Understanding cellular organisation - from archaea to eukaryotes


Funding Image
Agency: Wellcome Trust
Type: Collaborative Award in Science
Principal Investigator: Buzz Baum
Investigators: Buzz Baum, Mohan Balasubramanian, Jan Löwe, Ricardo Henriques, Ann-Christin Lindas, Thijs Ettema, Ethan Garner
Start-date: December 2016
End-date: December 2021

Life is diverse, but similarities in sub-cellular organization exist across plants, animals, and fungi due to their common origin as eukaryotes. The mechanisms behind the establishment and maintenance of these membrane-bound compartments are not fully understood, partly due to a lack of experimental models that bridge eukaryotic and non-eukaryotic cells. However, relatives of molecular machines defining eukaryotic cell organization have been found in archaea, providing stripped-down systems to understand eukaryotic cell biology. Our research aims to better comprehend eukaryotic cell biology, including malaria, cancer, and stem cells, by studying the archaeal molecular machines that contributed to the transition from prokaryotic to eukaryotic cell organization.

Technology explored


QuickPALM QuickPALM

Supported publications


High-fidelity 3D live-cell nanoscopy through data-driven enhanced super-resolution radial fluctuation
Romain F. Laine, Hannah S. Heil, Simao Coelho, Jonathon Nixon-Abell, Angélique Jimenez, Theresa Wiesner, Damián Martínez, Tommaso Galgani, Louise Régnier, Aki Stubb, Gautier Follain, Samantha Webster, Jesse Goyette, Aurelien Dauphin, Audrey Salles, Siân Culley, Guillaume Jacquemet, Bassam Hajj, Christophe Leterrier, Ricardo Henriques
Paper published in Nature Methods, November 2023
Technologies: CARE, NanoJ, NanoJ-eSRRF, NanoJ-SQUIRREL, NanoJ-SRRF, NanoPyx and Nuclear-Pores as references
Funded by: CZI, EMBO, ERC, FCT, H2021, H2022, InnOValley and Wellcome Trust
News: Photonics.com, The Science Times, Optics.org and Phys.org
Blogs: Springer Nature Protocols and Methods Community
DOI: 10.1038/s41592-023-02057-w
Mapping molecular complexes with super-resolution microscopy and single-particle analysis
Afonso Mendes, Hannah S. Heil, Simao Coelho, Christophe Leterrier, Ricardo Henriques
Paper published in Open Biology, July 2022
Technologies: NanoJ-VirusMapper, Nuclear-Pores as references and ZeroCostDL4Mic
Funded by: EMBO, ERC and Wellcome Trust
DOI: 10.1098/rsob.220079
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 and Wellcome Trust
DOI: 10.1038/s42003-022-03634-z
The LEGO® brick road to open science and biotechnology
Etienne Boulter, Julien Colombelli, Ricardo Henriques, Chloé C. Féral
Review published in Trends in Biotechnology, March 2022
Technologies: NanoJ, NanoJ-Fluidics and NanoJ-SRRF
Funded by: EMBO, ERC and Wellcome Trust
DOI: 10.1016/j.tibtech.2022.02.003
Physical mechanisms of ESCRT-III–driven cell division
Lena Harker-Kirschneck, Anne E. Hafner, Tina Yao, Christian Vanhille-Campos, Xiuyun Jiang, Andre Pulschen, Fredrik Hurtig, Dawid Hryniuk, Siân Culley, Ricardo Henriques, Buzz Baum, Anđela Šarić
Paper published in Proceedings of the National Academy of Sciences, January 2022
Funded by: Wellcome Trust
DOI: 10.1073/pnas.2107763119
Expansion Microscopy on Saccharomyces cerevisiae
AG Korovesi, L Morgado, M Fumasoni, R Henriques, HS Heil, M Del Rosario
Paper published in microPublication Biology, January 2022
Technologies: CARE
Funded by: EMBO, ERC and Wellcome Trust
DOI: 10.17912/micropub.biology.000566
eHooke - A tool for automated image analysis of spherical bacteria based on cell cycle progression
Bruno M. Saraiva, Ludwig Krippahl, Sérgio R. Filipe, Ricardo Henriques, Mariana G. Pinho
Paper published in Biological Imaging, September 2021
Technologies: CARE
Funded by: ERC and Wellcome Trust
DOI: 10.1017/s2633903x21000027
FtsZ treadmilling is essential for Z-ring condensation and septal constriction initiation in Bacillus subtilis cell division
Kevin D. Whitley, Calum Jukes, Nicholas Tregidgo, Eleni Karinou, Pedro Almada, Yann Cesbron, Ricardo Henriques, Cees Dekker, Séamus Holden
Paper published in Nature Communications, April 2021
Technologies: CARE and DeepAutoFocus
Funded by: BBSRC and Wellcome Trust
News: Nanowerk
DOI: 10.1038/s41467-021-22526-0
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
Application of Super-Resolution and Advanced Quantitative Microscopy to the Spatio-Temporal Analysis of Influenza Virus Replication
Emma Touizer, Christian Sieben, Ricardo Henriques, Mark Marsh, Romain F. Laine
Review published in Viruses, February 2021
Technologies: NanoJ-VirusMapper, Super-Beacons and ZeroCostDL4Mic
Funded by: Wellcome Trust
DOI: 10.3390/v13020233
Avoiding a replication crisis in deep-learning-based bioimage analysis
Romain F Laine, Ignacio Arganda-Carreras, Ricardo Henriques, Guillaume Jacquemet
Perspective published in Nature methods, January 2021
Technologies: CARE and ZeroCostDL4Mic
Funded by: EMBO, ERC and Wellcome Trust
DOI: 10.1038/s41592-021-01284-3
The field guide to 3D printing in microscopy
Mario Del Rosario, Hannah S Heil, Afonso Mendes, Vittorio Saggiomo, Ricardo Henriques
Review published in Adv. Biol., January 2021
Technologies: CARE, NanoJ, NanoJ-Fluidics and NanoJ-SRRF
Funded by: EMBO, ERC and Wellcome Trust
DOI: 10.1002/adbi.202100994
vLUME - 3D virtual reality for single-molecule localization microscopy
Alexander Spark, Alexandre Kitching, Daniel Esteban-Ferrer, Anoushka Handa, Alexander R. Carr, Lisa-Maria Needham, Aleks Ponjavic, Ana Mafalda Santos, James McColl, Christophe Leterrier, Simon J. Davis, Ricardo Henriques, Steven F. Lee
Paper published in Nature Methods, October 2020
Technologies: Nuclear-Pores as references, QuickPALM and vLume
Funded by: BBSRC and Wellcome Trust
News: La Razon (ESP), ZAP, Medium US and IEEE Spectrum
Blogs: Qubit, , Tech Explorist and Whats New
DOI: 10.1038/s41592-020-0962-1
Closed mitosis requires local disassembly of the nuclear envelope
Gautam Dey, Siân Culley, Scott Curran, Uwe Schmidt, Ricardo Henriques, Wanda Kukulski, Buzz Baum
Paper published in Nature, August 2020
Technologies: CARE, NanoJ, NanoJ-SRRF and Nuclear-Pores as references
Funded by: BBSRC and Wellcome Trust
News: Nature Asia
DOI: 10.1038/s41586-020-2648-3
The cell biologist's guide to super-resolution microscopy
Guillaume Jacquemet, Alexandre F. Carisey, Hellyeh Hamidi, Ricardo Henriques, Christophe Leterrier
Review published in Journal of Cell Science, June 2020
Technologies: CARE, NanoJ, NanoJ-Fluidics, NanoJ-SRRF, Nuclear-Pores as references and ZeroCostDL4Mic
Funded by: BBSRC and Wellcome Trust
News: ScienMag and EurekAlert!
DOI: 10.1242/jcs.240713
Between life and death - strategies to reduce phototoxicity in super-resolution microscopy
Kalina L Tosheva, Yue Yuan, Pedro Matos Pereira, Siân Culley, Ricardo Henriques
Review published in Journal of Physics D - Applied Physics, January 2020
Technologies: CARE, NanoJ, NanoJ-Fluidics and NanoJ-SRRF
Funded by: BBSRC and Wellcome Trust
DOI: 10.1088/1361-6463/ab6b95
Super‐beacons - Open‐source probes with spontaneous tuneable blinking compatible with live‐cell super‐resolution microscopy
Pedro M Pereira, Nils Gustafsson, Mark Marsh, Musa M Mhlanga, Ricardo Henriques
Paper published in Traffic, January 2020
Technologies: NanoJ, NanoJ-Fluidics, NanoJ-SQUIRREL, NanoJ-SRRF and Super-Beacons
Funded by: BBSRC and Wellcome Trust
DOI: 10.1111/tra.12728
Live imaging of a hyperthermophilic archaeon reveals distinct roles for two ESCRT-III homologs in ensuring a robust and symmetric division
Andre Arashiro Pulschen, Delyan R Mutavchiev, Siân Culley, Kim Nadine Sebastian, Jacques Roubinet, Marc Roubinet, Gabriel Tarrason Risa, Marleen van Wolferen, Chantal Roubinet, Uwe Schmidt, Gautam Dey, Sonja-Verena Albers, Ricardo Henriques, Buzz Baum
Paper published in Current Biology, January 2020
Technologies: Sulfoscope
Funded by: Wellcome Trust
DOI: 10.1016/j.cub.2020.05.021
Nuclear pores as versatile reference standards for quantitative superresolution microscopy
Jervis Vermal Thevathasan, Maurice Kahnwald, Konstanty Cieśliński, Philipp Hoess, Sudheer Kumar Peneti, Manuel Reitberger, Daniel Heid, Krishna Chaitanya Kasuba, Sarah Janice Hoerner, Yiming Li, Yu-Le Wu, Markus Mund, Ulf Matti, Pedro Matos Pereira, Ricardo Henriques, Bianca Nijmeijer, Moritz Kueblbeck, Vilma Jimenez Sabinina, Jan Ellenberg, Jonas Ries
Paper published in Nature Methods, September 2019
Technologies: CARE, NanoJ, NanoJ-SQUIRREL, NanoJ-SRRF and Nuclear-Pores as references
Funded by: BBSRC and Wellcome Trust
News: Mirage News
DOI: 10.1038/s41592-019-0574-9
Artificial intelligence for microscopy - what you should know
Lucas von Chamier, Romain F. Laine, Ricardo Henriques
Review published in Biochemical Society Transactions, July 2019
Technologies: CARE, NanoJ, NanoJ-Fluidics, NanoJ-SQUIRREL and NanoJ-SRRF
Funded by: BBSRC and Wellcome Trust
DOI: 10.1042/bst20180391
Nanoscale polarization of the entry fusion complex of vaccinia virus drives efficient fusion
Robert D. M. Gray, David Albrecht, Corina Beerli, Moona Huttunen, Gary H. Cohen, Ian J. White, Jemima J. Burden, Ricardo Henriques, Jason Mercer
Paper published in Nature Microbiology, July 2019
Technologies: NanoJ and NanoJ-VirusMapper
Funded by: BBSRC and Wellcome Trust
Blogs: Nature Microbiology Community
DOI: 10.1038/s41564-019-0488-4
Automating multimodal microscopy with NanoJ-Fluidics
Pedro Almada, Pedro M. Pereira, Siân Culley, Ghislaine Caillol, Fanny Boroni-Rueda, Christina L. Dix, Guillaume Charras, Buzz Baum, Romain F. Laine, Christophe Leterrier, Ricardo Henriques
Paper published in Nature Communications, March 2019
Technologies: NanoJ, NanoJ-Fluidics, NanoJ-SQUIRREL, NanoJ-SRRF and NanoJ-VirusMapper
Funded by: BBSRC and Wellcome Trust
News: Technology Times, MSN, DNYUZ and Express Informer
DOI: 10.1038/s41467-019-09231-9
NanoJ - a high-performance open-source super-resolution microscopy toolbox
Romain F Laine, Kalina L Tosheva, Nils Gustafsson, Robert D M Gray, Pedro Almada, David Albrecht, Gabriel T Risa, Fredrik Hurtig, Ann-Christin Lindås, Buzz Baum, Jason Mercer, Christophe Leterrier, Pedro M Pereira, Siân Culley, Ricardo Henriques
Paper published in Journal of Physics D - Applied Physics, January 2019
Technologies: NanoJ, NanoJ-Fluidics, NanoJ-SQUIRREL, NanoJ-SRRF, NanoJ-VirusMapper and QuickPALM
Funded by: BBSRC and Wellcome Trust
DOI: 10.1088/1361-6463/ab0261
Fix your membrane receptor imaging - actin cytoskeleton and CD4 membrane organization disruption by chemical fixation
Pedro M Pereira, David Albrecht, Siân Culley, Caron Jacobs, Mark Marsh, Jason Mercer, Ricardo Henriques
Published in Frontiers in immunology, January 2019
Technologies: CARE, NanoJ, NanoJ-Fluidics and NanoJ-SQUIRREL
Funded by: BBSRC and Wellcome Trust
DOI: 10.3389/fimmu.2019.00675
Content-aware image restoration - pushing the limits of fluorescence microscopy
Martin Weigert, Uwe Schmidt, Tobias Boothe, Andreas Müller, Alexandr Dibrov, Akanksha Jain, Benjamin Wilhelm, Deborah Schmidt, Coleman Broaddus, Siân Culley, Mauricio Rocha-Martins, Fabián Segovia-Miranda, Caren Norden, Ricardo Henriques, Marino Zerial, Michele Solimena, Jochen Rink, Pavel Tomancak, Loic Royer, Florian Jug, Eugene W. Myers
Paper published in Nature Methods, November 2018
Technologies: CARE, NanoJ-SQUIRREL and NanoJ-SRRF
Funded by: BBSRC and Wellcome Trust
News: Technology Networks, VBIO, Innovations Report and Informationsdienst Wissenschaft
DOI: 10.1038/s41592-018-0216-7
Heterogeneous localisation of membrane proteins in Staphylococcus aureus
Felix Weihs, Katarzyna Wacnik, Robert D. Turner, Siân Culley, Ricardo Henriques, Simon J. Foster
Paper published in Scientific Reports, February 2018
Technologies: NanoJ and NanoJ-SRRF
Funded by: BBSRC and Wellcome Trust
DOI: 10.1038/s41598-018-21750-x
Quantitative mapping and minimization of super-resolution optical imaging artifacts
Siân Culley, David Albrecht, Caron Jacobs, Pedro Matos Pereira, Christophe Leterrier, Jason Mercer, Ricardo Henriques
Paper published in Nature Methods, February 2018
Technologies: NanoJ, NanoJ-SQUIRREL, NanoJ-SRRF and QuickPALM
Funded by: BBSRC and Wellcome Trust
News: physicsworld.com
DOI: 10.1038/nmeth.4605
SRRF - Universal live-cell super-resolution microscopy
Siân Culley, Kalina L Tosheva, Pedro Matos Pereira, Ricardo Henriques
Paper published in The international journal of biochemistry & cell biology, January 2018
Technologies: NanoJ, NanoJ-SQUIRREL and NanoJ-SRRF
Funded by: BBSRC and Wellcome Trust
DOI: 10.1016/j.biocel.2018.05.014