2018 was a very successful year for the Central Analytical Facilities (CAF). Some of the things to be thankful for, is the Vibrational Spectroscopy Unit which was added and the DNA Sequencer Unit which celebrated 21 years.
[Please see highlights of each Unit below:]
Highlights at the CT Scanner facility include major contributions to research as evidenced by 26 citations of the facility in 2018, as well as successful completion of many industry projects. The largest industry project involved analysis of steel samples using both micro and nanoCT for understanding the integrity of the material and analysing the distribution of unwanted defects. The second largest project involved analysis of the distribution of contamination occurring during the life of a commercial product, and attempting to understand the extent and origin of this contamination. The facility also developed new standardized microCT test methods for additively manufactured metals which are summarized in a review paper and an associated series of method papers.[1]
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The Vibrational Spectroscopy facility opened its doors at the Department of Food Science with an official launch in March. In February, a technician from Norsk Electro Otikk (NEO, Norway) successfully set up the three hyperspectral imaging systems in the unit. The instruments were optimized for routine analysis using software from Prediktera. Students were given the opportunity to learn more about this technology by attending a two-day workshop at the annual CAF training initiative held in June. During the workshop participants received hands-on training on the instruments and could experiment with the multivariate data analysis software (Evince), available on processing computers in the unit. Interest in the use of these instruments has been growing steadily as students and supervisors realize the benefits of incorporating NIR hyperspectral imaging into their research. By generating calibration models, this technique enables rapid analysis of several quantitative and qualitative properties. Large number of samples can be analysed non-destructively and imaging generates chemical maps to visualize spatial distribution of analytes within samples. Some exciting research projects, which are still ongoing, include identification of meat obtained from different species, detection of plant and cereal diseases, screening of fruit defects and quantification of lignin content in paper samples.
The Unit is managed by Dr Janine Colling. She completed her undergraduate and post-graduate degrees at the Institute for Plant Biotechnology at Stellenbosch University with the main focus on medicinal plant biotechnology. She obtained a Joint PhD degree from the University of Stellenbosch and Ghent University in 2016. Before joining the Central Analytical Facility, she did a post-doc at the Department of Horticulture, investigating the biochemical factors involved in regulating dormancy in apple trees.
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The Electron Microscopy facility had a fast-paced year filled with exciting research and support challenges, outreach and networking opportunities, and moving forward in building a platform in biological electron microscopy. Maintaining instrumentation in an excellent working condition was an additional aspect of our day-to-day running that often held many challenges, even requiring some ingenious MacGyver skills. The midyear workshops in Analytical and Biological Electron Microscopy, as well as Correlative Light and Electron Microscopy (CLEM), were attended by keen groups of students from universities in the Western and Eastern Cape.
Prof Lydia-Marie Joubert (manager) had the opportunity to introduce their work at the Crick African Network Symposium in January at Spier. Another opportunity for networking with local and international scientists arose at the SA BioImaging Symposium at the end of October at STIAS. “Here we strengthened ties with the Global BioImaging Network that was established by EMBL in Germany, and discussed major challenges in imaging sciences in Africa" Lydia said.
Dr Elrika Harmzen-Pretorius (senior analyst) attended a course in Advanced Quantitative Analysis at Oxford Instruments in London, to support our capacity building in engineering and earth sciences. Lydia recently attended an Array Tomography workshop in Oxford, UK, where academic researchers from Europe met with industrial partners who are involved in developing 3D Electron Microscopy.
Madelaine Frazenburg's (senior analyst) tireless efforts to meet deadlines and support the mineral exploration clients despite extended delays in instrumentation repairs was indeed remarkable. The Unit again recruited a small group of proficient EM users as student analysts, which gave excellent after hour support to their industry clients.
They gradually acquired small equipment for their bio-EM applications and are redesigning their lab infrastructure to also provide 'wet lab' services. Acquiring running water and a fume hood in the lab are top items on the list. With the publication of the Faculty of Science centenary book, 'A particular frame of mind', various images from EM students and staff were included to emphasize the importance of visual and analytical data in the growth of Natural Sciences. A copy was also presented to the Directors of Stanford Beckman Center, Lydia's previous academic home. “We are happy to report increased collaboration with our neighbours at UWC and from Tygerberg campus, and look forward to welcoming visitors from our international EM community" Lydia said.
Photo on the right: Prof Lydia-Marie Joubert with prof Lucy Shapiro, Director of Beckman Center
and Mr Mark Shepard, Associate Director of Beckman Center with a copy of 'A particular frame of mind'.
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The Fluorescence Microscopy facility experienced a successful year, reaching cost efficiency in 2018, with growth in income of more than 20%. A new fluorescence microscope has been acquired for the Tygerberg Medical Campus, which should contribute greatly to research on this campus. 
With regard to flow cytometry, the first successful single cell sorting has been performed for a study on bacterial populations in soil, a protocol was optimised for the analysis of Protea pollen grains and a new course on flow cytometry data analysis was introduced this year. From the confocal microscope a few great publications saw the light, ranging from the first CLEM results on polymer fibres to modulation of mitochondrial bioenergetics. The first CLEM results using both super-resolution and SEM on fibrin fibres from patients with Parkinson's disease, Alzheimer's disease and diabetes has also been accepted for publication.
Photo on the right: Lize Engelbrecht, manager, with students at a workshop during the CAF Training Initiative in June.
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The Nuclear Magnetic Resonance facility made important advances this year in expanding Solid State NMR to prominent commercial and foreign clients.
Very reliable results were obtained on SS NMR coal profiling for AC Boilers, Italy. Fortunately for us no other NMR unit globally could help them measure and calculate the structural and lattice parameters required as input data for the combustion modelling of coal in their new low NOx emission burners. The client travelled to SU to observe the analysis and made important contacts with other CAF units regarding their coal profiling needs. With over 150 years' experience in Steam Generation and Burner Technology and a track record of 1000 units exceeding 80,000 MW installed worldwide, AC BOILERS is the largest Italian original technology Boiler Manufacturer, providing the full range of Steam Generator Technologies.
An important service contract was signed with Sasol on full solid and liquid state NMR profiling of their waxes. A variety on Carbon-13 and Proton NMR experiments were employed for their needs. These include direct observation, cross-polarisation and several proton and carbon NMR relaxation studies.
A research collaboration on a SA wine profiling method was initiated with Dr Astrid Buica and her PhD student at the Department of Viticulture and Oenology. A Non-targeted fingerprinting approach is utilised, employing customised water and ethanol soft signal suppression in routine Proton NMR spectra of wine, to enable the direct observation of the wine metabolites in 20 minutes. Principal component multivariate analysis on the proton NMR 'fingerprint' is then employed to enable the generation variety of authentication parameters on the wines, including utilisation as a quality control mechanism. These authentication parameters include geographical origin, adulteration and differentiation of grape variety, amongst others. This research project plays an important role in initiating and motivating for the future fingerprinting of authentic South African wines and the resultant local and export authentication certification thus enabled through SU-CAF.
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The Mass Spectrometry Unit was appointed as the best performing CAF unit of the year for their enormous amount and diversity of research at SU. A new Mass Spectrometry laboratory was established at Tygerberg, the Biomedical LCMS laboratory with a new staff member Hannes van der Merwe. Hannes studied at 
KOVSIES, after which he worked for a year in the TB group at Medical Micro. In 2003, he received a position at Farmovs-PAREXEL, later just PAREXEL, as analyst involved in method development and analysis with LC-MS equipment. He then moved to the regulatory group where he was involved with GLP, GCLP and ISO audits of the labs and studies. In 2010, SYNEXA offered him a post where he was the head of quality and later the MS lab, until 2018 when he joined CAF. The new laboratory at Tygerberg follows from a number of collaborative studies conducted by researchers at Tygerberg and staff of the Stellenbosch CAF laboratory, involving the development of LCMS methods for determination of morphine, PAS, glutamine, rifampicin and esomeprazole in plasma from hospital patients. These studies are ongoing and the aim is to transfer all the developed methods to the new Tygerberg laboratory.
“We are not always aware of the final outcome of the data that we generate on behalf of clients, but there are certain achievements of which we are justly proud, including a paper published Dr Cluver et al in American Journal of Obstetrics & Gynecology on esomeprazole to treat preeclampsia, as well as a prize won by Kim Adams for the best presentation by a student at CoBNeST" Dr Marietjie Stander (manager) said.
The Microbiology group of Prof Gideon Wolfaardt, with Edward Archer as the project leader has successfully conducted a proficiency test with SCORE. The European Monitoring Centre for Drugs and Drug Addiction's (EMCDDA) Sewage CORE analysis group (SCORE). The analysis involves urban water profiling through the detection of pharmaceuticals and illicit drugs in wastewater and environmental surface waters. This approach will assist to track pharmaceutical use and substance abuse patterns on a community level in order to address both public- and ecological health risk assessment.
The ion mobility functionality of the Synapt was used to publish 3 papers in 2018 by users, this is a first for South Africa. One of the highlights is a paper by Pieter Venter and co-workers from Prof Andre de Villiers that was published in Analytical Chemistry: Comprehensive 3-dimensional LC×LC×ion mobility spectrometry separation combined with high resolution MS for the analysis of complex samples.
The UPC2 system is still an excellent tool for steriod research and a record number of papers were again published this year on it, four by the Dr Storbeck's group and four of the post graduate students won prizes for posters and talks at international conferences: Desmaré van Rooyen, Lise Barnard, Monique Barnard and Therina du Toit (two awards), post doc of Prof Amanda Swart.
The laboratory has conducted a few interesting industry studies this year, one on fruit juice quality and adulteration, another on the adulteration of honey. They also improved our knowledge and experience on the analysis of polyphenolic compounds and flavonoids in a number of studies in conjunction with other universities including UJ and UP. Several in-depth studies were conducted during the year with regard to what should be present and what shouldn't be present in rooibos tea, involving numerous samples from the South African Rooibos tea industry.
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The Neuromechanics facility significantly increased its services to neuroscience researchers in 2018, with applications ranging from athlete concussion management to reading comprehension and mind-controlled devices. More than 10 postgraduate students from Stellenbosch University's biomedical engineering research group made use of the unit's high-density electroencephalography (EEG) equipment, and the unit staff also facilitated their first two big projects for users from external universities. The unit also successfully delivered a number of long-term, large-scale projects related to the 3D analysis of how physical movement and posture are affected by factors such different prosthetic limb designs, accelerated aging due in the HIV population and the ergonomics of classroom furniture in schools. These projects dramatically expanded the unit's capabilities for collecting measurements of different functional activities as well as managing and 
analysing large datasets. Lastly, the unit also piloted a range of new analytical services for sports athletes and is now well positioned to expand on these services next year.
Tamsin Purkis joined the Neuromechanics team in January 2018. Before joining CAF, Tamsin obtained her Undergraduate, Honours and Master's degrees in Mechanical Engineering at the University of Pretoria, while working in the Mechatronics and Micro-Manufacturing unit at the Council for Scientific and Industrial Research. Her work and thesis centred around her passion for Biomechanics and included the development of a wearable gait analysis system and a low-cost paediatric prosthetic knee."
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At DNA Sequencing the biggest highlight of the year was the growth in the NGS service. The number of runs increased from 129 in 2017 to 202 (until 16 Nov). The underlying increase in sample numbers (more than 1000 samples for the year) is driven by a larger pool of users making use of the facility (currently more than 34 different research groups in 11 different institutes) which also came with a greater diversity of types of analysis performed. Human exome sequencing remains the most frequently used service but other assays like 600bp partial genome sequencing and whole genome sequencing is now also being used more. More than 150 bacterial and fungal genomes have been sequenced along with more than 60 viral isolates.
Photo on the right: The Unit celebrated 21 years since their start in 1997 with colleagues and clients in September this year.
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The ICP-MS & XRF laboratory had a challenging year, with a number of unexpected breakdowns, but the team excelled in making the unit as cost-effective as possible while continuously improving service to customers and expertise within the unit. To this end, Riana Rossouw (manager) and Dr Laura Bracciali (U-(Th)-Pb Geochronology division manager) attended a one week advanced Thermo SF ICP-MS training course in Bremen, Germany in early March. “The course was extremely well structured and tremendously valuable to our applications in the lab, and well worth swopping the SA summer weather for freezing cold Europe" Riana said. “We are looking forward to welcoming our ICP analyst Charney's little one next year, and hope she will enjoy temporarily swopping her CHNS sample boat folding skills for the fun task of nappy folding!"
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With so many highlights there are more than enough reasons to be thankful and look forward to next year. Prof Gary Stevens, director, is excited about 2019: “The Electron Microscopy Unit and the Fluorescence Microscopy Unit will be expanding to offer services at the Tygerberg campus. We will also be growing the Pharmacology Division."
[1] du Plessis, A., Yadroitsev, I., Yadroitsava, I. and Le Roux, S.G., 2018. X-Ray Microcomputed Tomography in Additive Manufacturing: A Review of the Current Technology and Applications. 3D Printing and Additive Manufacturing, 5(3), pp.227-247.
