Periodic Reporting for period 1 - e.Biofilm (Creation of a group of Excellence on Engineered Biofilms)
Okres sprawozdawczy: 2023-03-01 do 2024-06-30
Biofilms are interactive communities of interface-associated microbial cells, enclosed in a matrix of extracellular polymeric substances. Biofilms are ubiquitous both in nature and human-built environments, and impact clinical infections, environmental sustainability, and industrial processes. Consequently, biofilms are central to many of the domains of research and innovation identified in the Treaty on the Functioning of the European Union, and exert considerable economic pressure across healthcare, environment, and industry. As our fundamental knowledge of biofilm increases, so does the need for guidance on how to regulate biocides, medical devices, and processes designed to control, kill, remove, or exploit biofilms. The main objective of this proposal project is to establish a Group of Excellence on Engineered Biofilms at the Faculty of Engineering of the University of Porto (UPorto). Worldwide impact requires not only excellence in the stated biofilm research foci, but also a technology transfer program that promotes innovation, a thriving educational and training program, and communication and dissemination strategies that establish links with the scientific community, other relevant stakeholders, and the public. To achieve these objectives, e.Biofilm will build on existing expertise from the ERA Chair holder Darla Goeres from the Center for Biofilm Engineering of Montana State University (MSU). The main goals of e.Biofilm are: 1) establish better links between research and innovation to shorten the path from fundamental research on biofilms to industrial and clinical solutions; 2) serve as a training and networking hub for young students and professionals, with a profound, yet wide, understanding of the field of biofilms in healthcare and industry, and the tools/knowledge needed to develop biofilm-related technologies; 3) simultaneously inform the general public and other relevant stakeholders in the European Research Area (ERA) about innovative technologies that enable biofilms to be engineered in a reproducible way.
During the 1st year significant progress was made towards creating a group of excellence:
-Built a biosafety level II laboratory that resulted in a research space that will provide sustainability for the program.
-Established a senior research team, including the prospective leader of the project, hired the first year as a permanent assistant researcher. This allows the leader to be mentored by Darla Goeres during the course of the project.
-ALiCE (Associate Laboratory in Chemical Engineering) and DEQ (Chemical Engineering Department) provided in kind strategic fundings to acquire state of the art research equipment.
-Established four Research Focus Areas (Industrial Systems; Chronic Wound Infections; Imaging Analysis; Computational modeling) that are the research foundation of e.Biofilm.
-Recruited a supervision committee for each Research Focus Area and 4 PhD students (3 financially supported by e.Biofilm) who started conducting research related to WP2 and WP3.
-Trained 3 master students and one bachelor student.
-Completed the first Training School on the Fundamentals of Biofilm Engineering.
-Invited 3 professors to present seminars in the areas of statistics, importance of considering diversity of thought in science, and ecology.
-Established secondments between e.Biofilm researchers and academic collaborators.
-Developed a strategy to engage with industry and initiated contacts to promote innovation with the purpose of registering projects with biofilm claims.
- Obtained additional funding through a COST Action (CA23152 - Building Consensus on Biofilm Regulatory Decision Making - RegulatoryToolBox).
-Built a biosafety level II laboratory that resulted in a research space that will provide sustainability for the program.
-Established a senior research team, including the prospective leader of the project, hired the first year as a permanent assistant researcher. This allows the leader to be mentored by Darla Goeres during the course of the project.
-ALiCE (Associate Laboratory in Chemical Engineering) and DEQ (Chemical Engineering Department) provided in kind strategic fundings to acquire state of the art research equipment.
-Established four Research Focus Areas (Industrial Systems; Chronic Wound Infections; Imaging Analysis; Computational modeling) that are the research foundation of e.Biofilm.
-Recruited a supervision committee for each Research Focus Area and 4 PhD students (3 financially supported by e.Biofilm) who started conducting research related to WP2 and WP3.
-Trained 3 master students and one bachelor student.
-Completed the first Training School on the Fundamentals of Biofilm Engineering.
-Invited 3 professors to present seminars in the areas of statistics, importance of considering diversity of thought in science, and ecology.
-Established secondments between e.Biofilm researchers and academic collaborators.
-Developed a strategy to engage with industry and initiated contacts to promote innovation with the purpose of registering projects with biofilm claims.
- Obtained additional funding through a COST Action (CA23152 - Building Consensus on Biofilm Regulatory Decision Making - RegulatoryToolBox).
e.Biofilm aims to advance biofilm research using imaging and molecular characterization by using various technologies (e.g. bioreactors, molecular biology, microscopy, statistics, and computational simulation) to gain a deeper understanding of the biogeography of biofilms. The project is focused on two case studies: industrial systems (Focus Area 1, FA1) and clinical settings (Focus Area 2, FA2). Imaging analysis tools will be developed to effectively discriminate between bacteria and matrix components in multi-species biofilms generated by FA1 and FA2 and accurately record their spatial distribution. The resulting images will be securely stored in a database that incorporates the 3D aspects of the method (Focus Area 3, FA3). This innovative approach is designed to characterize multiple components, ultimately leading to more meaningful, statistically relevant data using computational models (Focus Area 4, FA4).
Ongoing research is being carried out by the PhD students. Two PhD students are actively working on FA1. To date, the research has resulted in the development of a spatial transcriptomic method, using multiplex mRNA PNA-FISH, providing essential data on gene expression in individual Legionella pneumophila cells, both in the planktonic and sessile states, while also recording functionality and spatial information. The second PhD student is giving the first steps towards characterizing Klebsiella pneumoniae and L. pneumophila matrix components. The PhD student of FA2 is focused on studying the spatial distribution of Pseudomonas aeruginosa / Staphylococcus aureus biofilms in a chronic wound model. To date, the PhD student assign for FA3 conducted a review of the literature on image analysis techniques and methods used to analyze confocal microscopy images to identify and locate microorganisms and biofilm matrix components. Also, the basis of the database development has been conducted. Undergraduate students also conducted research on FA1, which included designing NAM probes for representative genes of the transmissive and replicative phases of L. pneumophila and utilizing microfluidics to monitor biofilm development, and on FA4, focusing on identifying and exploiting the most promising machine learning methods to speed up simulations of agent-based modeling of biofilms.
Ongoing research is being carried out by the PhD students. Two PhD students are actively working on FA1. To date, the research has resulted in the development of a spatial transcriptomic method, using multiplex mRNA PNA-FISH, providing essential data on gene expression in individual Legionella pneumophila cells, both in the planktonic and sessile states, while also recording functionality and spatial information. The second PhD student is giving the first steps towards characterizing Klebsiella pneumoniae and L. pneumophila matrix components. The PhD student of FA2 is focused on studying the spatial distribution of Pseudomonas aeruginosa / Staphylococcus aureus biofilms in a chronic wound model. To date, the PhD student assign for FA3 conducted a review of the literature on image analysis techniques and methods used to analyze confocal microscopy images to identify and locate microorganisms and biofilm matrix components. Also, the basis of the database development has been conducted. Undergraduate students also conducted research on FA1, which included designing NAM probes for representative genes of the transmissive and replicative phases of L. pneumophila and utilizing microfluidics to monitor biofilm development, and on FA4, focusing on identifying and exploiting the most promising machine learning methods to speed up simulations of agent-based modeling of biofilms.