Annual Report of the Central Analytical Facilities › english › faculty › science › CAF... · CAF Neuromechanics Unit; the use of ultra-performance convergence chromatography

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2016 / 2017

STELLENBOSCH UNIVERSITY

C e n t r a lA n a l y t i c a lF a c i l i t i e s

Annual Reportof the

Central AnalyticalFacilities

contents

Overview ................................................................................................................................................................1

Building the CAF client database ......................................................................................................................3

Neuromechanics: new unit for interdisciplinary research ...........................................................................6

Steroid analysis at the Mass Spectrometry unit reaches new heights ................................................... 11

From Stellenbosch to Stanford University and back: new manager Electron Microscopy unit ........ 14

Financial Reports .............................................................................................................................................. 17



www.sun.ac.za/caf

in the scientific community by providing

exceptional analytical services.

The aim of the Central Analytical Facilities

is to

1

overview

The stories chosen for this report relate to the need to create and maintain an

up-to-date and comprehensive set of data on CAF clients; the development of the CAF Neuromechanics Unit; the use of ultra-performance convergence chromatography for steroid analysis in the Mass Spectrometry Unit; and, a profile on Dr Lydia-Marie Joubert, the new manager of the CAF Electron Microscopy Unit. Collectively, these stories provide insight into several important fundamentals of CAF policy and functioning.

Firstly, the equipment managed within CAF has to have a broad footprint of service to research and we have to collect accurate data to demonstrate this.

This is critical to justifying the very large investment in CAF equipment by Stellenbosch University and the Department of Science and Technology, via the National Research Foundation’s National Equipment Program (NEP). The data now becoming available via the client information database shows that CAF is an important national research support

resource, with 28% of academic clients being from other South African universities. Industry clients make up a relatively small proportion of CAF clients (15%), but of these industry clients 15% are companies based in other countries, indicating a developing international private sector market for CAF services. This may in future become important to the sustainability of CAF.

Secondly, there has to be a strong focus within CAF of trying to get the absolute best out of equipment in terms of analytical performance and the development of novel analytical methods.

Natural partnerships then develop between large analytical equipment, novel method development, high-level training of postgraduate students, multi-disciplinary research, research productivity, and human capacity development. Thus, CAF is a key link in the chain of research and human capital production at Stellenbosch University, and it is very important that the CAF units are suitably strongly orientated

As had become traditional, this report covers the financial performance of the Central Analytical Facilities (CAF) for the period 1 January 2016 to 30 June 2017; a projection for the 2nd half of 2017 is included.

The report also presents selected short articles about important developments within CAF during 2016 and 2017.

2 Central Analytical Facilities • Annual Report 2016/2017

towards service delivery to enable this role to be played optimally.

Thirdly, CAF has to be proactive in developing facilities outside of its traditional realm of spectroscopy and microscopy.

This is important to broadening the range of researchers and postgraduate students who can draw benefit from access to well managed large analytical infrastructure and it is also important to the university developing more multi-disciplinary research. The article on the development of the Neuromechanics Unit illustrates well the potential of new equipment and the development of new laboratories to stimulate research between disciplines. In the second half of 2017 a new CAF unit for Vibrational Spectroscopy will be created in the Food Science environment, which will both stimulate research between disciplines as well as address a basic need at Stellenbosch University for this type of analytical service.

A further very interesting development which is likely to take place early in 2018 is that CAF will develop and manage a node of the Nuclear Medicine Research Initiative (NuMeRI) structure.

NuMeRI is a product of the South African Research Infrastructure Roadmap (SARIR) initiative of the Department of Science and Technology (DST) and CAF will manage the Node for Infection Imaging (NII) which will be housed within the PET/CT Center at Tygerberg Hospital. The NII is intended to support and advance Molecular Medicine research within the Nuclear Medicine community of South Africa and will be based around a new PET/CT scanner and an expansion to the existing radiopharmacy at the PET/CT centre.

The key partners in this, in addition to NuMeRI and DST, are Tygerberg Hospital and the

Division of Nuclear Medicine in the Faculty of Health Sciences.

Thus, it is clear that there will be many exciting and important developments within CAF in the next 12 months. The financial data presented in this report shows that CAF is meeting its mandate to operate sustainably, whilst also managing to expand the range of analytical services and keep the price of services to researchers firmly in check.

However, one large looming challenge may be the need to recapatalise our equipment base in the absence of the NEP programme. This is certainly the case for 2017, with the possibility that there will also not be a NEP round in 2018.

With the financial pressures on state funding of tertiary education, as well as on university budgets that have come with the student fees crisis it may be that we need to consider that CAF will have to function within a fundamentally different financial framework in future.

I am completely confident that CAF is capable of rising to the challenge to do this, whilst sustainably serving research at Stellenbosch University.

PROF GARY STEVENSDIRECTOR

Please note:

The following additional information is on the CAF website: www.sun.ac.za/caf

• CAF Training Initiative • List of accredited journal articles that

presented data generated in CAF labs

3

The NRF now requires the university to report a comprehensive profile for each

person who uses NEP funded equipment for a period of five years after the commissioning of the equipment.

CAF created an effective system for collecting this information that does not place a significant time demand on clients. Clients are requested to provide basic infor mation required by the

NRF as well as contact details required by CAF via an online form and only have to register once to have access to all CAF facilities.

A unique CAF ID-number is generated which is required whenever clients make a booking or use any of the facilities. The graphs below indicate the sort of information which can readily be derived from the resultant database (data as on 5 July 2017).

Academics (1136)

Industry (199)

The number of CAF clients from different sectors:

As of 1 April 2017, all CAF clients need a client ID number in order to use CAF services. The reason for this is that the NRF now requires comprehensive information to be reported annually on those who use equipment funded by the National Equipment Programme (NEP). In addition, more comprehensive information on who has used CAF equipment and for what purpose, is important strategic information in planning equipment upgrades and new equipment aquisitions.

Building the CAF client databaseby Prof Gary Stevens & Elbie Els


Non RSA universities (0,7%)

Other RSA universities (28%)

RSA research institutions (4,3%)

Stellenbosch University (65.5%)

Other (1,5%)

RSA clients (85%)

International clients (15%)

The clients from industry:

The academic clients:

5

Other (4%)Research assistant (3,2%)

Researcher (28,1%)

Students (50,2%)

Unspecified (14,5%)

The types of CAF users:

The students according to the degree they are registered for:

Honours (8%)

Masters (39,5%)

Other (1,3%)

PhD (43,9%)

Post doctoral (3%)

Undergraduate (4,9%)

The students according to the faculty they are registered at:

Agrisciences (22,4%)

Engineering (12,4%)

Medicine & Health Sciences (14,7%)

Science (49,2%)

Other (1,3%)


One of the research fields emerging to meet this challenge is neuromechanics,

which is the multidisciplinary study of how the nervous and musculoskeletal systems interact to control movement.

Neuromechanics research typically requires multiple analytical techniques to be performed simultaneously and non-invasively, which is technically challenging.

This includes analysis of skeletal motion, the internal and external forces producing the motion and the electrical activity in the nervous system related to motor control. In recent years there have been significant advancements in the accuracy, connectivity and portability of

analytical instruments used in neuromechanics. These improvements have created new and exciting possibilities for studying movement; both in terms of more integrated and advanced fundamental science experiments as well as simpler and more ecologically valid field experiments.

As a result, a new unit for Neuromechanics was recently established within the Central Analytical Facilities (CAF) to accelerate multidisciplinary research in healthcare, engineering and sport.

Physical movement is fundamental to our full participation in society, and is so ubiquitous that we seldom take note of it. Nevertheless, it is a surprisingly intricate phenomenon with a complex relationship to health and performance that is not yet clearly understood.

(a) Indoor testing (b) Outdoor testingFigure 1: Place-kicking experiments carried out using the unit’s infrared camera system were initially conducted (a) indoors (with a net and a target on the wall) at the unit’s Tygerberg laboratory and more recently, (b) outdoors using the unit’s new equipment. Spherical body markers were attached to the body (left) and tracked with millimetre precision in 3D (right).

Multidisciplinary research at new Neuromechanics unitby Dr John Cockcroft

7

Knowledge of how human movement is controlled and organized in different contexts, as well as changes therein as a function of development, learning, impairment and rehabilitation, plays a critical role in efforts to improve quality of life. It supports the development of better health care for persons with impaired movement due to aging, injury, disability or disease. This encompasses a wide range of disciplines including biomedical engineering, orthopaedics, physiotherapy, exercise science and sports medicine.

Neuromechanics can also facilitate advance-ments in the optimization of physical perfor -mance. This allows, for example, the develop-ment of ergonomic interventions and products that optimize productivity and health and safety within various work environments.

Similarly, it can be useful to fitness trainers aiming to improve strength and conditioning programs, or coaches and athletes seeking to improve technique and reduce injury risk.

One study being conducted at the unit is using advanced 3D motion capture technology to develop evidence-based methods for coaching rugby goal-kicking.

In 2014 the top 15 goal-kickers in South Africa were tested at the unit’s indoor facility, and field-testing recently began this year (Figure 1).Due to a scarcity of published information on the relationship between elite goal-kicking technique and performance, the first phase of the project – carried out by the Mechanical Engineering department before the establishment of the Neuromechanics unit - was exploratory.

The objectives were to investigate how variable movement technique was amongst professional goal-kickers and how consistently individuals performed the movement. The first aspect of technique which was analysed was the approach to the ball, specifically the positioning and angulation of different body segments (feet, pelvis and trunk) relative to the tee and the target at different key moments (Figure 2).

Figure 3 demonstrates how a 3D motion capture system can provide information that is either difficult or impossible to extract from two-dimensional video.

(a) Time events and phases (b) Outcomes of interest for the analysis of the run-up

Figure 2: A top view of the approach to the ball (final two steps) illustrating the (a) breakdown of the kick into functional time periods and (b) measurements of foot positioning and body alignment to tee and target at key points in the movement.


Position and angulation were measured at a high temporal and spatial resolution (sub-millimetre accuracy at 400Hz) from an infinite number of view angles, providing measurements precise enough to reliably detected small differences in movement. Another advantage of using 3D motion capture is that it can be used to assess speed and acceleration variables that are not quantifiable

with the naked eye or video analysis. This facilitates crucial insight into how the body generates and transfers momentum down the kinetic chain to produce the foot speed required to kick the rugby ball a sufficient distance. For example, the rugby project involved an assessment of the approach speed profile was performed to investigate the relationship between the deceleration of the centre of mass and the speed of the kicking foot at ball contact.

(a) Foot positioning (b) Body alignment

Figure 3: A top view of the measured (a) foot positioning during the final two steps of the run-up and (b) the average angulation of the approach and the alignment of the feet during support foot contact and kicking foot ball contact.

Figure 4: Individual and group approach speeds over time at key points in the kick. The support leg foot off event (S1) was chosen as the zero point in time, such that participants with a walking ghost step i.e. an initial kicking leg foot contact (K1) before S1, are reflected as beginning at a negative point in time. The subsequent distributions of individual speeds at K2, S2 and K3 are relative to S1 and thus express the cumulative variability of the preceding phases.

KFO

SFC (support foot contact))

Flight phaseStrike phase Ball contact

9

KFO

SFC (support foot contact))

Flight phaseStrike phase Ball contact

The major advantage of using motion capture technology lies in the ability to track changes in skeletal posture in 3D. In the rugby project, the researchers investigated patterns in the angular positions of skeletal joints and segments related the role of the upper body and arm in preserving balance and increasing power production in the kicking leg. An analysis of the angular velocity of the joints and segments also revealed a clear kinematic sequence in which the contribution of individual body segments was observed (Figure 5). Negative values in the kinematic sequence represent the ‘backswing’ component of the movement (in coaching terms this is known as ‘coiling the leg’), and positive values represent the downswing (power generation phase) of a specific joint or segment. It can be observed that the pelvis and hip initiate the downswing while the player is still airborne, while the knee begins contributing positively to foot speed just before mid-way through the strike phase.

The first phase of the project produced some interesting insights. Individual professional kickers were most consistent in terms of approach angle to the ball and body angulation to the target (1-2 degrees of variability) and phase timing (5-15ms), and least consistent in terms of the phase acceleration and deceleration of the body (8 – 18%). Foot positioning was also consistent across repeated kicks (variability of 1-2cm), as was approach speed (2%). As expected, intra-individual variability increased

towards ball contact while inter-subject variability decreased. Most notably, foot speed at ball contact (an important performance variable) was most similar across the group even though kicking technique differed more than expected across the group (10 – 30% depending on the metric). This suggested that expert technique is highly specific to the individual kicker, which presented a challenge to the development of standardized coaching. Furthermore, before the Neuromechanics unit was established, the project faced two barriers. Firstly, it was unclear what the ecological validity of the findings were because the experiments had been carried out indoors. Secondly, there was a lack of sports science expertise needed to fully translate the analytical results into coaching practise.

The establishment of the Neuromechanics unit has played an important role in advancing the rugby goal-kicking project into its second phase. The unit’s new outdoor-enabled camera system is now enabling comparisons to be made between expert kickers using data collected on the field instead of in the laboratory.

Figure 5: Illustrations of the type of instantaneous angular postural data that was measured using 3D motion capture for the rugby project: transverse plane rotation of the lumbar spine (left) and proximal-to-distal sequencing patterns (a build up of momentum through coordinated movements).


The unit staff have also introduced the principle investigator from Mechanical Engineering to colleagues from the Sports Science department who were interested in collaborating on the project. This multidisciplinary collaboration has expanded the project scope and team, which now includes two Masters students (Sports Science and Engineering) and a doctoral student (Sports Science).

The postgraduate engineering student is developing data mining algorithms for extracting complex features from the movement data that are not accessible with normal data reduction methods. These results will then inform the design of an evidence-based coaching program by the Sports Science department, who will determine key performance indicators from an analysis of differences between expert and amateur kickers.

The unit manager is also training and co-supervising the postgraduate students so that they can gain additional skills and make full use of the motion capture technology.

The unit is unique in South Africa in terms of its facilities, equipment and staff. It operates from an established laboratory on the Tygerberg campus and a large, new, purpose-built laboratory recently launched at the Coetzenberg Sports Complex, which together house a world-class array of neuromechanics equipment managed by a team of three full-time biomedical engineers.

The unit’s laboratory-based analytical system is the unit’s premier platform for fundamental research, funded in 2015 by the NRF’s National Equipment Program. It includes a dual-belt, incline-adjustable treadmill for measuring 3D forces on each foot, a wireless high-density (128 channel) EEG system, a new optical motion capture system, 16 wireless EMG probes for measuring muscle activity, a wireless cardiopulmonary exercise testing system. This instrumentation gives the unit cutting-edge capabilities for mapping and correlating brain and body function during activities involving walking, running, jumping or balancing.

The unit also houses a high-end portable analysis platform that consists of wearable sensor technologies (with similar analytical capabilities) that can be easily transported in a single suitcase and rapidly deployed in remote or uncontrolled environments. Projects current ly planning to make use of the new unit facility cover a wide range of topics including humanoid robotics design, athlete concussion, prosthetic limb testing, accelerated aging in the HIV population and balance deficits in children with Foetal-Alcohol Syndrome. The unit is also aiming to leverage its equipment for third-stream income. Currently, this includes routine analytical services to the conditioning staff in Maties High Performance Program, and clinical gait analysis services (pre- and post-surgery assessment) to the Red Cross hospital for children with cerebral palsy.

Athlete Anthony Clark in the new Neuromechanics unit at Coetzenburg.

11

The new ultra-performance convergence chromatography (UPC2) system, funded by the National Equipment Programme (NEP), has changed the game in steroid research at Stellenbosch University. The NEP application was headed by Prof Pieter Swart and Dr Karl Storbeck, both from the Department of Biochemistry.

Jonathan Quanson, a PhD student of Dr Storbeck, has made a huge contribution

towards the success of this new equipment. Quanson’s research investigates the role of adrenal steroid hormones in the development of castration resistant prostate cancer (CRPC).

Prostate cancer is dependent on male sex hormones known as androgens. As such the primary treatment for advanced cases of prostate cancer is androgen deprivation therapy which prevents the production of testosterone, the primary androgen in men, and is produced by the testes. While removal of the testes initially demonstrates excellent results, in most cases the cancer later returns and is then termed CRPC. Research has revealed that CRPC remains androgen dependent and has the ability to convert androgen precursors of adrenal origin to active androgens which drive its progression.

Quanson has therefore developed and published a high-throughput method to separate and quantify nineteen structurally related androgen precursors and androgens which have been implicated in CRPC. The sensitivity and selectivity achieved by this method makes it

ideally suited for multiple in vitro and in vivo applications, such as investigations into CRPC and other hormone dependent cancers. The quantification range is ideal for the use in cell culture, xenograft, tissue, serum and plasma analysis (Quanson et al, 2016). According to Quanson this method unlocks possibilities for new applications which can benefit from the enhanced separation and detection offered by UPC2-MS/MS.

Dr Marietjie Stander, manager of the Mass Spectrometry (MS) Unit, said that (to their knowledge) this was the first publication on the use of UPC2-MS/MS for the analysis of steroid hormones.

Jonathan Quanson at the ultra-performance convergence chromatography system.

Steroid analysis at the MS Unit reaches new heightsby Dr Marietjie Stander & Elbie Els


The UPC2 instrument uses carbon dioxide (CO2) as the primary carrier solvent to separate the different steroids on a silica based column under supercritical fluid conditions. A supercritical fluid is any substance at a temperature and pressure above its critical point, where distinct liquid and gas phases do not exist. A supercritical fluid takes on properties of both a gas and a liquid - high diffusivity and low viscosity. Unlike conventional supercritical systems, the UPC2 instrument can combine supercritical CO2 with organic solvent, thereby significantly increasing the ability to separate compounds with similar structures from each other. This system is connected to a very sensitive mass spectrometer that can distinguish between molecules based on their molecular mass and chemical structure, and can quantify compounds, including steroids, at levels of less than one picogram injected onto the system. The instrument is orders of magnitude more sensitive than its predecessor thereby enabling researchers to measure physiologically relevant concentrations of steroids in a variety of samples.

“We have performed comparisons of the UPC2 against a UPLC system on the same mass analyser and found a 2-10 times increase in signal on the UPC2 for analytes we are working with” Quanson said. “This method has clearly demonstrated that the selectivity and reduced run times achieved by UPC2 are ideal for both clinical and research settings as they allow for the simultaneous quantification of numerous steroid metabolites, while at the same time achieving high throughput.” The chromatographic efficiency is also greatly increased as they are able to separate more compounds over a shorter run. According to him this is also a green system because it generates a lot less waste, as supercritical CO2 is much less damaging to the environ-ment than organic solvents. It is also cheaper.

Ultimately “the cherry on the cake is that the separation on this system is so effective that we are able to separate some compounds with only a chiral difference from one another” Quanson said.

Since the instrument’s installation in 2015, 26 547 injections (until 15 June 2017) have been performed and the research groups at Biochemistry have published numerous papers in reputable journals like the Journal of Steroid Biochemistry & Molecular Biology, Plos One, The Journal of Clinical Endocrinology & Metabolism and the Journal of Chromatography B. Many new collaborations have also been initiated. Waters (the manufacturer of the instrument) reported that Stellenbosch University’s Biochemistry Department published more papers than any of their other clients using this state-of-the-art technology in the field of steroid research world-wide in 2016.

Dr Storbeck was recently awarded an Advanced Newton Fellowship from the Academy of Medical Sciences in the UK based on the success achieved using the UPC2 instrument for steroid analysis. This project, conducted in collaboration with the group of Prof Wiebke Arlt at the Institute of Metabolism and

The separation of the same six compounds on [1] UPLC versus [2] UPC2 . This displays the fantastic separation that is possible with the UPC2 in the same run time. (Quanson et al, 2016).

[1] UPLC

[2] UPC2

13

Systems Research, University of Birmingham, is investigating the potential of UPC2-MS/MS as an alternative to Gas Chromatography Mass Spectrometry (GC-MS) for the diagnosis of a variety of clinical conditions. While GC-MS is currently considered the gold standard in steroid analysis, it is very laborious and time consuming due to intensive sample preparation which is required. UPC2-MS/MS offers a high throughput alternative which could significantly improve the throughput of clinical laboratories.

All of the work performed on the instrument is carried out using methods developed by the staff and students themselves, making the new instrument an excellent training facility.

The number of users of the ultra-performance convergence chromatography (UPC2) system - from 2015 until the end of February 2017.

Postgraduate students

Academic staff

SU: Stellenbosch UniversityUCT: University of Cape Town

References:Jonathan L. Quanson, Marietjie A. Stander, Elzette Pretorius, Carl Jenkinson, Angela E. Taylor, Karl-Heinz Storbeck, 2016. High-throughput analysis of 19 endogenous androgenic steroids byultra-performance convergence chromatography tandem massspectrometry. Journal of Chromatography B, 1031

“It gives many students the opportunity to not only work on state-of-the-art equipment to generate the best possible results, but also allows them to operate these instruments themselves, thereby acquiring a new skillset that will give them a huge advantage in the future when they enter the job market” Stander said.

UCT

IND

SU

SU

UCT

IND: Industry

Industry clients


After more than 10 years as Electron Microscopist and Senior Research Professional at the Cell Sciences Imaging Facility (CSIF) at Stanford University (USA), dr Lydia-Marie Joubert comes back to South Africa to manage CAF’s Electron Microscopy unit.

I am very much a South African at heart, and Stellenbosch University (SU) provides me the opportunity to lead a team in Electron

Microscopy (EM) at a core facility that is already very functional and bring South Africa prominently into the international microscopy, correlative imaging and 3D microscopy fields” Joubert said.

“The niche I want to fill here is to develop the biological background that is lacking here currently.” She strongly feels that people leaving South Africa should always look for an opportunity to give something back.

“South Africans have made a great international contribution and I think our obligation is to, not necessarily come back physically, but to plough back intellectually and to create opportunities for collaboration.”

In her role as EM specialist and manager at Stanford University, she was responsible for Scanning Electron Microscopy (SEM) related research projects, EM technique development, teaching and consultation, and management of an ongoing kidney stereology project involving TEM and light microscopy analysis. Her major interests are 3D SEM technique development and computation, as well as Correlative Light and EM techniques (CLEM) and she has focused a lot on 3D electron microscopy and application of novel techniques into new niche areas at Stanford.

“What I achieved at Stanford was connected to the people I worked with, and the developments there that are specifically in three dimensional analysis in biological electron microscopy, and to correlate high resolution fluorescence microscopy with the ultrastructural context provided by electron microscopy. One new big advantage in electron microscopy is that it is no longer a challenge imaging and capturing beautiful and informative pictures, since cutting-edge equipment has evolved rapidly over the last decade. Automation (of instruments) is

“

Dr Lydia-Marie Joubert

From Stellenbosch to Stanford University and backby Elbie Els

15

still a challenge and then also computation.” According to her, Stanford is probably the most interdisciplinary university in the world and they always had integration of the biological field with the engineering side. “Material development, biomaterials and the imaging of biomaterials under conditions that are needed for biomedical application (VP-SEM application) are some of the major things I learned and got involved in at Stanford.”

Another breakthrough development by Joubert, some colleagues and postdoctoral students at Stanford University is Array Tomography. She explains that Array Tomography is based on serial sections of cells and tissues that are gathered on conductive glass panels that can be used for light microscopy and the sections can then be reconstructed in a three dimensional volume. The same sections can then be used for scanning electron microscopy, to obtain internal ultrastructure and stacks of images that can be correlated with the 3D volume from light microscopy. Comparisons between fluorescence microscopy and electron micros-copy result in a much better resolution than using only light microscopy, and gives us a better understanding of structure as well as function.

“I also hope to bring Array Tomography to Stellenbosch, because it is a novel and powerful technique, and people here haven’t tried it yet probably because they are not that familiar with the applications” she said. To prepare biological tissue for these applications they often delve into the publications of the 60s, 70s and 80s that were the initial high days of electron microscopy.

Her biggest challenge and vision for the SU Electron Microscopy unit is to expand onto the Tygerberg Campus. “Because of the clinical field I was in at Stanford at both the medical school and bioengineering, I would like to expand the EM unit to have a point of service in the medical research environment.”

One of the things that she also wants to develop further at Stellenbosch is the CLEM (correlative light and EM) imaging platform that was launched in 2016. According to Joubert this is a strikingly new field to be in and there also is a learning curve for clients because it is at the front end of microscopy and a lot of troubleshooting is still needed. After talking to some of the staff at SU, Joubert said that the research questions and the equipment are here already and that it is a case of bringing them together.

“How can you answer the research questions with the equipment we have? I am very impressed with the current staff and the equipment here at Stellenbosch – there are a lot of cutting edge tools, and smart and dedicated staff here.”

Joubert also feels that it is important to publish your work and attend conferences and network with other researchers. She plans to bring international collaborators and speakers to Stellenbosch. “Some of my colleagues from Stanford University and the greater Bay Area are specifically delighted about this opportunity, because from a medical side they have been looking for someone to connect to in SA to have a hub here and transfer technology and expertise.” Joubert said that people in the

Joubert at the ‘March for Science’ in San Francisco


USA are usually very impressed by the level of science they find in SA. According to her it is also no longer expected that one person should do everything in a research project and therefore collaborators are very important. “One can move frontiers much more efficiently if a group of researchers work together, each applying their expertise in a niche area.” Project management then becomes crucial for success.

She also has a creative side and was the winner in the illustration category at the International Science and Engineering Visualization Challenge (SciVis) in 2013 with her image “The Hand.” She took multiple micrographs of colonies of live and dead bacteria, enlarged them 400 times, and superimposed them on a sculpture of a human hand. “I just played around with interesting images and then also had more time off to try different things.” She is also focused on photography and explains that when she was a student in the 80s (and up to about 2000) they captured their images (‘electron micrographs’) on negatives. A photography course was compulsory before starting their electron microscopy course because they had to know how to develop their own negatives and make photographic prints. “Film was better resolution than you could capture with CCD cameras until very recently. You could visualize ultrastructure with the instruments in high resolution, but you couldn’t capture digital images in high resolution.” She also received an American Microscopy Society Award in 2009 for her breakthrough development of new methods to investigate hydrogels – an honor that a scientist is allowed to win only once.

Her passion for the electron microscopy field comes from her graduate studies in the 1980s at SU with prof Jan Coetzee.

“I was always a very visual person and I loved physics. I think applying the physics of electron microscopy in the biological field just put it all together.”

She also mentioned that the very inspiring people at the Botany Department at SU during her graduate studies, helped her choose between botany and her other major, mathematics, for her post-graduate studies. “The computational side of biological EM today indeed provides a full circle back to all my intellectual interests.”

She is glad that she was part of electron microscopy in South Africa in the 70s and 80s. “In contrast to a few years ago, it nowadays is good to refer to sources from the 70’s in publications or talks, because that is when electron microscopy really started.” Joubert matriculated as dux scholar at Outeniqua High School in George, obtained 4 degrees at Stellenbosch University and then obtained her PhD at the University of Pretoria, spent some time doing research at the Indiana University (USA) and started off her career as lecturer in Microscopy Techniques and Plant Sciences at Stellenbosch University. She also studied at Weizmann Institute in Israel during her post-graduate years, before getting married and raising 3 boys. After a few positions as researcher, doing world-class research in botany, microbiology and microscopy, Joubert headed to Stanford University in 2006.

With her passion and extraordinary knowledge and experience the CAF Electron Microscopy unit can surely look forward to a very exciting phase of growth and development.

Joubert’s award winning illustration ‘The Hand’.

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MS UNIT Internal invoicing 2 113 784 1 969 796 876 060 1 664 513

External invoicing 4 274 813 4 754 380 2 872 546 5 457 837

Total logbook income 6 388 598 6 724 176 3 748 606 7 122 351

Expenses

Salaries 2 955 982 2 787 168 1 479 985 2 959 969

Running costs 955 287 1 042 577 478 741 957 482

Maintenance 607 627 632 923 512 879 1 025 757

Travel Costs 2 380 948 15 309 30 618

Small Equipment & KKW 12 736 91 539 0 0

Total Expenses 4 534 012 4 555 155 2 486 913 4 973 826

FM UNIT Internal invoicing 663 703 848 044 417 394 834 789

External invoicing 31 493 39 136 112 658 134 208

Total logbook income 695 195 887 180 530 052 968 997

Expenses

Salaries 807 244 1 056 051 525 493 1 050 987

Running costs 168 609 218 819 144 742 289 485

Maintenance 41 815 38 610 0 0

Travel Costs 31 817 9 468 7 025 14 050

Small Equipment & KKW 31 430 4 686 0 0

Total Expenses 1 080 915 1 327 634 677 261 1 354 522

SEM UNIT Internal invoicing 422 687 656 850 307 330 614 660

External invoicing 419 190 913 020 619 243 1 238 486

Total logbook income 841 878 1 569 870 926 573 1 853 146

Expenses

Salaries 716 526 1 049 188 598 464 1 418 607

Running costs 35 925 143 704 67 124 134 248

Maintenance 169 080 98 971 61 145 122 290

Travel Costs 32 493 14 476 26 795 53 590

Small Equipment & KKW 34 310 131 804 43 740 87 480

Total Expenses 988 335 1 438 144 797 268 1 816 215

ICP & XRF UNIT Internal invoicing 800 336 761 409 477 911 1 013 172

External invoicing 1 390 363 1 828 224 796 289 1 688 133


Expenses

Salaries 2 125 561 1 533 321 863 551 2 007 404

Running costs 580 638 591 558 348 742 697 484

Maintenance 140 647 232 660 139 953 279 906

Travel Costs 29 990 95 634 7 788 15 576


Total Expenses 2 892 718 2 457 816 1 410 372 3 050 708

January 2015- 31 December

2015


2016

Actual:January 2017- 30 June 2017

Projection: January 2017-

Dec 2017

Financial Reportsby Fransien Kamper



2015


2016



Dec 2017

DNA UNIT Internal invoicing 3 058 897 3 198 595 1 458 850 2 917 701

External invoicing 4 964 903 4 902 329 2 199 288 4 398 576


Expenses

Salaries 2 261 695 2 301 652 1 170 627 2 341 253

Running costs 4 211 622 4 382 754 1 772 175 3 544 350

Maintenance 371 367 199 323 159 736 319 472

Travel Costs 20 427 916 2 493 4 986


Total Expenses 6 885 699 7 071 156 3 125 551 6 251 101

NMR UNIT Internal invoicing 669 227 847 097 265 361 530 723

External invoicing 478 053 500 894 583 719 1 167 438

Total logbook income 1 147 279 1 347 991 849 080 1 698 160

Expenses

Salaries 932 580 1 099 918 581 779 1 163 558

Running costs 295 759 296 141 166 884 333 768

Maintenance 40 184 63 570 1 531 3 062

Travel Costs 1 271 0 0 0

Small Equipment & KKW 0 0 0 0

Total Expenses 1 269 794 1 459 629 750 194 1 500 388

CT UNIT Internal invoicing 293 869 445 672 390 063 780 125

External invoicing 1 200 353 1 595 162 729 680 1 459 360


Expenses

Salaries 921 886 1 083 401 574 228 1 148 456

Running costs 226 192 176 930 226 613 453 226

Maintenance 169 200 550 312 224 861 449 722

Travel Costs 84 462 55 697 29 934 59 868


Total Expenses 1 432 867 1 887 746 1 065 590 2 131 179

NEUROMECHANICS UNIT Internal invoicing 213 844 463 998 171 900 343 800

External invoicing 58 250 534 742 355 426 710 851

Total logbook income 272 094 998 740 527 326 1 054 651

Expenses

Salaries 505 769 748 201 622 428 1 244 856

Running costs 1 312 139 797 29 366 58 732

Maintenance 0 25 779 0 0

Travel Costs 0 0 14 338 28 676

Small Equipment & KKW 0 143 845 23 055 46 110

Total Expenses 507 081 1 057 622 689 187 1 378 374

19


2015


2016



Dec 2017

TOTAL UNITS INCOME Total internal income 8 236 346 9 191 460 4 364 869 8 699 483

Total external income 12 817 419 15 067 887 8 268 849 16 254 890

Total Income: All Units 21 053 765 24 259 347 12 633 718 24 954 373

ADDITIONAL INCOME

Interest Received 935 186 658 894 475 319 525 319

Funds Received VR(R) 1 000 000 1 000 000 375 000 750 000

Salary Contribution VR(R) 3 171 000 3 392 970 1 798 274 3 596 548

VAT Refund on Equipment 1 234 455 772 588 559 595 988 595

TOTAL ADDITIONAL INCOME

6 340 641 5 824 452 3 208 188 5 860 462

TOTAL INCOME 27 394 406 30 083 799 15 841 906 30 814 835

EXPENDITURE TOTAL EXPENDITURE

Expenses

Salaries: Admin 1 310 533 1 558 230 892 402 1 784 803

Salaries: sum of units 11 227 243 11 658 900 6 416 555 13 335 091

Salaries: Bonus 216 378 299 718 366 750 366 750

17% Levy (IKVK) 2 178 961 2 561 541 1 405 704 2 763 331

Running costs (sum of units) 6 475 344 6 992 280 3 234 387 6 468 775

Maintanance (sum of units) 1 539 920 1 842 148 1 100 105 2 200 209

Travel Costs (sum of units) 202 840 177 139 103 682 207 364

Small Equipment & KKW (sum of units) 146 073 584 434 147 607 244 876

CAF General Running Costs 431 663 473 143 294 273 584 645

Travel Costs-Courier 55 684 72 556 31 455 62 910

Infrastructure 644 500 1 262 331 74 692 98 496

Equipment 1 162 848 931 176 435 279 717 939

Equipment Repair fund 867 200 500 000 250 000 500 000

CAF Vehicle Fund 0 20 000 15 000 30 000

Loan VR(R) 540 000 540 000 0 0

Totalnormal operational costs 26 999 188 29 473 596 14 767 890 29 365 189

Surplus per year 395 217 610 203 1 074 016 1 449 646

CAF Overdraft (Originally R5mil Facility) 4 000 000 3 500 000 0 0

EQUIPMENT EXPENDITURE 27 106 909 25 258 792 15 381 046 0

NRF-NEP Total grants 20 004 000 17 300 000 10 254 030

ALT/US Funds 5 000 000 6 217 076 5 127 016

Departments/ Faculties/ VR(R) Contributions 1 002 211 647 806

CAF Contribution 1 100 698 1 093 910



2015


2016



Dec 2017

NEP EQUIPMENT DETAILS 27 106 909 25 258 792 7 380 393 7 975 320

Pegasus GCxGC-HRT-MS 8 956 372

ELYRA P1 with 3D PALM and ELY CO2/T management component

4 115 544

Carl Zeiss Merlin Field Emission Scanning Electron Microscope with STEM for Correlative Microscopy

10 102 222

Agilent 7900 ICP-MS 3 932 772

Integrated real-time neurophysiological and biomechanical analysis system

9 520 169

Capillary Sequencer 4 074 549

Waters Ultra Performance Convergence Chromatograph (UPC2) connected to a Waters Xevo TQ-S MS

11 664 074

BD FACSMelody Cell sorter 7 380 393

LabScanner, Prediktera Software and Via-Spec transmission access

7 975 320

FUNDS

Emergency Equipment Repair Fund

474 480 1 036 543 1 185 315 1 435 315

Vehicle Replacement 59 686 75 860 92 000

Reserve, Food Security Project

1 035 185 1 109 835 1 142 680 1 175 000

Maintenance Fund Equipment: BD FACS Jazz sorter (2013)

1 089 483 1 168 049 1 202 616 1 235 000

21

Internal Clients Faculty Use: 2016 Income

Total 2016 income: Internal and External

Total % Internal income (38%)

Total % External income: Industry (35%)

Science (47,49%)

Agri Sciences (29,78%)

Medicine and Health Science (17,29%)

Engineering (5,07%)

Arts and Social Siences (0,20%)

Not Indicated (0,16%)

Total % External income: Other SA Universities (27%)


2016 Income from other South African Universities (excluding Stellenbosch University):

University of Cape Town (22,79%)

University of Johannesburg (12,89%)

Nelson Mandela Metropolitan University (9,79%)University of Pretoria

(9,42%)

University of Kwazulu-Natal (8,92%)

University of the Western Cape (7,28%)

Rhodes University (4,99%)

University of the Free State (4,57%)

University of the Witwatersrand (4,50%)

University of Venda (2,12%)Other (12,74%)

www.sun.ac.za/caf



Documents

Annual Report of the Central Analytical Facilities › english › faculty › science › CAF... · CAF Neuromechanics Unit; the use of ultra-performance convergence chromatography