The department DTU Bioengineering at the Technical University of Denmark invites applications for a position as a PhD student in Intracellular Metabolites as Fermentation Indicators (IMFI). The position is part of the FBM Initiative, which is funded by the Novo Nordisk Foundation.
The FBM Initiative is a collaboration between offers rDTU Bioengineering
This position will be placed in the Microbial Signalling and Regulation group, in Department of Biotechnology and Biomedicine, section for Microbial and Chemical Ecology. The section is working withapplied microbial diversity, evolution and community dynamics by both classical microbiological, genetic and biochemical approaches, and hosts the metabolomics platform where a combination of GC and LC coupled to DAD and QTOF MS/MS is commonly used for analyses of microbial secondary metabolites.
Responsibilities and Tasks
The project is a joint venture between DTU bioengineering, DTU Chemical engineering, and Glycom, a world leading producer of human milk oligosaccharides (HMO) by fermentation. The PhD student will develop a pipeline for the extraction and quantification of intracellular metabolites, including nucleotides and secondary messengers from bacteria grown under various physiological conditions. After development the procedure will be implemented at both the DTU Metabolomics platform and at Glycom. For intelligent modulation of the interplay between metabolite fluxes and metabolite concentrations in regulated metabolic pathways, the PhD student will adopt a stochastic (Gillespie) model, designed in the Metabolic Signalling and Regulation Group, to be able to predict the effects of regulatory mutations.
In this project, you will
- Be part of a large FBM network, and participate in a collaborative environment with participants from Glycom and two institutes at DTU
- Apply bacterial growth physiology and molecular microbiology to obtain reproducible metabolite concentrations under various conditions
- Develop a quenching procedure to stop cellular metabolism and allowing extraction of intracellular metabolites
- Develop an LCMS method for simultaneous quantification of more than 25 intracellular metabolites based upon HILIC separation
- Use quantification of metabolites for discovering potential metabolic bottlenecks during industrial production of HMO
- Use adaptive laboratory evolution to identify mutations that relieve strains from stress due to metabolic dysregulation or bottlenecks
- Adopt a stochastic model for use in simulation of regulated pathways
Candidates should have a Master's degree in engineering or a similar degree with an academic level equivalent to the Master's degree in engineering.
We are looking for a candidate with a solid background in
- Bacterial physiology and molecular microbiology
- Programming in Matlab or similar programs
We will prefer a candidate with skills in one or several of the following areas
- Quantification of metabolites by LCMS
- Regulation of gene expression
- Quenching of microbial cells
- Adaptive laboratory evolution
DTU is a leading technical university globally recognized for the excellence of its research, education, innovation and scientific advice. We offer a rewarding and challenging job in an international environment. We strive for academic excellence in an environment characterized by collegial respect and academic freedom tempered by responsibility.
Applications must be submitted as one PDF file containing all materials to be given consideration. To apply, please open the link "Apply online", fill out the online application form, and attach all your materials in English in one PDF file.
The file must include
- A letter motivating the application (cover letter)
- Curriculum Vitae
- Grade transcripts and BSc/MSc diploma
- Excel sheet with translation of grades to the Danish grading system (see guidelines and Excel spreadsheet here)