CAF
Welcome to Stellenbosch University

Training Initiative: The Workshops

Please note:

  • All workshops are in Stellenbosch, except Mass Spectrometry based Proteomics in Tygerberg.
  • All workshops are presented in the week of 19-23 June 2017 except Mass Spectrometry based Proteomics in September 2017.

Select a workshop: 

  1. Mass Spectrometry of Small Molecules: LC-MS
  2. Mass Spectrometry of Small Molecules:GC-MS
  3. Mass Spectrometry based Proteomics 
  4. Solution State Nuclear Magnetic Resonance Spectroscopy
  5. Flow Cytometry and Cell Sorting
  6. Confocal and Super-resolution Microscopy
  7. Correlative Light and Electron Microscopy
  8. Introduction to X-ray Micro- and Nano-CT
  9. Nucleic Acid Preparation, QC and Library building for Next Generation Sequencing
  10. Vicon neuromachanical analysis (kinematics, kinetics and EMG)
  11. Noraxon mobile neuromechanical analysis (kinematics, kinetics and EMG)
  12. Solution ICP-MS in Environmental analysis of major and trace elements
  13. Practical XRF Spectrometry
  14. Introduction to U/Pb Geochronology and data processing

Mass Spectrometry (MS)

1. Mass Spectrometry of Small Molecules: LC-MS

Presenters: Dr Marietjie Stander, Mr Erick van Schalkwyk and Mr Malcolm Taylor

Duration: 1 Day

2. Mass Spectrometry of Small Molecules: GC-MS

Presenter: Mr Lucky Mokwena

Duration: 3 Days

The GC-MS training on small molecules will be separated as follow:

  1. Day 1: Theoretical background of GC-MS
  2. Day 2: Sample preparation techniques, Instrumentation and application; (2 groups)
  3. Day 3: Data processing and manipulation (2 groups)

Days 2 and 3 will be divided into  2 groups for the morning and afternoons sessions.

3. Mass Spectrometry based Proteomics

Presenter: Dr Maré Vlok

Duration: 3 Days

After this 3-day workshop the student will know the basic principles of mass spectrometry, be able to prepare biological samples for mass spectrometry-based analysis and be able to use global databases for mass spectrometry-based data in order to identify proteins. Finally, the student will be able to recognise the value of mass spectrometry for their own research.

Course will comprise of the following:

  • Theoretical component: basic principles of mass spectrometry and proteomics, overview of various proteomics and mass spectrometry based applications.
  • Tutorials: Design of proteomics and mass spectrometry based experiments.
  • Practicals: Preparation of biological samples for mass spectrometry with the specific aim of proteomics based applications. Therefore, samples will be used from gels and will be cleaned, trypsin digested and finally prepared for identification by mass spectrometry. Data obtained from the practical will then be used for database searches in order to teach the student the basic principles that are important for database searches.
  • Discussions: After each component time is allocated for questions and answers, the course is also ended with an in depth discussion from the students and how they would apply mass spectrometry within their own projects.

Day 1:
Lecture: Introduction to Proteomics, sample extraction and preparation for digest
Practical: Prepare samples for in-gel and in-solution digest
Discussion: Any questions on the day?

Day 2:
Practical: Extraction and clean-up of peptides
Practical: Preparation of MS system
Lecture: Chromatographic separation and enrichment techniques
Lecture: Mass spectrometry
Lecture: Quantitative proteomics
Discussion: Questions?

Day 3:
Practical: Preparing database search
Practical: Investigating data
Lecture: Data analysis and statistics
Discussion: Students feedback on how they can apply Mass spectrometry based proteomics in their projects.

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Nuclear Magnetic Resonance (NMR)

4. Solution State NMR

Presenter: Dr Jaco Brand

Duration: 1 Day

The purpose of the workshop is to connect the theory to applications in modern solution state NMR. The aim is to reintroduce participants to the theory and on the practical aspects of the technique. Examples from different application areas such as chemistry, biochemistry, pharmaceuticals, polymers and petrochemicals will be used to highlight the importance of the technique in structure elucidation, absolute stereochemistry determination as well as chemical composition determination and reaction kinetics. Structure determination is the main strength of the technique and will receive the most attention.

The following topics will be discussed:

Morning Session:
  • NMR theory lecture
  • Hands-on sample preparation techniques and choosing solvents for your samples
  • Running selected 1D and 2D experiments by participants on the instrument
  • Evaluating and processing data, Spinworks or Mestrenova processing
Afternoon Session:
  • What can I do with NMR?
  • From structure determination to reaction kinetics, metabolomics, medical and biological applications
  • Hands-on interactive session on the interpretation of 1D and 2D data of selected organic structures
  • Lecture on the use of Chiral shift reagents to determine absolute stereochemistry

Fluorescence Microscopy

5. Flow Cytometry and Cell Sorting

Presenter: Ms Rozanne Adams

Duration: 1 Day 

This course introduces the participant to flow cytometry and the applications of this technology. Participants will get the chance for hands-on acquisition of samples to familiarise themselves with the work flow on a flow cytometer, the setup and calibration of the instrument and data analysis.

The content that will be covered includes:

  • Basic understanding of the components of a flow cytometer
  • Knowledge of key concepts: light and colour, scatter, laser delay, pulse area and width, spillover
  • Hands-on acquisition
  • Data analysis using FACSDiva

6. Confocal and Super-resolution Microscopy

Presenters:  Ms Lize Engelbrecht and Ms Dumisile Lumkwana

Duration: 1 Day

This course introduces participants to theory and applications of confocal microscopy and the super-resolution microscopy techniques structured illumination (SR-SIM), photoactivation localization (PALM) and stochastic optical reconstruction (STORM) microscopy.

The content that will be covered includes:

Morning session:

  • Theory session on fluorescence and confocal microscopy
  • Hands on acquisition of samples in confocal mode
  • Data processing of acquired images

Afternoon session:

  • Theory session on super-resolution techniques
  • Calibration of the system for super-resolution microscopy
  • Hands-on acquisition of samples in the SR-SIM module
  • Data processing of acquired images

Scanning Electron Microscopy

7. Correlative Light and Electron Microscopy

Presenters: Ms Lize Engelbrecht, Ms Madelaine Frazenburg and MS Elrika Harmzen

Duration: 1 Day

Morning session:
A short presentation will be followed by image acquisition on the confocal microscope in the Fluorescence Microscopy Unit. Various strategies to set up a CLEM experiment will be introduced. A selection of fluorescently labelled samples will be imaged during this session.

Afternoon session:

In the afternoon, the samples imaged in the morning on the confocal microscope will be transferred to the Scanning Electron Microscopy Unit. Using the Shuttle and Find feature on the Merlin FE SEM, the same samples will be imaged and overlaid to produce correlative fluorescence and electron micrographs.

CT Scanner

8. Introduction to X-ray Micro- and Nano-CT

Presenter: Mr Stephan le Roux

Duration: 1 Day

The workshop will cover the basics of X-ray Micro-CT and Nano-CT.

Course content will include:

  • Specific examples
  • How the method works
  • What kind of information can be found
  • Advantages of X-ray 3D imaging

Systems will be demonstrated and prepared data will be used for demonstrating 3D data analysis. This will cover basic 3D visualization, image segmentation, defect analysis, part to part comparison and many more. The course focuses on new users and is ideal for researchers and students new to the field of non-destructive "X-ray microscopy".

DNA Sequencer

9. Nucleic Acid Preparation, QC and Library building for Next Generation Sequencing

Presenters: Ms Alvera Vorster and Mr Carel van Heerden

Duration: 3 Days

The focus of the workshop will be the preparation and quality control (QC) of nucleic acids (DNA and RNA) for next-generation sequencing applications. During the workshop basic DNA and RNA extraction theory will be presented which will be followed by practical sessions. The nucleic acids extracted during the practical sessions will be quantified and QC’ed using the NanoDrop ND-1000 and the Qubit 2.0 fluorometer. Further QC (integrity) will be performed using a real-time based qPCR assay (DNA) and the Agilent 2100 BioAnalyzer (pro- and eukaryotic RNA). This will be followed with theoretical sessions on library preparation for next-generation sequencing (Ion Torrent). A hands-on session for quantifying and assessing the quality of NGS-libraries will follow. The workshop will conclude with some basic analysis and interpretation of NGS-data as generated by the Ion Torrent platforms.

Human Movement Analysis

10. Vicon neuromechanical analysis (kinematics, kinetics and EMG)

Presenters: Dr John Cockcroft, Ms Madelein Dreyer, Ms Cara Mills

Duration: 2 Days

Venue: Coetzenberg laboratory
 

In this workshop participants will be trained to operate a synchronized motion capture system (Vicon), force-plate system (Bertec instrumented treadmill) and wireless EMG system (Noraxon) to perform neuromechanical testing and analysis of human movement. Participants will also be given a structured methodology for creating and implementing data processing pipelines and quality control measures. There will be a strong focus on subject preparation and calibration, as well as on understanding the underlying analytical techniques employed to produce outcomes.

11. Noraxon mobile neuromechanical analysis (kinematics, kinetics and EMG)

Presenters: Dr John Cockcroft, Ms Madelein Dreyer, Ms Cara Mills

Duration: 2 Days

Venue: Coetzenberg laboratory

In this workshop participants will be trained to operate a synchronized portable motion capture system (Noraxon MyoMotion), mobile force-plate system (Bertec) and wireless EMG system (Noraxon) to perform neuromechanical testing and analysis of human movement. Participants will also be given a structured methodology for creating and implementing data processing pipelines and quality control measures. There will be a strong focus on subject preparation and calibration, as well as on understanding the underlying analytical techniques employed to produce outcomes.

ICP-MS & XRF

12. Solution ICP-MS in Environmental analysis of major and trace elements

Presenter: Ms Riana Rossouw

Duration: 1 Day

The 1-day workshop aims to give students and ICP analysts a broader knowledge of ICP analysis principles and instrument parameters to be better equipped for the accurate analysis of a variety of solution sample matrices by ICP-MS.

We will cover the following topics during a short lecture session:

  • Sampling techniques, sample storage & sample processing, as this is the most important part of the analytical procedure.
  • Clean working conditions
  • Principles of ICP-MS analysis
  • Interferences from different sample types
  • Quality control & data processing

In the afternoon we will have a practical session demonstrating how all the above is applied.

13. Practical XRF Spectrometry

Presenter: Ms Mareli Grobbelaar

Duration: 1 Day

The workshop will provide an introduction to WXRF spectrometry as well as the importance of correct sample preparation for users to get optimal results, introduce user to the analytical techniques to obtain qualitative and quantitative elemental results.

  • Morning session:

A short presentation will be given on the theory of how XRF spectrometry works, instrument components, introduction to instrument parameter selection as well as sample preparation. This will be followed by a practical session of sample preparation on different samples types.

  • Afternoon session:

Practical session on the XRF spectrometer will cover the theory topics that were discussed in the morning. Samples prepared in the morning practical will be analysed to show qualitative and quantitative results of the instrument.

14. Introduction to U/Pb Geochronology and data processing

Presenter: Dr Jeanne Taylor

Duration: 1 Day

This one day training workshop will cover the basics of U-Th-Pb theory and background to LA-ICP-MS geochronology, as well as hands-on training in data processing and interpretation using Iolite, VisualAge and Isoplot software.

Topics that will be covered include:

  • U-Th-Pb isotope systematics
  • Interpreting U-Pb Concordia diagrams and ages
  • The analytical challenges of dating by LA-ICP-MS
  • Practical exercise in Iolite and VisualAge data reduction.
  • Practical exercise in using Iosplot to calculate ages.