The Center for Microbial Biotechnology (CMB), Department of Systems Biology, Technical University of Denmark (DTU) would like to invite applications for two 3-year PhD student positions starting in May 2013, or shortly thereafter. The hired PhD students will work on a new project concerning production of natural pigments in microbial cell factories, a partnership between DTU and Chr. Hansen A/S. The Danish National Advanced Technology Foundation financially supports the project.

Project description
The overall aim of the project is to develop a microbial platform for biotransformation of low value plant derived pigments to yield high value natural pigments with enhanced properties, e.g. stability, and colour shades. The PhD students will work as a team to identify enzymes capable of catalysing the desired modifications, establish biosynthetic pathways to provide the necessary building blocks and methods for controlling import and export of pigments in/out of the engineered microorganisms.
The first PhD project (PhD1) will focus on identifying candidate genes encoding enzymes capable of catalysing the desired modifications of pigment, construction of gene libraries and screening for the desired enzymatic activity. The second PhD project (PhD2) will concentrate on analysing and optimizing transport in and out of the chosen microbial cell factories, and the develop a platform for chemical analysis of the compounds from the biotransformation process.
The PhD students will become members of a project group consisting of two other PhD students and a post-doc, which will be supervised by Professor Uffe H. Mortensen, Associated Professor Ulf Thrane, Associated Professor Thomas O. Larsen and Assistant Professor Rasmus J. N. Frandsen in close collaboration with relevant experts from Chr. Hansen A/S.

PhD1 – Theme: Identification and characterization of transferases
This PhD project aims to build a microbial platform that allows efficient screening of libraries of genes encoding potential pigment modifying enzymes (transferases). This includes identification and characterization of this class of enzymes by mining public sequence databases and via genome/transcriptome sequencing of pigment producing plant species. Additionally, enzyme-coding genes will be expressed in various heterologous host strains using high-throughput USER cloning and screening for enzymes that can provide targeted pigment structures. Further characterization of the positive hits in the libraries will consist of a detailed analysis of substrate specificity. The project will deliver industrial value, in the form of enzymes for refining food relevant pigments, and scientific value by a comprehensive understanding of the transferase class of enzymes.

PhD2 – Theme: Toxicity, import and export of pigment in yeast
This PhD project first aims at determining and describing any toxicity of natural pigments to yeast. Subsequently, it will establish, optimize and analyse the interaction between pigments and yeast in terms of uptake of the native pigments and export of the refined compounds. This includes a determination of the intracellular pigment structure, intermediates and other substrates for the enzymatic processes. To do this, the project will also aim at setting up an analytical platform for monitoring the known and biotransformed pigments in collaboration with the Metabolomic Facility at DTU Systems Biology. A UV-library of known and new pigments will be created and used for automated detection of these compounds by target mass spectrometric analysis. The exact structure of all significant pigments will be elucidated by NMR spectroscopy. The project will deliver important industrial value in terms of new and refined pigment as well as scientific value by a thorough understanding of the transport mechanisms in microbial cell factories.

Qualifications
Candidates must have a M.Sc. degree within a relevant field, such as molecular biology, biochemistry, biotechnology, microbiology or equivalent academic qualifications. Candidates for project 1 must be able to document solid experimental experience in genetic engineering and biochemistry, and for project 2 in biochemistry, microbiology and analytical chemistry. Furthermore, preference will be given to candidates who can document that they are knowledgeable in some or all of the following specific areas: gene discovery, genome annotation, heterologous expression in E. coli and Saccharomyces cerevisiae, metabolic engineering, development of enzymatic screening assays, use of pipetting robots and metabolomics techniques using UPLC-HRMS systems. The size of the project group and diverse skill sets required for successful completion of the project, calls for persons with a mind-set for collaboration and a desire to master new scientific disciplines. Lastly, a good grasp of the English language is essential.

Further information
Further information concerning the project can be obtained from Professor Uffe H. Mortensen (um@bio.dtu.dk, +45 4525 2701), Associate Professor Ulf Thrane (ut@bio.dtu.dk, +45 4525 2630) and Assistant Professor Rasmus J. N. Frandsen (rasf@bio.dtu.dk, +45 4525 2708).

Approval and Enrolment
The scholarships for the PhD degree are subject to academic approval, and the candidates will be enrolled in one of the general degree programmes of DTU. For information about the general requirements for enrolment and the general planning of the scholarship studies, please see the DTU PhD Guide.

Salary and appointment terms
The salary and appointment terms are consistent with the current Danish rules for PhD degree students.

Application
We must have your online application by 2 April 2013.

Applications must be submitted as one pdf file containing all materials to be given consideration. To apply, please open the link « Apply online, » fill in 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)
• A clear indication of which PhD position you apply for
• Curriculum vitae
• Documentation of a relevant completed M.Sc. degree
• Course and grade list of Bachelor and Master degrees
• Excel sheet with translation of grades to the Danish grading system (see guidelines and excel spreadsheet here)

Candidates may apply prior to obtaining their master’s degree, but cannot begin before having received it.

All interested candidates irrespective of age, gender, race, disability, religion or ethnic background are encouraged to apply.

Work place
The Department of Systems Biology represents a large concentration of academic biotechnological research in Denmark, including protein and enzyme chemistry, food biochemistry, bioinformatics, systems biology, molecular biology, fermentation technology, physiology and genetics of industrial microorganisms and medical microbiology. The department hosts around 35 senior and 50 junior faculty members and post-doctoral fellows, 65 PhD students and 80 technical/administrative personnel. In addition to bachelor, master and PhD education, collaborative research and innovation together with national and international universities and industries is given high priority at the Department.

Center for Microbial Biotechnology (www.cmb.bio.dtu.dk/English.aspx) has 13 senior and 6 junior faculty and post-doctoral fellows and 25 PhD students as well as technical/administrative staff. The research is on industrial biotechnology, including fermentation, fungal biodiversity, heterologous expression of secondary metabolites in new hosts, mycotoxins, and metabolic engineering.