
Probe microscopy-based functional tracking of respiratory viruses to identify virus tropism
We aim to characterise virus tropism by identifying permissive cell types that support complete virus replication by using Tip-enhanced Raman Spectroscopy (TERS). TERS integrates atomic force microscopy (AFM) and near-field optical recordings with Raman spectroscopy, enabling direct, label-free characterisation of molecular organisation and thus visualisation of virus entry and exit at nanometer resolution.
As a result, tropism ultimately defines whether productive replication occurs and thereby shapes virus pathogenesis, disease progression, and transmission. However, inferring tropism from virus properties alone remains difficult and typically requires elaborate infection experiments.
In this project, TERS will be employed to resolve virus entry and exit strategies with unprecedented spatial detail, Fig. C02.1. Beyond imaging, TERS provides molecular fingerprints and resolves nano scale surface structures, thereby revealing chemical and conformational changes that accompany virus-cell interactions. Time-resolved nanoscale studies will further allow us to monitor replication at the level of single infection events and to detect heterogeneous infection patterns that are masked in bulk analyses. By combining structural and temporal information, we aim to precisely define the host cell factors and physiological states that permit or restrict virus replication, thus contributing directly to research goals G3 and G4. Our approach represents a novel, rapid, label-free, and phenotypic method to define virus tropism. In addition to TERS, we will employ nanoscale infrared spectroscopy (nanoIR), a technique that combines AFM with IR absorption to provide chemical composition and conformational information at nanometer resolution. The combination of nanoIR and TERS will yield complementary spectroscopic data to unravel structural changes during virus-cell interactions, potentially down to amino acid resolution. To further dissect the influence of host determinants on virus tropism, we will additionally apply a cellular senescence model.
- WP 1: Experimental setup and model development (Deckert/Deinhardt-Emmer)
- WP 2: Nanoscale time-lapse study of virus and membrane samples (Deckert/Deinhardt-Emmer)
- WP 3: Correlative TERS, nanoIR, and topography analysis of virus infection (Deckert/Deinhardt-Emmer)
Team Members
N. N.
Doctoral Researcher
N. N.
Doctoral Researcher
Project-Specific Publications
2025
Höppener, Christiane; Sobotta, Fabian H.; Höppener, Stephanie; Deckert, Volker; Brendel, Johannes C.
Unraveling the hierarchical self-assembly of amphiphilic block copolymer-peptide conjugates by tip-enhanced Raman spectroscopy. Journal Article
In: Small, vol. 21, iss. 32, pp. e2502157, 2025, ISSN: 1613-6829.
@article{Hoeppener:25,
title = {Unraveling the hierarchical self-assembly of amphiphilic block copolymer-peptide conjugates by tip-enhanced Raman spectroscopy.},
author = { Christiane Höppener and Fabian H. Sobotta and Stephanie Höppener and Volker Deckert and Johannes C. Brendel},
url = {https://pubmed.ncbi.nlm.nih.gov/40519054/},
doi = {10.1002/smll.202502157},
issn = {1613-6829},
year = {2025},
date = {2025-08-01},
urldate = {2025-08-01},
journal = {Small},
volume = {21},
issue = {32},
pages = {e2502157},
abstract = {Self-assembly of block copolymers in solution provides access to different nanostructures depending on block composition and processing conditions. However, more complex hierarchical nanostructures as found in nature remain challenging to achieve. In this study, the influence of a β-sheet forming tetrapeptide sequence (GFFG) is investigated at the interface of an amphiphilic block copolymer based on poly(butyl acrylate) (PBA) and poly(ethylene oxide) (PEO). Using atomic force microscopy (AFM) and tip-enhanced Raman spectroscopy (TERS), nanoscale insights are provided into the structural organisation and mechanical properties of these hybrid materials. Both the tetrapeptide-containing block copolymer and a control block copolymer without the peptide linker form wormlike micelles in water. However, the incorporation of the peptide linker alters the micelle morphology by increasing the contour length sixfold compared to the control polymer and by altering the mechanical properties of the wormlike micelles. TERS analysis confirms the presence of ordered β-sheet structures at the hydrophilic/hydrophobic interface, which increase the bending stiffness of the micelles. The introduction of additional secondary interactions, such as those induced by the peptide linker, therefore appears as an interesting lever to manipulate the structure formation and mechanical properties block copolymer micelles, opening up interesting design strategies for tailor-made hierarchically structured nanomaterials.},
keywords = {},
pubstate = {published},
tppubtype = {article}
}
Deinhardt-Emmer, Stefanie; Chousterman, Benjamin G; Schefold, Joerg C; Flohé, Stefanie B; Skirecki, Tomasz; Kox, Matthijs; Winkler, Martin S; Cossarizza, Andrea; Wiersinga, W Joost; Poll, Tom; others,
Sepsis in patients who are immunocompromised: diagnostic challenges and future therapies Journal Article
In: The Lancet Respiratory Medicine, vol. 13, no. 7, pp. 623–637, 2025.
@article{deinhardt2025sepsis,
title = {Sepsis in patients who are immunocompromised: diagnostic challenges and future therapies},
author = {Stefanie Deinhardt-Emmer and Benjamin G Chousterman and Joerg C Schefold and Stefanie B Flohé and Tomasz Skirecki and Matthijs Kox and Martin S Winkler and Andrea Cossarizza and W Joost Wiersinga and Tom Poll and others},
url = {https://www.thelancet.com/journals/lanres/article/PIIS2213-2600(25)00124-9/fulltext},
doi = {https://doi.org/10.1016/S2213-2600(25)00124-9},
year = {2025},
date = {2025-01-01},
urldate = {2025-01-01},
journal = {The Lancet Respiratory Medicine},
volume = {13},
number = {7},
pages = {623–637},
publisher = {Elsevier},
keywords = {},
pubstate = {published},
tppubtype = {article}
}
Hornung, Franziska; SureshKumar, Harini K.; Klement, Laura; Reisser, Yasmina; Wernike, Christoph; Nischang, Vivien; Jordan, Paul M.; Werz, Oliver; Hoffmann, Carsten; Löffler, Bettina; Deinhardt-Emmer, Stefanie
High-fat diet impairs microbial metabolite production and aggravates influenza A infection Journal Article
In: Cell Communication and Signaling, vol. 23, no. 1, pp. 359, 2025, ISSN: 1478-811X.
@article{Hornung:25,
title = {High-fat diet impairs microbial metabolite production and aggravates influenza A infection},
author = { Franziska Hornung and Harini K. SureshKumar and Laura Klement and Yasmina Reisser and Christoph Wernike and Vivien Nischang and Paul M. Jordan and Oliver Werz and Carsten Hoffmann and Bettina Löffler and Stefanie Deinhardt-Emmer},
url = {https://pubmed.ncbi.nlm.nih.gov/40745568/},
doi = {10.1186/s12964-025-02367-w},
issn = {1478-811X},
year = {2025},
date = {2025-01-01},
urldate = {2025-01-01},
journal = {Cell Communication and Signaling},
volume = {23},
number = {1},
pages = {359},
publisher = {Springer},
keywords = {},
pubstate = {published},
tppubtype = {article}
}
2024
Höppener, Christiane; Aizpurua, Javier; Chen, Huan; Gräfe, Stefanie; Jorio, Ado; Kupfer, Stephan; Zhang, Zhenglong; Deckert, Volker
Tip-enhanced Raman scattering Journal Article
In: Nature Reviews Methods Primers, vol. 4, no. 1, pp. 47, 2024.
@article{hoppener2024tip,
title = {Tip-enhanced Raman scattering},
author = {Christiane Höppener and Javier Aizpurua and Huan Chen and Stefanie Gräfe and Ado Jorio and Stephan Kupfer and Zhenglong Zhang and Volker Deckert},
url = {https://www.nature.com/articles/s43586-024-00323-5},
doi = {https://doi.org/10.1038/s43586-024-00323-5},
year = {2024},
date = {2024-01-01},
urldate = {2024-01-01},
journal = {Nature Reviews Methods Primers},
volume = {4},
number = {1},
pages = {47},
publisher = {Nature Publishing Group UK London},
keywords = {},
pubstate = {published},
tppubtype = {article}
}
2023
Schulz, Luise; Hornung, Franziska; Häder, Antje; Radosa, Lukáš; Brakhage, Axel A; Löffler, Bettina; Deinhardt-Emmer, Stefanie
Influenza virus-induced paracrine cellular senescence of the lung contributes to enhanced viral load Journal Article
In: Aging and disease, vol. 14, no. 4, pp. 1331, 2023.
@article{schulz2023influenza,
title = {Influenza virus-induced paracrine cellular senescence of the lung contributes to enhanced viral load},
author = {Luise Schulz and Franziska Hornung and Antje Häder and Lukáš Radosa and Axel A Brakhage and Bettina Löffler and Stefanie Deinhardt-Emmer},
url = {https://pmc.ncbi.nlm.nih.gov/articles/PMC10389813/},
doi = {https://doi.org/10.14336/AD.2023.0310},
year = {2023},
date = {2023-01-01},
urldate = {2023-01-01},
journal = {Aging and disease},
volume = {14},
number = {4},
pages = {1331},
keywords = {},
pubstate = {published},
tppubtype = {article}
}
Höppener, Christiane; Elter, Johanna K; Schacher, Felix H; Deckert, Volker
Inside Block Copolymer Micelles—Tracing Interfacial Influences on Crosslinking Efficiency in Nanoscale Confined Spaces Journal Article
In: Small, vol. 19, no. 20, pp. 2206451, 2023.
@article{hoppener2023inside,
title = {Inside Block Copolymer Micelles—Tracing Interfacial Influences on Crosslinking Efficiency in Nanoscale Confined Spaces},
author = {Christiane Höppener and Johanna K Elter and Felix H Schacher and Volker Deckert},
url = {https://onlinelibrary.wiley.com/doi/full/10.1002/smll.202206451},
doi = {https://doi.org/10.1002/smll.202206451},
year = {2023},
date = {2023-01-01},
urldate = {2023-01-01},
journal = {Small},
volume = {19},
number = {20},
pages = {2206451},
publisher = {Wiley Online Library},
keywords = {},
pubstate = {published},
tppubtype = {article}
}
Deckert-Gaudig, Tanja; Yao, Xiaobin; Darussalam, Erwan; Hornung, Franziska; Carravilla, Pablo; Zhao, Ziliang; Rezaei, Kourosh; Eggeling, Christian; Deinhardt-Emmer, Stefanie; Deckert, Volker
Identification of RNA-containing virus particles using a triple correlative morphological and microscopic approach Journal Article
In: accepted in: J Translat Med, 2023.
@article{DeckertGaudig:23,
title = {Identification of RNA-containing virus particles using a triple correlative morphological and microscopic approach},
author = {Tanja Deckert-Gaudig and Xiaobin Yao and Erwan Darussalam and Franziska Hornung and Pablo Carravilla and Ziliang Zhao and Kourosh Rezaei and Christian Eggeling and Stefanie Deinhardt-Emmer and Volker Deckert},
url = {https://chemrxiv.org/engage/chemrxiv/article-details/64e8c60279853bbd786af71a},
doi = {10.26434/chemrxiv-2023-b9mr1},
year = {2023},
date = {2023-01-01},
urldate = {2023-01-01},
journal = {accepted in: J Translat Med},
publisher = {American Chemical Society (ACS)},
keywords = {},
pubstate = {published},
tppubtype = {article}
}
2021
Deinhardt-Emmer, Stefanie; Wittschieber, Daniel; Sanft, Juliane; Kleemann, Sandra; Elschner, Stefan; Haupt, Karoline Frieda; Vau, Vanessa; Häring, Clio; Rödel, Jürgen; Henke, Andreas; Ehrhardt, Christina; Bauer, Michael; Philipp, Mike; Gaßler, Nikolaus; Nietzsche, Sandor; Löffler, Bettina; Mall, Gita
Early postmortem mapping of SARS-CoV-2 RNA in patients with COVID-19 and the correlation with tissue damage Journal Article
In: Elife, vol. 10, pp. e60361, 2021.
@article{deinhardt2021early,
title = {Early postmortem mapping of SARS-CoV-2 RNA in patients with COVID-19 and the correlation with tissue damage},
author = {Deinhardt-Emmer, Stefanie and Wittschieber, Daniel and Sanft, Juliane and Kleemann, Sandra and Elschner, Stefan and Haupt, Karoline Frieda and Vau, Vanessa and Häring, Clio and Rödel, Jürgen and Henke, Andreas and Ehrhardt, Christina and Bauer, Michael and Philipp, Mike and Gaßler, Nikolaus and Nietzsche, Sandor and Löffler, Bettina and Mall, Gita},
url = {https://elifesciences.org/articles/60361},
doi = {https://doi.org/10.7554/eLife.60361},
year = {2021},
date = {2021-01-01},
urldate = {2021-01-01},
journal = {Elife},
volume = {10},
pages = {e60361},
publisher = {eLife Sciences Publications, Ltd},
keywords = {},
pubstate = {published},
tppubtype = {article}
}
2020
Deckert, Volker; Deckert-Gaudig, Tanja; Cialla-May, Dana; Popp, Jürgen; Zell, Roland; Deinhard-Emmer, Stefanie; Sokolov, Alexei V; Yi, Zhenhuan; Scully, Marlan O
Laser spectroscopic technique for direct identification of a single virus I: FASTER CARS Journal Article
In: Proc Natl Acad Sci, vol. 117, iss. 45, pp. 27820–27824, 2020.
@article{Deckert:20,
title = {Laser spectroscopic technique for direct identification of a single virus I: FASTER CARS},
author = { Volker Deckert and Tanja Deckert-Gaudig and Dana Cialla-May and Jürgen Popp and Roland Zell and Stefanie Deinhard-Emmer and Alexei V Sokolov and Zhenhuan Yi and Marlan O Scully},
url = {https://www.pnas.org/doi/abs/10.1073/pnas.2013169117},
doi = {10.1073/pnas.2013169117},
year = {2020},
date = {2020-01-01},
urldate = {2020-01-01},
journal = {Proc Natl Acad Sci},
volume = {117},
issue = {45},
pages = {27820–27824},
keywords = {},
pubstate = {published},
tppubtype = {article}
}
2015
Olschewski, Konstanze; Kämmer, Evelyn; Stöckel, Stephan; Bocklitz, Thomas; Deckert-Gaudig, Tanja; Zell, Roland; Cialla-May, Dana; Weber, Karina; Deckert, Volker; Popp, Jürgen
A manual and an automatic TERS based virus discrimination Journal Article
In: Nanoscale, vol. 7, iss. 10, pp. 4545–4552, 2015, ISSN: 2040-3372.
@article{Olschewski:15,
title = {A manual and an automatic TERS based virus discrimination},
author = { Konstanze Olschewski and Evelyn Kämmer and Stephan Stöckel and Thomas Bocklitz and Tanja Deckert-Gaudig and Roland Zell and Dana Cialla-May and Karina Weber and Volker Deckert and Jürgen Popp},
url = {https://pubmed.ncbi.nlm.nih.gov/25686406/},
doi = {10.1039/c4nr07033j},
issn = {2040-3372},
year = {2015},
date = {2015-03-01},
urldate = {2015-03-01},
journal = {Nanoscale},
volume = {7},
issue = {10},
pages = {4545–4552},
keywords = {},
pubstate = {published},
tppubtype = {article}
}
