Přehled
Title: Computational Characterization of Enzymes for Sustainable Design of Bioplastics
Study program: Biomedical Technology and Bioinformatics
Supervisor: Assoc. Prof. Karel Sedlář, PhD
Topic description:
White biotechnology, i.e. a technology that uses living cells to produce value added chemicals, usually loses the competition with standard petrochemical production due to higher financial costs. The biological production of plastics is not an exception, mainly because of insufficient characterization of enzymes responsible for synthesis of various polymers. Although these enzymes are quite abundant in bacteria, systematic computational research based on analysis of their sequences has not been performed so far.
The topic is focused on developing a computational pipeline for analysis of sequences of polyhydroxyalkanoate (PHA) synthases with the ultimate goal of creating their comprehensive database. PHA are microbial polyesters synthesized by various prokaryotic microorganisms with great potential for plastics industry. However, their wider use is still limited by a lack of fundamental knowledge on key genes/enzymes in various prokaryotes responsible for their synthesis, preventing the use of the most suitable organisms and their potential genetic engineering necessary to establish economically feasible processes. The aim of the research is to analyse all currently available genome sequences in order to classify them into four known classes or to propose their novel classification. Additionally, particular classes will be characterized by matching sequences with physicochemical properties of polymers they synthesize. Proposed computational pipelines for analysis of close and
distant orthologues will be deployed together with a database of PHA synthases.
The project will be solved mainly at the Department of Biomedical Engineering. However, cooperation with our national (University Hospital Brno, the Faculty of Chemistry BUT, and Czech Collection of Microorganisms) and foreign partners (Ludwig-Maximilians-Universität München in Germany and HESSO Valais-Wallis in Switzerland) is expected. PhD students will complete a six-month internship at attractive partner universities abroad. UBMI provides doctoral students with a stipend and/or a parttime contract beyond the state stipend when joining a grant project or engaging in teaching.
Your task:
- Analysis of all currently available bacterial genomes.
- Deploy your own computation pipelines.
Requirements:
- Previous education in bioinformatics or biotechnology.
- Good communications skills and desire to work on yourself.
We offer:
- To join young investigator’s team solving cutting-edge projects.
- Possibility to travel to foreign conferences and cooperating institutions.
For more information about this topic please contact Karel Sedlář – sedlar@vut.cz
How to apply:
Please apply and submit your motivation letter and CV via university website from April 1 to April 30, https://www.vut.cz/eprihlaska/cs/zadani/vybrat-obor/fakulta/5
Funding:
Funding is provided as a combination of part-time or full-time research projects and/or regular scholarships.
