PhD student in Intracellular Metabolites as Fermentation Indicators (IMFI)

Updated: 2 months ago
Job Type: FullTime
Deadline: 07 Aug 2020

The department DTU Bioengineering at the Technical University of Denmark invites applications for a position as a PhD student <strong>in Intracellular Metabolites as Fermentation Indicators (IMFI). </strong>The position is part of the FBM Initiative, which is funded by the Novo Nordisk Foundation.<br />The FBM Initiative is a collaboration between DTU Chemical Engineering, DTU Bioengineering, and the Novo Nordisk Foundation Center for Biosustainability. It offers research-based education in Fermentation Based Biomanufacturing for Master- and PhD- students, and professionals.<br />This position will be hosted at DTU Bioengineering and is one of seven PhD student positions available for the FBM PhD program this year.<br /><br />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 with applied 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.<br /><br /><strong>Responsibilities and Tasks</strong><br />The project is a joint venture between DTU bioengineering, DTU Chemical engineering, and Glycom, a world leading producer of human milk oligosaccharides (HMO) by <em>Escherichia coli </em> 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.<br /><br />In this project, you will:<ul><li>Be part of a large FBM network, and participate in a collaborative environment with participants from Glycom and two institutes at DTU</li><li>Apply bacterial growth physiology and molecular microbiology to obtain reproducible metabolite concentrations under various conditions </li><li>Develop a quenching procedure to stop cellular metabolism and allowing extraction of intracellular metabolites</li><li>Develop an LCMS method for simultaneous quantification of more than 25 intracellular metabolites based upon HILIC separation</li><li>Use quantification of metabolites for discovering potential metabolic bottlenecks during industrial production of HMO</li><li>Use adaptive laboratory evolution to identify mutations that relieve strains from stress due to metabolic dysregulation or bottlenecks</li><li>Adopt a stochastic model for use in simulation of regulated pathways</li></ul><br /><strong>Qualifications</strong><br />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.<br /><br />We are looking for a candidate with a solid background in:<br /> <ul><li>Bacterial physiology and molecular microbiology</li><li>Programming in Matlab or similar programs</li></ul><br />We will prefer a candidate with skills in one or several of the following areas:<br /> <ul><li>Quantification of metabolites by LCMS</li><li>Regulation of gene expression</li><li>Quenching of microbial cells </li><li>Adaptive laboratory evolution</li></ul><br />We expect that you are an efficient team worker, have good communication skills, and have a critical approach to the formulation and testing of hypotheses. Also, a good sense of humor will be appreciated.<br /><br /><strong>Approval and Enrolment</strong><br />The scholarship for the PhD degree is subject to academic approval, and the candidate will be enrolled in one of the general degree programs at DTU. For information about our enrolment requirements and the general planning of the PhD study program, please see the <a href="http://www.dtu.dk/english/Education/PhD/Rules/PhDguide" target="_blank">DTU PhD Guide</a>.<br /><br /><strong>Assessment</strong><br />The assessment of the applicants will be made by Mogens Kilstrup and approved by an internal PhD assessment committee.<br /><br /><strong>We offer</strong><br />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.<br /><br /><strong>Salary and Appointment Terms</strong><br />The appointment will be based on the collective agreement with the Danish Confederation of Professional Associations. The allowance will be agreed upon with the relevant union. The period of employment is 3 years.<br /><br />You can read more about <a href="http://www.dtu.dk/english/about/job-and-career/working-at-dtu/career-paths" target="_blank">career paths at DTU here</a>.<br /><br /><strong>Further information</strong><br />Further information may be obtained from Mogens Kilstrup, <a href="mailto:mki@bio.dtu.dk," target="_blank">mki@bio.dtu.dk ,</a> or +45 21138815.<br /><br />You can read more about DTU Bioengineering at <a href="http://www.Bioengineering.dtu.dk" target="_blank">.<br">www.Bioengineering.dtu.dk</a>.<br /><br /><strong>Application</strong><br />Please submit your online application no later than <strong>7 August 2020 (23:59 local time)</strong>. Apply online at <a href="http://www.career.dtu.dk/" target="_blank"><br">www.career.dtu.dk</a><br /><br />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:<br /> <ul><li>A letter motivating the application (cover letter)</li><li>Curriculum Vitae</li><li>Grade transcripts and BSc/MSc diploma</li><li>Excel sheet with translation of grades to the Danish grading system (see guidelines and <a href="http://www.dtu.dk/english/Education/phd/Applicant/Pre_acceptance-1-" target="_blank">Excel spreadsheet here</a>)</li></ul><br />Candidates may apply prior to ob­tai­ning their Master's degree but cannot begin before having received it.<br /><br />All interested candidates irrespective of age, gender, race, disability, religion or ethnic background are encouraged to apply.<br /><br /><em>The Fermentation Based Biomanufacturing (FBM) Initiative was founded as a response to the biotech industry’s increasing demand for specialized expertise in the fermentation area. Cutting-edge research, covering all aspects from fundamental physiology of production organisms/cell factories, synthetic biology and metabolic engineering, to scale-up process technology and downstream processing, provides the basis for the specialized FBM Education. The educational activities are developed in close dialogue with industry partners.<br />The FBM Initiative at DTU educates top-candidates at MSc and PhD level, and provides research-based expertise for the biotechnological, chemical, and pharmaceutical fermentation based biomanufacturing industry. </em><br /><br /><em>The Department of Biotechnology and Biomedicine (DTU Bioengineering) conducts research, educates future bio-engineers, provides scientific advice and innovate within the areas of microbiology, biochemistry, biotechnology and biomedicine. The research at DTU Bioengineering is at the highest international level and focuses on the societal and scientific challenges within the field. Research is conducted within three main areas: Microbial ecology and physiology, Industrial biotechnology and cell factories, and Biomedicine and health. The department has extensive collaboration with national and international research units and industries. DTU Bioengineering has approx. 160 employees, of which 2/3 is scientific staff and is expanding rapidly in 2020. The department is located at DTU Lyngby Campus.</em><br /><br /><strong><em>Technology for people</em></strong><br /><em>DTU develops technology for people. With our international elite research and study programmes, we are helping to create a better world and to solve the global challenges formulated in the UN’s 17 Sustainable Development Goals. Hans Christian Ørsted founded DTU in 1829 with a clear vision to develop and create value using science and engineering to benefit society. That vision lives on today. DTU has 11,500 students and 6,000 employees. We work in an international atmosphere and have an inclusive, evolving, and informal working environment. Our main campus is in


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