23rd Feb 2016
The 6th ACGT Proteomics workshop kicked off at the University of Pretoria (UP) on the 1st of February 2016. Returning workshop facilitator, Prof Lennart Martens (from Ghent University) presented a two-day workshop to an enthusiastic group of delegates represented by UP, the Agricultural Research Council, the Council for Scientific and Industrial Research , University of Free State and the National Health Laboratory Services.
Prof Martens gave a series of lectures and practicals on de novo sequencing, protein identification issues, protein inference and metaproteins. Ms Tracey Hurrell, a senior PhD student at UP, stood in for Prof Kathryn Lilley at the UP leg of the workshop. Ms Hurrell spent 18 months in Prof Lilley’s lab in Cambridge as a fellow and therefore was the perfect stand-in for Prof Lilley. Ms Hurrell gave lectures on post translational modifications, protein-protein and protein-RNA interactions, and spatio-temporal proteomics.
The lectures were well received by the delegates and the round table discussion sessions afforded the delegates the opportunity to interact with the experts and ask for guidance with regards to their own research. Prof Duncan Cromarty from UP and Dr Stoyan Stochev from CSIR (both experts in the proteomics field) were there to assist with the round table discussions.
The two-day workshop was replicated in Cape Town at the University of Cape Town (UCT) on the 4th to the 5th of February. Prof Jonathan Blackburn’s lab at UCT hosted the workshop in conjunction with ACGT; with Prof Martens and Prof Lilley facilitating the workshops.
The delegates who attended the UCT workshop were from UCT, Stellenbosch University, K-RITH and CPGR. The facilitators used the same programme that they used at UP. Some of the Western Cape proteomics experts that assisted the facilitators during the round table discussions included Drs Zack McDonald and Nelson Soares, and Proffs David Tabb and Jonathan Blackburn.
Talks about forming a formal Proteomics Society came up after the UCT leg of the workshop. The ACGT plans to have a Proteomics symposium later this year. A formal discussion about the Proteomics society can be held at the symposium. The ACGT will also host a Skyline workshop in December for data analysis. Details about the two events will be circulated in due course.
The organizers and facilitators wish to express their sincere gratitude for the financial assistance provided by the Bioinformatics Service Platform (BSP).
7th Dec 2015
The ACGT had its first Plant Biotechnology Research Infrastructure Exhibition day on the 12th of November 2016. This event took place at the University of Pretoria’s Plant Science Complex and was attended by 20 students, lecturers and researchers from all the ACGT partner institutions.
The ACGT usually has two Plant Biotechnology Forums per year but this year only one plant forum was held at the beginning of the year and the exhibition day replaced the 2nd forum for the year. The aim of this exhibition day was to afford the ACGT partner institutions the opportunity to showcase their shared equipment/facilities that cater to the plant biotechnology community. The event was informal and the attendees had the platform to interact with the facilities managers (or representatives). Attendees were provided information about the equipment and services offered as well as discussed future collaborative projects.
The following partner institutions exhibited the following facilities:
1. University of Pretoria (UP): UP showcased their QuantStudioTM 12K Flex Real-Time PCR platform. This platform aims to promote large-scale quantitative real-time PCR-based functional research at UP and at a national level.
2. Council for Scientific and Industrial Research (CSIR): The CSIR exhibited their Biosciences proteomics and Biomolecule Characterisation facility. This facility applies a range of techniques (including high resolution, high mass accuracy mass spectrometry) to quantitatively characterize complex lysates as well as recombinant peptides, proteins and antibodies.
3. Agricultural Research Council (ARC): The ARC displayed their Illumina MiSeq and Illumina HiSeq2500 platforms that generate NGS datasets ranging from 125 to 300bp in size. The platform also hosts a Laser Capture Microdissection (LCM) microscope , high throughput, automated liquid handling robotics systems, and a high performance compute cluster for data analysis and data storage.
4. University of Pretoria (UP): UP showcased their Ion Torrent Sequencing Facility that provides high-quality high-throughput sequencing solutions to researchers in South Africa. The Ion Torrent Personal Genome Machine housed in a dedicated laboratory in the new Plant Sciences Complex is capable of generating up to 2 GB sequence data from single or multiplexed samples.
5. University of Johannesburg (UJ): UJ exhibited some of their recent results on the use of LC-MS based Metabolomics approaches in Plant Biotechnology research as well as MS-based phytohormone analysis. The Shimadzu Nexera UPLC ultra-fast LC , Shimadzu LC-IT-TOF-MS and Shimadzu 2010 Ultra GC-MS equipment were showcased.
6. University of Pretoria (UP): UP also exhibited their ACGT Microarray Facility. This facility supports research projects utilizing the Agilent platform for microarray studies. Catalog arrays for model organisms, or custom arrays with flexible array configurations provide a good balance between cost and data throughput. All the required hardware for hybridising Agilent slides are available in the facility.
The ACGT hopes to have another exhibition day in the near future. The 1st plant event for 2016 will be the 12th Plant Biotechnology forum to be held at the Council for Scientific and Industrial Research.
26th Nov 2015
Using a groundbreaking gene editing technique, scientists have created a strain of mosquitoes capable of rapidly introducing malaria-blocking genes into a mosquito population through its progeny, ultimately eliminating the insects’ ability to transmit the disease to humans. This new model represents a notable advance in the effort to establish an antimalarial mosquito population, which with further development could help eradicate a disease that sickens millions worldwide each year.
For full article, please click on the following link: Science Daily
8th Oct 2015
2015 marks the first year that a student team from the University of Pretoria (UP) participated in the International Genetically Engineered Machines (iGEM) competition and only the third time that an African team participated in this prestigious event.
The International Genetically Engineered Machines (iGEM) competition which started at the Massachusetts Institute of Technology (MIT) annually draws hundreds of high school and university teams from around the world to compete in what has become the premier international synthetic biology student competition. Synthetic biology is an emerging field that combines modern molecular biology and systems engineering concepts to develop innovative solutions, such as cancer-targeting viruses, novel biosensors, or even DIY biological 3D printers.
The Forest Molecular Genetics (FMG) Programme, with support from the Department of Science and Technology (DST), sponsored seven undergraduate and one BSc Honours student to participate in the iGEM 2015 competition. The team (Pretoria_UP) was mentored by Dr Steven Hussey and additionally advised by Prof Zander Myburg and Dr Eshchar Mizrachi from the Department of Genetics and Forestry and Agricultural Biotechnology Institute (FABI) at UP.
Pretoria_UP team representatives, Mr Gert Pietersen and Ms Nomakula Zim won a bronze medal at the 2015 iGEM Giant Jamboree in Boston, MA (24-28 September) where they presented their “Switch-coli” project to an international audience. They gained valuable insight into the iGEM organisation, which they will share with the rest of the team in preparation for the 2016 competition where the team aims to make their mark. The team used DNA BioBricks, the standard parts of synthetic biology, to design a genetic program controlling bacterial chemotaxis (movement in response to a chemical gradient). Their design improves a “bio-tweet” principle by the WITS-CSIR_SA team in 2011. This means that motile bacteria travel from a sender position to a recipient position, turn around synchronously only when most of them have arrived at the recipient, and then travel back to the sender, relaying information on the state of the recipient.
They registered seven new BioBricks in the Standard Registry of DNA parts, synthesized six and submitted three BioBrick DNA samples to the Registry. They also compiled a comprehensive wiki of their project, delivered an oral presentation, as well as a poster, to the iGEM community and judges. In addition, the team reached out to Grade 11 learners in the previously disadvantaged community of Mamelodi, educating them about synthetic biology and conducting a survey assessing differences in awareness, perception, attitude, and future projections of synthetic biology among learners from schools in previously disadvantaged and advantaged backgrounds. This work comprised the team’s Human Practices portfolio and revealed striking socio-economic influences on synthetic biology acceptance and awareness.
The Pretoria_UP iGEM initiative is a community project within the FMG Programme, which aims to attract and develop scarce skills in synthetic biology innovation. The vision of this project is to participate in iGEM regularly and to encourage other South African institutions to form teams, and thereby stimulate a new generation of students who will develop synthetic biology solutions for the South African Bio- economy.
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 az.ca1566727614.ju@e1566727614illaf1566727614
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 az.ca1566727614.ju@e1566727614illaf1566727614
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 az.ca1566727614.ju@e1566727614illaf1566727614
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.ca1566727614.ju@e1566727614illaf1566727614)