Stellenbosch University
Welcome to Stellenbosch University
Hands-on training encourages
Author: Elbie Els
Published: 29/06/2018

Seventeen different workshops were offered at the annual Training Initiative of the Central Analytical Facilities (CAF) from 18-22 June. Participants received high quality, hands-on training on the use and functioning of a range of high-end analytical equipment not readily available at all universities in South Africa. Postgraduate students (MSc, PhD) and researchers, as well as university and industry technical staff attended the workshops. At the opening function on 19 June, Prof Gary Stevens, director of CAF, encouraged participants to pursue a career in the analytical field and said that there is a need for more equipped scientists. Leaders in serving science like Zeiss, Separations, ThermoFisher, LecoAfrica, Microsep and Perkin Elmer sponsored the workshops.

Ania Botha and Grant Martin from Zeiss with Prof Gary Stevens, director of CAF, at the Welcome Dinner.

Participants from all seventeen workshops joined together at the Welcome Dinner.​

​Sibylle von Boetticher from Separations at  their display at the Welcome Dinner.

Participants at the CLEM workshop with Lize Engelbrecht and Prof Lydia-Marie Joubert.

Participants at the GC-MS workshop with Lucky Mokwena.

​Participants at the Neuromechanics Noraxon workshop.

The Solution State Nuclear Magnetic Resonance Spectroscopy workshop covered sample preparation, the setup and acquisition of some 1H and 13C NMR spectra on their samples, practise using 1D and 2D NMR experiments to solve several different structures and several other aspects.

“I enjoyed the hands-on experience preparing samples and getting to work and learn the different types of software available for data analysis." (Participant)

The Practical XRF Spectrometry workshop started off with a theory session in the morning. Topics covered included the basic principles of XRF spectrometry, instrument components of a WDXRF, sample preparation and data acquisition. This was followed by a practical session of sample preparation where fused beads and press powder pellets were prepared. In the afternoon session the prepared samples were analysed with qualitative and quantitative analysis under different instrument conditions. The course was concluded with a discussion of the results.

“It was very good, I cannot think of anything that could have made it better." (Participant)

The theory of ICP-MS analysis as well as the importance of high quality sampling and sample preparation techniques were discussed, after which time was spent on the instrument to understand all the factors playing a role in accurately measuring trace elements in various sample matrices.

“The workshop was very good." (Participant)

The Introduction to U-(Th)-Pb Geochronology by LA ICP-MS workshop consisted of an initial theoretical introduction to radioactive decay, with particular reference to the spontaneous decay of U and Th isotopes to Pb isotopes in common accessory minerals of rocks and how this can be used to obtain age constraints on geological processes; how to plot U-Pb data; a schematic description of the LA ICP-MS instrumentation available at CAF; comparison to other dating U-(Th)-Pb methods (SIMS, TIMS), with mention to accuracy and precision. Thereafter they spent some time in the LA ICP-MS laboratory familiarising with the laser and mass spectrometer, their main hardware components, the software used to run the instruments and how to set-up an analytical sequence. This was followed by a discussion of the key aspects of data reduction, with a brief overview of the software application (Iolite) used at CAF and including examples of already processed data assessed against micro-textural evidence (CL images) from the same zircon samples. The final part of the workshop consisted in the presentation and discussion with the participants of U-(Th)-Pb dating applications from various published geological case studies. The participants were encouraged to engage in the discussion and asked several questions throughout the workshop.

“I enjoyed the presentation related to geological application." (Participant)

The Biological Electron Microscopy: Introduction and Advanced Applications workshop was attended by 6 postgraduate students, whose academic background varied from Engineering (MSc) to Biological Sciences (MSc, PhD and post-doctoral). The morning lecture focused on basic principles of Electron Microscopy design and operation, fundamentals in biological EM, and the development of novel 3D EM techniques. Demonstration of processing techniques included negative staining and sample prep of microorganisms, tissue prep for resin embedding, and 3D array tomography. The afternoon was spent at the Zeiss Merlin FESEM, where a variety of specimens and detectors were used to illustrate the principles taught in the morning session. A representative of Carl Zeiss Microscopy, who was the sponsor of bags and notebooks, also attended the morning workshop. The delightful group of students had various interesting suggestions for novel tools and development in electron microscopy. Zeiss displayed the Zeiss Digital Classroom at the welcome dinner. The foundation of microscopy starts at undergraduate level and thus Zeiss designed a system that not only is fun and interactive for students but can be used as a tool for lecturers to assure for successful students in their microscopy classrooms. Blended learning has become of utter importance in this growing digital world and gives students a glimpse into the world of microscopy in an interactive way. This solution is not limited to only for student microscopes but can be added to all light microscopes.

“The practical part was amazing. To see the images that the machine could capture had all of us awestruck." (participant)

Our CLEM workshop was hosted in collaboration with the Fluorescence Microscopy Unit, and presentations by unit managers Lize Engelbrecht and Lydia-Marie Joubert introduced the students to basic principles, novel concepts, tools and challenges in Correlative Light and Electron Microscopy. A practical session at the Zeiss confocal microscope, and an introduction to sectioning of biological material, was followed by an afternoon session in the Electron Microscopy Unit where Zeiss's Shuttle-and-Find navigation system and software for CLEM was demonstrated.

“The whole Correlative light and electron microscopy workshop was extremely interesting and useful." (Participant)

The Analytical Electron Microscopy workshop was hosted to an international group of postgraduate (PhD) Engineering students from Nelson Mandela University, and Geological Sciences (MSc) at Stellenbosch University. Morning lectures by unit manager Lydia-Marie Joubert and senior analysts Madelaine Frazenburg and Elrika Harmzen-Pretorius was followed by an afternoon session in the lab, where operation of analytical detectors and software applications on the Zeiss EVO and Zeiss MERLIN scanning electron Microscopes were demonstrated. We were entertained by an exciting group of students with a keen interest and applications for analytical EM in their research projects. Challenges in analytical EM, and the way forward to future collaboration, were discussed.

“The electron microscopy was especially interesting to learn of sampel preparation and to look at how much magnification can be achieved with the microscope." (Participant)

The 600bp genome sequencing workshop received a generous donation of two bark beetle species from Dr Francois Roets to sequence for the training initiative. This allowed us to maximise the value of the workshop, with the hope that the resulting data might be used for publication purposes.  On day one, the attendees extracted DNA from both the invading and indigenous bark beetle species. The extracted DNA was evaluated with quality control procedures to prioritise and select the best possible template for massively parallel sequencing.  On day two, the bark beetle DNA was fragmented and used for library construction.  In particular, the extended range templating chemistry was employed to generate 600bp reads for sequencing on the Ion Torrent S5 platform.  On the final workshop day, the data was evaluated with a preliminary analysis, to demonstrate possible avenues that might be pursued to compare DNA sequences that were obtained from these beetles. ThermoFisher was one of DNA's three sponsors and their mission is to enable customers to make the world healthier, cleaner and safer. They help customers accelerate life sciences research, solve complex analytical challenges, improve patient diagnostics, deliver medicines to market and increase laboratory productivity. Perkin Elmer (sponsor) imagines a world where people can detect health issues sooner to treat them more effectively, where food and water are always safe and where scientific and medical research are enhanced to solve the greatest challenges of our time. Separations (sponsor) is a laboratory, biopharmaceutical process and lab automation specialist company. They have highly specialist consultants like Sibylle von Boetticher who was excited to be part of this training initiative and meeting their users.

“The whole workshop was very interesting and useful as it directly spoke to my phd." (Participant)

The Introduction to X-ray Micro and nano-CT workshop was a great experience to meet and engage with students and researchers from different fields and other institutions.  “We received lots of interest and positive feedback. The training got us and the participants excited into thinking of different ways to use MicroCT in their fields of study" said Stephan le Roux, presenter.

All aspects of the workshop were very interesting and useful to me." (Participant)

The super-resolution microscopy workshop included a short presentation on the different super-resolution microscopy techniques available at the CAF Fluorescence Microscopy Unit. With the PALM and STORM platforms participants samples of bacteria and fibroblast cells and learned of the many challenges that comes with high resolution microscopy. Participants were amazed at the quality of the images of epithelial cells stained with various colours when visualised using Structured Illumination Microscopy (SIM).

“The background to the technique formed a good basis for understanding the technique specifics. This assisted us to form an idea of how we could apply the technique in our own work, how we could improve our samples to use the technique and what the technique is actually able to do." (Participant)

The Cell sorting course on the BD FACSMelody™ presented an introduction into flow cytometry and the principles of the technique and fluorescence, as well as the principle and theory of cell sorting. The participants were active in the course, enquiring about methods and also applications of the theory. For the practical session, we demonstrated the differences between the BD FACSMelody™ cell sorter and the BD FACSAria II cell sorter. The participants were able to see a demonstration on cell sorting. Overall, the feedback for the course was very positive and everyone gained a better understanding of the applications of flow cytometry.

“I enjoyed the practical session." (Participant)

The Flow Cytometry data analysis course was aimed at providing information to participants on flow cytometric gating, data analyses and interpretation of results, as well as a how-to on basic data analysis in FlowJo® software.  The participants thoroughly enjoyed the hands-on tutorial and the question and answer sessions. All in all, they feedback indicated that they gained new understanding and the course was able to address many of their questions.

“The data analysis was very interesting." (Participant)

Trainees attending the first workshop for the Hyperspectral imaging unit were welcomed at the Food Science department from the 19th – 20th of June 2018.  On the first day of training, the morning was dedicated to a basic introduction on NIR Spectroscopy and NIR hyperspectral imaging.  The lecture was followed by a practical demonstration of the hyperspectral imaging equipment in the CAF unit, to give participants an opportunity to get first-hand experience operating the instruments.  Participants could image samples such as coffee beans, leaves and maize kernels to obtain a representation of the images and data, which are collected with the SWIR and VNIR cameras.  The second day of training focused on the basics of Multivariate data analysis.  The theoretical part was completed in the morning, after which participants moved to the lab to practice their chemometrics skills using the Evince software and tutorials provided by Prediktera.  Interested users can also download a free 30 day trail of this software to practice their skills at home.  The intention of this course was to provide new users with a basic introduction to this equipment and data processing software. 

“I enjoyed the practical experience using Evince software." (Participant)

The GC-MS workshop was held over 3 days. Day 1 was dedicated to the theory, day 2 was the practical session and day 3 the data interpretation. For the practical and data presentation, the participants were divided into 2 groups for the morning and afternoon sessions. The practical and data interpretations sessions were conducted in the CAF lab at the JH Neethling Building under the supervision of Mr Mokwena with the assistance of Mr William Arries (CAF GC-MS Units). On completion of the workshop, all the participating candidates were issued with attendance certificates. LecoAfrica sponsored the GC-MS workshop. LECO Corporation has for over 75 years remained a worldwide leader in the development of top quality analytical instrumentation, mass spectrometers, metallography, optical equipment and related consumables. Leco serves life sciencies, environmental and agriculture, food, energy and fuels, and the mined materials and metals markets.

I found the troubleshooting of the GCMS machine very interesting." (Participant)

Several students from various academic institutions throughout South Africa as well as from industry, took part in the LCMS workshop. They were trained in the basic theory and practical usage of LC Triple Quadrupole or Tandem Mass Spectometry (LC-MSMS) and LC Time of Flight (LC-qTOF) techniques. Microsep who sponsored this workshop distributes and supports internationally recognised market-leading brands in Southern Africa. Their goal is to provide high quality products and innovative solutions to satisfy the needs of their customers. The company's focus is in the laboratory, industrial and retail market segments, providing systems and solutions to the separations science, water purification, analytical instrumentation, microporous membrane filtration, high precision weighing, metal detection, dimensioning, logistics and retail automation industries.

“Lectures explaining the LCMS were of a high standard. The hands on preparations were of great value." (Participant)

The Neuromechanics Unit hosted a two-day Noraxon mobile neuromechanical analysis workshop on advanced technologies for measuring and analyzing human movement. The instruments included a Noraxon wearable sensor system that wirelessly tracks skeletal motion (kinematics) using inertial sensors and the electrical activity of the muscles (EMG) using surface electrodes placed on the skin. A Bertec instrumented treadmill was also used to measure the ground reaction forces produced during certain movements (e.g. walking, running, jumping, etc.). Attendees were instructed on how to operate the Noraxon MyoResearch software platform to capture and analyse the kinematic, EMG and force data. There was a strong focus on test participant preparation and the sensor placement required to obtain high quality, accurate data. During the practical session on the second day, attendees completed the entire workflow from participant preparation through to data analysis indepedently. During this process attendees were encouraged to generate hypotheses around certain movements and then practically test and evaluate these using the available technologies and the data they captured.

The EMG analysis was very good." (Participant)

Over the course of three days participants at the Proteomics workshop were introduced to proteomics in general and the techniques employed in particular. Everyday consisted of both theoretical sessions followed by practical sessions where the theory discussed were applied. During the practical sessions participants prepared their own samples for analysis and were showed what the sample should – and should not – look like.

“It was a well presented workshop and the fact that it was hands-on made it to be of great value. Only when you do the work do you really understand all the concepts." (Participant)