Postgraduate Vacancies

 ONE PHD STUDENT AND ONE POSTDOCTORAL STUDENT

MSc project opportunity - Hybridisation of Chorister and Red-capped Robin-Chats
An NRF funded MSc project is offered at the School of Animal, Plant and Environmental Sciences, University of the Witwatersrand, to investigate hybridisation in two closely related robin-chat species, i.e. Chorister Robin- Chat Cossypha dichroa and Red-capped Robin C. natalensis.
Contact: Dr Craig Symes, School of Animal, Plant and Environmental Sciences, University of the Witwatersrand, P/Bag 3, WITS, 2050, South Africa. email: craig.symes@wits.ac.za
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ADVERTISEMENT :  ONE MSc. AND ONE  POSTDOCTORAL STUDENT

PLANT BIOTECHNOLOGY LABORATORY, SCHOOL OF MOLECULAR AND CELL BIOLOGY, UNIVERSITY OF THE WITWATERSRAND

START DATE: January 2012 (AS SOON AS POSSIBLE)

REQUIREMENTS: Both student positions require the appropriate qualifications and should preferably be South African permanent residents or citizens.  The background required to do this project would be microbiology (preferably some plant virology); molecular biology; plant biotechnology and some knowledge and practice of general plant transformation and tissue culture.  Some basic bioinformatics is also required.

Applications should be sent by email along with three reference contacts (with email contacts); CV; and academic transcripts. 

CONTACT:  PROFESSOR CHRISSIE REY EMAIL: Chrissie.rey@wits.ac.za; telephone: 011-7176324

IMPROVEMENT OF CASSAVA AS A CROP

BACKGROUND

Cassava is an important food security crop and source of starch for industrial applications and

Biofuels cassava mosaic disease (CMD), caused by cassava mosaic geminiviruses (CMGs) and transmitted by whitefly Bemisia tabaci Gennadius is one of the two most important viral diseases of cassava in Africa.

Our laboratory is interested in exploring new aspects to host-pathogen interactions which will help

to devise strategies for managing or reducing crop losses. These projects include genetic engineering for virus resistance; genomics for identifying natural resistance genes in cassava; or characterizing the recovery phenotype in cassava cultivars that show symptom and disease recovery after infection

MASTERS PROJECT

RNA silencing is a process that suppresses the expression of certain genes through sequence-specific interactions with RNA at the post-transcriptional stage (PTGS), involving small interfering RNAs (siRNAs), or at transcription (usually induced by DNA methylation), and can also be used to engineer virus resistance.   Recovery is a phenotype observed in virus-infected plant hosts characterised by initially severe symptoms which are observed to gradually attenuate until the host appears almost symptomless. It has been reported that a correlation exists between the cassava recovery phenotype post infection with ACMV and SLCMV and the production of virus-derived siRNAs through post-transcriptional gene silencing (PTGS). However, much research remains to be done to better understand the recovery phenotype observed in cassava post infection by other CMGs such as South African cassava mosaic virus (SACMV).

Research Objectives

The overall objectives of this research are to understand the mechanisms of disease resistance or recovery  in

relation to cassava begomoviruses.

Specific Aims

1. To deep sequence the siRNA species populations occurring in the greatest numbers from the enriched siRNA isolates of TME3 (tolerant cultivar) and T200 (susceptible cultivar) at the 3 time points post infection, including 67dpi, when the recovery phenotype is expected to be observable. Deep sequencing of the isolated siRNAs will be performed at the ARC-Biotechnology Platform at Onderstepoort using the Illumina iScan. 

To use bioinformatics tools to analyse the siRNA populations in order to determine if the siRNAs that contribute toward the recovery phenotype being induced in the resistant host plant TME3 are different in virus target regions or numbers compared with the susceptible variety.  Deep sequencing the isolated siRNAs will allow for observation of which parts of the genome of SACMV are targeted. The data collected from the deep sequencing may also aid in comparison of the abundance (quantities) of vsRNAs at each time point and between the susceptible and recovery-phenotype cassava landraces.

POSTDOCTORATE STUDENT

There are arguably only two approaches to controlling or reducing virus disease and preventing crop yield losses: Genetic engineering using a pathogen-derived approach which induces basal innate immunity (RNA silencing); or to mine genes that are involved in susceptibility or resistance in crops, such as cassava, and use those to manipulate the host plant.   In order to identify candidate genes, one approach is to compare the entire transciptome of a resistant and susceptible cassava plant.  Today, sequencing and assembly methodologies are automated and can be applied to entire genomes. The recent new innovations in Genome Sequence Analyzers (such as the Roche GS 20/FLX (454 parallel sequencing platform), Illumina Solexa Technology or Applied Biosystem SOLiD) can generate millions of bases of DNA, allowing for an increase in the scale of research centred on the discovery of new genes.   Furthermore, these high throughput systems allow the sequencing and quantification of entire transcriptomes, which is a powerful tool to compare expressed genes in pathogen-resistant and susceptible plant hosts. Deep-sequencing of  two cassava transcriptomes (susceptible and resistant at 3 dpi for each) was carried out using multiplex sequencing and the sequencing platform of the recently upgraded SOLiD 4 SYSTEM Genome Analyzer at the University of Zurich Functional Genomics Center and data in now available to compare susceptible and resistant varieties. We are interested in identifying genes involved in disease or resistance traits.

Aims

1. To use bioinformatics tools to compare and analyse subsets of the data.
2. Identification of up-or down-regulated genes possibly involved in virus disease replication or movement or in resistance
3. Validation of gene functionality using virus-induced gene silencing

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ADVERTISEMENT: Two M. Sc students

Field: Environmental Biotechnology, School of Molecular and Cell Biology, University of the Witwatersrand

Start Date: Immediately

Requirements: Interested candidates must be in possession of a B. Sc (Honours) degree and must be South African citizens or permanent residents. Candidates will be expected to maintain a high standard of work, leading to at least one publication in a recognised peer-reviewed journal.

Interested applicants should submit a CV, academic transcript with 3 referees to Dr. Kulsum Kondiah at Kulsum.Kondiah@wits.ac.za. Enquiries can be directed to the provided e-mail address or telephonically at 27 11 717 6312.

BACKGROUND:

The research group is interested in investigating cheap yet innovative detection and treatment strategies for heavy metals present in acid mine drainage. Metallophilic bacteria surviving in such extreme environments have evolved mechanisms that sequester or detoxify heavy metal ions that can easily be exploited for biosensing and bioremediation.

MASTER’S OPPORTUNITY 1:

Expression of metal-binding genes for application in a portable biosensor

Metallophilic bacteria use a number of strategies to survive in high concentrations of heavy metals that would otherwise be toxic to normal cellular activities. Such mechanisms include efflux pumps, extracellular sequestration and enzymatic detoxification and reduction which are all driven by proteins. Metalloregulatory proteins such as metallothioneins can bind heavy metal ions leading to regulation of proteins involved with the sequestration or reduction of heavy metals. Such metal binding proteins can be exploited in the construction of a nanobiosensor as the biological component that binds the ions resulting in an output that can be converted into a detectable signal.

Aim: To express and purify metal binding proteins for use in the construction of an electrochemical nanobiosensor.

The project will require skills in molecular biology and proteinomics.

MASTER’S OPPORTUNITY 1:

Investigation of the bioremediation potential of metallophilic bacteria

Metallophilic bacteria that are capable of bioaccumulating or reducing toxic heavy metal ions find application in bioremediation. These bacteria can remove the heavy metal ions from the water by adsorbing them onto their cell walls or accumulating them within vesicles in the cell. Alternatively, some metallophiles can reduce toxic heavy metal ions that result in carcinogenesis and neurotoxicity to less toxic forms that are safer when ingested.

Aim: To investigate the potential for metallophilic bacterial isolates to bioaccumulate lead, nickel and cobalt

The project will require skills in bacteriology.