Research Team


Christoph Spahn

Christoph Spahn

Postdoc (now PI)


Started in: February 2020

Ended in: December 2020

Funding: EMBO Fellowship


Christoph was a 1-year Postdoc (now PI) in our research group. Worked on 3 publications. Contributed to 2 technologies. Collaborated with 9 labs.

My past: I studied biology in the beautiful and romantic city Würzburg in Germany. Afterwards, I moved to Frankfurt to do my PhD in Mike Heilemann research group, investigating nucleoid architecture in E. coli cells using single-molecule localization microscopy (SMLM), a super-resolution approach that provides near molecular resolution. After figuring out how to directly label the nucleoid and how to combine different super-resolution methods (which took some time), my work resulted in several imaging approaches that allow for three-color SMLM in individual cells at spatial resolutions of ~ 20 – 40 nm. This is exactly what we require to explore the inner life of bugs at the nanoscale and understand how different processes and stimuli affect bacterial homeostasis and nucleoid organization.
My present: With the developed toolbox, I investigate how E. coli cells replicate and segregate their chromosome and how biological processes such as transcription and translation shape the nucleoid in a dynamic manner. As most of my work was performed in fixed specimen, I am very happy to join the Henriques group as an EMBO short term fellow, to perform live-cell imaging and ultimately provide a dynamic, super-resolved picture of bacterial chromosome replication.
My future: I want to use super-resolution microscopy to gain a deep understanding of how antimicrobial compounds perturb microbial cell homeostasis. This knowledge will become extremely important for fighting antimicrobial resistance and designing new drugs.


In the news


Collaborations

Christophe Leterrier

Christophe Leterrier

Aix Marseille Université, CNRS, INP
Marseille, France

Joint: 10

Florian Jug

Florian Jug

Human Technopole
Milan, Italy

Joint: 3 1

Guillaume Jacquemet

Guillaume Jacquemet

Abo Akademi University
Turku, Finland

Joint: 16 1

Loïc Royer

Loïc Royer

Chan Zuckerberg Biohub
San Francisco, USA

Joint: 2

Mariana Pinho

Mariana Pinho

ITQB NOVA
Oeiras, Portugal

Joint: 4 1 2

Mike Heilemann

Mike Heilemann

Goethe University
Frankfurt, Germany

Joint: 3 1

Pedro Matos Pereira

Pedro Matos Pereira

ITQB NOVA
Oeiras, Portugal

Joint: 20 3

Séamus Holden

Séamus Holden

Warwick University
Warwick, UK

Joint: 5

Yoav Shechtman

Yoav Shechtman

Technion - Israel Institute of Technology
Haifa, Israel

Joint: 4


Technologies

DeepBacs DeepBacs
ZeroCostDL4Mic ZeroCostDL4Mic

Publications with our group (see more on Google Scholar)

Transertion and cell geometry organize the Escherichia coli nucleoid during rapid growth
Christoph Spahn, Stuart Middlemiss, Estibaliz Gómez-de-Mariscal, Ricardo Henriques, Helge B. Bode, Séamus Holden, Mike Heilemann
Preprint published in bioRxiv, October 2023
Technologies: CARE, DeepBacs and ZeroCostDL4Mic
Funded by: EMBO, ERC, H2021 and H2022
DOI: 10.1101/2023.10.16.562172
DeepBacs for multi-task bacterial image analysis using open-source deep learning approaches
Christoph Spahn, Estibaliz Gómez-de-Mariscal, Romain F. Laine, Pedro M. Pereira, Lucas von Chamier, Mia Conduit, Mariana G. Pinho, Guillaume Jacquemet, Séamus Holden, Mike Heilemann, Ricardo Henriques
Paper published in Communications Biology, July 2022
Technologies: BioImage Model Zoo, CARE, DeepBacs, NanoJ, NanoJ-SQUIRREL, NanoJ-SRRF and ZeroCostDL4Mic
Funded by: CZI, ERC, FCT and Wellcome Trust
DOI: 10.1038/s42003-022-03634-z
Democratising deep learning for microscopy with ZeroCostDL4Mic
Lucas von Chamier, Romain F. Laine, Johanna Jukkala, Christoph Spahn, Daniel Krentzel, Elias Nehme, Martina Lerche, Sara Hernández-Pérez, Pieta K. Mattila, Eleni Karinou, Séamus Holden, Ahmet Can Solak, Alexander Krull, Tim-Oliver Buchholz, Martin L. Jones, Loïc A. Royer, Christophe Leterrier, Yoav Shechtman, Florian Jug, Mike Heilemann, Guillaume Jacquemet, Ricardo Henriques
Paper published in Nature Communications, April 2021
Technologies: CARE, FBSR-TFM, NanoJ, NanoJ-SQUIRREL, NanoJ-SRRF and ZeroCostDL4Mic
Funded by: EMBO, ERC and Wellcome Trust
News: AZO Life Sciences, Drug Target Review, Nanotechnology Now and The Medical News
Blogs: Microbiome Digest - Bik's Picks
DOI: 10.1038/s41467-021-22518-0