16th Sep 2015
Forests worldwide are continually under threat from introduced insects and pathogens despite the best biosecurity efforts. Without a concerted global effort to understand and control invasive pests the problem is expected to worsen as international trade increases.
In a review article, published in the prominent journal Science, Prof Mike Wingfield and his co-authors from the Forestry and Biodiversity Institute (FABI) at the University of Pretoria (UP) assert that an integrated global strategy is urgently needed to protect our forests.
Profs Wingfield, Bernard Slippers, Brenda Wingfield from FABI and Dr Eckehard Brockerhoff, Principal Scientist at Scion in New Zealand, considers the urgent need for a global strategy to keep planted forests healthy. They reflect on the global value of plantation forests that are seriously threatened by invasive pathogens and insect pests. Globalisation is compounding this issue, and while there are solutions – including biosecurity, biological control, breeding, genetic engineering, environmentally safe chemical control and more – to protect forests, the lack of investment, capacity, and coordination of global efforts are barriers.
‘More and more pests are emerging. Their impact is a growing concern as one in every six people rely on forests for food globally, and many more depend on them for climate regulation, carbon storage, health (through improved water and air quality) as well as the wood and wood-product industries,’ explained Prof Wingfield. In South Africa, forestry contributes around R45 billion a year to the economy.
‘Keeping invasive pests out of forests should be a top priority for all countries,’ he said.
The authors added that global biosecurity is only as strong as the weakest link. ‘Many countries don’t have the resources to put biosecurity measures in place for plants and plant products. Once a pest becomes established it can be impossible to eradicate, and the pest can use the new country as a stepping stone for further invasions.’
The authors said that the only way to realistically deal with tree pests will be through global collaboration – sharing experience and research findings. While bodies like the International Union of Forest Research Organizations (IUFRO)help to facilitate collaboration, there is no single body or funding structure to support a global strategy for dealing with pests in planted forests.
According to the researchers, the perfect time to talk about this issue is now, as the World Forestry Congress of the Food and Agriculture Organisation (FAO) of the United Nations (UN) is focusing on forest health and sustainability when it meets in September in South Africa.
Paper and other details
1 Wingfield, M.J., Brockerhoff, E.G., Wingfield, B.D. & Slippers, B. (2015). Planted forest health: The need for a global strategy. Science (in press) DOI
2 See Fig. 2 of the paper for the spread of pitch canker.
An introduction to the special issue of Science and the other review papers are available here or visit http://www.sciencemag.org/content/349/6250/800.full
16th Sep 2015
On 10 September, the highly anticipated Alliance for Accelerating Excellence in Science in Africa (AESA) was launched in Nairobi, Kenya.
This initiative of the African Academy of Sciences (AAS) is supported inter alia by the New Partnership for Africa’s Development (NEPAD), the Bill and Melinda Gates Foundation (BMGF), the Wellcome Trust (WT) and the UK Department for International Development (DFID).
AESA is a jointly-funded pan-African platform established to support the development of long-term sustainable funding, research leadership, and scientific excellence and innovation in Africa. AESA was endorsed by the African Union to champion the development of research for health capacities in Africa and represents an exciting new model for long term development of research leadership and excellence in Africa. AESA will fund and manage science programmes, work in partnership to develop health research strategies, and monitor investments in science on behalf of African and global partners.
Two major programmes, DELTAS and the Grand Challenges Programme, are included.
The launch and academic programme was attended by African and global science leaders, policy and decision makers, industry and non-governmental organizations, and representatives from the NRF, MRC, and ICSU ROA.
On 11-12 September, the launch is followed by the initiation of the large-scale NRF-IDRC-DFID programme to strengthen Science Granting Councils in Sub-Saharan Africa.
Story by NRF media room, 10 September 2015
7th Sep 2015
The CLC Genomics Workbench, commercially available through Qiagen, is used for the analysis and visualization of next generation sequencing data. It includes a number of features and tools within the fields of genomics, transcriptomics and epigenomics. Furthermore, CLC genomics workbench currently supports all the major next generation sequencing platforms, such as SOLiD, Ion Torrent, Complete Genomics, 454, Illumina Genome Analyzer and Sanger sequencing.
In 2013 and 2014, the ACGT successfully hosted two previous CLC bio/CLC Genomics workbench respectively. Surveys and feedback from previous attendees suggested that this workshop was extremely useful and relevant in this current “omics” era and recommended that more workshops be hosted in the future. It was this in mind that the ACGT partnered with Inqaba biotec to successfully host a third workshop in 2015. Attendees were representative of the following institutions: UP, Wits, ARC, UNISA and UJ. This workshop was hosted at The Centre for Bioinformatics and Computational Biology Computer Lab at the University of Pretoria between the 24th and 27th of August 2015.
Field Application Scientist, Dr Anne Arens (Qiagen, Belgium) assisted by Dr. Hamilton Ganesan (Inqaba biotec) both did an excellent job at demonstrating the versatility of this software package and presented the various applications and work-flows that can be performed within the CLC Genomics Workbench. The first two days (24-25th August) of the workshop was dedicated to addressing the most popular topics requested by attendees (i.e. Resequencing, phylogenetics, RNA-Seq: differential expression analysis, Blast2Go and 16S rRNA Metagenomics). The second two days (26-27th) was dedicated to one-on-one sessions with the trainer in order to deal with specific problems that attendees may have encountered during their own analysis.
Feedback from those who attended found that the course was relevant, at the right pace and level for them and was well organized. One of the delegates were extremely complementary and had this to say: “…. This was a very insightful training and I would like to acknowledge Anne for such great explanations of each concept and for being a great trainer”. Similar comments from others indicated that overall the workshop was informative, useful and well received.
For more information on upcoming bioinformatics training events, visit the events page on the ACGT website www.acgt.co.za), like us on Facebook (http://www.facebook.com/ACGT.biotec) or contact Farhahna Allie at
30th Aug 2015
Metabolomics is a newly emerging field of ‘omics’ that aims to investigate the global metabolic changes in a biological system. The two major technologies, mass spectrometry (MS) and nuclear magnetic resonance (NMR) spectroscopy, is commonly used for identifying and quantifying the full range of metabolites in biological samples and each produce large amounts of spectral data. The conversion of this data into biologically meaningful information requires considerable data processing. With the recent establishment and growth of metabolomics-based studies in South Africa, it has become important to consider the computational tools available to handle and interpret the large amounts of metabolomics data that is generated by these high-throughput technologies. SIMCA, offered through the commercial vendor Umetrics, is one of the leading software packages currently available for the analysis and interpretation of metabolomics data sets. Providing training in a software package such as SIMCA would greatly build the capacity of principal investigators and postgraduate students in metabolomics multivariate data analysis and experimental design.
The ACGT, in conjunction with The Department of Science and Technology (DST), successfully hosted a SIMCA metabolomics data analysis workshop at the Centre for Bioinformatics and Computational Biology Computer Lab at the University of Pretoria between the 3rd and 7th of August 2015. Two trainers were invited from Imperial College (London) to facilitate the workshop. Trainers included Dr. Ruey-Leng Loo and Mr. Torben Kimhofer. Both trainers are specifically knowledgeable and experienced in various important components of metabolomics data analysis specifically using the SIMCA software package. Twenty six attendees from various institutions NWU, UP, ARC, CSIR, UJ, UNISA and Wits attended the workshop. The five day workshop kicked off with a brief welcome and opening remarks by Dr Farhahna Allie as well as the trainers. Each of the attendees then had the opportunity to introduce themselves and their research topics and how they best envisaged benefiting from this workshop. Workshop days started off with a lecture session in the morning and a hands-on session in the afternoon. Moreover, the workshop also offered the attendees with a great opportunity to network and share their knowledge and experience with in their diverse metabolomics projects, further encouraging them to foster future collaboration.
Feedback from the attendees demonstrated that the course was relevant and that it was presented at the right pace and level for them, as well as that the workshop was well organized. Overall, the positive feedback from delegates indicated that the course was useful. The trainers were equally pleased with the execution of the workshop and they were specifically impressed with the enthusiasm and active participation of the attendees.
For more information on upcoming bioinformatics training events, visit the events page on the ACGT website (www.acgt.co.za), like us on Facebook (http://www.facebook.com/ACGT.biotec) or contact Farhahna Allie at
29th Aug 2015
RNA-Seq has become increasingly popular in transcriptome profiling and is used primarily to determine differential expression of genes or transcripts as well as identifying novel transcripts. The analysis of RNA-seq data most commonly includes: quality control, filtering, read alignment, assigning reads to genes or transcripts, and estimating transcript abundance. There is currently a vast number of tools that are currently available and accessible, such as Galaxy, which help simplify the processing and analysis of RNA-Seq data. Galaxy is a user-friendly web-based platform that offers all of the tools necessary for creating and performing a complete intensive RNA–seq data analysis workflow or pipeline.
A Galaxy workshop was co-hosted by ACGT and The Genomics Research Institute (GRI) between the 1st and 3rd of July 2015 at the University of Pretoria. This workshop forms part of a series of open-source bioinformatics training workshops planned for 2015 that is being co-sponsored by the Bioinformatics Service Platform (BSP) and the ACGT. The overall aim of this workshop was to provide a hands-on tutorial for different aspects of RNA-Seq analyses, from data preparation, through to statistical testing for differential gene expression. This workshop was specifically designed to teach participants how to integrate data, and perform simple and complex analysis within Galaxy using the “Tuxedo” suite of tools. The Tuxedo suite is specially comprised of Bowtie (alignment), Tophat (mapping) and Cufflinks (transcript abundance).
The first day of the workshop kicked off with a brief welcome and opening remarks by Dr Farhahna Allie (ACGT Support Scientist) and Prof Fourie Joubert. This was followed by a brief “ice-breaker” introduction by the attendees. Each day of the workshop started off with 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. Datasets for the workshop was provided and although the workshop required that attendees have some basic understanding and knowledge of Linux commands and/or R commands, these commands were fully documented and provided to each participant.
Overall, the positive feedback from delegates indicated that the course was presented well and useful. This workshop was particularly successful as it highlighted the expertise of local South African trainers: Prof Fourie Joubert, Dr Charles Hefer and Dr. Oliver Bezuidt.
For more information on upcoming bioinformatics training events, visit the events page on the ACGT website (www.acgt.co.za), like us on Facebook (http://www.facebook.com/ACGT.biotec or contact Farhahna Allie at
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 ()
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
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:
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:
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
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
• 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
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