Application of multi-color super-resolution microscopy to bacterial cells to investigate essential cellular processes on the nanoscale.
Started February, 2020; ended December, 2020
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.
Research themes with our lab
Publications with our group (see more on Google Scholar)
| 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
Published in Nature Communications Biology, July 2022 (see publication)
| 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
Published in Nature communications, April 2021 (see publication)