The Central Analytical Facility (CAF) at Stellenbosch University is in a unique position to provide 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. A consolidated training event will be provided within CAF during the week 9 to 13 July 2012. The training will be in the form of workshops and is aimed at providing participants with exposure to equipment to reinforce theoretical principles and develop the necessary practical, hands-on skills. In most cases, data interpretation will also be covered.

The training is aimed at postgraduate students (MSc, PhD), as well as researchers and university and industry technical staff. Places are limited as most workshops can only accommodate up to 7 participants due to limited space in the laboratories for hands-on exposure to equipment. Preference will be given to applicants who can motivate that their participation will directly benefit their own research or the research of others.

An outline of the workshops and their scheduling is provided below. As far as is practically possible, the courses have been scheduled to allow participants who would like to take advantage of two courses the opportunity to do so.

Certificates of participation will be issued at the end of the workshop.

THE APPLICATION PROCESS AND COST OF PARTICIPATION

• The application process will be open from 10 May 2012 up to and including 8 June 2012.
• All researchers, postgraduate students and university and industry technical staff may apply.
• Participants may apply for a maximum of 2 workshops, provided these do not clash in terms of scheduling. In the event of a conflict, the first workshop will be selected.
• Only electronic submissions will be accepted. Please use the online submission form below, or download the application form and e-mail to lianin@sun.ac.za.
• If you are applying via the downloaded form, please send only the downloaded page copied into your message, and make the subject of your e-mail: Training Initiative July 2012 – workshop title, your institution
• Participants will be selected on the basis of their application and specifically their motivation.
• The training is free to staff and students at South African universities.
• Travel, accommodation and meal expenses are for the participant’s or their institution’s own cost.
• Participants from industry will be charged R2500 per workshop.
• The successful candidates will be notified by e-mail no later than 12 June 2012.

SCHEDULING

THE WORKSHOPS:

There will be three Mass Spectrometry training workshops, two for non-proteomic applications and one for proteomic applications. Other units presenting more than one workshop include: The Live Cell Imaging Unit who will present on Fluorescent Microscopy and Basic Flow Cytometry; and the NMR Unit, who will present on Solution and Solid State NMR. All workshops are described below.

* Learn more about each presenter by clicking on his / her name below.

1. MASS SPECTROMETRY OF SMALL MOLECULES: LC-MS

Presented by: Dr Marietjie Stander, Fletcher Hiten, Meryl Adonis

Duration: 1 Day

2. MASS SPECTROMETRY OF SMALL MOLECULES: GC-MS

Presented by: Lucky Mokwena

Duration: 1 Day

The training on small molecules (and to some extent polymers) will be separated into an LC-MS and GC-MS component. Each component will be presented as a full day workshop and will be repeated two times during the training week. Both workshops will have a theoretical and practical component and will incorporate the topics outlined below.

3. MASS SPECTROMETRY OF SMALL MOLECULES: GC-MS

Presented by: Dr Salome Smit

Duration: 2 Days

After this 2-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.

NUCLEAR MAGNETIC RESONANCE (NMR)

4. SOLUTION STATE NMR

Presented by: Dr Jaco Brand

Duration: 1 Day

The purpose of the workshop is to connect theory to applications in modern solution state NMR. The aim is to reintroduce participants to the theory, but emphasis will be 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. Structure determination is the main strength of the technique and will receive the most attention.

1. Basic principles of NMR
2. Sample preparation
3. Running selected experiments
4. Processing data

1. What can I do with NMR?
2. Selected examples on interpretation of 1D and 2D data
3. The use of Chiral shift reagents to determine absolute stereochemistry

5. SOLID STATE NMR

Presented by: Dr Susanne Causemann

Duration: 2 Days

Solid State NMR is based on the same principles as the widely-used solution state NMR however the spectra of solids are very different from these of liquid samples and often difficult to acquire as well to interpret. In the solid state, several interactions are present between the nuclear spins and the surrounding internal magnetic and electronic fields. On the one hand these interactions are the origin of extremely broad and featureless solid state NMR spectra, but on the other hand these interactions contain structural information as well as information about the dynamics of the sample. The art of solid state NMR is to overcome these challenges by applying special techniques followed by careful interpretation of the results with respect to the nuclei and sample specific properties. Only then, can Solid State NMR provide unique information of the structure and dynamics present in a high variety of samples (organic – inorganic, crystalline – amorphous solids). These can be probed on different timescales depending on the property being evaluated.

The Solid State NMR workshop is addressed to researchers with a sound knowledge of the general NMR basics.

• to give an introduction to the theoretical background of Solid State NMR
• to give an overview that will lead to a better understanding of commonly used solid state NMR methods
• to facilitate a better understanding of the influence of sample properties on the acquisition and the results
• to enable data processing and interpretation
• to enable data processing and interpretation
• to provide a better understanding of Solid State NMR literature
• to discuss Solid State NMR applications in the research projects of the participants where possible

The workshop will take place over two days and will include lectures, demonstration of the instrument as well as exercises in processing and interpretation of Solid State NMR results.

Participants are advised to bring along their laptops so that they can participate in the data fitting exercises.

LIVE CELL IMAGING

6. FLUORESCENT MICROSCOPY

Presented by: Dr. Ben Loos

Duration: 2 Days

This workshop introduces the participant to fluorescence microscopy techniques. The mornings are compiled of a series of talks discussing principles and practice of fluorescence, 3D imaging, intensity-based analysis, fluorescence resonance energy transfer (FRET) and colocalization. The afternoons are spent in acquiring samples, from simple single colour to 3 colour, to z-stacking and time-lapsing. Concepts such as spectral unmixing and bleedthrough will be discussed. The acquired data will then be used for image processing and analysis. The 2 day long course is limited to 6 participants and will be repeated if sufficient demand exists.

• Theory and hands-on acquisition & analysis
• Principles of microscopy: light and colour, resolving power, types of microscopy
• Fluorescence microscopy, intro and applications
• Advanced imaging techniques (3-D imaging, deconvolution, spectral un-mixing, FRET, FRAP)
• Cell^R image acquisition
• Cell^R image analysis
• Introduction to super-resolution microscopy

7. BASIC FLOW CYTOMETRY

Presented by: Mrs. L Engelbrecht

Duration: 2 Days

This workshop 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 as well as data analysis. Emphasis will be placed on the principles of planning a multi-colour experiment for flow cytometry with the necessary control and setup requirements. The course will run over 2 days and is limited to six participants.

• 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, FlowJo and ModFit
• Planning of a multi-colour experiment
• Knowledge of possible applications of flow cytometry

8. SCANNING ELECTRON MICROSCOPY (SEM)

Presented by: Ms Madelaine Frazenburg

Duration: 3 Days

A 3 day workshop will be presented to introduce participants to the basic SEM principles and operation. The topics that will be covered include:

• The importance of sample preparation
• Different techniques

• Analyzer
• Point and ID
• Mapping
• Automation

• EDS Spectrometer
• WDS Spectrometer

• Gold coating
• Carbon coating
• Critical point drying of biological samples

• SE images
• BSE images
• CL images
• Standard Setup
• Quantitative analyses
• Data reduction

9. COMPUTED TOMOGRAPHY (CT) SCANNER WORKSHOP

Presented by: Dr Anton du Plessis

Duration: 1 Day

This short-course will be presented over 1 day and repeated every day, 10-13 July 2012. It will comprise the following:

• Introduction & welcoming to the CT Scanning facility
• Lecture on the physics of X-ray micro-CT scanning
• Informal discussions
• A sample chosen by the group will be scanned and analyzed, with hands-on training during the process. This includes time for Q&A

10. NEXT GENERATION SEQUENCING BIOINFORMATICS WORKSHOP

Presented by: Anelda van der Walt

Duration: 3 Days

The DNA Sequencing Unit invites researchers to participate in a 3-day Next Generation Sequencing Bio-informatics workshop. Participants, who already have SOLiD or Ion Torrent NGS datasets or are in the process of generating data, are invited to join and learn how to analyze their results. The course will include theoretical sessions as well as hands-on practical sessions.

• Study design for NGS projects
• Theory behind SOLiD and Ion Torrent sequencing
• QC of datasets
• Mapping to a reference
• De novo assembly
• QC of mapping / de novo assemblies
• Downstream analysis

TRAVEL & ACCOMMODATION

The training is free to staff and students at South African universities, however travel and accommodation expenses are for the participant’s or their institution’s own cost. Participants from industry will be charged R750 per day.

Participants must make their own accommodation arrangements.

The following accommodation is available close to the course venue (within one/two blocks). The University Flats are the most affordable.

Clik on a link below for accommodation options:
• University flats
• d'Ouwe Werf Hotel
• Caledon Villa Guest house
• River Manor Guest house
• Ryneveld Lodge/Guest house
• Roosenwijn Guest house
• Other University Accommodation

Shuttle services : Stellenbosch – Cape Town International Airport

BETTINA SHUTTLE SERVICES
Tel: +27 (0)21 887 0702
Fax: +27 (0)21 887 2402
E-mail: info@bettinashuttle.co.za
Web: www.bettinashuttle.co.za

CL HEYNES SHUTTLE & TOURS
Tel: 021 887 6967
Fax: 021 887 0971
E-Mail: CALVYNSTOURS@YAHOO.COM

ABOUT THE PRESENTERS

LC-MS Workshop Presenters: Dr Marietjie Stander (middle), Fletcher Hiten(left), Meryl Adonis (right)

Dr Marietjie Stander graduated with an MSc cum laude in 1997 under Prof Ben Burger at Stellenbosch University using mostly GC-MS in her research. She obtained her PhD in Chemistry in 1999 at North West University under Prof Piet Steyn where she acquired her first experience on LC-MS. She did a postdoc at Stellenbosch University on mycotoxin research and was appointed Applications Specialist by Microsep in 2001. During her 3 years at Microsep she gained further experience and training on HPLC and LC-MS equipment. In 2003 she moved back to the Western Cape to become an Analytical Chemist for Synexa Life Sciences and in 2005 she took up her current position at Stellenbosch University where she manages the Mass Spectrometry unit. The MS unit consists of 4 laboratories: LC-MS, GC-MS, Proteomics and Maldi and has 7 full time staff members. Fletcher and Meryl are two experienced analysts in the LC-MS laboratory and will be assisting Marietjie in presenting the workshop.

GC-MS Workshops Presenter: Mr Lucky Mokwena,

Lucky is an experimental Analytical Chemist with a Master’s Degree in Analytical Chemistry obtained at the University of Stellenbosch in 2009. He has acquired extensive experience and know-how in GC-MS in the last 15 years as Analytical Chemist in the employ of ARC, KWV, CSIR and Stellenbosch University (SU). His research interest is in chromatographic method development and validation. Currently he is employed as a Senior Analyst at the Central Analytical Facility (CAF) at SU, managing the GC-MS Division of the Mass Spectrometry Unit. He has developed and validated methods using GC-MS equipped with Purge and Trap, Thermal Desorption and Headspace for the analysis of environmental samples (air, water, wine and soil). He has worked with, Volatile Organic Compounds (VOCs) and Semi-volatile Organic Compounds (SVOCs), as well as Volatile phenols and thiols in wine. He has a strong background in a variety of sample preparation techniques: solid phase extraction (SPE), solid phase micro extraction (SPME), solid phase dynamic extraction (SPDE) and liquid-liquid extraction (LLE). He has developed his skills in chromatographic problem solving and instrument troubleshooting on both HPLC and GC-MS, as well as data processing, especially using principal component analysis (PCA) as a statistical tool.

Proteomics Workshop Presenter: Dr Salome Smit

Salome completed her PhD in Biochemistry at the University of Pretoria in 2011. She is experienced in the field of functional genomics and has now focused her attention on the daunting field of proteomics. She is currently heading up the Proteomics lab at the Central Analytical Facility, University of Stellenbosch. It is the only facility of its kind in Africa with the addition of the LTQ Orbitrap Velos Mass spectrometer. At the lab they strive to do world class proteomic research. The aim of the research is to identify thousands of proteins of any organism and hence determine the proteome of each organism we work on.

Solution State NMR Workshop Presenter: Dr Jaco Brand

Jaco is an organic chemist with a keen research interest in the use of NMR to solve various research questions. He completed his PhD in Organic Chemistry in 2007 at Kovsies (UOFS), and after 3 years at Farmovs Parexel International, doing LC-MS quantification of drugs in human plasma, he has moved to Sellenbosch University to pursue his love for the use of NMR in various fields. His own research interests are in structure elucidation, molecular modeling, natural products, physical organic chemistry and the application and behaviour of NMR chiral derivatizing agents in determining absolute stereochemistry.

Solid State NMR Workshop Presenter: Dr Susanne Causemann

Susanne has been employed as Solid State NMR application specialist and researcher at CAF, Stellenbosch University for the past year. During this time she has supported various research projects using Solid State NMR methods to study different materials ranging from various organic compounds like coals and cellulose, but also inorganic materials like amorphous aluminas, catalysts, zeolites and many other materials. Susanne obtained her PhD degree in 2010 in physical chemistry from the University of Münster in Germany where she studied Solid State NMR on a fundamental level. In addition, she was involved in solving various chemical and physical research questions using Solid State NMR methods. She appreciates the challenge to develop and implement Solid State NMR spectroscopy as a new research tool in South Africa.

Fluorescence Microscopy Workshop Presenter: Dr Ben Loos

Ben is a physiologist with experience in cellular imaging. His research interests are the dynamic processes of cell death and survival, systems physiology and neurodegeneration. He has “started” the Cell Imaging Unit in 2006, with a Wide Field Life Cell Imaging platform, and fostered the development and utilization of fluorescence microscopy in research. The unit is equipped for various fluorescence-based imaging techniques, and will soon enter the field of super-resolution confocal microscopy. Ben completed his PhD in 2009 during which he spent 300 days out of 360 days (!) on the microscope. He is now a lecturer in Physiology and supports CAF and microscopy from this position.

Flow Cytometry Workshop Presenter: Lize Engelbrecht

Lize is a physiologist who joined the Central Analytical Facility at Stellenbosch University, during 2011. Her position in the unit has provided her with much valued experience in various flow cytometric applications, such as multi-parameter analysis, cell cycle analysis, cell viability assays and cell sorting, using a wide variety of biological material. During her own research on the regeneration of skeletal muscle, she characterised isolated satellite cells using multiple parameters for flow cytometry. She had been a science teacher in the UK for 4 years before returning to the research field, so she is always eager to teach others and share her expertise to better equip them.

SEM Workshop Presenter: Madelaine Frazenburg

Madelaine is a biologist with experience in biological and mineralogical research, and various diverse fields. She completed her BSc (Hons) at UNISA, and after 15 years of working in the geological industry she has taken on the challenge in the X-ray micro-beam unit of Stellenbosch University. Her own research interest are in the Palynological diversity in the Oxalis hirta species in the Cape floral region and currently is focusing on developing protocols for the SEM and TEM application for different types of materials.

CT Scanner Workshop Presenter: Presenter: Dr Anton du Plessis

Anton is an experimental physicist with experience in laser and photonics based research, applied to various diverse fields. He completed his PhD in 2005 at Stellenbosch, and after 6 years at the CSIR in Pretoria doing full time research, he has recently moved from visible photons to X-ray photons and has taken on the challenge of ensuring the X-ray micro-CT scanner at Stellenbosch University is put to good use. His own research interests are in applications of technology and currently he is focusing on developing protocols for improving the contrast and resolution of the CT scanner for different types of materials.

NGS Bioinformatics Workshop Presenter: Anelda van der Walt

Anelda holds an undergraduate degree in Genetics and Biochemistry from the University of Pretoria. She completed an MSc in Bioinformatics at the South African National Bioinformatics Institute in the Western Cape in 2004, where she also worked in the field of HIV Bioinformatics for some time. She joined the Centre for Proteomics and Genomics Research in 2010 where she was introduced to the new field of Next Generation Sequencing (NGS). At CPGR she was mainly involved in two large consortium projects in the Agri Biotech field – both funded by TIA. Her main function on both projects was the analysis of Illumina RNA-seq and microRNA-seq data. She was also involved in a project where Illumina and 454 data were combined to perform de novo transcriptome assembly of a marine animal to identify novel SNP markers. In 2011 she joined the Central Analytical Facilities at Stellenbosch University (SU) and is currently supporting the recently acquired NGS platforms at the DNA Sequencing Facility. Projects she is currently involved in includes using transcriptome sequencing, de novo genome sequencing, genome re-sequencing, and amplicon sequencing on both the SOLiD and Ion Torrent platforms available at SU.