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 18-22 June 2018
  • The Opening Function is on 19 June 2018 at 17:30 in Stellenbosch

Select a workshop: 

  1. Vicon neuromechanical analysis (kinematics, kinetics and EMG) (2 days)

  2. Noraxon mobile neuromechanical analysis (kinematics, kinetics and EMG) (2 days)

  3. Whole genome sequencing of 600bp libraries; from specimen to analysis (4 days)

  4. Cell Sorting on the BD FACS Melody (1 day)

  5. Super-resolution Microscopy: SR SIM and PALM/STORM (1 day)

  6. Correlative Light and Electron Microscopy (1 day)

  7. Flow Cytometry Data Analysis Workshop (1 day)

  8. Introduction to Hyperspectral imaging and chemometrics (2 days)

  9. Introduction to Biological Electron Microscopy (1 day)

  10. Introduction to Analytical Electron Microscopy (1 day)

  11. Advanced Applications in Biological Electron Microscopy (1 day)

  12. Mass Spectrometry of Small Molecules: LC-MS (1 day)

  13. Mass Spectrometry of Small Molecules: GC-MS (3 days)

  14. Mass Spectrometry Based Proteomics (3 days)

  15. Solution State Nuclear Magnetic Resonance Spectroscopy (1 day)

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

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

  18. Practical XRF Spectrometry (1 day)

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

1.Vicon Neuromechanical Analysis

Presenters: Dr John Cockcroft, Ms Tamsin Purkis, 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.

 

2.Noraxon Mobile Neuromechanical Analysis

Presenters: Dr John Cockcroft, Ms Tamsin Purkis, 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.

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3. Whole genome sequencing of 600bp libraries; from specimen to analysis

Presenters: Ms Alvera Vorster and Mr Carel van Heerden

Duration: 4 Days

This workshop starts with the preparation and quality control (QC) of genomic DNA for whole genome sequencing. Basic DNA extraction theory will be presented, which will be followed by practical sessions. The DNA, extracted during the practical sessions, will be quantified and assessed for quality using fluorometry (Qubit4), spectrophotometry (Nanodrop) and microfluidic capillary electrophoresis (LabChip® GX Touch). This will be followed with theoretical sessions on library preparation for next-generation sequencing (Ion Torrent). The hands-on session for construction, quantification and quality assessment of 600bp libraries is scheduled across the first two days of this workshop.  The workshop will conclude with some basic analysis and interpretation of whole genome sequencing data that was generated by the Ion Torrent S5 platform during the course of this workshop.

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4. Cell Sorting on the BD FACS Melody

Presenter: Ms Rozanne Adams

Duration: 1 Day

Students interested in sorting samples of single cell or particles suspensions for further analysis, can attend our one-day cell sorting workshop on the new BD FACSMelody. The course is 70% hands on training and aimed at users with some prior flow cytometry experience who understand the principles of the method. The course will cover instrument setup for sorting and quality control, as well as training on tube sorting, single cell sorting in plate format and single cell sorting onto microscope slides. The training will also cover optimisation of the sample preparation for sorting and further culture.  

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5. Super-resolution Microscopy: SR SIM and PALM/STORM

Presenter: Ms Lize Engelbrecht

Duration: 1 Day

Super-resolution microscopy enables the researcher to acquire information of the subcellular structures at a much higher resolution than conventional confocal microscopy. At the Fluorescence Microscopy Unit at Stellenbosch, two such super-resolution microscopy platforms are available namely SR SIM and PALM/STORM. This one day course will cover the theoretical background of both platforms, followed by hands-on sessions during which these two techniques will be demonstrated. The course will also include a discussion on sample preparation, imaging conditions and workflow, as well as post-processing principles.

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 6. Correlative Light and Electron Microscopy

Presenters: Ms Lize Engelbrecht and Prof Lydia-Marie Joubert

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.

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 7. Flow Cytometry Data Analysis Workshop

Presenters: Ms Rozanne Adams

Duration: 1 Day

With this one-day course we aim to teach users basic data analysis of their flow cytometric data in FlowJo, a popular third party software package for analysis. We will cover data input, compensation, gating, creating tables  and layouts for visual and data output. This course is aimed at allowing users to become more independent with their data analysis.

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8. Introduction to Hyperspectral imaging and chemometrics

 Presenter: Dr Janine Colling

Duration: 2 Days

Day 1: Introduction to Hyperspectral imaging and Practical session

Morning session:

Overview of what hyperspectral imaging is and typical applications which make use of this instrument.

Afternoon session:

Demonstrate the set up of the Hyperspectral imaging VNIR and SWIR system to acquire images of different samples.

Day 2: Introduction to Multivariate data analysis

An introduction to the Evince software for image analysis and an overview of the methods used for qualitative and quantitative analysis and creating models.

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9. Introduction to Biological Electron Microscopy

Presenter: Prof Lydia-Marie Joubert

Duration: 1 Day

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10. Introduction to Analytical Electron Microscopy

Presenters: Ms Madelaine Frazenburg and Dr Elrika Harmzen-Pretorius

Duration: 1 Day

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11. Advanced Applications in Biological Electron Microscopy

Presenter: Prof Lydia-Marie Joubert

Duration: 1 Day

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12. Mass Spectrometry of Small Molecules: LC-MS

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

Duration: 1 Day

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13. Mass Spectrometry of Small Molecules: GC-MS              

Presenters: Mr Lucky Mokwena, Mr William Arries

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.

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14. 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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15. Solution State Nuclear Magnetic Resonance Spectroscopy        

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

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16. 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".

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

Presenter: Mrs 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.

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18. Practical XRF Spectrometry        

Presenter: Mrs Mareli Moolman

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.

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19. Introduction to U-(Th)-Pb Geochronology by LA ICP-MS      

Presenter: Dr Laura Bracciali

Duration: 1 Day

This one day training workshop will cover the basics of U-(Th)-Pb dating by LA ICP-MS, including a short laboratory session and introduction to data reduction approaches.

The following topics will be covered:

  • U-(Th)-Pb isotope systematics
  • Introduction to laser ablation inductively-coupled plasma mass spectrometry
  • LA U-(Th)-Pb dating of accessory minerals, with an emphasis on zircon and rutile
  • Setting up and running an automated analytical sequence
  • Data reduction approaches
  • Applications to the Earth Sciences