
Project Area C
Projects of the CRC 1768
Project Area C
Tools for morphology, entry, and photonic signatures
This project area focuses on the direct visualisation and characterisation of viruses and virus-host interactions using photonic tools. It is motivated by the lack of optical tools to predict infectivity and impact from microscopy-based data. This need has been identified by the virology community. In particular, Project Area A and Project Area B have generated a strong demand for characterising and distinguishing virus sub-types, specifically based on their morphology, molecular organisation, virus-host interaction, and host response. As highlighted in the section on existing tools and their limitations, many tools are available for visualising and analysing virus morphologies, virus entry, or virus-host response, such as microscopy and photonic solutions. However, most of these methods lack highthroughput capabilities, often require specialised and sometimes complex, extensive sample preparation such as labelling or fixation, and need optimisation to enable rapid and straightforward prediction of host-cell fate decisions from parameters such as morphology, virus entry mechanism, and virus presence and replication dynamics. Only then can aims such as virus sorting based on predicted infectivity from morphological, cell-entry, or single-cell-based quantification of host responses be realised.
In Project Area C, we will therefore explore straightforward and accurate approaches for investigating molecular details during virus entry and uncoating, precise determination and discrimination of virus morphology and virus surface, establishment of non-specific or label-free imaging of viruses and host cell responses, and sorting of viruses.
Recent developments in visualisation and photonic tools have highlighted current observation technologies such as electron microscopy (EM) (Z03), super-resolution optical microscopy (SRM) (C01, C03), and near-field microscopy (C02), which enable the characterisation of individual viruses with high spatial resolution down to the nanometre range. This is supported by the rapidly increasing performance of computer technology to analyse image-based microscopy data efficiently, including artificial intelligence algorithms (C03). The latter are particularly useful in detailing label-free observation approaches, such as scattering or specifically Raman spectroscopic readouts, with improved sensitivity, allowing us to generate virus-specific fingerprints (C01, C02, C04). Furthermore, multimodal combination or correlation of all these techniques, such as in correlative electron-light microscopy (CLEM) (Z03) or scattering with fluorescence readout (C01), will help to increase the information content and thus the accuracy of virus characterisation, and the use of tools such as fibres as a flow system will help to enhance throughput. The availability of such novel tools, and most importantly their improvement and simplification as planned within this CRC, will be an important breakthrough in preparedness to improve and accelerate the fight against novel emerging viruses.
High-resolution and high-throughput optical detection and characterisation of viruses
Project Leaders
Prof. Dr. Christian Eggeling
Institute of Applied Optics and Biophysics,
Friedrich Schiller University Jena
Prof. Dr. Markus A. Schmidt
Leibniz Institute of Photonic Technology
Probe microscopy-based functional tracking of respiratory viruses to identify virus tropism
Project Leaders
Prof. Dr. Volker Deckert
Institute of Physical Chemistry,
Friedrich Schiller University Jena
PD Dr. Stefanie Deinhardt-Emmer
Institute of Medical Microbiology,
Jena University Hospital,
Deciphering virus-membrane interactions with advanced optical microscopy and machine learning-supported image analysis
A critical step in virus infection is the initial uptake of viruses into host cells. Interestingly, and perhaps counterintuitively, a particular virus may use different modes of crossing the plasma membrane, either in the same cell or depending on cell type. Even for members of the same virus family, different modes of uptake have been observed. The main uptake pathways include the use of membrane fusion or endocytosis. A number of endocytic mechanisms have been discovered and these depend on multiple factors, such as cell type and surface receptors, as well as cell membrane properties. Importantly, the uptake path usually determines the fate and infectivity of a virus. Thus, predicting the mode of entry is important for choosing and optimising preventative or impeding measures of infections. However, determining an uptake mechanism is challenging due to multiple factors involving assay design and observation technology. An accurate investigation requires an adapted experimental design for each virus, receptor and host cell, analysing binding, uptake, routing, and the infection cycle of cellular and virus proteins. At the same time, direct microscopic imaging of the viruses and other molecules involved in the uptake into living cells should employ as high a temporal and spatial resolution as possible, since every entry mode displays specific spatiotemporal dynamics of virus and molecular movements at the cell and virus surface. Finally, data analysis needs to be tailored to correlate a “microscopic signature” of entry events with fusion signatures and particular endocytic mechanisms, which would then make it possible to identify the mode(s) of entry of an emerging virus. Unfortunately, the realisation of high-resolution microscope experiments of virus uptake is usually too complex to accomplish a straightforward and quick prediction of entry modes of newly emerging viruses. This is, however, within the overall aim of this CRC VirusREvolution, which is to set up tools to quickly react to potential pandemic threats. We therefore propose to realise a fast and facile tool to predict the mode(s) of virus entry from standard low-resolution live-cell microscopy data. To achieve this, we will combine high spatiotemporal resolution microscopy data with methods from Machine Learning (ML) / Artificial Intelligence (AI) for fast, objective, and quantitative analysis to establish a tool that allows correlation with the standard microscopy data of lower spatiotemporal resolution. This shall enable the characterisation and differentiation of the membrane interactions of virtually any virus, using widely used standard and less complex microscopy approaches, such as widefield or confocal microscopy. We will employ a machine learning approach that builds on the experience gained from working with a variety of viruses. Thus, the performance of our tool will gradually improve as more and more virus data becomes available. Our experimental and computational tools will contribute to answering the research questions of the CRC VirusREvolution, such as revealing mechanisms of virus entry and tackling the goals of the description and prediction of the infectivity of viruses and their hosts.
Project Leaders
Prof. Dr. Christian Eggeling
Institute of Applied Optics and Biophysics,
Friedrich Schiller University Jena
Prof. Dr. Marc Thilo Figge
Faculty of Biological Sciences,
Friedrich Schiller University Jena,
Leibniz Institute for Natural Product Research and Infection Biology – Hans Knöll Institute
Prof. Dr. Mario Schelhaas
Institute of Cellular Virology,
University of Münster
Raman spectroscopy: A tool for host response and virus characterisation
Project Leaders
Prof. Dr. med. vet. Martin Beer
Institute of Diagnostic Virology,
Friedrich-Loeffler-Institut
Prof. Dr. Jürgen Popp
Friedrich Schiller University Jena,
Institute of Physical Chemistry (IPC)