PhD scholarship in Diversity and Evolution of bacterial Biosynthetic Gene Clusters at the Center for Microbial Secondary Metabolites, CeMiSt

torsdag 12 aug 21

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Frist 24. september 2021
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We offer a PhD fellowship at Department of Biotechnology and Biomedicine (DTU Bioengineering) at the Technical University of Denmark. The PhD project is part of the Center for Microbial Secondary Metabolites, CeMiSt and will be carried out in the Bacterial Interactions and Evolution Group headed by Professor Ákos T. Kovács at DTU Bioengineering and in the Natural Products Genome Mining group headed by Tilmann Weber at DTU Biosustain.

CeMiSt is a Center of Excellence funded by the Danish National Research Foundation. The Center started in 2018 and will run for six years with an option for a four-year extension. The Center is based at the Technical University of Denmark and hosted by Department of Biotechnology and Biomedicine (DTU Bioengineering). Three DTU departments and 10 senior faculty participate in the Center and >15 PhD students and postdocs are hired. The purpose of CeMiSt is to unravel the biological role of microbial secondary metabolites in natural microbiological communities. The Center is led by Professor Lone Gram.

We are seeking a candidate to study the diversity of bacterial secondary metabolite production using genome analysis and metagenome sequencing. You will be involved in a fun PhD project on bioinformatic analysis of genome sequences, with strong international connections, a productive scientific environment, and a good work-life balance.

Responsibilities and qualifications
Your PhD project will contribute to our understanding of the diversity and evolutionary changes of gene clusters related to microbial secondary metabolite (SM) production. You will perform bioinformatic analysis of publicly available and in-house sequenced genomes of the Bacillus genus, in addition to enriched metagenome data. In addition, you will determine the genome phylogeny in the Bacillus genus to determine the turnover and evolutionary rates of biosynthetic gene clusters.

Your experience within the areas of computational or evolutionary biology will be an advantage, including:

  • Experience in working with large sequencing datasets
  • Knowledge about genome and/or metagenome sequence analysis and assembly strategies
  • Experience in R or preferably Python
  • Knowledge about evolutionary rate analysis and evolutionary theory

Previous knowledge about microbial secondary metabolite biosynthesis and experience with DNA extraction is advantageous or the willingness to learn is required. You may collaborate with natural product chemistry scientists to elucidate structures of key compounds associated to the biosynthetic gene clusters.

Expected starting date: December 2021 or shortly thereafter.

You must have a two-year master's degree (120 ECTS points) molecular biology, biology, engineering or a similar degree with an academic level equivalent to a two-year master's degree.

Approval and Enrolment
The scholarship for the PhD degree is subject to academic approval, and the candidate will be enrolled in one of the general degree programmes at DTU. For information about our enrolment requirements and the general planning of the PhD study programme, please see the DTU PhD Guide.

Assessment
The assessment of the applicants will be made by by Professor Ákos T. Kovács and Professor Tilmann Weber.

We offer
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 an academic freedom tempered by responsibility.

Salary and appointment terms
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.

You can read more about career paths at DTU here.

Further information
Further information may be obtained from Professor Ákos T. Kovács, tel.: +45 4525 2527, atkovacs@dtu.dk  

Please do not send applications to this e-mail address; follow the electronic application and submission procedure as explained below.

You can read more about DTU Bioengineering on http://www.bioengineering.dtu.dk and a DTU podcast introduces the Center that is also described at www.cemist.dtu.dk.

If you are applying from abroad, you may find useful information on working in Denmark and at DTU at DTU – Moving to Denmark.

Application
Please submit your online application no later than 24 September 2021 (Danish time).

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) - Please provide contact details for two referees in your motivation 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)

You may apply prior to ob­tai­ning your 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.

The Center for Microbial Secondary Metabolites aims to establish what effect microbial secondary metabolites have on other microorganisms in their natural environment. We have traditionally perceived them as ‘competition substances’, but in natural environments they are rarely produced in quantities of antibiotic effect. The Center’s hypothesis is that secondary metabolites constitute a network of signal molecules that directly affect gene expression, behaviour, and metabolism of the microorganisms and thus play a decisive role in the composition and function of microbiological communities. We will explore this in an interdisciplinary collaboration with the use of sequence-based, analytical-chemical, molecular, bioinformatic, and classic microbiological methods.

The Department of Biotechnology and Biomedicine (DTU Bioengineering) addresses challenges of societal and scientific importance within biotechnology, biomedicine, food technology and human health. The department is based on both basic and applied research and employs tools from biochemistry, biophysics, chemistry, cellular biology, immunology, microbial ecology and physiology, bioinformatics and bio-engineering. 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. 300 employees, of which 2/3 is scientific staff. The department is located at DTU Lyngby Campus.

Technology for people
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 12,900 students and 6,000 employees. We work in an international atmosphere and have an inclusive, evolving, and informal working environment. DTU has campuses in all parts of Denmark and in Greenland, and we collaborate with the best universities around the world.