Extraction of biofilm matrix for proteomic analyses - A proof-of-concept study

Project type: Master

In nature, the predominant lifestyle of bacteria is living in polymicrobial communities. Most bacteria live in so-called biofilm communities in which cells are embedded in a self-produced extracellular matrix. The main components of the biofilm matrix are extracellular polymeric substances (EPS), including amyloid-like fibers.

Biofilms provide many advantages for the members, such as protection from antibacterial compounds or generation of local niches, which facilitates cell specification. We hypothesize that many of these advantages are linked to the structure and composition of the biofilm matrix, which is explored in the present project. 

 In the Section of Microbiology, we use a four-species bacterial model community displaying synergistic features. We aim to understand the inter-species dynamics between the four members with various approaches, such as genetic manipulation, bioinformatic analyses, phenotypic assays, and microscopy. A specific research focus is the identification and quantification of proteins present in the biofilm matrix of different community compositions.
In this project, we will separate biofilm cells and matrix and perform proteomic analyses of the matrix fraction based on mass spectrometry analysis. To validate the matrix extraction, you will apply molecular techniques to follow and optimize the extraction protocol. Once the MS data is acquired, you will apply bioinformatic pipelines for proteomic comparisons of the matrix proteomes of wild-type strains and specific biofilm mutants.

 The project will be conducted at the Section of Microbiology at Nørre Campus in Copenhagen. We have a diverse lab environment with researchers focusing on various aspects of microbiology and a high level of interproject interactions. You will have a day-to-day supervisor in the lab that will assist you with practical and scientific tasks and ensure your smooth transition into the group. The project is flexible and will be well-suited for a microbiology or biochemistry student interested in microbiology and bioinformatics. Do not hesitate to contact us for more information, and feel free to come by and have a chat about how to shape the project to match your interests.

For more information, please contact:
Mette Burmølle, E-mail: burmolle@bio.ku.dk
Heiko T. Kiesewalter, E-mail: heiko.kiesewalter@bio.ku.dk

READ MORE AT: https://www1.bio.ku.dk/english/research/microbiology/

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