Independent ResearchersHead of Research UnitOverviewMembersPublicationsProjects & CollaborationsProjects & Collaborations OverviewMembersPublicationsProjects & Collaborations Projects & Collaborations 3 foundShow per page10 10 20 50 The role of cell-cell interactions in the development and virulence of multispecies biofilms Research Project | 2 Project MembersMicrobial infections are a leading cause of death and especially for chronic infections we still lack effective treatment strategies. To find new treatments, we first need a thorough understanding of the dynamics and functioning of the microbial communities that cause these chronic infections. In the past, bacterial pathogenesis has mostly been studied using single species grown in batch cultures. In contrast, many chronic infections are caused by multiple species growing in spatially structured biofilms. Interactions between these species can affect the growth, virulence, and stress tolerance of cells and can thus affect disease outcome, yet we still poorly understand these dynamics. Here, we will address this knowledge gap by studying how intra- and interspecies interactions affect the development and function of the multispecies biofilms that cause chronic lung infections. WE will focus on three species that often co-occur: the two major pathogens Pseudomonas aeruginosa and Staphylococcus aureus and the mucus-degrading commensal Streptococcus parasanguinis . Previous studies have found a complex set of interactions between these species. However, these interactions are not constant in space and time: each interaction has a different spatial range and is important during different phases of biofilm development, yet for most interactions these spatiotemporal properties have not been characterized. Moreover, we lack a quantitative approach to predict how these interactions combine to affect the development and function of biofilms. Here, we will use recent technological advances to measure the activity of cells in biofilms at high spatiotemporal resolution to characterize the spatiotemporal properties of intra- and interspecies interactions. Moreover, we will develop a quantitative framework to predict how these interactions combine to affect the development, virulence gene expression, and antibiotic tolerance of the biofilms that cause chronic infections. We will use a combination of single-cell microscopy and transcriptomics to characterize the spatiotemporal properties of known intra- and interspecies interactions and to identify novel interactions. We will integrate these interactions in a mathematical model which will allow us to identify which interactions have the strongest effects on biofilm development, virulence gene expression, and antibiotic tolerance. By identifying these interactions, we could potentially identify new strategies that can be used to suppress biofilm development or to reduce antibiotic tolerance. Moreover, the concepts and approaches developed here can help us better understand how cell-cell interactions affect the development and function of other microbial communities that play important roles in health and disease, industry, and the environment. Microfluidic sample preparation for high-resolution structure determination by cryogenic electron microscopy Research Project | 1 Project MembersElectron microscopy (EM) introduced a fast and lasting change to structural and cellular biology. Direct electron detector cameras and improved image processing algorithms now allow structure determination of large biomolecules by cryogenic EM (cryo-EM) at atomic resolution using a single particle approach. For the latter, only thousands to a few million particles must be imaged, to measure high-resolution structures. This amount of protein can be delivered by microfluidic technologies. I this project we explore to the potential of combining microfluidics and electron microscopy to study protein structures for drug discovery. Microfluidic Sample Preparation for High-Resolution Electron Microscopy, Visual Proteomics and Electron Tomography Research Project | 2 Project MembersElectron microscopy (EM) introduced a fast and lasting change to structural and cellular biology. Direct electron detector cameras and improved image processing algorithms now allow structure determination of large biomolecules by cryogenic EM (cryo-EM) at atomic resolution using a single particle approach. Strategies to study the cellular ultrastructure, such as electron tomography (ET), correlative light and electron microscopy (CLEM), and the lamella milling of eukaryotic cells, opened new windows allowing biologists to study the mechanism of cellular processes at unprecedented precision. Unfortunately, sample preparation remains a bottleneck, and, surprisingly, EM is rarely used as a bioanalytical tool despite its immense potential to detect proteins on the single-molecule level. Both (i) new single-cell analysis tools and (ii) advanced methods for protein isolation and cryo-EM sample preparation are urgently needed. Here, we aim at (i) the development of a versatile system for the fast protein production, protein isolation, and cryo-EM sample preparation for the structural analysis of sensitive protein complexes, (ii) the development of a new targeted and untargeted single-cell analysis method named "single-cell visual proteomics," and (iii) the development of a new strategy for the blotting-free cryopreservation of eukaryotic cells to study cellular structures by ET. 1 1 OverviewMembersPublicationsProjects & Collaborations
Projects & Collaborations 3 foundShow per page10 10 20 50 The role of cell-cell interactions in the development and virulence of multispecies biofilms Research Project | 2 Project MembersMicrobial infections are a leading cause of death and especially for chronic infections we still lack effective treatment strategies. To find new treatments, we first need a thorough understanding of the dynamics and functioning of the microbial communities that cause these chronic infections. In the past, bacterial pathogenesis has mostly been studied using single species grown in batch cultures. In contrast, many chronic infections are caused by multiple species growing in spatially structured biofilms. Interactions between these species can affect the growth, virulence, and stress tolerance of cells and can thus affect disease outcome, yet we still poorly understand these dynamics. Here, we will address this knowledge gap by studying how intra- and interspecies interactions affect the development and function of the multispecies biofilms that cause chronic lung infections. WE will focus on three species that often co-occur: the two major pathogens Pseudomonas aeruginosa and Staphylococcus aureus and the mucus-degrading commensal Streptococcus parasanguinis . Previous studies have found a complex set of interactions between these species. However, these interactions are not constant in space and time: each interaction has a different spatial range and is important during different phases of biofilm development, yet for most interactions these spatiotemporal properties have not been characterized. Moreover, we lack a quantitative approach to predict how these interactions combine to affect the development and function of biofilms. Here, we will use recent technological advances to measure the activity of cells in biofilms at high spatiotemporal resolution to characterize the spatiotemporal properties of intra- and interspecies interactions. Moreover, we will develop a quantitative framework to predict how these interactions combine to affect the development, virulence gene expression, and antibiotic tolerance of the biofilms that cause chronic infections. We will use a combination of single-cell microscopy and transcriptomics to characterize the spatiotemporal properties of known intra- and interspecies interactions and to identify novel interactions. We will integrate these interactions in a mathematical model which will allow us to identify which interactions have the strongest effects on biofilm development, virulence gene expression, and antibiotic tolerance. By identifying these interactions, we could potentially identify new strategies that can be used to suppress biofilm development or to reduce antibiotic tolerance. Moreover, the concepts and approaches developed here can help us better understand how cell-cell interactions affect the development and function of other microbial communities that play important roles in health and disease, industry, and the environment. Microfluidic sample preparation for high-resolution structure determination by cryogenic electron microscopy Research Project | 1 Project MembersElectron microscopy (EM) introduced a fast and lasting change to structural and cellular biology. Direct electron detector cameras and improved image processing algorithms now allow structure determination of large biomolecules by cryogenic EM (cryo-EM) at atomic resolution using a single particle approach. For the latter, only thousands to a few million particles must be imaged, to measure high-resolution structures. This amount of protein can be delivered by microfluidic technologies. I this project we explore to the potential of combining microfluidics and electron microscopy to study protein structures for drug discovery. Microfluidic Sample Preparation for High-Resolution Electron Microscopy, Visual Proteomics and Electron Tomography Research Project | 2 Project MembersElectron microscopy (EM) introduced a fast and lasting change to structural and cellular biology. Direct electron detector cameras and improved image processing algorithms now allow structure determination of large biomolecules by cryogenic EM (cryo-EM) at atomic resolution using a single particle approach. Strategies to study the cellular ultrastructure, such as electron tomography (ET), correlative light and electron microscopy (CLEM), and the lamella milling of eukaryotic cells, opened new windows allowing biologists to study the mechanism of cellular processes at unprecedented precision. Unfortunately, sample preparation remains a bottleneck, and, surprisingly, EM is rarely used as a bioanalytical tool despite its immense potential to detect proteins on the single-molecule level. Both (i) new single-cell analysis tools and (ii) advanced methods for protein isolation and cryo-EM sample preparation are urgently needed. Here, we aim at (i) the development of a versatile system for the fast protein production, protein isolation, and cryo-EM sample preparation for the structural analysis of sensitive protein complexes, (ii) the development of a new targeted and untargeted single-cell analysis method named "single-cell visual proteomics," and (iii) the development of a new strategy for the blotting-free cryopreservation of eukaryotic cells to study cellular structures by ET. 1 1
The role of cell-cell interactions in the development and virulence of multispecies biofilms Research Project | 2 Project MembersMicrobial infections are a leading cause of death and especially for chronic infections we still lack effective treatment strategies. To find new treatments, we first need a thorough understanding of the dynamics and functioning of the microbial communities that cause these chronic infections. In the past, bacterial pathogenesis has mostly been studied using single species grown in batch cultures. In contrast, many chronic infections are caused by multiple species growing in spatially structured biofilms. Interactions between these species can affect the growth, virulence, and stress tolerance of cells and can thus affect disease outcome, yet we still poorly understand these dynamics. Here, we will address this knowledge gap by studying how intra- and interspecies interactions affect the development and function of the multispecies biofilms that cause chronic lung infections. WE will focus on three species that often co-occur: the two major pathogens Pseudomonas aeruginosa and Staphylococcus aureus and the mucus-degrading commensal Streptococcus parasanguinis . Previous studies have found a complex set of interactions between these species. However, these interactions are not constant in space and time: each interaction has a different spatial range and is important during different phases of biofilm development, yet for most interactions these spatiotemporal properties have not been characterized. Moreover, we lack a quantitative approach to predict how these interactions combine to affect the development and function of biofilms. Here, we will use recent technological advances to measure the activity of cells in biofilms at high spatiotemporal resolution to characterize the spatiotemporal properties of intra- and interspecies interactions. Moreover, we will develop a quantitative framework to predict how these interactions combine to affect the development, virulence gene expression, and antibiotic tolerance of the biofilms that cause chronic infections. We will use a combination of single-cell microscopy and transcriptomics to characterize the spatiotemporal properties of known intra- and interspecies interactions and to identify novel interactions. We will integrate these interactions in a mathematical model which will allow us to identify which interactions have the strongest effects on biofilm development, virulence gene expression, and antibiotic tolerance. By identifying these interactions, we could potentially identify new strategies that can be used to suppress biofilm development or to reduce antibiotic tolerance. Moreover, the concepts and approaches developed here can help us better understand how cell-cell interactions affect the development and function of other microbial communities that play important roles in health and disease, industry, and the environment.
Microfluidic sample preparation for high-resolution structure determination by cryogenic electron microscopy Research Project | 1 Project MembersElectron microscopy (EM) introduced a fast and lasting change to structural and cellular biology. Direct electron detector cameras and improved image processing algorithms now allow structure determination of large biomolecules by cryogenic EM (cryo-EM) at atomic resolution using a single particle approach. For the latter, only thousands to a few million particles must be imaged, to measure high-resolution structures. This amount of protein can be delivered by microfluidic technologies. I this project we explore to the potential of combining microfluidics and electron microscopy to study protein structures for drug discovery.
Microfluidic Sample Preparation for High-Resolution Electron Microscopy, Visual Proteomics and Electron Tomography Research Project | 2 Project MembersElectron microscopy (EM) introduced a fast and lasting change to structural and cellular biology. Direct electron detector cameras and improved image processing algorithms now allow structure determination of large biomolecules by cryogenic EM (cryo-EM) at atomic resolution using a single particle approach. Strategies to study the cellular ultrastructure, such as electron tomography (ET), correlative light and electron microscopy (CLEM), and the lamella milling of eukaryotic cells, opened new windows allowing biologists to study the mechanism of cellular processes at unprecedented precision. Unfortunately, sample preparation remains a bottleneck, and, surprisingly, EM is rarely used as a bioanalytical tool despite its immense potential to detect proteins on the single-molecule level. Both (i) new single-cell analysis tools and (ii) advanced methods for protein isolation and cryo-EM sample preparation are urgently needed. Here, we aim at (i) the development of a versatile system for the fast protein production, protein isolation, and cryo-EM sample preparation for the structural analysis of sensitive protein complexes, (ii) the development of a new targeted and untargeted single-cell analysis method named "single-cell visual proteomics," and (iii) the development of a new strategy for the blotting-free cryopreservation of eukaryotic cells to study cellular structures by ET.
