Facilities - ARC


  • National Agricultural Proteomics Research & Services Unit (NAPRSU)

    2nd October 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:  az.ca1527106910.cwu@1527106910abmid1527106910nb1527106910/ az.ci1527106910rga.c1527106910ra@Ba1527106910bmidN1527106910

    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

    Background

    The ARC Biotechnology Platform (ARC BTP), situated on the historic Onderstepoort Campus, was established in 2010 as a major strategic priority of the ARC, aimed at increasing technical expertise in advanced and high throughput agricultural biotechnology. The role of the ARC BTP is to create the high throughput, high technology resources required for the application in advanced genomics, quantitative genetics, marker assisted breeding and bioinformatics, within the agricultural sector, in the areas of plant and animal improvement and protection. The ARC BTP was therefore built as both a research and a service driven institution, thus providing an environment in which the next generation of highly skilled young researchers can be developed. The technologies established within the platform are accessible as services to the whole ARC, collaborators, companies, science councils and researchers across the continent.

    The ARC BTP has developed and implemented high throughput DNA and RNA sequencing and genotyping technologies, with the capacity to analyse thousands of samples, or to generate very large volumes of data from single samples, with full automation of sample preparation and analyses. The current technology includes both Illumina sequencing and genotyping systems. Other technologies that enable high throughput workflow implementation, such as liquid handling robotics, laboratory information managing system (LIMS) and high-performance computing, have also been established. Targeted sampling is addressed in the platform by the implementation of a Laser Capture Micro-dissection microscope.

    Though these facilities are already in place at the ARC BTP, we encourage discussions with potential clients to ensure experiments and expectations are achievable.

    Equipment

    The BTP houses various high-throughput technologies, including:

    •  Next generation sequencing platforms (see table 1)
    • HiScanSQ (Illumina)
    • MiSeqs (2x, Illumina)

     

    Table 1. Next Generation Sequencing Capacity at BTP

    NGS Platforms

    Standard Flowcells

    Gb per run

    Estimated sequencing   turn-around times

    MiSeq
    HiScanSQ 100 bp x 2 ±150 Gb ±2 months

     *Hiseq2500 expected to arrive in January- 600GB (High Output Mode) 100bp x 100bp, 180GB (Rapid Mode) 150bp x 150bp.


    • Star (Hamilton)
    • StarPlus (2x, Hamilton)

     

    Laser Capture Micro-dissection Microscope:

    • Zeiss PALM 4, with a Calibri system and florescence capability

     

    A high-performance computing cluster for bioinformatics analyses:

    • Hewlett Packard, 12 Computing Nodes, ~ 1TB of RAM connected with high speed Infini-band to the Storage Array

    * It is recommend that potential clients contact the BTP Core Facility for project discussions and access to the facilities.

    Services

    The BTP provides both Next Generation Sequencing and SNP Genotyping Services.

    Next Generation Sequencing Services:

    The ARC BTP operates three next generation Illumina sequencers, a HiScanSQ 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.

    SNP Genotyping Services:

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

     *It is recomnended potential clients contact the BTP Core Facility for project discussions and pricing.

     

    Contact information 

    The ARC BTP NGS Core Facility could be contacted electronically at BTP-Core[at]arc.agric.za or telephonically as follows :

     

    Dr Jasper Rees,

    The Head of the Biotechnology Platform

    + 27 82 415 9295

    Dr Dirk Swanevelder,

    Senior Researcher, ARC Biotechnology Platform

    + 27 79 506 8617

    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:  az.ci1527106910rga.c1527106910ra@ah1527106910sinar1527106910P1527106910 / az.ci1527106910rga.c1527106910ra@ag1527106910natN1527106910 / az.ci1527106910rga.c1527106910ra@ll1527106910iJ1527106910

    Tele:  012 – 672 9218 / 9027 / 9008

    Fax:  012 – 672 9214

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