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Nucleating the growth of biofilms for biocatalysis with polymer chemistry

Primary Supervisor: Dr Paco Fernandez-Trillo (PFT), School of Chemistry

Secondary supervisor: Robin C May (RCM) and Sara Jabbari (SJ)

PhD project title: Nucleating the growth of biofilms for biocatalysis with polymer chemistry

University of Registration: University of Birmingham

Project outline:

Bacteria often attach to surfaces in the form of biofilms. Biofilms represent a problem in many medical and industrial settings as they are physically tough and hard to kill or remove from surfaces. However, these characteristics make biofilms a potentially very useful platform for biocatalysis, where bacteria are used to make chemicals for a variety of purposes. This project will focus on controlling the way in which bacteria attach to surfaces, so we can specify when and where biofilms form.

In this project we will investigate the use of synthetic polymers to nucleate the growth of biofilms that will be utilised as a platform for biocatalysis. Previous work in FFT’s laboratory has demonstrated the potential of polymers to induce the clustering of bacteria and dictate the phenotype of the formed biofilm (F. Fernandez-Trillo et al. bioRxiv 2016). This expertise will be coupled with TWO’s expertise in the use of biofilms as a platform for biocatalysis. We will develop a high-throughput platform to evaluate how polymer length and composition determines the phenotype of the formed biofilms and their potential to produce relevant metabolites. This work has relevance in the production of pharmaceuticals, and potential applications for synthesis of fine chemicals.

A key question in this project is how polymers interact with bacterial surfaces and envelopes. The Gram-negative cell envelope is a complex, multi-layered structure that changes in response to growth and environmental conditions. As such, interactions of bacteria with polymers would be expected to change in response to these environmental conditions. This brings about the exciting possibility that interactions between polymers and bacteria can be tuned from both sides: changes in polymer chemistry (eg charge, hydrophobicity); and changes in envelope (eg outer membrane physicochemical properties).

Research Objectives: Our high-throughput strategy is based on the modification of a polymer scaffold (P1) to give us access to a library of modulated polymers (P2) with a broad range of chemical functionalities in highly efficient way (Scheme). Chemical functionality will be selected from a range of moieties known to mediate bacterial adhesion to surfaces and hosts, such as cationic residues, carbohydrates and peptides. These functional polymers will be then incubated with non-pathogenic strains of Escherichia coli, and the characteristics of the formed biofilms evaluated. Detailed objectives are:

O1. Synthesis of Polymer Scaffolds and Modulated Polymers:

O2. Biofilm characterization, growth and catalysis:

We will employ an iterative process so that biofilm morphology and biocatalysis performance will inform “modulated” polymer synthesis and the choice of aldehydes. Overall, we aim to identify “modulated” polymers that can nucleate the growth of robust biofilms with a high catalytic activity.

O3. Lab-scale Bioreactor Design and Development:

BBSRC Strategic Research Priority: Renewable Resources and Clean Growth: Industrial Biotechnology

Techniques that will be undertaken during the project:

Due to the multidisciplinary approach, the PhD student will develop a wide range of experimental skill described in the following training objectives:

Training 1-Microbiology:

  • -Microbial culture: Post-graduate will receive training in standard techniques for microbial culture and identification. Post graduate will also receive training in flow cytometry and molecular microbiology methods. This expertise will be key for the completion of Objective 2-3.

  • Biofim Growth and Analysis: Post-graduate will receive training in techniques for biofilm generation and analysis, including Fluorescence and Raman Confocal Microscopy, Electron Microscopy. This expertise will be key for the completion of Objective 2-3.

  • Analysis of bacterial envelope properties: goiniometry, determination of inhibitory concentrations of envelope-active compounds, confocal microscopy.

  • Biocatalysis: Post-graduate will receive training in techniques to analysise biocatalyst performance including HPLC, and other assays as determined by the biocatalytic systems used. This expertise will be key for the completion of Objectives 2-3.

Training 2-Statistics and Data analysis:

The skills developed as part of the Foundation Skills Modules (i.e.: Large Dataset Handling, Quantitative Biology) will be supported by training in the following software packages:

  • GraphPad Prism: This software combines scientific graphing, curve fitting, statistics, and data organisation, and is specially designed for experimental biologists. This software will be key throughout the project, Objectives 1-3.

  • Design of Experiments: Post-graduate will receive training in R, a language and environment for statistical computing and graphics. Training in this package will allow student to implement a design of experiments approach and use surface response methodology to rapidly optimise experimental conditions, Objectives 1- 3.

Training 3-(Polymer) synthesis and Characterisation: Controlled polymerisation (i.e. free radical), combinatorial chemistry, (bio)conjugation using efficient chemistries (i.e. hydrazine-aldehyde condensation), polymer characterisation (NMR, GPC, IR). This expertise will be key for the completion of Objective 1.

Training 4-Bioreactor Design and Development: Postgraduate will receive basic training in design of packing parameters, such as support geometry, size or density. Postgraduate will also receive training in bioreactor operation and optimization, including flow rate and retention time. This expertise will be key for the completion of Objective 3.

Contact: Dr Paco Fernandez Trillo, University of Birmingham