Africa Centre for DNA Barcoding
DNA Barcoding the flora of the Kruger National Park
Senior researchers: Michelle van der Bank and Vincent Savolainen
Post-doctoral positions: Sylvie Duthoit and Renaud Lahaye
PhD: Olivier Maurin
MSc: Matlou Jerminah Moeaha
Collaborator: Yanis Bouchenak-Khelladi
What is DNA barcoding — In 2004 the Consortium of Barcode of Life (www.barcodinglife.com) has launched an initiative to promote DNA barcoding, a process enabling the rapid and inexpensive identification of the estimated 10 million species on Earth. It is a diagnostic technique in which short gene sequence(s) can be used for species identification. In animals, the mitochondrial cox1 gene (CO1) has been identified as a suitable DNA barcode, however, in plants it is still unclear which marker(s) could be used as a DNA barcode. Scientists from 11 institutions all over the world, supported by the Plant Working Group (http:/kew.org.uk/barcoding/index.html), are searching for this short fragment(s) of DNA. Once the potential “barcode” is identified, all 300.000 species of plants on Earth will have to be barcoded.
Benefits of DNA barcoding — (i) enabling species identification, including any life stage or fragment, (ii) facilitating species discoveries based on cluster analyses of gene sequences, (iii, and providing insight into the diversity of life (iv) promoting development of handheld DNA “barcoder” that can be applied in the field for biodiversity inventories. When this technology becomes available it will help many non-scientists to quickly and inexpensively identify known species and retrieve information about them.
The KNP and its flora — The KNP was established in 1898 to protect the wildlife of the South African Lowveld. It provides an ideal environment for a plant barcoding study since it is one of the largest protected areas in Africa. This large protected area of 20 000 km2 is roughly the same size as Wales. It now forms part of the Great Limpopo Transfrontier Park, which links the KNP with Gonarezhou National Park in Zimbabwe and the Limpopo National Park in Mozambique. UNESCO has designated this new Transfrontier Park as a World Heritage Site. Since its creation in 2000, fences between the Parks have started to come down allowing the animals to take up their old migratory routes that had previously been blocked due to political boundaries. Various habitats and ecological regions exist within the boundary of the Kruger, with at least 16 recognized ‘ecozones’, each one characterize by specific vegetation, geology, soils, rainfall rate, and temperature. For example the vegetation and plant diversity found in the Malelane Bushveld Mountain is very distinctive of what can be found in the Lebombo Mountains located on the border with Mozambique. In the northern part of the Park the Sandveld is divided in several fragments and represent a particularly interesting area in term of plant diversity. This area has many highly localized species, which just enter from Mozambique or the Limpopo valley. Large rivers like the Limpopo, the Elephant and the Crocodile as well as rocky outcrops spreading all over the Park also represents places of botanical interest. Surprisingly, no comprehensive botanical inventory has recently been done in the KNP.
Collecting in the KNP — Since the beginning of this project in September 2005, we have collected more than 2 000 plant specimens. This represents the most complete and recent inventory of the Parks flora, which will be useful to update datasets of the Scientific Services of the KNP. This is also the largest and most diverse sampling ever made for barcoding purposes in a protected area.
Producing a DNA barcode for the flora of the KNP — Results based on eight plastid DNA markers (coding and non-coding) were evaluated, across a phylogenetically diverse set of taxa, which include 19 families, 22 genera and 38 species. The results suggest that a combination of genes is recommended as a barcode for the flora of the KNP, although matK alone correctly identified >90% of the species. The first data from this study has recently been presented at the Second barcode of life conference in Taipei and a scientific paper was submitted to PNAS entitled “DNA barcoding the floras of biodiversity hotspots”.
This study will improve the knowledge of plant biodiversity of the KNP, as well as conservation management, by providing exact localities of native, alien, rare and endangered plants. DNA-barcoding will also facilitate the future monitoring of botanical plots throughout the park by providing DNA-based taxonomic identification tools. Lastly this study will also reduce plant bio-prospecting in the KNP because herbarium specimens and DNA samples will be made available to the scientific community.
DNA barcoding of all trees and shrubs species is now nearly completed (300 spp) and the DNA barcoding program of herbs, grasses and bulbs is also well on its way.
DNA Bank for the Flora of the KNP at UJ — A DNA bank was set up at the University of Johannesburg where DNA extracts for the flora of KNP will be held centrally and made available for the scientific community. DNA extracts will also be duplicated and transferred to the DNA bank of the South African Biodiversity Institute (SANBI) in Kirstenbosch near Cape Town, South Africa, and the Royal Botanic Gardens, Kew in the United Kingdom.
The DNA, from the field to the lab...
The DNA barcoding project raises some interest and curiosity in the press...
Centre for Aquatic Research
Directed by Prof Ina Wagenaar. It carries out basic research in the aquatic environment and sustainable management of aquatic resources.
Centre for Catalysis Research
Directed by Prof James Darkwa, researches homogeneous catalysis, strongly underpinned by organic and organo-metallic synthesis, especially of new classes of ligands and catalyst precursors.
Centre of Excellence (CoE) in Food Security
The Department of Biotechnology and Food Technology of the Faculty of Science, University of Johannesburg (UJ), is part of the new Centre of Excellence (CoE) in Food Security, awarded to the University of Pretoria (UP) and the University of the Western Cape as co-hosts .
This CoE will focus on five key areas, i.e., sustainable production; post-harvest technology and processing; access to food; consumer demand, food utilization and nutritional outcomes; and knowledge transfer and leadership in the food system.
Centre for Nanomaterials Science Research
The Centre for Nanomaterials Science Research (CNSR) facilitates and supports individual and collaborative research in the Department of Applied Chemistry. Its members are mostly active academic staff members some of whom are affiliated with a number of professional organizations including the South African Chemical Institute, the Water Institute of Southern Africa, the South African Nanotechnology Initiative, the American Chemical Society and the Royal Society of Chemistry among various organizations.
The CNSR at the University of Johannesburg was established in 2007 and consisted of four “Pillars” of research, all having a nanomaterials science foundation. While other nano-based activities exist within the University. These four pillars or focus areas reflects the strategic focus within the Faculty of Science and the university at large. The primary aim of the CNSR is to highlight the nanomaterials expertise at the University of Johannesburg, while providing a platform for the high-level training of researchers in Materials Science.
The CNSR forms part of the DST/NRF Centre of Excellence in Strong Materials established by the NRF and Department of Science and Technology, which focuses on the synthesis, functionalization, characterisation and applications of carbon-based nanomaterials i.e. carbon nanotubes and strong composites. Research staff in the CNSR are part of the academic staff of the University of Johannesburg, having several strong collaborations with other regional, national, and international institutions. On average the CNSR aims to fund two postdoctoral fellows and a senior research associate’s running costs, for three years, together with a number of postgraduate students.
- Nanomaterials for water treatment including nanocomposite membranes
- Nanomaterials for catalysis applications in water treatment and energy
- Bio-nanomaterials for drug delivery and water purification
- Nanomaterials for sensors and photovoltaic applications in clinical and environmental analysis
The Centre also supports research that involves analytical and electrochemistry with emphasis on water analysis and treatment, which may contain contamination by nanomaterials.
Examples of on-going research in this group include projects on the synthesis of nano materials for catalysis, the synthesis and characterisation of aligned and N/B-doped multi- walled nanotubes chemical vapour deposition and the use of structurally modified nano materials in water purification. Much of this research is multidisciplinary and our postgraduate students gain wide range of experience ranging from synthetic techniques to electron microscopic characterisation. Other projects involve greener methods using microwave irradiation to synthesize nanocomposites materials incorporation doped carbon nanotubes and other metal nanoparticles. Some of the materials synthesized under this banner are listed below.
Activities in this area include fabrication and functionalization of commercial and in-house synthetic microfiltration-, ultrafiltration, nanofiltration and reverse osmosis membranes. The membranes are applied for removal of inorganics, organics and degradation of microbes in water. For degradation of organics and microbes in water, the membranes are impregnated with nanoparticles are im
The research activities involve electrospinning of synthetic and biopolymer solutions under applied voltage to produce nanofibers. The starting materials are synthetic- and biopolymers. The nanofibers are used as filters for removal of both inorganic and organic pollutants in water purification
Ceramics and nanomaterials
The prime research domain in this field is the development of silicon/carbon nanomaterials from carbonaceous waste material using sol-gel technology. These wastes include lignin, low-value coals, coal ash, medical waste, and polymers. The nanocomposite materials are then used for various applications.
Polymer composites and nanocomposites are widely used in the diversified area of material science. It has also been used to develop high energy thermal and packaging devices. The research focus in this division of nanomaterial research has been expanded to include the application of these composite/nanocomposites in the removal of heavy metals and organic pollutants based on adsorption chemistry.
Phosphorus Chemistry Research
The phosphorus chemistry research activities cover synthesis and biological evaluation of new bisphosphonate derivatives as anti-tumour and anti-viral agents. The bisphosphonate derivatives are important because of their anti-metastatic activity in cancer patients and their antiviral activity against HIV-1, HIV-2 and other retroviruses. Current projects focus on phosphorylation of single-walled and double-walled carbon nanotubes. The phosphorylated carbon nanotubes have also been applied in the treatment of radioactive waste and in the removal of toxic metal ions such as Cr(VI) and Hg(II). The Department has had joint anti-cancer research projects with the radiopharmaceutical unit at NECSA (Nuclear Energy Corporation of South Africa).
Water research group
The water research group is one of the apex research niche areas of University of Johannesburg, namely the Water and Health Group (UJWHG). The UJWHG is a unique multidisciplinary organisation that involves engineering, health, and social science disciplines.
There are various thrusts in the water research field. One area focuses on the use of nanoporous polymers (alias nanosponges) for removing organic pollutants in water purification. The activities involve the synthesis of water-insoluble cyclodextrin- and calixarene-based polymers and their derivatives and testing of various forms of the materials, which is a collaboration with the industry partners, to remove organic pollutants. Nanosponges bind organic molecules in aqueous media, but release the same contaminants in organic media, which makes them ideal not only for this application but for chromatography, separation science, and for potential sensor applications. Another area involves electrospinning of polymers to produce nanofiber filters used in form of membranes and cartridges. In another focus area, research activities have recently intensified on nanocomposite membranes decorated with bimetallic nanoparticles for catalytic degradation of organic and microbiological water pollutants. Catalytic nanocomposite membranes is one of the focus areas of Mintek’s nanotechnology innovation centre’s (NIC) research activities. The Department of Applied Chemistry is hosting one of the NIC centres in nanotechnology and water.
The electrochemistry research in the Department focuses on the following: Electrochemical sensors and biosensors based on nanocomposite (dendrimer, gold nanoparticles, graphene and quantum dots) platforms for biomedical, water and environmental applications.
Photoelectrochemistry: i) synthesis and photo/electro-characterisation of novel photoactive composite materials such as graphene, graphite, polymers/dendrimers, and other nanomaterials; ii) development of reactors for water treatment. Application of electrochemistry in the analysis of organic, inorganic and natural products. Current research involves development of chemical sensors for selected organic and inorganic water pollutants, aptamer biosensor for HIV protein detection, cholera biosensor, smart polymer based enzyme biosensors, exfoliated graphite based photoelectrochemical reactors for the removal of organics from water (water treatment), onsite electrochemical sensor for arsenic, among other metals.
DST/Mintek Nanotechnology Innovation Centre (NIC)
The DST/Mintek is a national facility that is geographically spread across the country and was established at Mintek in 2007 by the Department of Science and Technology. The Mintek NIC activities are aimed at addressing national priorities highlighted by both the national nanotechnology strategy and national research and development (R&D) strategy. Importantly, the Mintek NIC structure was built on the foundation of the national system of innovations (NSI) to focus on driving South Africa’s transformation from resource-based economy towards knowledge based economy using nanotechnology. The Mintek NIC activities focus on a number of issues, including the development of research platforms, encouraging and promoting the formation of collaborative networks, addressing human capital development and bridging the “innovation chasm”.
The Department of Applied Chemistry collaborates with the DST/Mintek NIC in an attempt to develop nanomaterials-based solutions to solve problems relating to water treatment (Water Platform). The NIC operates under the umbrella of the Water and Health Research Group, which is a multidisciplinary sounding board within the University for water-related issues including the treatment, distribution, and social consequences of water resources. Its vision is to provide nanotechnology solutions for effective treatment of water to improve the quality of life of the people of South Africa. It seeks to address the objectives of the National Nanotechnology Strategy of South Africa in respect of improving the quality of life by pursuing research and development in water treatment utilizing nanotechnology and membrane technology.
The centre focuses on the use of polymeric materials and zeolites that can be used in a broad range of applications such as filter-beds and ion-exchange columns. These materials are broadly adaptable to different forms including granules, beads and films. Functionality is added by suitable immobilisation of nano-scale metal, inorganic and organic units. The centre’s main area of expertise is the application of synthesis and characterisation techniques to these “functional nanomaterials”. The functional nanomaterials are then applied to the detection, trapping, and destruction of water-borne pollutants, especially trace organic molecules. The centre works closely with local and international research institutions such as the University of the Western Cape, Durban University of Technology, and TU Delft in the Netherlands. It also has close links with science councils and water-bodies such as the Water Research Commission. Thirdly the participation from industrial partners like Rand-Water, ESKOM, and Industrial Urethanes allows us to develop the technology in tandem with the science. The centre has a strong focus on postgraduate student development, and short-term visits by collaborating partners are encouraged.
The following Nanotechnology research activities are carried out
- Nanostructured polymeric adsorbent for capturing organics and heavy metals. Adsorption modules with low pressure drops for fast removal of organics and heavy metals.
- Membrane supported nanocatalysts as treatment options for polluted water and wastewater. Total mineralisation and degradation of organic compounds using membrane supported nanocatalysts which have high degradation rates towards selected compounds are developed and fabricated in-house.
- Hydrophilic nanostructured polymeric membranes for portable water production. Imparting hydrophilicity to old and newly formulated polymeric membranes as a way of minimising fouling and increasing membrane lifespan is generally accepted as the best method.
- The kinetic studies of the nanocomposite membrane treatment is of interest and activities are on-going to understand the science involved. The fate and behaviour of the nanomaterials in the environment is another area of interest. How the nanomaterials interest with environmental matrices in water and sediments, for example is of particular interest. How the aquatic organisms interact with the nanomaterials is another area in which research activities are on-going.
Centre of Excellence for Strong Materials (COESM)
The centre falls within the framework of the Department of Science &Technology and National Research Foundation (DST/NRF) Centre of Excellence in Strong Materials. CoESM focuses on carbon nanomaterials for various applications including water treatment among other applications. The centre’s director is situated at Wits, School of Chemistry with a chapter in the Department of Applied Chemistry at UJ. The centre has strong membership from from the department.
Institute of Nanotechnology and Water
The establishment of the Institute for Nanotechnology and Water at the University of Johannesburg, affiliated with the Department of Applied Chemistry, will position the University as a significant player in realizing the potential of nanotechnology applications to ameliorate many of South Africa’s water problems the results of which can be applied to other countries in Africa. Positioning of UJ on the world map of nanotechnology and water facilitate contact with international experts in this field. As a means of encouraging growth and sustainability, the Institute will mentor younger staff and integrate the project activities into on-going research efforts. The Institute will facilitate research and development projects that arise from the work done in a state-of-the-art laboratories. The establishment of such laboratories will be for the purpose of conducting fundamental research in a model facility which undertakes essential studies that place particular emphasis on performance and quality evaluation of the products produced.
The facility will also host the SARChI Chair in Nanotechnology for Water.
The Paleoproterozoic represents one of the richest mineralized eras in geological history. The understanding of the evolution of System Earth in this era is thus of great relevancy for future exploration for mineral deposits. The era hosts orders of magnitude by far the largest concentrations of iron, manganese, platinum and chromium in the world, in addition to very large concentrations of gold, base metals, fluorspar, graphite, etc. Many of the deposits appear to be time-bounded; related to unique environmental changes like oxy-atmoversion and oxyhydroversion, and establishment of first major supercontinents with associated rift zones and collisional mountain belts. The objectives of the research work conducted by the Paleoproterozoic Mineralization Research Centre are
- to study and model the relationship between environmental change and styles of mineralization in the Precambrian, with a specific focus on the Paleoproterozoic Era.
- to apply the knowledge for evaluating the mineral exploration and beneficiation potential of rock formations formed during that era (1,6 - 2,5 billion years ago) on a global scale.
- to ensure a competitive edge for industrial partners in global mineral exploration and acquisition markets by studying the temporal and spatial distribution, composition, and origin of mineral deposit, on local and regional scale.
- to train postgraduate students in the field of Economic Geology.
The Research Centre is primarily funded by grants from theUJ University Research Council, and further supported by Industry and the National Research Foundation.. Research is undertaken by a team, each member with a specific expertise, in partnership with national and international collaborators. Scientific methods involve integrated stratigraphic, sedimentological and tectonic studies of selected time-bounded deposits and successions, aided by petrographical, mineralogical, geochemical, paleomagnetic and geochronological Studies.
Understanding time-bounded events of mineralization is a major thrust for which intercontinental sequence stratigraphy, absolute age dating, geochemical trends and paleomagnetic reconstruction are essential. Characterisation of the composition of time-bounded ores in the Paleoproterozoic is an important component of the applied economic geology part of the project in order to try and ensure cost-effective extraction and beneficiation of the deposits.
In April 2014 the multi-university DST-NRF Centre of ExcellenceIn April 2014 the multi-university DST-NRF Centre of Excellence “Centre for Integrated Mineral and Energy Resource Analysis” (CIMERA) was launched, which is hosted by PPM and co-hosted by the Economic Geology Research Institute at Wits University, highlighting the close working relationship between the two Centres. In April 2014 the multi-university DST-NRF Centre of Excellence “Centre for Integrated Mineral and Energy Resource Analysis” (CIMERA) was launched, which is hosted by PPM and co-hosted by the Economic Geology Research Institute at Wits University, highlighting the close working relationship between the two Centres.