Stellenbosch University
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Hands-on training at workshops
Author: Elbie Els
Published: 10/07/2019

Seventeen different workshops were offered at the annual Training Initiative of the Central Analytical Facilities (CAF) in 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, researchers and university and industry technical staff attended the workshops. Participants were welcomed by Prof Gary Stevens, CAF director, at STIAS. Leaders in serving science like Zeiss, Separations, Labotec, ThermoFisher, LecoAfrica, Microsep and Perkin Elmer sponsored the workshops.


Introduction to U-(Th)-Pb Geochronology by LA ICP-MS (1 day)

This workshop started with a classroom session in which the theoretical background of radioactive decay was introduced as well the basics of mass spectrometry. The different U-(Th)-Pb dating methods available to the Earth Science community were introduced and compared, and advantages and disadvantages of each technique highlighted. The students were encouraged to apply a critical and aware approach when choosing the right techniques to address the key questions of their research projects. A detailed description of the LA ICP-MS analytical set-up of the CAF laboratory was provided.

This was followed by a brief visit to the sample preparation laboratory where single grain samples are picked and mounted in epoxy discs and a more extensive visit to the LA ICP-MS laboratory to see the instruments (laser and mass spectrometer). The general layout and requirements of an analytical laboratory and potential issues that can arise during an analytical session were discussed. After a description of the key components of both instruments, the initial part of a real analytical run was simulated (involving turning on the Ar plasma of the mass spectrometer). The relationship between software applications used to run complex instruments and such instruments was discussed.

The afternoon was dedicated to a general discussion on data reduction approaches and overview of the software application Iolite. The last classroom session focused on the vast range of applications of U-(Th)-Pb dating to the Earth Sciences, with an emphasis on the different geological meaning that U-(Th)-Pb dates of different minerals have in relation to their closure temperature and the phenomenon of Pb diffusion. It was an intense but rewarding one-day training session, in which the main theoretical and practical aspects of U-(Th)-Pb chronology by LA ICP-MS were covered. The participation of interested students who asked many questions stimulated the discussion and made the experience enjoyable and rewarding for everyone.

“I gained a lot during the training; the presenters Dr Bracciali (U-(Th)-Pb) and Mrs Grobbelaar (XRF) delivered effectively and efficiently despite the time constraints. It gave me a better idea of how to do my analyses and the background has been helpful in interpretation of my geochemical results."

Practical XRF Spectrometry (1 day)

Participants received an introduction to the basic theoretical principles of XRF Spectrometry. A sample preparation demonstration followed where participants were given the opportunity to do hands-on preparations. Different sample preparation methods were also discussed relevant to the participant's research and interests. The workshop was ended with an analytical session on the XRF spectrometer demonstrating topics discussed in the theory session. All the participants were very engaging and enjoyed the workshop.

Solution ICP-MS in Environmental analysis of major and trace elements (1 day)

The Solution ICP-MS workshop was attended by a diverse group of researchers from different institutions and fields of interest. Everyone interacted well in sharing their own research questions, and they were all in agreement that the course benefitted their approach to major and trace element analysis in their own research.


Introduction to Hyperspectral Imaging and chemometrics (2 days)

The value of this workshop is that it offers a first-hand experience in NIR spectroscopy, hyperspectral imaging and data analysis techniques – a relatively big task to accomplish in two days. Six enthusiastic participants with backgrounds ranging from medicinal plants, food science, genetic breeding and viticulture accepted the challenge, even traveling from as far as Fort Hare. When learning a new skill it is important to lay down a solid knowledge foundation, which you can build your research and planning on. Therefore, day one of training focused on understanding the theory of NIR spectroscopy and providing an overview of the data analysis techniques for exploratory analysis and developing models. For day two, we planned a more hands on approach to cement the knowledge bricks into their rightful place. The morning kicked off with an interactive presentation by Ms Eileen Fouche from Labotec as she shared her expertise with NIR spectroscopy and its applications in the industry. This was followed by a practical demonstration where we tested the ability of two desktop Buchi NIR instruments with calibrations to predict various parameters such as the protein, moisture and fat content in wheat flour.

Equipped with a better understanding of this technique, participants took this one level further by integrating training on the hyperspectral imaging equipment. This entailed learning how to set up the instrument, followed by a demonstration of how to develop a classification model to distinguish between pharmaceutical products based on their chemical contents. Participants also worked through tutorials to practice their data analysis skills. The workshop ended on a high note by sharing pizzas over lunch and discussing research interests, travel stories and learning from each other's experiences.


Nucleic Acid Preparation, QC and Library building for NGS (4 days)

Rooibos (tea) is a part of the Western Cape economy and natural biodiversity, but very little is known of its genome.  Therefore, this year's training centred on generating a partial genomic sequence of Rooibos (Aspalathus linearis).  The course started with a pipetting master-class; kindly sponsored by Separations.  This was followed by DNA extraction, quantification and quality assessment.  The 12 attendees each successfully extracted high quality genomic DNA from 12 different plants.  Each attendee built their own NGS library and size-selected the library for the optimum size, prior to quantifying the library.  These libraries were combined and sequenced on the Ion Torrent S5 Prime.  For the final part of the training the data was used in de novo assembly to generate a partial genomic sequence.

Cell sorting on the BD FACS Melody (1 day)

The Fluorescence Microscopy Unit houses a BD FACSMelody cell sorter, on which six participants were trained during the CAF Training Initiative. The background of flow cytometry and cell sorting was first presented after which the participants received a demonstration on the instrument. Aspects which were addressed on the instrument included the correct setup of the instrument for sorting how to troubleshoot problems during this procedure. Fibroblast cells transfected with Green Fluorescent Protein were then analysed and sorted onto microscope slides and subsequently into 96 well plates.

Super-resolution microscopy (1 day)

Super-resolution microscopy allows the researcher to capture images of intracellular detail at a much higher resolution than conventional confocal microscopy. During this workshop, the principles of two types of super-resolution microscopy were introduced. Samples prepared in similar ways were then imaged with confocal microscopy, SIM and PALM/STORM to compare the results of each. Although confocal microscopy provides great results in many experiments, super-resolution just gives that extra resolution one needs to study intracellular organelles.

Correlative Light and Electron Microscopy (1 day)

The CLEM workshop was co-presented by the Fluorescence Microscopy and Electron Microscopy units who usually collaborate on correlative microscopy. Participants were presented with the background of both fluorescence microscopy and electron microscopy, as well as the workflow of the procedure to achieve correlation between these modalities. After presentations the group received a demonstration on confocal microscopy in the Fluorescence Microscopy Unit. A sample of orange skin and sample of fibroblast cells, which were prepared in different ways for CLEM, were then imaged on the confocal microscope. The last session was in the Electron Microscopy Unit where these samples were localised using Zeiss's 'shuttle-and-find' system, and imaged on the electron microscope. Participants assisted in the final overlay of confocal and electron microscopy images.


Biological Electron Microscopy (1 day)

Participants were introduced to the fundamentals of electron microscopy, followed by a presentation on advanced and novel EM applications. They then had the opportunity to prepare a bacterial sample for STEM analysis using a negative staining protocol and Uranyl Acetate, as well as TEM grids with nanoparticles. Demonstrations were also included on preparation of specimens for conventional and array tomography SEM, using resin embedding and ultramicrotomy. Workshop attendees got familiar with all ancillary equipment needed for sample preparation, and detectors used for imaging and analysis of a variety of biological samples, ranging from human placenta to polychaete worms and Mycobacterium tuberculosis (MTB) bacteria.

“The workshop was very useful and a pleasure to attend. Prof Joubert is a very passionate about her work and shares with it great generosity. Thank you!"

Introduction to Analytical Electron Microscopy (1 day)

The attendees were introduced to basic principles of scanning electron microscopy by unit manager prof. Lydia Joubert. An invited speaker with a long career in geometallurgy, Mrs Lesley Andrews, gave a very informative talk on analytical EM applications and image analysis in industry, after which PhD candidate Nonkuselo Madlakana demonstrated the use of various analytical detectors and analytical software at the EVO SEM. Different secondary, backscattered and scanning transmission imaging detectors and cathodoluminescence (CL) detection of zircons was also demonstrated on the Merlin FESEM.

Solution State Nuclear Magnetic Resonance Spectroscopy (1 day)

The 2019 NMR training day consisted of a small group of students from Stellenbosch University and iTemba labs. The day began with a tour of the facility and getting an overview of the three liquid state and one solid state NMR instruments. This gave attendees insight on their capabilities and applications in chemistry research and beyond. This was followed by hands-on sample preparation and the taking of their own NMR spectra. With this background on the process they got a thorough two hour lecture on NMR theory and how to interpret their spectra with insight and understanding.

After lunch they worked through a 2 hour tutorial on the interpretation of and assignment of signals using 1D and 2D NMR spectra. They started with spectra of a small molecule and worked their way up to progressively larger molecules. Each step added a small piece to the previous structure which helped in working their way up slowly from simple to more complex spectra, including homonuclear and heteronuclear two-dimensional correlation spectra, their interpretation and application. The students then had an interactive session on proper processing of their 1D and 2D data using the Mestrenova software package.

The workshop concluded with a supplementary topic on the use of chiral derivatising agents to determine the absolute configuration of molecules. All structures theoretically have an exact mirror image and this method is used to determine which one your structure belongs to, using NMR.

Introduction to X-ray Micro- and Nano-CT (1 day)

Attendees learned about the typical procedure followed when setting up a scan, reconstructing and analysing the data. The presenter highlighted the general uses of CT by presenting examples of the facility's previous work and explained applications of CT specific to the attendees' research interests.

“The use of the CT-Scan to develop a 3D visual image of samples was very interesting and useful."


Noraxon mobile neuromechanical analysis (2 days)

In this workshop participants learned how to use the Noraxon MyoResearch software, processing several unique examples, to expose them to thinking from start to finish about their protocols and projects. Participants also prepped subjects and captured their own data using several synchronised systems. They produced research questions which led to interesting group discussions.

Vicon neuromechanical analysis (2 days)

Participants learned how to use the Vicon Nexus software, processing some ideal data and then troubleshooting intentionally badly captured data, to expose them to thinking from start to finish about their protocols and projects. Participants also prepped subjects and captured their own data using several synchronised systems. After processing their data they produced research questions which they then presented to the rest of the group. This led to interesting group discussions.

LC-MS (2 days)

Numerous reseachers from various academic institutions throughout South Africa as well as from industry, took part in our LCMS training initiative. 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.

“The practical side of both workshops (LC-MS and GC-MS) is the important connection to the theory, in order to be able to apply what was taught. Seeing the machines "in action" was very useful and solidified the information provided beforehand.

GC-MS (3 days)

The GC-MS workshop was conducted by Mr Lucky Mokwena assisted by Mr William Arries (both from the CAF GC-MS Unit) and Mr Mark Pieterse (Leco Africa). The training format was adjusted this year. In 2019, Day 01 (Wednesday) was dedicated to both the sample preparation technique and practical demonstration, day 02 (Thursday) dedicated to the theory of the instrumentation including the demonstration and the final day (Friday) was dedicated to data interpretation. For the practical and data presentation, the participants were divided into two groups for the morning and afternoon sessions.

Proteomics (3 days)

Participants were introduced to proteomics in general and the techniques employed in particular. All three days 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.

“The Proteomics practicals were enjoyable. I also appreciate that the presenter took the time to speak to each of us individually and provided input on our projects."