Background

The clinical and botanical supplies unit is a state-of-the-art medicinal plant processing facility designed to produce pharmaceutical grade herbal products, bridging the gap between laboratory research and clinical trials. The facility is HACCP-accredited (a food safety management system that enables food processing and catering industries to introduce and maintain a cost effective, on-going and safety programme). It is equipped to develop and demonstrate technologies that are beyond laboratory scale, up to a 100 litre scale. This facility allows the CSIR to take biotechnology, agro-processing and chemistry-based project leads from proof of concept to a tangible commercial product through stringent process development and piloting.

This facility is specifically aimed at the development and supply of small quantities of pharmaceutical raw material based on indigenous plants. The main purpose of this facility is to allow the early clinical validation of patented botanicals, prior to licensing to multinational pharmaceutical companies.

Key infrastructure and equipment

Infrastructure is available to support bioprospecting, agroprocessing and algae technology development, which are aimed to support agreed national priorities.

The facility has a 150 litre reactor (extraction vessel), herb dryer, drum drier, automated vibratory washing machine, automated slicer (1 – 45 mm thickness), industrial mincer, high performance liquid chromatographer instrumentation, bench top capsule-making machine, spray drier (8 -15 litre per hour), and hydraulic press (50 litre capacity, 400 Bar maximum pressure).

Chemistry pilot plant:

The chemistry pilot plant houses various organic and inorganic reactors, centrifuges, condensers/evaporators (scrubber/vacuum system) 40 litre solvent recovery, a wiped film evaporator, short path distillation equipment, six-inch fractionating column, continuous counter current extraction equipment and many more. The facilities can accommodate research and production from as little as a 10 litre scale, up to a pilot scale of about 400 litre.

Food and feed processing plant:

The facility is also equipped with food and feed pilot production equipment that can be used to undertake research for the food, beverage, fishing and agro-processing industries. This is a fully-equipped food and feed processing plant, with both a twin screw extruder and a single screw extruder suitable for production of specialised foods and feeds. Availability of such equipment allows for the manufacturing of aqua feeds in a multitude of shapes, sizes, densities and textures, which can be both floating and sinking feeds. It also has a small fish tank system for dedicated studies on live fish that is used to assist in developing novel aqua feeds for specific species.

The facility also has access to supporting laboratories for specific analytical and microbiological studies. It is also used to provide training for food science and engineering students, as well as training local communities in agro-processing and food processing methods.

Algal research laboratory:

The facility also boasts a fully equipped algal research laboratory with flow cytometer; fluorescent spectrophotometers; ultraviolet-visible spectrophotometer; gas chromatography-mass spectroscopy; liquid chromatography and liquid chromatography mass spectrometry (a method that combines the features of gas-liquid chromatography and mass spectrometry to identify different substances within a test sample); liquid extraction equipment and many more.

Skills and competences

The team that works in this facility is made up of bioprocess engineers, process chemists, natural product chemists, as well as food and chemical engineers. The group has extensive expertise in the areas of process chemistry, protein and plant extractions, food and feed engineering; and algal biotechnology with their respective skills ranging from process and product development and optimisation, process trouble-shooting, process flow sheeting, process design, techno-economic (feasibility) assessments, technology packaging, technology transfer and implementation.

The team’s competitive advantage lies in its strong product and development skills, as well as its experience of industry needs and challenges. The group boasts a combined process and product development knowledge gained over 50 years with a long track record of successful project execution and completion.

Contact information

Mr Dheepak Maharajh

email:

Tele: +27826508542

The CSIR BIDC is a world class facility established to translate biotechnology based concepts into market ready products and services. The facility offers competency throughout the value chain from laboratory scale concept validation through to demonstration of technology, prototyping and pilot manufacture. The BIDC focuses on industrial biologics (enzymes, whole cell catalysts, biological treatment solutions, reagents) and products for human and animal health care (vaccines, diagnostics, probiotics).

The facility comprises laboratories for molecular biology, applied biochemistry and biocatalysis as well as laboratory scale process development. These facilities are complemented by high-end analytical infrastructure and skills within CSIR Biosciences. The final component of the BIDC is the recently established BioIndustry Development Hub (BDH) which focuses on commercialization of technologies through large scale process development, toll manufacture and technical incubation of entrepreneurs and small businesses.

The BIDC is available to the entire national system of innovation to provide contract R&D, process development, process optimisation, scale-up, regulatory support, commercial manufacturing services and incubation of SMMEs to enable the development of a vibrant and sustainable bioeconomy in South Africa and throughout the African continent.

For more information and to contact the CSIR BIDC  click here.

 

The Molecular Technologies facility provides access to expertise and modern technologies for the generation and expansion of small compound libraries, the development of analogue series, and the identification, characterisation and quantification of specific compounds and natural extracts through its broad range of analytical expertise.

Equipment:

• State-of-the-art technologies for chemical synthesis (Chemspeed robotic and microwave synthesis platforms)
• Semi-preparatory and preparatory chromatography (including TLC, HPLC, CCC)
• Associated detection methods (UV/VIS, fluorescence, MS)
• NMR technologies and in-silico platforms for the identification of molecules and the elucidation of their 3D structure.

The facilities capabilities include:

Chemical library management:

• Compound management and hosting
• Miniaturization
• Natural and synthetic collections
• Library generation based on specific chemotypes

For small and natural compounds:

• Identification and isolation from complex matrices
• Natural and simplified ADME model
• Chemical modifications
• Bioactivation/inactivation models
• In-silico modelling and design

Analysis of small and large molecules:

• Biomarker ID and quantification in products (QC)
• Biomarker ID and quantification in complex matrices (PK, Clinical studies)
• Characterisation and quantification of specific analytes
• Purity determination
• Method development and validation

Contact:
Library and compound synthesis
Dr Edwin MMutlane
Molecular Technologies
CSIR Biosciences
Tel: 012 841 4282
Email:

Compound analysis
Dr Paul Steenkamp
Molecular Technologies
CSIR Biosciences
Tel: 012 841 3260
Email:

The pharmacology and bioassay facility designs, develops and validates pharmacological assays for drug benefit and risk assessment, which are applied in biomolecular screening campaigns of small to medium sized chemical and extract libraries.

Equipment:

• State-of-the-art liquid handling and high-throughput robotic assay facilities
• High-end spectrophometry for absorbance/fluorescence measurements
• Realtime PCR
• Agilent Bioanalyzer analysis for RNA, DNA and protein integrity

Services:

In vitro models for drug benefit and risk assessment include:

Pathogens and infectious disease

• Antiviral screens including HIV pseudovirus
• Malaria (conventional and transmission blocking screens)
• Antimicrobial screens
• Antifungal screens
• Drug signature profiling

 

Mammalian cell tissue culture

• Cancer and oncology screens
• Drug permeability
• Drug cytotoxicity screening
• Drug signature profiling

The facility also develops and applies assays for cosmeceuticals testing. In vitro models include:

Enzyme and cell-based assays

• Elastase, collagenase, hyaluronidase screening for activity inhibition
• Elastin and collagen screening for protein production

Targeted and whole genome assays

• Cell-based TaqMan and microarray expression profiling of molecular biomarkers specific to youthful skin and ageing

Contact:
Ms Natasha Kolesnikova / Dr Malefa Tselanyane
Biomedical Technologies
Tel: 012 841 4735 / 012 841 4045
Email: /

The biomarker discovery/validation and biomolecule analysis facility characterises and quantifies specific compounds through a broad range of analytical services.

Equipment:

Electrophoresis
Ettan IPGphor I/II IEF (GE Amersham)
Rotofor Cell (Bio-Rad)
Dalt II Separation Unit (GE Amersham)
Protean Plus DodecaCell (Bio-Rad)
Ettan SE600 Ruby gel electrophoresis system with auto gel stainer
Ettan DALTtwelve, running 12 large format gels in parallel

Imaging
PharosFX (Bio-Rad)
EXQuest automated spotcutter (Bio-Rad)
PDQuest (Bio-Rad)
Image Master 2D scanner and software

HPLC
1100 nanoHPLC (Agilent Technologies)

Mass spectrometry
MAPII AutoPrep MALDI Robot system (Bruker Daltonics)
Bruker autoflex® Daltonics MALDI-TOF mass spectrometer with post-source decay
QStar Elite (ESI/MALDI) (Applied Biosystems)
Qtrap (ESI) (Applied Biosystems)

Protein-interaction
Biocore 3000 (GE Amersham)

Services:

Proteomics services are available to internal and external customers. The following services are available:

Biomarker & Drug-target discovery and validation

Gel-based proteomics

• • Fractionation: 1D / 2D PAGE;
  • Protein visualisation / isolation: gel staining (Coommassie, Silver, SYPRO-Ruby, Cy dye, and Flamingo)
  • Gel imaging (fluorescence, colorimetric and radioisotopic) (Biorad PharosFX)
  • High-throughput spot picking (Biorad ExQuest); and
  • 1D / 2D PAGE band/spot identification/confirmation  (Dionex Ultimate 3000 and AB Sciex QStar Elite).

Solution-based (gel-free) proteomics

• Off-line and on-line fractionation:

• In-solution peptide/protein IEF (Biorad MicroRotofor)
• 2D HPLC (Dionex Ultimate 3000 nanoRSLC

• Shotgun and targeted biomarker/drug target discovery  (AB Sciex QStar Elite and AB Sciex 4000 QTRAP)

• MRM-based During ‘validation’, putative targets are confirmed by a targeted approach where fewer analytes are monitored in a larger sample size. The main aim of this stage is to assess marker sensitivity (likelihood that an affected/diseased sample will test positive). In ‘verification’ the analysis is further extended with 100s of samples analysed in order to examine variations due to environmental, genetic and/or biological factors. Thus, candidate biomarker sensitivity is affirmed while specificity (likelihood that an unaffected/healthy sample will test negative) is gauged.”

• Mass spectrometry (iTRAQTM, peptide identification, peptide sequence identification, glycan analysis, posttranslational modification analysis)
• Protein characterisation (protein-protein / ligand interaction)

Microarrays (cDNA oligo)

•     Sample preparation and hybridisation
•     Conventional and high-resolution scanning*
•     Expression analysis
•     Quantitative Real-Time PCR

Contact information
Dr Stoyan Stoychev

Molecular Technologies

Tel: +27 12 841 2270/3001

Fax: +27 12 841 2388

Email:

Molecular and Biomedical Technologies (MBT) is a service-orientated area providing non-routine, innovative, validated bio-molecule, value adding analytical, chemical, genomic and pharmacological services that support research and development (R&D) initiatives through working closely with higher education institutes (HEIs), science councils and companies at different stages of growth.

Core services offered by MBT:

• Drug and cosmetic screening
• Chemical synthesis and analysis
• Biomarker discovery/Validation and biomolecule analysis  

Contact details:

Specific enquiries can be directed to the respective individuals indicated on the pages of the core service areas listed above.

For more information about MBT contact:

Dr Dalu Mancama

Biomedical Technologies

CSIR Biosciences

Telephone: +27 (0) 12 841 4533

Email:

Physical address:

CSIR Biosciences

Building 20

Meiring Naude Road

Brummeria

Pretoria

One of the ACGT partners, CSIR, signed a Memorandum of Agreement (MoA) with UNISA, that officially sealed a partnership, for the commissioning of a 600 MHz Nuclear Magnetic Resonance (NMR) Instrument – the first of its kind, to be purchased and commissioned in the Gauteng region.

Generating a magnetic force 300,000 times stronger than the magnetic field of Earth, the NMR Instrument can be used to fully characterise the structures and molecular dynamics of isolated compounds of interest, particularly of those which cannot be crystallized. This is done by using one of two different probe systems, namely a dual broadband probe (for smaller molecules), or using the triple resonance probe for C, N and H analysis of larger protein molecules. Studies and increased understanding of protein- substrate interactions, in biological systems, will allow for the design of better and more effective drugs against a variety of disease-causing agents and will also be useful in nutrition research.

While the instrument was purchased by UNISA, the CSIR, has provided a suitable Housing Facility, with subsequent maintenance costs being allocated, on a pro rata basis, between users. In accordance with the MOA, both CSIR and UNISA are contributing to Human capital development, by allowing UNISA post-graduate students, studying in the field of biotechnology, to perform practical work and receive training in CSIR laboratories. These students will be jointly supervised by UNISA and CSIR staff.

Dr Martin Myer, Senior Lecturer and research coordinator in the Department of Life Sciences and Consumer Sciences at UNISA, is the Operations Manager of the Facility.

Contact information

Dr Martin Myer, Tel: +27 12 841 2356/3260

The Aptamer technology platform at CSIR Biosciences headed by Dr Khati runs a Biacore-based surface plasmon resonance (SPR) facility. This biosensor technology allows the real-time detection and monitoring of biomolecular binding events. In a Biacore experiment, one of the interacting molecules (the ligand) is bound to the biosensor surface, whereas the other (the analyte) is delivered to the surface in a continuous flow through a microfluidic system. Binding of the analyte to the ligand is monitored on real-time by surface plasmon resonance, which detects the mass concentrations at the surface. The response is directly proportional to the mass of analyte that bind to the surface. A range of different sensor chips is available for different application purposes.

The technology requires no labelling and provides quantitative information on kinetic parameters (association and dissocation rate constants, ka and kd), affinity constants (K_D) and stoichiometry. Applications include epitope mapping, molecular assembly and small molecule screening. Moreover, experiments can be performed using crude media (cell lysates, tissue extracts, sera and biological fluids) allowing, in combination with mass spectrometry, the identification of binding partners of a given molecular target immobilized on the biosensor.

The facility operates a Biacore 3000 instrument. This instrument is fully automated and supports 4 channels that can be used individually, in series or as pairs (on-line reference subtraction). The facility is opened to scientists from ACGT affiliated institutions (and beyond) and provides training and support for the use of this biosensor technology.

Contact information

Dr Makobetsa Khati

Tel: +27 12 841 4770, Fax: +27 12 841 3651

Dr Lionel Gresh

Tel: +27 12 841 3583, Fax: +27 12 841 4790

The Roche LightCycler instrument at the ACGT enables the quantitative real-time PCR amplification experiments. This helps to determine the amount of a specific DNA sequence of interest. There are major applications in the detection of GM food, but real-time PCR is also an important step for the validation of expression data generated by cDNA microarray screening and other gene discovery techniques.

The broad range of applications that run on LightCycler instruments has significantly contributed to the existing expertise in quantitative PCR. The instrument combines a thermal cycler platform with a fluorescence detection system, software modules and high-quality reagents, making it an ideal tool for research in the field of gene analysis.

Contact information

Tel: +27 12 841 3221

Proteomics represents an important new phase in the post-genomics era, providing the opportunity to analyze the entire protein complement of a cell under different physiological conditions.

Researchers in the Proteomics section of the Systems Biology group at CSIR apply techniques that allow global analysis of the state of proteins in biological systems. This ability to probe expression, posttranslational modifications and interaction of proteins at any given time is an important component of the systems biology approach. The ultimate goal is to integrate proteomics data with genomic, transcriptomic, metabolomic, and structural bioinformatics data to get a more complete view of the biological system. This represents a vital tool in the search for new drug targets, which may provide opportunities for rational drug design, as well as providing links between methods of identifying the genetic predisposition to disease.

The ACGT proteomics facility is equipped with the following equipment:

• 1x Dionex nanoRSLC with UV detector and fraction collector
• 1x Dionex proflow nanoRSLC (funded by Diplomics)
• 1x AB Sciex 6600 TripleTOF mass spectrometer
• 1x Bruker Autoflex MALDI TOF mass spectrometer
• 3x Thermofisher King Fisher Duo magnetic handling stations
• 1x CentriVap Proteomics vacuum concentrator system (funded by Diplomics)
• 1x Agilent 2D HPLC
• 1x LEAP HDx-3 PAL hydrogen deuterium exchange preparatory system
• 1x Applied Photophysics Chirascan circular dichroism spectrophotometer
• 1x Shimadzu Fluorescence spectrophotometer
• 1x BioTek PowerWave HT UV-Vis plate reader
• 1x Pressure Biosciences PCT barocyler

Software:

• AB Sciex Protein Pilot and Peak View database search and spectra integration software
• AB Sciex Biopharmaview intact protein deconvolution software
• Peaks v6 database search software
• Biognosys QuiC quality control software for DDA and DIA data
• Skyline and MSStats targeted proteomics data extraction software
• MaxQuant and Perseus quantitative proteomics software
• SearchGui and Peptide Shaker database search and visualization software

Services:

The Proteomics facility is used for a range of research programmes within the ACGT. In addition, Proteomics services are available to internal and external customers.

The types of analysis performed within the facility can be split into two major areas (i) Proteomics and (ii) Biomolecule characterization.

1. Proteomics: the main focus in this respect is to perform bottom-up analysis for biomarker identification and drug-target discovery and verification, as well as to identify mechanisms of action in certain studies. The main technique applied for this is SWATH via fast scanning time of flight (TOF) instrumentation coupled to electrospray ionization (ESI) and nanoflow ultra-high-pressure liquid chromatography (nano UPLC). The following assays are routinely run in our lab (major associated equipment is indicated in brackets):

• • Protein and peptide lysate concentration determination using range of colorimetric and fluorescence assays (BioTek PowerWave HT UV-Vis plate reader)
  • Automated protein capture, clean-up and on-bead digestion for complex lysates using MagReSyn® microparticles and magnetic handling stations (KingFisher® Duo)
  • Automated phosphopeptide enrichment using MagReSyn® microparticles and magnetic handling stations (KingFisher® Duo)
  • FFPE sample extraction and processing of archival tissue (Pressure Biosciences PCT barocyler)
  • Spectral library building for SWATH assays using 1D and 2D chromatography (Dionex UV nanoRSLC coupled to Sciex 6600 TripleTOF)
  • Label-free SWATH based quantitative profiling of complex lysates with and without phosphopeptide enrichment (Dionex UV nanoRSLC coupled to Sciex 6600 TripleTOF)
  • In-gel and in-solution based protein identification and confirmation (Dionex nanoRSLC coupled to AB Sciex 6600 TripleTOF)

2.  Biomolecule characterization: the primary focus is on the structural characterisation of recombinantly produced proteins and antibodies (Ab):

• • UV based protein concertation determination (BioTek PowerWave® HT UV-Vis plate reader)
  • Intact mass analysis (Dionex UV nanoRSLC coupled to Sciex 6600 TripleTOF)
  • N-glycan profiling and polymer analysis (Bruker Autoflex MALDI-TOF)
  • In-solution sequence confirmation and PTM analysis (Dionex UV nanoRSLC coupled to Sciex 6600 TripleTOF)
  • Probing structural dynamics to understand the effects of mutations, buffer additives and stabilizers, ligand binding and protein-protein interactions using continuous and pulsed hydrogen-deuterium exchange (HDX) coupled mass spectrometry (LEAP HDx-3 PAL coupled to Agilent 2D HPLC coupled to AB Sciex 6600 TripleTOF)
  • Probing secondary structure conformation (Applied Photophysics Chirascan)
  • Probing tertiary and higher order structure conformation (Shimadzu Fluorescence spectrophotometer)

 

Contact information:
Dr Stoyan Stoychev, email:
Dr Previn Naicker, email: