We are looking for a capable and energetic PhD student to work on a multidisciplinary project on the microbiome of wheat under Conservation Agriculture. The project will involve high throughput amplicon sequencing and qPCR methods, among others. The project is funded by the NRF, and there is a bursary available, however, preference will be given to students who already have their own bursary. The ideal candidate should have completed a MSc degree in Microbiology, Genetics or Biochemistry or any related field with a strong background in molecular biology. Preference will also be given to South African citizens.
Project Title: Regional microbial signatures in South African and Austrian vineyards
Scope of Research: The project is focused on understanding vineyard microbial ecosystems, in particular the influence of region of origin on the mycobiota of grapes. The postdoctoral candidate will have the opportunity to work on individual research as well as to work within a team (doctoral, masters and Hons level students), and in addition, to gain experience in supervision.
Postdoctoral Research Fellowship (18‐month appointment)
Project Title: Engineering yeast strains for biofuel production
The National Research Foundation has awarded the South African Research Chairs Initiative (SARChI): Biofuels and Other Clean Alternative Fuels to prof. WH (Emile) van Zyl at the Department of Microbiology, Stellenbosch University. The Research Chair focuses on the development of technologies for commercial production of secondgeneration bio-energy from lignocellulosic biomass in South Africa.
Plant biomass-derived bioethanol is regarded as a leading alternative energy source in a fossil fuel dependent energy paradigm. Bioethanol functions as octane enhancer, and can be used to replace up to 15% of petrol. It also acts as a fuel oxygenate in petrol blends allowing more complete combustion and hence, decreased polluting emissions. The departments of Microbiology and Process Engineering at Stellenbosch University, through the South African Research Chair (SARChI) in Biofuels, are at the forefront of South African research to address the shortcomings of plant polysaccharide conversion to bioethanol. Strains of Saccharomyces cerevisiae were engineered to simultaneously hydrolyse plant materials (cellulose and raw starch) and ferment the resulting monosaccharides through the development of enabling technologies such as advanced plant polysaccharides pretreatment and advanced Consolidated Bioprocessing (CBP). Simplification and cost-reduction of the hydrolysis-fermentation process can be further achieved by integrating superior enzymatic hydrolysis and fermentation with more robust yeast into a single unit operation. To achieve this, supportive bioinformatics research dedicated to solving current problems in bioethanol biotechnology, specifically improved industrial performance of yeast strains and improved catalytic efficiency of enzyme hydrolysis, remain key.
The Next Generation Sequencing Unit at the Central Analytical Facilities (CAF) is seeking a highly motivated Postdoctoral Fellow to join the NGS team and expand the Bioinformatics capacity.
Project title: NGS data analysis in projects related to wheat and wheat diseases
Duration: 2 years
Scope of Research:
CAF currently boasts a SOLiD 5500xl and an Ion Torrent PGM together with conventional sequencing equipment. The DNA Sequencing unit has been operational for over 12 years with recent expansion into the NGS market, and delivers a service to local and international clients from academia as well as industry.
The successful candidate will initially mainly be involved in analysis of data relevant to two projects in the Agri Biotech field.
The first project will generate genomic NGS data for 4 fungal races of the same species. The genomes have to be assembled and annotated. Comparative analysis between the four races will be part of the project in collaboration with the client.
The second project entails transcriptome sequencing of wheat. RNA-seq data will be analyzed and differentially expressed genes be identified for our international collaborator.
The candidate might also be requested to get involved in other projects running at CAF.
Requirements: PhD in Genetics, Bioinformatics, Computer Science or related field (must have graduated within the last five years.
The successful candidate will have at least 2 years experience in the analysis of NGS data preferably with experience of SOLiD data.
- The accepted applicant should have strong written and communication skills, and be proficient in the following:
- Open source command line Bioinformatics software
- HPC (not required)
- Perl or Python and shell scripts
- Understanding of basic genetics and molecular techniques
Successful applicants will be subject to University policies and procedures.
Commencement of duties: As soon as possible
Remuneration: A bursary will be available – value depends on experience of successful candidate
Closing date: 7 April 2013
- Postdoctoral fellows do not hold posts or positions; neither do they enter into an employment contract with the University.
- They receive a fellowship in order to conduct research, and do not receive a salary or remuneration for contract research or teaching.
- Their bursaries are paid out via the bursary system and not Human Resources.
- They are not part of the teaching staff of the university, neither are they contract researchers.
- They are not postgraduate students