Facilities - ARC


  • National Agricultural Proteomics Research & Services Unit (NAPRSU)

    2nd Oct 2013

    Background

    Our unit (jointly owned by UWC and ARC), provides State of the Art Proteomics research and services, mostly to Agricultural and Biotechnology researchers and private companies in South Africa. This work is mostly funded by the Department of Science and Technology (DST) through the National Equipment Programme (NEP) of the National Research Foundation (NRF).

    Proteomics is a collection of relatively new tools and expertise for Biologists and (Bio) chemists and its practical applications are growing fast (see below). Proteomics is the term that describes a multitude of tools and expertise used primarily to profile and identify proteins of interest in any organism at a large scale. Proteins are the functional/operational units in cells, and proteins of interests’ often include biomarkers for certain diseases or physiological/developmental status. We have post graduate students ranging from BSc interns, Honours, Masters, PhD and Postdocs applying proteomics in their own various biological experiments.

    For example, one could use proteomics to investigate effects of pathogens on cells/tissues/organs/organism protein expression levels and patterns. This information could be used to identify targets/strategies for the improvement of pathogen resistance by both plants and animals.

    Services & Equipment

    Proteomics:

    – Experimental Design
    – 1D & 2D SDS PAGE
    – Staining & Imaging
    – Spot picking & Identification
    – Data Analysis

    Biotyping:

    Our MALDI Biotyper enables molecular identification, and classification of microorganisms like bacteria, yeasts and fungi. This application is achieved reliably and quickly using peptide mass finger-printing by high-throughput MALDI-TOF mass spectrometry.

    Other services include:

      •  Polymer Analysis
      • nanoHPLC
      • MALDI Imaging
      • Protein Extraction
      • Robotic Spot Picking
      • Metabolite Analysis
      • Protein Separation

     

    * To view the NAPRSU brochure, click here.

    Pricing information:

    For detailed pricing information, contact the service provider listed below.

    Contact information:

    Name of contact person:  Prof. Bongani Ndimba

    Email address:  /

    Tele:  021 – 959 2215/2648

    Location: Proteomics Research & Services Unit, Department of Biotechnology, University of the Western Cape, Robert Sobukwe Road, Bellville, Cape Town, South Africa

  • The ARC Biotechnology Platform

    The ARC Biotechnology Platform
    29th May 2013

    Located on the Agricultural Research Council’s Onderstepoort Veterinary Research campus, the Biotechnology Platform (ARC-BTP) was established in 2010 as a major strategic priority of the ARC. The role of the ARC-BTP is to create the high-throughput resources and technologies required for applications in genomics, quantitative genetics, marker assisted breeding and bioinformatics within the agricultural sector. The focus of the ARC-BTP is to establish itself as both a research and service driven institution, providing an environment in which highly skilled researchers can be hosted and trained. The technologies established within the platform are accessible as services to the ARC, collaborators, companies, science councils and researchers across the continent.

     

    The ARC-BTP has implemented high-throughput DNA and RNA sequencing and genotyping technologies within the platform, with the capacity to genotype thousands of samples, or generates large volumes of data from single samples.

    The current technologies available in the platform include:

    • Next generation sequencing and genotyping platforms
    • Liquid handling robotics systems
    • Laser capture micro-dissection microscope​

     

    Next Generation Sequencing services 

    The ARC-BTP operates three next generation Illumina sequencers, a HiSeq2500 and two MiSeq systems. Different sample preparation protocols are available for NGS library preparations, depending on the type of samples and/or the application. This is an area that gets regularly updated and the facility keeps abreast with these. The best approach with the current available technologies will be determined during initial discussion with clients.

     

    Applications:

    • Whole genome DNA sequencing
    • 16S rRNA amplicon sequencing
    • Whole genome DNA re-sequencing
    • RNA sequencing

     

     

     

     

     

    RNA Sequencing Services:

    RNA-seq allows researchers to detect both known and novel features in a single assays, enabling the detection of gene fusions, single nucleotide variants and allele-specific gene expression without requiring prior knowledge.

    RNA-seq is the gold standard for mapping transcriptomes, profiling changes in splicing and measuring gene expression levels.

    Applications:

    • High throughtput (RNAtag) sequencing
    • mRNA and small RNA sequencing
    • Total RNA (Ribozero) sequencing
    • Ultra low input RNA sequencing

     

     

     

     

     

    SNP Genotyping Services 

    Genotyping enables the measurement of genetic variation between members of a species on the basis of single nucleotide polymorphisms (SNPs). Illumina BeadChips have been developed in collaboration with leading agricultural researchers. This means the SNP technology has been tried and tested by numerous agricultural organizations, industry and academia.

    Application:

    • Copy Number Variation analyses

      Image courtesy of Illumina Inc.

    • Biobank sample analyses
    • Parentage analyses
    • Plant, Animal and Human screening panels
    • Targeted disease or rare variant panels
    • QTLs, GWAS, SNP discovery and forensics

     

     

     

    SNP genotyping is performed using the Infinium bead chip technology of Illumina (plants, animals and human). Both commercial and custom made Infinium bead chips, ranging from 1000 up to more than a± 3 K-1 million,000 K SNPs, are available from Illumina (www.illumina.com). We recommend that clients contact us for ordering and pricing of these, since reagents have expiry dates and we need to schedule the work around these dates.

    Image courtesy of Illumina Inc.

     

    High throughput nucleic acid extraction 

    The Hamilton star Plus is used for high throughput DNA extractions that. uses the Magnetic Bead Technology, it allows highly efficient nucleic acid isolation from a variety of samples at any throughput.

    Key features:

    • High throughput  
    • No cross contamination
    • Multiple sample types
    • Adjustable protocols

     

     

     

    Focused Ultrasonificator for Sample Preparation

    The Covaris focused-ultrasonicator uses the acoustic technology: Adaptive Focused Acoustics™ (AFA), that mechanically shears the sample by applying very high frequency ultrasound waves or acoustic bursts. The shearing process is un-biased from temperature, sample GC content or concentration. It is able to produce consistent shearing of fragments ranging in size from 150 bp to 5 kb, for between one and ninety-six samples.

     

    Applications of the COVARIS E220:

    • DNA/RNA shearing
    • Biomarker extraction
    • FFPE Nucleic acid extraction
    • Epigenomics
    • RNA-seq
    • Cell lysis

     

     

     

    Laser Capture Micro-Dissection Microscope (LCM)

    A highly specific specimen can be isolated with the focused laser of the PALM MicroBeam LCM and transferred to a collection tube. This allows researchers to separate their desired specimen from a population of cells or tissues at an early stage of their research work.  The system is ideal for single-cell isolation for use in downstream applications as cells remain viable.

    Applications of the PALM MicroBeam Microscope (Zeiss):

    • Sample manipulation at microscopic scale
    • Highly specific cell and feature selection
    • Contamination-free isolation
    • Contact-free isolation

     

     

     

     

    Technology under development: 

    Optical Mapping

    Use the Irys to produce fingerprints of large DNA molecules for the construction of genome wide maps. The Irys is able to directly image intact and labelled genomic DNA to enable high-resolution detection of structural variations in both plants and animal genomes. This technology is particularly useful for species with large repetitive regions.

    Applications of the Bionano Irys:

    • Whole genome mapping
    • Structural variation detection
    • Sequence assembly
    • Sequence scaffolding

     

     

     

     

     

    Real-time sequencing with ultra-long reads

    The Oxford Nanopore technology has made the sequencing of ultra-long reads possible. Each MinION consists of 512 nanopore channels that are able to generate 5kb to 20kb or longer reads in real-time. Read lengths are determined by sample preparation, and is now approaching 1 Mb for a single read. This has particular benefits when assembling large, complex genomes, resolving structural variation or wishing to explore large metagenomic communities.

    Applications of the ONT MinION:

    • Sequence assembly
    • Sequence scaffolding
    • Direct DNA or RNA sequencing

     

     

     

     

     

     

     

    Contact Information:

    General enquiry about ARC BTP Core Facility/Service:

    Email:  

    Phone: Phone: +27 12 529 9483

     

    Dr Farai Muchadeyi

    Senior Manager ARC Biotechnology Platform

    Phone: +27 12 529 9352

    Email: 

     

    Lerato Mpye

    Project Co-coordinator ARC Biotechnology Platform

    Phone: + 27 79 506 8617

    Email: 

     

    Dr Dirk Swanevelder

    Senior Researcher ARC Biotechnology Platform

    Phone: +27 12 529 9472

    Email: 

     

    Dr Magriet Van Der Nest 

    Senior Researcher ARC Biotechnology Platform

    Phone: +27 12 529 9472

    Email:

     

    Dr Nokuthula Mchunu

    Senior Researcher ARC Biotechnology Platform

    Phone: +27 12 529 9356

    Email:

     

    Dr Rian Pierneef

    Researcher ARC Biotechnology Platform

    Phone: +27 12 529 9356

    Email: 

     

    Location

    The ARC BTP is housed on the ARC Onderstepoort Campus

    Agricultural Research Council

    Onderstepoort Campus

    100 Old Soutpan Road (M35)

    Biotechnology Platform Building (Building 38)

    GPS co-ordinates:

    25°39’03.10″S

    28°11’03.10″E

     

  • Animal Genetics, Irene

    20th May 2013

    Background

    The Animal Genetics department undertakes basic and applied research and strives to apply current knowledge for the improvement of farm animals of both large and small-scale farmers.  A DNA forensic service is also offered to the South African Police Service (SAPS) in stock theft cases.  Microsatellite based DNA profiling forms the basis of all the molecular genetics research and services in the Animal Genetics department.  The technology is also applied in parentage determination and the identification of individual animals for registration purposes.

    The department also has an established national DNA reference catalogue called Lidcat – Livestock Identification Catalogue.  The system is aimed at establishing an affordable and irrefutable identification system for animals by collecting a biological sample (hair) from individuals and storing it under ideal conditions.

    Microsatellite markers are also available for certain game species.  These include buffalo, kudu, impala, eland, rhino, wildebeest, duiker, blesbok and sable.

    Services & Pricing

    The DNA parentage services are available to stud and commercial breeders as well as small-scale farmers and individual livestock owners.

    The South African Police Services is the main client for the Forensic service offered.  Private individuals also make use of the Forensic service in the case of livestock disputes.

    Species identification tests are available to private clients, chain stores as well as the SAPS.

    The Lidcat service is used in the case of theft or parentage/ownership disputes, the system can be used to identify the animal.

    List of Services:

    • Animal Forensics (Livestock and Game species)
    • DNA profiling for Livestock Species (Parentage verification and individual identification)
    • Species identification
    • Genetic disorders – Dexter Chondrodysplasia
    • Lidcat and Biobank

     

     

    SERVICE

    AMOUNT INCL. VAT

    DNA PROFILING:

    CATTLE

    R150-00 (sliding scale available)

    HORSES

    R250-00 or sliding scale on request

    PIGS

    R150-00

    SHEEP

    R200-00

    GOATS

    R150-00

    FORENSICS

    R550-00

    DEXTER CHONDRODYSPLASIA

    R228-00

    SPECIES IDENTIFICATION:

    PRIVATE

    R300-00 (sliding scale available)

    FORENSICS

    R550-00

    LIDCAT:

    STORAGE                                     

            

    R15 / lidcat kit (please note additional charge if  DNA typing is required)

    *The prices are reviewed annually. Contact service provider for quotation.

    Equipment:

    PCR:

    • GeneAmp 9700 (x3)
    • Applied Biosystems Real-Time PCR 7500
    • Illumina Eco Real-Time PCR

    Genotyping/Sequencing:

    • ABI 3130XL

    Contact information:

    Name of contact person:  Pranisha Soma / Olivia Maopholi / Jill Anigworth

    Email address:  / /

    Tele:  012 – 672 9218 / 9027 / 9008

    Fax:  012 – 672 9214

    Location: Agricultural Research Council, Animal Production Institute, Animal Genetics Division, Irene.