affected areas. Goodfellow returned a third time to study the virus at a molecular level using the sequencing technology.

    “Sequencing the genome of a virus can tell us a lot about how it spreads and changes as it passes from person to person. While this information is invaluable to researchers, the rapid sharing of data does not always occur,” said Professor of the Virus Genomics laboratory at the Wellcome Trust Sanger Institute, Paul Kellam, Ph.D, who is leading the team to map the genomic data captured by Goodfellow and his colleagues.

    “It used to take months to process samples that had to be brought back to labs in the UK for analysis. Having sequencing capabilities on the ground helps generate data in a matter of days or at the longest weeks, which should have a profound impact on how the Ebola virus is researched and inevitably addressed on a global scale,” continued Kellam.
    Rapid sequencing enables epidemiologists to decipher the source of individual strains, helping to eliminate the need to rely on Ebola patients to find out how and where they contracted the Ebola virus, as different strains can be tracked as they are transmitted from person to person.

    “Only by understanding the Ebola virus and other pathogens, which cause so much suffering in countries like Sierra Leone, can we take meaningful steps to protect communities from future outbreaks,” said Goodfellow. “My hope is that this technology will be used by the next generation of Sierra Leonean scientists and researchers to help provide a sustainable research and surveillance system in the future.”

    The next-generation sequencing system was installed at the laboratory adjacent to an Ebola Treatment Centre in Makeni, which was funded by the UK’s Department for International Development. The next-generation sequencing system is also expected to be installed at the University of Makeni, where it will be used by local scientists to study Ebola and other pathogens that affect the region.

    “We’ve learned many painful lessons from the Ebola outbreak, not least of which is that as a scientific community we must become less secretive with the data that is generated,” said Director of the Wellcome Trust, Dr Jeremy Farrar.

    “The collective expertise of the world’s infectious disease experts is more powerful than any single lab, and the best way of tapping into this is to enhance the capacity to generate the data in the countries affected, rather than having to fly samples out to other countries and then to make the data openly and safely available, as soon as possible,” concluded Farrar.

    Story by: Terri Chowles, eHealthNews.co.za

  • In the front line of the fight against malaria

    27th May 2015

    Saturday, 25 April was World Malaria Day. This year’s theme was ‘Invest in the future, defeat malaria’. The University of Pretoria’s Centre for Sustainable Malaria Control (UP CSMC) believes that research is critical in combating malaria in a manner that is sustainable and without the potentially adverse health effects of toxic chemicals.

    One of the ways in which the Centre interpreted this year’s theme, is that we should invest in our up-and-coming malaria researchers who develop new and innovative intervention methods to defeat this disease. As part of the Centre’s World Malaria Day activities, a group of 18 postgraduate students of the UP CSMC, who are working on malaria-related projects, travelled to rural Tonga in Mpumalanga Province, South Africa, to visit the Tonga Malaria Training Station, where they could get a more practical view of how the disease is fought on ground level.

    Mr Aaron Mabuza, Malaria Control Programme Manager for Mpumalanga, spoke to the students about the work that he and his team are doing. He explained that one of the key programmes that the Tonga Malaria Training Station is involved with is the training and consequent management of insecticide spray workers who play a major role in Mpumalanga’s and South Africa’s control of the malaria vector (mosquito) itself.
    Because malaria vectors are considered endophilic, meaning that the mosquito vectors rest inside houses after taking a blood meal, it is possible to control the prevalence of the insects that carry the disease through indoor residual spraying (IRS). As the name implies, IRS involves applying a residual insecticide to the walls and other surfaces of a house. The insecticide will then kill mosquitoes and other insects that come into contact with these surfaces for several months. It is important to note that the process does not necessarily prevent people from being bitten by mosquitoes, but rather kills the insects when they come to rest on the surface after they have fed, thus preventing transmission of infection to other persons.

    The Tonga Station is equipped with training facilities and accommodation for the spray workers undergoing training. Training usually takes place in August so that enough sprayers are available to cover the target area, because to be effective, IRS has to be applied to a very high proportion of households in an area – usually more than 80%. For the 2014/2015 malaria season, 321 temporary spray operators were trained and employed. In addition to the training of spray workers, the Station also runs yearly awareness and education campaigns to educate affected communities about malaria control and prevention strategies.

    South Africa is one of the few countries in the world where dichlorodiphenyltrichloroethane, better known by the acronym DDT, is still used for vector control. Although use of this chemical is contentious, the responsible application thereof has been successful in reducing malaria transmission and related deaths in the three malaria-endemic provinces – Limpopo, Mpumalanga and KwaZulu-Natal. As the benefits in using chemicals for the control of malaria outweigh the human and environmental risks associated with these chemicals, there is agreement that public health efforts are needed to reduce reliance on chemicals. In an effort to find sustainable ways toward eliminating malaria, researchers at the UP CSMC are currently involved with various projects inter alia to determine the effects that chemicals used for insect control have on people living in the affected communities and also to find safer alternatives for vector control. Recently both Prof Tiaan de Jager (Director of the UP CSMC) and Prof Riana Bornman delivered plenary lectures on the topic at an international congress in Copenhagen. The UP CSMC’s work on insecticide exposure and health effects is internationally recognised.

    According to Mr Mabuza there was an increase in the total number of malaria cases reported during the past season. He says that 75% of reported cases were however imported from other malaria areas and countries outside Mpumalanga, meaning that only 25% of cases contracted the disease locally in Mpumalanga. The case fatality rate was only slightly above the national and provincial norm of 0,5%. This relatively low mortality rate, he says, can be attributed to successful vector control through the spraying of houses, which is done between September and December each year. Another contributing factor to the low mortality rate in the province is the high rate of early diagnosis and treatment of malaria cases achieved by health workers in the province. Most diagnoses are still made using antigen-based malaria rapid diagnostic tests (RDTs) when a patient presents with symptoms at a clinic, but it is the second, more proactive testing approach employed by the programme that allows health workers to identify the majority of cases before they become too serious.

    When a patient is diagnosed with malaria, health workers take blood smear samples from the patient’s immediate family members and close neighbours to determine if they were infected by the same parasite carrying mosquito. At present the blood smears are sent to the National Institute for Communicable Diseases (NICD) in Johannesburg for analysis, but the Station plans to analyse all samples locally once their own laboratory becomes operational.

    Apart from the laboratory that will be available to staff at the Tonga Malaria Training Station in the future, the Station has also taken the first steps towards establishing a state-of-the-art insectary, which will allow researchers at the Station to study the behaviour of the mosquitoes that carry the deadly malaria parasite, thereby enabling them to develop more effective methods of vector control. The Station may also serve as a future field station for UP CSMC staff and students. The UP CSMC already has a satellite research facility in Vhembe District in Limpopo Province and Dr Sunday Ukpe from the UP CSMC is actively involved in promoting early diagnosis and the effective treatment of malaria in Mpumalanga.

    The dedicated staff at the Tonga Malaria Training Station has been an inspiration to all the students who have had the opportunity to experience the practical side of the fight against a disease that they normally only get to study in a laboratory. All indications are that the team at the Station have made strides towards eliminating the disease in South Africa. According to Mr Mabuza, the largest remaining challenge is for them to find a way to effectively control the spread of the disease from neighbouring countries, where effective control strategies are largely lacking. He says that he firmly believes that it will be possible to eliminate the disease in South Africa by 2018, provided that countries where the disease is endemic work together towards achieving this goal. According to Prof de Jager, the UP CSMC is doing innovative and leading research to support the country and the African continent in efforts to eliminate malaria.

    Story by: Ansa Heyl, University of Pretoria

  • Enhancing biopharming for an emerging bioeconomy

    Enhancing biopharming for an emerging bioeconomy
    11th Feb 2015

    In the world of health and medicine, the word tobacco usually brings to mind cancer, emphysema and heart disease. But in recent years the plant’s tarnished reputation is getting a makeover from the development of pharmaceuticals through an effective, swift and cost-cutting technique that has been dubbed “biopharming.”

    For more than seven years, the CSIR has been at the forefront of biopharming research and development (R&D) in South Africa and has active partnerships with global leaders in the field. Now, the CSIR’s antibody expression platform aims to enhance the organisation’s preparedness for hosting a national biopharming platform in support of an emerging South African bioeconomy. Consequently, the CSIR is poised to play a leadership role in support of the Department of Science and Technology’s new bioeconomy strategy.

    According to Dr Tsepo Tsekoa, principal investigator of the antibody expression platform,”Technological development has resulted in plants increasingly becoming an attractive host for the recombinant production of proteins destined for agro-industrial, biomedical and pharmaceutical application. With the recent approval of a number of plant-produced biologics for human health use – and a strong pipeline in clinical trials – the concept of using plants as a source to produce recombinant vaccines and other biopharmaceutical proteins is now being realised. An example of this is the use of antibody-producing tobacco plants employed in the battle against rabies.”

    Dr Tsepo Tsekoa

    “Plant-based expression systems are relatively inexpensive, readily scalable and fast; leveraging a niche in vaccines for neglected diseases, pandemic vaccines or emerging disease vaccines where other means of production may be too slow to respond or too expensive for mass roll-out,” noted Tsekoa.

    Over the next few years, the platform will develop biopharming-related human capital and strengthen state-of-the-art competence through research exchanges; evaluate recombinant vaccine manufacturing technologies for rapid response to pandemic influenza in South Africa; and complete a proof of concept for expression of highly active and broadly neutralising HIV antibodies in preparation for national roll-out in partnership with a large international consortium.

    “In addition, the production of ‘biobetters’ – which refers to a recombinant protein drug that is in the same class as an existing biopharmaceutical but is improved over the original, is an attractive option, as plant expression systems have been shown to produce biopharmaceuticals free of human infective viruses, prions and bacterial contaminants such as endotoxins. The technology has the potential to become a commercially attractive and universally accepted approach for vaccine, therapeutic and reagent protein manufacturing,” said Tsekoa.

    The CSIR has a sound track record when it comes to biopharming R&D. The organisation has produced vaccines such as RabiVir, a plant-made antibody cocktail for rabies prophylaxis, plant-made subunit animal vaccines as well as a pipeline of other veterinary vaccine production technologies, including virus-like particles.

    Story by: Kulani Chauke, Council for Scientific and Industrial Research

  • Spotlight on malaria case management

    10th Feb 2015

    The University of Pretoria (UP)’s vision acknowledges this institution’s prominent role in Africa and its commitment to fulfilling its social responsibilities. In this context it is clear that malaria, which has a devastating impact on the health of the citizens and the economies of many African countries, has been and continues to be a significant focus of research at UP. The University of Pretoria Centre for Sustainable Malaria Control (UP CSMC) is currently one of the leaders in malaria research in South Africa and is known for its unique integrated focus on malaria parasite biology, functional genomics, drug discovery efforts, innovative mosquito control strategies, public health management and community engagement. The Centre cooperates closely with the National Department of Health and other partner institutions throughout the country in their efforts to eradicate malaria in South Africa by 2018.

    Worldwide an estimated 250 million clinical cases of malaria occur annually, and more than half a million deaths are reported. The majority of these deaths occur in sub-Saharan Africa and the victims are mostly children under the age of five years. Despite a marked reduction in the incidence of malaria over the past decade, fatality rates due to malaria remain high in South Africa. Since the malaria season is currently at its peak, the focus of many health care professionals is firmly on the timely diagnosis and treatment of this disease.

    Malaria is endemic in three provinces in South Africa (Limpopo, Mpumalanga and KwaZulu-Natal), but this does not mean that the other provinces are malaria free. The disease is transmitted by female Anopheles mosquitoes that carry the malaria parasite, and although malaria prevention and control strategies are being vigorously implemented in the provinces where malaria is endemic, similar strategies in the rest of the country are unfortunately lagging behind.

    It is interesting to note that even though malaria is not endemic in Gauteng, this province is none the less classified as one of the high-incidence malaria areas in South Africa, with most of the reported cases occurring in the Ekurhuleni, Johannesburg and West Rand Districts. More than 80% of the patients diagnosed with malaria in these districts hail from Mozambique and other African countries and have travelled to South Africa in search of employment.

    Since many of these migrants are in the country illegally, they are reluctant to seek medical attention when they become ill. This often leads to delayed diagnosis and treatment, and consequently to a high mortality rate among people from this group. Unfortunately the Gauteng Department of Health’s campaign aimed at educating migrants about the disease has been hampered by the fact that they are difficult to reach as they often have no fixed addresses or are afraid of prosecution should their illegal status become known.

    In recent years ‘taxi malaria’ or ’Odyssean malaria’ – which refers to malaria transmitted by translocated parasite-carrying mosquitoes – has become another cause for concern in the South African provinces where malaria is non-endemic, since malaria is often excluded as a possible diagnosis in the case of patients who have not visited areas where the disease is endemic. According to the National Institute for Communicable Diseases (NICD), road traffic arriving from areas in and around South Africa where malaria is endemic is a very likely source of most of the infected mosquitoes responsible for Odyssean malaria cases.

    As the disease mimics many other conditions, such as influenza, meningitis, viral hepatitis, septicaemia and tick-bite fever, misdiagnosis is common and results in treatment being delayed, which in turn leads to a high incidence of severe and complicated malaria and a high fatality rate.

    The Plasmodium falciparum malaria strain, which accounts for the majority of malaria cases in South Africa, causes almost all severe and fatal instances of the disease. Symptoms of malaria typically include fever, rigours, headache and muscle pain, but a definitive diagnosis can usually be made by the detection of the parasite during a microscopic examination of a blood smear, or by using a rapid malaria antigen test. Most hospitals and clinics in the country have the capacity to make a definitive diagnosis by using either one of these methods. Malaria is generally treated with antimalarial drugs combined with medications to control fever, anti-seizure medications when needed, and fluids and electrolytes. The severity of a patient’s condition and the likelihood of chloroquine resistance will determine the types of medication administered.

    In October 2014 the UP CSMC was awarded the status of Medical Research Council (MRC) Collaborating Centre for Malaria Research, which means that it is now part of a network of MRC Collaborating Centres for Malaria Research that will collectively provide a multi-disciplinary approach to malaria research; synergise efforts on malaria research to achieve common goals; and facilitate scientific collaboration among malaria researchers in southern Africa. The Centre will also receive funding from the MRC to further develop the infrastructure needed in order to continue to engage in cutting-edge research on innovative, safe and effective vector control methods.

    In recent years the management and treatment of malaria has improved significantly and there is even talk of a vaccine that could eradicate the burden of this devastating disease in many of the world’s poorest countries. With the huge increase in available resources and brainpower focused on fighting this disease, it is beginning to seem more likely that the ambitious goal of eradicating malaria by 2018 could indeed be achieved.

    Story by: Ansa Heyl, University of Pretoria

  • The Universities of Pretoria and Stellenbosch Host the 5th Proteomics Workshop

    The Universities of Pretoria and Stellenbosch Host the 5th Proteomics Workshop
    11th Dec 2014

    The ACGT hosted the 5th national proteomics workshop in September 2014; facilitated by two world renowned proteomics experts, Prof Kathryn Lilley from Cambridge University and Prof Lennart Martens from Ghent University. The workshops were held at two nodes; at the University of Pretoria from the 10th-12th of September and at Stellenbosch University from the 15th – 17th of September.

    This three-day workshop was a follow-up from the 2012 and 2013 Proteomics workshops that were facilitated by Prof Lilley and the 2013 Proteomics-Bioinformatics workshop facilitated by Prof Martens. The 1st two days of the workshop were packed with a series of lectures and practical sessions from both professors. The topics covered on day 1 and 2 included: introduction to proteomics, basics of mass spectrometry, quantitative proteomics approaches, data processing of quantitative methods, identification and interpretation of MS proteomics data, experimental design and protein inference. On the 3rd day, round-table discussions were conducted and the participants had the opportunity to engage with the two professors, as well as local proteomics experts, regarding their own projects and discuss topics such as sample preparation; experimental design; quantifying methods to be employed, biological interpretation of MS data and validation methods.

    The Gauteng leg of the workshop was well represented by attendees from the ACGT partner institutions (Council for Scientific and Industrial Research, Agricultural Research Council, the Universities of Johannesburg, Pretoria and Witwatersrand). There were also attendees from Rhodes University, University of South Africa, University of Free State and Protechnik Laboratories. The Western Cape leg of the workshop had participants from Stellenbosch University, University of Cape Town, the Agricultural Research Council and Cape Peninsula University of technology.

    The workshop was very well received at both nodes with some of the participants sharing comments such as “Both speakers were very knowledgeable and were good at explaining difficult concepts. I thought the course was excellent and extremely useful”, and “The lecturers (Profs Lilley and Martens) were excellent at conveying complex topics in an easy to understand way. They were extremely knowledgeable and helpful during discussion sessions. I would highly recommend utilising their expertise in future workshops.”

    The facilitators were also impressed with the attendees and were able to pitch the lectures according to the needs of the participants at the different nodes. The success of the workshop made it possible for the both facilitators informing the ACGT team that they would be happy to come back in 2015 and present a more evolved proteomics workshop.

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  • Wits’ Professional Development Hub hosts the 10th Regional Plant Biotechnology Forum

    Wits’ Professional Development Hub hosts the 10th Regional Plant Biotechnology Forum
    3rd Dec 2014

    The 10th Regional Plant Forum was held on the 30th of October 2014 at the University of the Witwatersrand’s Professional Development Hub. The ACGT partnered with Prof Chrissie Rey, from the University of the Witwatersrand, to plan and organise the 10th Forum under the theme of “Crop Improvement and Genetic Transformation”.

    The forum drew an audience of over 50 people representing all the ACGT partner institutions as well as outside attendees, including the African Centre for Crop Improvement (ACCI) in KZN as well as the Department of Science and Technology. The attendees had the pleasure of hearing talks from two prominent scientists in the field and keynote speakers for the forum, Dr Sandy Snyman and Prof Johan Burger.

    Dr Sandy Snyman is a senior researcher in the biotechnology facility at the South African Sugercane Research Institute (SASRI) based in Kwa-Zulu Natal. Whilst with SASRI, Dr Snyman has initiated and implemented several tissue culture protocols in different aspects of the institute. She also has a particular interest in biosafety risk assessment relating to genetically modified organisms (GMOs).

    Prof Johan Burger is Chair of the Genetics department of Stellenbosch University and his research programme deals with viral diseases as well as molecular genomics of grapevine. Prof Burger serves on a number of steering committees that deal with the study of virus and virus-like diseases of grapevine as well as grape genome programs.

    The forum also included talks from Dr Lerato Matsaunyane from University of Johannesburg/ Agricultural Research Council (ARC), Dr Inge Gazendam from the ARC, Prof Chrissie Rey from Wits, Dr Kingstone Mashingaidze from the ARC and Mr Wayne Barnes from the forum sponsor, Thermo Fisher Scientific.

    The forum served as an opportunity for the 50+ delegates to network and talk about future collaborative efforts. A need for workshops for plant biotechnologists was also highlighted and the ACGT will look into ways of bringing such workshops within reach for its partner institutions as from 2015.

    To access the presentations, please click on the title below:

    Dr Sandy Snyman (SASRI) – “In vitro manipulations and strategies for the improvement of sugarcane cultivars in South Africa”
    Dr Lerato Matsaunyane (UJ) – “Analysis of the unintended and unexpected effects of transgene insertion on the endogenous host genome”
    Prof Johan Burger (SU) – “Of vineyards, viromes and VNPs – lessons in virus variability and versatility”
    Dr Inge Gazendam (ARC) – “The application of genetic transformation at the ARC-VOPI to improve plant traits”
    Prof Chrissie Rey (Wits) – “Stacking genes for multiple trait genetic modification”
    Dr Kingstone Mashingaidze –  “Public-private partnerships for deployment of GM traits to smallholder farmers

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