The ultimate goal of the BaSyC programme is to create a life-like entity that is able to autonomously grow, transmit information, and divide. Consequently, the envisioned vesicle-based synthetic cell will need three core functionalities or modules:
1) Cell Fuelling: the ability to produce the correct amount of energy carriers and molecular building blocks
2) DNA Processing: the ability to transcribe, translate, and duplicate information carried by DNA
3) Cell Division: the ability to physically divide into two new cells
In addition, the cell needs to be able to coordinate and integrate these modules in space and time.
The production of material needs to be compatible with volume, area, and shape constraints of the growing vesicle, the rates of growth and DNA replication need to be tuned to the timing of cell division, and spatial cues need to be in place to ensure the proper distribution of genetic material. As a final requirement, the synthetic cell needs to be autonomous. All protein components that will provide the machinery to carry out the core functionalities eventually need to be coded on a single genome controlled and replicated by the synthetic cell itself.
To achieve the above, BaSyC centres its operations on 6 research lines: System mathematical and computational modelling, Cell Fuelling, DNA Processing, Cell Division, Spatio-Temporal Integration, Towards Autonomy of the synthetic cell. Through these research lines runs a set of interrelated projects on which senior and junior members of the programme collaborate in different group combinations.
In addition, an overarching research line on Philosophy, Ethics and Public Debate is included that deals with the possible impact on society of the eventual realization of a synthetic cell. Throughout the project, we will reflect on philosophical aspects, ethical dilemmas as well as societal opportunities associated with creating synthetic life, raise awareness with our researchers on these topics, and actively engage in public debate.
In order to address the challenge of building the first synthetic cell from the bottom up, the BaSyC consortium will bring 17 principal investigators (PI’s) together in a truly interdisciplinary pool of cutting-edge expertise for the first time.
The researchers have complementary expertise, covering all aspects involved in this research, from biochemistry and biophysics to (genome) engineering and genetics, microbiology and theory and ethics and philosophical aspects. They share a common vision that the ability to build a synthetic cell from its basic constituents will result in a deep molecular understanding of life. They are renowned for their multidisciplinary research, bridging disciplines and bringing different fields together, and are highly committed to a long-term collaboration within the BaSyC programme and beyond.
| Agata Szuba | Alberto Blanch Jover | Alex Cumberworth | Alka Rao | Ana Restrepo Sierra |
| Andreas Biebricher | Anne Jacobs | Anne Schwabe | Bettina Graupe | David Foschepoth |
| Diego Alonso Martinez | Elisa Godino | Ernest Yu Liu | Federico Fanalista | Flora Yang |
| George Dadunashvili | Giulia Bergamaschi | Gitta Buskermolen | Ilina Bareja | Joep Houkes |
| Lennard van Buren | Lorenzo Olivi | Lucia Baldauf | Ludo Schoenmakers | Mahesh Vibhute |
| Mareike Berger | Maria Tsanai | Marco van den Noort | Marten Exterkate | Mattia Rovetta |
| Max den Uijl | Max Finger Bou | Melanie Konig | Minco Polinder | Nicola de Franceschi |
| Pauline Lefrançois | Roel Maas | Sabrina Meindlhumer | Thijs Ettema | Thijs Nieuwkoop |
| Tom van de Weijer | Weria Pezeshkian | Zhanar Abil |
Zhanar Abil, Ana María Restrepo Sierra, Andreea R. Stan, Amélie Châne, Alicia del Prado, Miguel de Vega, Yannick Rondelez and Christophe Danelon
Darwinian Evolution of Self-Replicating DNA in a Synthetic Protocell
22 October 2024, Nature Communications, 15, 9091
https://doi.org/10.1038/s41467-024-53226-0
Laura Heinen, Marco van den Noort , Martin S. King, Edmund R. S. Kunji and Bert Poolman
Synthetic syntrophy for adenine nucleotide cross-feeding between metabolically active nanoreactors
21 October 2024, Nature Nanotechnology
https://doi.org/10.1038/s41565-024-01811-1
Yu Liu, Chunxiuzi Liu, Shaohua Tang, Hui Xiao, Xinlin Wu, Yunru Peng, Xianyi Wang, Linjie Que, Zengru Di, Da Zhou and Matthias Heinemann
The ‘‘weaken-fill-repair’’ model for cell budding: Linking cell wall biosynthesis with mechanics
18 October 2024, iScience, 27, 110981
https://doi.org/10.1016/j.isci.2024.110981
Lori Van de Cauter, Yash K. Jawale, Daniel Tam, Lucia Baldauf, Lennard van Buren, Gijsje H. Koenderink, Marileen Dogterom and Kristina A. Ganzinger
High-Speed Imaging of Giant Unilamellar Vesicle Formation in cDICE
25 September 2024, ACS Omega, 9, 42278-42288
https://doi.org/10.1021/acsomega.4c04825
Miyer F. Patiño-Ruiz, Zaid Ramdhan Anshari, Bauke Gaastra, Dirk J. Slotboom and Bert Poolman
Chemiosmotic nutrient transport in synthetic cells powered by electrogenic antiport coupled to decarboxylation
12 September 2024, Nature Communications, 15, 7976
https://doi.org/10.1038/s41467-024-52085-z
Meindlhumer, S.
Spiraling Towards Understanding In Vitro Min Protein Surface Patterns
11 September 2024, doctoral thesis, Delft University of Technology
Yilmaz, S.
Metabolic makeover: how to gain weight fast on a formate diet. Exploring and engineering synthetic metabolism in E. coli for optimal growth on formate
06 September 2024, doctoral thesis, Wageningen University
https://doi.org/10.18174/662566
Alexander J. Foster, Marco van den Noort and Bert Poolman
Bacterial cell volume regulation and the importance of cyclic di-AMP
27 June 2024, Microbiology and Molecular Biology Reviews, Rev 88:e00181-23
https://doi.org/10.1128/mmbr.00181-23
Barth, R.
Exploring SMC motor proteins and how to stop them
21 June 2024, doctoral thesis, Delft University of Technology
Daphne Broeks, Tarja Knuuttila and Henk de Regt
Understanding, Virtually: How Does the Synthetic Cell Matter?
01 June 2024, Perspectives on Science, 32, 3
https://doi.org/10.1162/posc_a_00612
E. Bailoni, M.F. Patiño-Ruiz, A.R. Stan, G.K. Schuurman-Wolters, M. Exterkate, A.J.M. Driessen and B. Poolman
Synthetic Vesicles for Sustainable Energy Recycling and Delivery of Building Blocks for Lipid Biosynthesis
17 May 2024, ACS Synthetic Biology, 13, 1549-1561
https://doi.org/10.1021/acssynbio.4c00073
Van den Noort, M.
It is all under control: Tuning the activity of the osmoregulatory ABC-importer OpuA
14 May 2024, doctoral thesis, 1-296, University of Groningen
https://doi.org/10.33612/diss.944974302
VilaChãLosa, J.
Bridging the gap between metabolism and the physics of the cytoplasm
13 May 2024, doctoral thesis, University of Groningen
https://doi.org/10.33612/diss.972628238
Bergamaschi, G.
Making waves: active microrheology of complex systems
03 May 2024, doctoral thesis, Vrije Universiteit Amsterdam
https://doi.org/10.5463/thesis.533
M. van den Noort, P. Drougkas, C. Paulino and B. Poolman
The substrate-binding domains of the osmoregulatory ABC importer OpuA transiently interact
02 May 2024, eLife, 12, RP90996
https://doi.org/10.7554/eLife.90996
Leonardo Morini, Andrei Sakai, Mahesh A. Vibhute, Zef Koch, Margo Voss, Ludo L. J. Schoenmakers and Wilhelm T. S. Huck
Leveraging Active Learning to Establish Efficient In Vitro Transcription and Translation from Bacterial Chromosomal DNA
16 April 2024, ACS Omega, 9, 19227-19235
https://doi.org/10.1021/acsomega.4c00111
J. Coenradij, E. Bailoni and B. Poolman
Construction of Out-of-Equilibrium Metabolic Networks in Nano- and Micrometer-Sized Vesicles
12 April 2024, J. Vis. Exp., e66627, 1-25
https://doi.org/10.3791/66627
Restrepo Sierra, A.M.
Engineering Synthetic Cells through Module Integration and Evolution
11 April 2024, doctoral thesis, 1-204, Delft University of Technology
https://doi.org/10.4233/uuid:2f2dfc76-5e29-4a04-84c1-3d337e3bf645
Olivi, L.
To Rebehold the Cell: Natural and Synthetic Cell Cycles Through the Lenses of Macromolecular Motion
22 March 2024, doctoral thesis, 1-248, Wageningen University
B. Monterroso, W. Margolin, A.J. Boersma, G. Rivas, B. Poolman and S. Zorrilla
Macromolecular Crowding, Phase Separation, and Homeostasis in the Orchestration of Bacterial Cellular Functions
28 February 2024, Chemical Reviews, 124, 1899-1949
https://doi.org/10.1021/acs.chemrev.3c00622
Richard Janissen, Roman Barth, Minco Polinder, Jaco van der Torre and Cees Dekker
Single-molecule visualization of twin-supercoiled domains generated during transcription
28 February 2024, Nucleic Acids Research, 52, 4, 1677-1687
https://doi.org/10.1093/nar/gkad1181
König, M.
From lipid to life: using simulations to connect molecular structure and membrane function
30 January 2024, doctoral thesis, 1-289, University of Groningen
https://hdl.handle.net/11370/3a84029f-5981-41c0-807d-660a80b561f6
Marco PA van Tilburg, Siewert J Marrink, Melanie König and Fabian Grünewald
Shocker-a molecular dynamics protocol and tool for accelerating and analyzing the effects of osmotic shocks
January 2024, Journal of Chemical Theory and Computation, 20, 1, 212-223
https://doi.org/10.1021/acs.jctc.3c00961
Nicola De Franceschi, Roman Barth, Sabrina Meindlhumer, Alessio Fragasso and Cees Dekker
Dynamin A as a one-component division machinery for synthetic cells
January 2024, Nature Nanotechnology, 19, 70-76
https://doi.org/10.1038/s41565-023-01510-3
Sakai, A.
Towards the bottom-up construction of a minimal synthetic cell
04 December 2023, doctoral thesis, 1-151, Radboud University
https://hdl.handle.net/2066/297618
Castro Linares, G.
The septin circus: an unforgettable show of cellular choreography
30 November 2023, doctoral thesis, 1-295, Delft University of Technology
https://doi.org/10.4233/uuid:d641823e-eaab-4fca-b856-fe3b0a500f88
Ireneusz Rosłon, Aleksandre Japaridze, Stef Rodenhuis, Lieke Hamoen, Murali Krishna Ghatkesar, Peter Steeneken, Cees Dekker and Farbod Alijani
Microwell-enhanced optical rapid antibiotic susceptibility testing of single bacteria
17 November 2023, CellPress, iScience 26, 108268
https://doi.org/10.1016/ j.isci.2023.108268
Rao, A.
Exploring Complex Cellular Membranes: Lipid Modifications in Extremophilic Archaea and Filamentous Fungi
14 November 2023, doctoral thesis, University of Groningen
https://doi.org/10.33612/diss.812181288
Xin Shi, Anna-Katharina Pumm, Christopher Maffeo, Fabian Kohler, Elija Feigl, Wenxuan Zhao, Daniel Verschueren, Ramin Golestanian, Aleksei Aksimentiev, Hendrik Dietz and Cees Dekker
A DNA turbine powered by a transmembrane potential across a nanopore
26 October 2023, Nature Nanotechnology
https://doi.org/10.1038/s41565-023-01527-8
Miloš Tišma, Richard Janissen, Hammam Antar, Alejandro Martin-Gonzalez, Roman Barth, Twan Beekman, Jaco van der Torre, Davide Michieletto, Stephan Gruber and Cees Dekker
Dynamic ParB–DNA interactions initiate and maintain a partition condensate for bacterial chromosome segregation
18 October 2023, Nucleic Acids Research, 1-20
https://doi.org/10.1093/nar/gkad868
den Uijl, M.J.
Membrane protein insertion in liposomes: implications for the synthetic cell
03 October 2023, doctoral thesis, University of Groningen
https://doi.org/10.33612/diss.774570878
Koster, C.
Exploring the potential of yeast mitochondria for synthetic cell research
22 September 2023, doctoral thesis, 1-205, Delft University of Technology
https://doi.org/10.4233/uuid:ef3e6834-988c-4d61-99f3-94133e005f1d
Schoenmakers, L.
Functionalizing Synthetic Cells Membranes and Condensates
19 September 2023, doctoral thesis, 1-202, Radboud University
https://repository.ubn.ru.nl/handle/2066/295327
Finger-Bou, M.
Not So Giant Steps On Tuning Protein Expression and Diminished Genomes
08 September 2023, doctoral thesis, 1-239, Wageningen University
https://doi.org/10.18174/632756
Charlotte C. Koster, Askar A. Kleefeldt, Marcel van den Broek, Marijke Luttik, Jean‐Marc Daran and Pascale Daran‐Lapujade
Long‐read direct RNA sequencing of the mitochondrial transcriptome of Saccharomyces cerevisiae reveals condition-dependent intron abundance
29 August 2023, Yeast, 1-23
https://doi.org/10.1002/yea.3893
Benjamin R. Gilbert, Zane R. Thornburg, Troy A. Brier, Jan A. Stevens, Fabian , John E. Stone, Siewert J. Marrink and Zaida Luthey-Schulten
Dynamics of chromosome organization in a minimal bacterial cell
9 August 2023, Frontiers in Cell and Developmental Biology, 11:1214962
https://doi.org/10.3389/fcell.2023.1214962
Mareike Berger and Pieter Rein ten Wolde
Synchronous replication initiation of multiple origins
8 August 2023, Physical Review X Life 1, 013007 (2023)
https://doi.org/10.1103/PRXLife.1.013007
L van de Cauter, L van Buren, GH Koenderink and KA Ganzinger
Exploring Giant Uniflagellar Vesicle Production for Artificial Cells – Current Challenges and Future Directions
18 July 2023, Small Methods, 18:e2300416
https://doi.org/10.1002/smtd.202300416
Alexander Cumberworth and Pieter Rein ten Wolde
Constriction of Actin Rings by Passive Crosslinkers
17 July 2023, Phys. Rev. Lett. 131, 038401
https://journals.aps.org/prl/abstract/10.1103/PhysRevLett.131.038401
Bailoni, E.
Recycling to grow Cofactor conservation for sustainable phospholipid biosynthesis in synthetic cells
27 June 2023, doctoral thesis, University of Groningen
https://doi.org/10.33612/diss.645664160
Andrei Sakai, Aafke J. Jonker, Frank H. T. Nelissen, Evan M. Kalb, Bob van Sluijs, Hans A. Heus, Katarzyna P. Adamala, John I. Glass, and Wilhelm T. S. Huck
Cell-Free Expression System Derived from a Near-Minimal Synthetic Bacterium
6 June 2023, ACS Synthetic Biology, 12, 6, 1616–1623
https://doi.org/10.1021/acssynbio.3c00114
Roman Barth, Biswajit Pradhan, Eugene Kim, Iain F. Davidson, Jaco van der Torre, Jan‑Michael Peters and Cees Dekker
Testing pseudotopological and nontopological models for SMC‑driven DNA loop extrusion against roadblock‑traversal experiments
19 May 2023, Scientific Reports, 13, Article number: 8100
https://doi.org/10.1038/s41598-023-35359-2
Elisa Godino, Ana Maria Restrepo Sierra and Christophe Danelon
Imaging Flow Cytometry for High-Throughput Phenotyping of Synthetic Cells
8 May 2023, ACS Synthetic Biology, 12, 7, 2015–2028
https://doi.org/10.1021/acssynbio.3c00074
Eugene Kim, Roman Barth and Cees Dekker
Looping the Genome with SMC Complexes
3 May 2023, Annual Reviews of Biochemistry 92:15–41
https://doi.org/10.1146/annurev-biochem-032620-110506
Berger, M.
Controlling DNA replication initiation: from living to synthetic cells
3 May 2023, doctoral thesis, 1-232, AMOLF and VU Amsterdam
https://doi.org/10.5463/thesis.125
Michele Partipilo, Nico J. Claassens and Dirk Jan Slotboom
A Hitchhiker’s Guide to Supplying Enzymatic Reducing Power into Synthetic Cells
13 April 2023, ACS Synthetic Biology, Review, 12, 4, 947–962
https://doi.org/10.1021/acssynbio.3c00070
Eleonora Bailoni, Michele Partipilo, Jelmer Coenradij, Douwe A. J. Grundel, Dirk J. Slotboom and Bert Poolman
Minimal Out-of-Equilibrium Metabolism for Synthetic Cells: A Membrane Perspective
7 April 2023, ACS Synthetic Biology, Review, 12, 4, 922–946
https://doi.org/10.1021/acssynbio.3c00062
Ryoya Nakagawa, Hisato Hirano, Satoshi N. Omura, Suchita Nety, Soumya Kannan, Han Altae-Tran, Xiao Yao, Yuriko Sakaguchi, Takayuki Ohira, Wen Y. Wu, Hiroshi Nakayama, Yutaro Shuto, Tatsuki Tanaka, Fumiya K. Sano, Tsukasa Kusakizako, Yoshiaki Kise, Yuzuru Itoh, Naoshi Dohmae, John van der Oost, Tsutomu Suzuki, Feng Zhang and Osamu Nureki
Cryo-EM structure of the transposon-associated TnpB enzyme
5 April 2023, Nature, 616, pages 390–397
https://doi.org/10.1038/s41586-023-05933-9
Zhanar Abil, Ana Maria Restrepo Sierra and Christophe Danelon
Clonal Amplification-Enhanced Gene Expression in Synthetic Vesicles
4 April 2023, ACS Synthetic Biology, 12, 4, 1187–1203
https://doi.org/10.1021/acssynbio.2c00668
Aleksandre Japaridze, Raman van Wee, Christos Gogou, Jacob W. J. Kerssemakers, Daan F. van den Berg and Cees Dekker
MukBEF-dependent chromosomal organization in widened Escherichia coli
3 March 2023, Frontiers in Microbiology, 14:1107093
https://doi.org/10.3389/fmicb.2023.1107093
Amini Hounejani, R.
Bacterial cytoskeletal filaments: Towards a DNA segregation system for a synthetic cell
8 March 2023, doctoral thesis, 1-116, Delft University of Technology
https://doi.org/10.4233/uuid:79de9e6e-8201-499b-8d41-7c52ae450257
Lucia Baldauf, Felix Frey, Marcos Arribas Perez, Timon Idema and Gijsje H. Koenderink
Branched actin cortices reconstituted in vesicles sense membrane curvature
17 February 2023, Biophysical Journal, 122, 1–14
https://doi.org/10.1016/j.bpj.2023.02.018
Sabrina Meindlhumer, Fridtjof Brauns, Jernej Rudi Finžgar, Jacob Kerssemakers, Cees Dekker and Erwin Frey
Directing Min protein patterns with advective bulk flow
27 January 2023, Nature Communications, 14:450
https://doi.org/10.1038/s41467-023-35997-0
Jan A. Stevens, Fabian Grünewald, P. A. Marco van Tilburg, Melanie König, Benjamin R. Gilbert, Troy A. Brier, Zane R. Thornburg, Zaida Luthey-Schulten and Siewert J. Marrink
Molecular dynamics simulation of an entire cell
18 January 2023, Frontiers in Chemistry, 11:1106495
https://doi.org/10.3389/fchem.2023.1106495
Alberto Blanch Jover and Cees Dekker
The archaeal Cdv cell division system
17 January 2023, Trends in Microbiology, review, 31, 6, p601-615
https://doi.org/10.1016/j.tim.2022.12.006
Thijs Nieuwkoop, Barbara R. Terlouw, Katherine G. Stevens, Richard A. Scheltema, Dick de Ridder, John van der Oost and Nico J. Claassens
Revealing determinants of translation efficiency via whole-gene codon randomization and machine learning
16 January 2023, Nucleic Acids Research, 51, 5, 2363–2376
https://doi.org/10.1093/nar/gkad035
Houkes, J.
Towards a synthetic cell: designing, testing and optimizing functional genomic modules in E. coli
11 January 2023, doctoral thesis, 1-177, Wageningen University & Research
https://doi.org/10.18174/582244
Elisa Godino and Christophe Danelon
Gene-Directed FtsZ Ring Assembly Generates Constricted Liposomes with Stable Membrane Necks
02 January 2023, Advanced Biology, 2200172
https://doi.org/10.1002/adbi.202200172
Baldauf, L.
Rebuilding Cytokinesis One Molecule at a Time
22 December 2022, doctoral thesis, 1-269, Delft University of Technology, cum laude
https://doi.org/10.4233/uuid:412a4272-9ec2-4aba-852d-981e392d64d0
Maas, R.
A microfluidic approach for forward design of modular cell-free genetic networks
13 December 2022, doctoral thesis, 1-175, Radboud University Nijmegen
https://hdl.handle.net/2066/285022
L. van Buren, G.H. Koenderink, C. Martinez-Torres
DisGUVery: a versatile open-source software for high-throughput image analysis of Giant Unilamellar Vesicles
12 December, ACS Synthetic Biology
https://pubs.acs.org/doi/10.1021/acssynbio.2c00407
Nicola De Franceschi, Weria Pezeshkian, Alessio Fragasso, Bart M. H. Bruininks, Sean Tsai, Siewert J. Marrink and Cees Dekker
Synthetic Membrane Shaper for Controlled Liposome Deformation
28 November 2022, ACS Nano
https://doi.org/10.1021/acsnano.2c06125
Tsanai, M.
Modeling of liquid-liquid phase separation in biological systems
15 November 2022, doctoral thesis, University of Groningen
https://doi.org/10.33612/diss.250581454
Blanch Jover, A.
Looking Back To Move Forward
Studying the Ancient Archaeal Cdv Cell Division Machinery for Synthetic Cells
11 November 2022, doctoral thesis, 1-122, Delft University of Technology
https://doi.org/10.4233/uuid:92945ff1-c8c3-406c-a7f2-fe538800a75e
Mareike Berger and Pieter Rein ten Wolde
Robust replication initiation from coupled homeostatic mechanisms
07 November 2022, nature communications, 13:6556
https://doi.org/10.1038/s41467-022-33886-6
Partipilo, M.
On the enzymatic provision of redox power in synthetic cells
25 October 2022, doctoral thesis, University of Groningen
https://doi.org/10.33612/diss.243330956
Biswajit Pradhan, Roman Barth, Eugene Kim, Iain F. Davidson, Benedikt Bauer, Theo van Laar, Wayne Yang, Je-Kyung Ryu, Jaco van der Torre, Jan-Michael Peters and Cees Dekker
SMC complexes can traverse physical roadblocks bigger than their ring size
18 October 2022, Cell Reports, 41, 111491
https://doi.org/10.1016/j.celrep.2022.111491
Lucia Baldauf, Lennard van Buren, Federico Fanalista and Gijsje Hendrika Koenderink
Actomyosin-Driven Division of a Synthetic Cell
27 September 2022, ACS Synthetic Biology, 11, 10, 3120–3133
https://doi.org/10.1021/acssynbio.2c00287
Dadunashvili, G.
Physical Principles of Membrane Reshaping; a theoretical study of self organization on membrane surfaces through membrane-mediated interactions
21 September 2022, doctoral thesis, 1-119, Delft University of Technology
https://doi.org/10.4233/uuid:4971c301-0234-4762-8a67-74337f6acbbc
Michele Partipilo, Guang Yang, Maria Laura Mascotti, Hein J. Wijma, Dirk Jan Slotboom and Marco W. Fraaije
A conserved sequence motif in the Escherichia coli soluble FAD-containing pyridine nucleotide transhydrogenase is important for reaction efficiency
September 2022, Journal of Biological Chemistry, 298(9) 102304
https://doi.org/10.1016/j.jbc.2022.102304
Yuval Mulla, Mario J. Avellaneda, Antoine Roland, Lucia Baldauf, Wonyeong Jung, Taeyoon Kim, Sander J. Tans and Gijsje H. Koenderink
Weak catch bonds make strong networks
25 August 2022, Nature Materials, 21, 1019-1023
https://doi.org/10.1038/s41563-022-01288-0
Jacopo Frallicciardi, Matteo Gabba and Bert Poolman
Determining small-molecule permeation through lipid membranes
24 August 2022, Nature Protocols
https://doi.org/10.1038/s41596-022-00734-2
Wojciech M Śmigiel, Luca Mantovanelli, Dmitrii S Linnik, Michiel Punter, Jakob Silberberg, Limin Xiang, Ke Xu, Bert Poolman
Protein diffusion in Escherichia coli cytoplasm scales with the mass of the complexes and is location dependent
12 August 2022, Science Advances, 8, 32, 5387
https://doi.org/10.1126/sciadv.abo5387
Eugene Kim, Alejandro Martin Gonzalez, Biswajit Pradhan, Jaco van der Torre and Cees Dekker
Condensin-driven loop extrusion on supercoiled DNA
14 July 2022, Nature Structural & Molecular Biology, 29, 719-727
https://doi.org/10.1038/s41594-022-00802-x
Subhas C Bera, Pim P B America, Santeri Maatsola, Mona Seifert, Eugeniu Ostrofet, Jelmer Cnossen, Monika Spermann, Flávia S Papini, Martin Depken, Anssi M Malinen and David Dulin
Quantitative parameters of bacterial RNA polymerase open-complex formation, stabilization and disruption on a consensus promoter
12 July 2022, Nucleic Acids Research, 50, 13, 7511–7528
https://doi.org/10.1093/nar/gkac560
Elisa Godino, Anne Doerr and Christophe Danelon
Min waves without MinC can pattern FtsA-anchored FtsZ filaments on model membranes
7 July 2022, Communications Biology, 5, 675
https://doi.org/10.1038/s42003-022-03640-1
Miloš Tišma, Maria Panoukidou, Hammam Antar, Young-Min Soh, Roman Barth, Biswajit Pradhan, Anders Barth, Jaco van der Torre, Davide Michieletto, Stephan Gruber and Cees Dekker
ParB proteins can bypass DNA-bound roadblocks via dimer-dimer recruitment
29 June 2022, Science Advances, 8, eabn3299
https://doi.org/10.1126/sciadv.abn3299
Bob van Sluijs, Roel J. M. Maas, Ardjan J. van der Linden, Tom F. A. de Greef and Wilhelm T. S. Huck
A microfluidic optimal experimental design platform for forward design of cell-free genetic networks
24 June 2022, Nature Communications, 13, 3626
https://doi.org/10.1038/s41467-022-31306-3
Vadim Bogatyr, Andreas S. Biebricher, Giulia Bergamaschi, Erwin J. G. Peterman, and Gijs J. L. Wuite
Quantitative Acoustophoresis
22 June 2022, ACS Nanoscience Au, 2, 4, 341–354
https://doi.org/10.1021/acsnanoscienceau.2c00002
van Buren, L.
Synthetic Cell Aspirations
24 May 2022, doctoral thesis, 1-276, Delft University of Technology
https://doi.org/10.4233/uuid:d0b7e1e5-7836-4914-993d-ff83e446a43f
Andrei Sakai, Christopher R. Deich, Frank H. T. Nelissen, Aafke J. Jonker, Daniela M. de C. Bittencourt, Christopher P. Kempes, Kim S. Wise, Hans A. Heus, Wilhelm T. S. Huck, Katarzyna P. Adamala and John I. Glass
Traditional protocols and optimization methods lead to absent expression in a mycoplasma cell-free gene expression platform
21 May 2022, Synthetic Biology, 7, 1
https://doi.org/10.1093/synbio/ysac008
Florian Chardon, Aleksandre Japaridze, Hannes Witt, Leonid Velikovsky, Camellia Chakraborty, Therese Wilhelm, Marie Dumont, Wayne Yang, Carlos Kikuti, Stephane Gangnard, Anne-Sophie Mace, Gijs Wuite, Cees Dekker and Daniele Fachinetti
CENP-B-mediated DNA loops regulate activity and stability of human centromeres
5 May 2022, Molecular Cell, 82, 9, 1751-1767.e8
https://doi.org/10.1016/j.molcel.2022.02.032
Godino, E.
Expression of a gene-encoded FtsZ-based minimal machinery to drive synthetic cell division
6 April 2022, doctoral thesis, 1-119, Delft University of Technology
https://doi.org/10.4233/uuid:c43c9b99-585a-4929-9bee-2c6d87a3b2c1
Eleonora Bailoni and Bert Poolman
ATP Recycling Fuels Sustainable Glycerol 3‑Phosphate Formation in Synthetic Cells Fed by Dynamic Dialysis
4 April 2022, ACS Synthetic Biology, 11, 7, 2348-2360
https://doi.org/10.1021/acssynbio.2c00075
Jose Losa, Simeon Leupold, Diego Alonso-Martinez, Petteri Vainikka, Sebastian Thallmair, Katarzyna M Tych, Siewert J Marrink and Matthias Heinemann
Perspective: a stirring role for metabolism in cells
1 April 2022, Molecular Systems Biology, 18: e10822
https://doi.org/10.15252/msb.202110822
Charlotte C. Koster, Eline D. Postma, Ewout Knibbe, Céline Cleij and Pascale Daran-Lapujade
Synthetic Genomics From a Yeast Perspective
21 March 2022, Frontiers in Bioengineering and Biotechnology, 10, 869486
https://doi.org/10.3389/fbioe.2022.869486
Alberto Blanch Jover, Nicola De Franceschi, Daphna Fenel, Winfried Weissenhorn and Cees Dekker
The archaeal division protein CdvB1 assembles into polymers that are depolymerized by CdvC
2 March 2022, FEBS Letters, 596, 7, 958-969
https://doi.org/10.1002/1873-3468.14324
Kevin D. Whitley, Stuart Middlemiss, Calum Jukes, Cees Dekker and Seamus Holden
High-resolution imaging of bacterial spatial organization with vertical cell imaging by nanostructured immobilization (VerCINI)
31 January 2022, natureprotocols, 17, 847-869
https://doi.org/10.1038/s41596-021-00668-1
Michel Bengtson, Mitasha Bharadwaj, Oskar Franch, Jaco van der Torre, Veronique Meerdink, Henk Schallig and Cees Dekker
CRISPR-dCas9 based DNA detection scheme for diagnostics in resource-limited settings
19 January 2022, Nanoscale, issue 5
https://doi.org/10.1039/d1nr06557b
Nieuwkoop, T.
Tuning for high protein production
08 December 2021, doctoral thesis, 1-195, Wageningen University
https://doi.org/10.18174/554205
Michele Partipilo, Eleanor J. Ewins, Jacopo Frallicciardi, Tom Robinson, Bert Poolman, and Dirk Jan Slotboom
Minimal Pathway for the Regeneration of Redox Cofactors
12 November 2021, JACS Au, 1, 2280−2293
https://doi.org/10.1021/jacsau.1c00406
Subhas Chandra Bera, Mona Seifert, Robert N. Kirchdoerfer, Pauline van Nies, Yibulayin Wubulikasimu, Salina Quack, Fla´ via S. Papini, Jamie J. Arnold, Bruno Canard, Craig E. Cameron, Martin Depken, and David Dulin
The nucleotide addition cycle of the SARS-CoV-2 polymerase
31 August 2021, Cell Reports, 36, 109650
https://doi.org/10.1016/j.celrep.2021.109650
Francois Iv, Carla Silva Martins, Gerard Castro-Linares, Cyntia Taveneau, Pascale Barbier, Pascal Verdier-Pinard, Luc Camoin, Stéphane Audebert, Feng-Ching Tsai, Laurie Ramond, Alex Llewellyn, Mayssa Belhabib, Koyomi Nakazawa, Aurélie Di Cicco, Renaud Vincentelli, Jerome Wenger, Stéphanie Cabantous, Gijsje H. Koenderink, Aurélie Bertin and Manos Mavrakis
Insights into animal septins using recombinant human septin octamers with distinct SEPT9 isoforms
5 August 2021, Journal of Cell Science, 134, jcs258484
https://doi.org/10.1242/jcs.258484
Weria Pezeshkian, Siewert J.Marrink
Simulating realistic membrane shapes
August 2021, Current Opinion in Cell Biology, 71, 103-111
https://doi.org/10.1016/j.ceb.2021.02.009
Lorenzo Olivi , Mareike Berger, Ramon N. P. Creyghton, Nicola De Franceschi, Cees Dekker, Bela M. Mulder, Nico J. Claassens, Pieter Rein ten Wolde and John van der Oost
Towards a synthetic cell cycle
26 July 2021, Nature Communications, 12:4531
https://doi.org/10.1038/s41467-021-24772-8
Marco van den Noort, Marijn de Boer and Bert Poolman
Stability of Ligand-induced Protein Conformation Influences Affinity in Maltose-binding Protein
23 July 2021, Journal of Molecular Biology, 433, 167036
https://doi.org/10.1016/j.jmb.2021.167036
Lori Van de Cauter, Federico Fanalista, Lennard van Buren, Nicola De Franceschi, Elisa Godino, Sharon Bouw, Christophe Danelon, Cees Dekker, Gijsje H. Koenderink and Kristina A. Ganzinger
Optimized cDICE for Efficient Reconstitution of Biological Systems in Giant Unilamellar Vesicles
29 June 2021, ACS Synthetic Biology, 10, 7, 1690–1702
https://doi.org/10.1021/acssynbio.1c00068
Alessio Fragasso, Nicola De Franceschi, Pierre Stömmer, Eli O. van der Sluis, Hendrik Dietz and Cees Dekker
Reconstitution of Ultrawide DNA Origami Pores in Liposomes for Transmembrane Transport of Macromolecules
25 June 2021, ACS Nano
https://doi.org/10.1021/acsnano.1c01669
Christos Gogou, Aleksandre Japaridze and Cees Dekker
Mechanisms for Chromosome Segregation in Bacteria
16 June 2021, Frontiers in Microbiology, 12, 685687
https://doi.org/10.3389/fmicb.2021.685687
Javier Antonio Alfaro, Peggy Bohländer, Mingjie Dai, Mike Filius, Cecil J. Howard, Xander F. van Kooten, Shilo Ohayon, Adam Pomorski, Sonja Schmid, Aleksei Aksimentiev, Eric V. Anslyn, Georges Bedran, Chan Cao, Mauro Chinappi, Etienne Coyaud, Cees Dekker, Gunnar Dittmar, Nicholas Drachman, Rienk Eelkema, David Goodlett, Sébastien Hentz, Umesh Kalathiya, Neil L. Kelleher, Ryan T. Kelly, Zvi Kelman, Sung Hyun Kim, Bernhard Kuster, David Rodriguez-Larrea, Stuart Lindsay, Giovanni Maglia, Edward M. Marcotte, John P. Marino, Christophe Masselon, Michael Mayer, Patroklos Samaras, Kumar Sarthak, Lusia Sepiashvili, Derek Stein, Meni Wanunu, Mathias Wilhelm, Peng Yin, Amit Meller and Chirlmin Joo
The emerging landscape of single-molecule protein sequencing technologies
7 June 2021, Nature Methods, 18, 604–617
https://doi.org/10.1038/s41592-021-01143-1
Fridtjof Brauns, Grzegorz Pawlik, Jacob Halatek, Jacob Kerssemakers, Erwin Frey and Cees Dekker
Bulk-surface coupling identifies the mechanistic connection between Min-protein patterns in vivo and in vitro
3 June 2021, Nature Communications, 12:3312
https://doi.org/10.1038/s41467-021-23412-5
Aleksandre Japaridze, Wayne Yang, Cees Dekker, William Nasser and Georgi Muskhelishvili
DNA sequence-directed cooperation between nucleoid-associated proteins
21 May 2021, iScience CellPress, 24, 102408
https://doi.org/10.1016/j.isci.2021.102408
Maria Tsanai, Pim W. J. M. Frederix, Carsten F. E. Schroer, Paulo C. T. Souza and Siewert J. Marrink
Coacervate formation studied by explicit solvent coarse-grain molecular dynamics with the Martini model
18 May 2021, Chemical Science, 12, 8521
https://doi.org/10.1039/d1sc00374g
Kevin D. Whitley, Calum Jukes, Nicholas Tregidgo, Eleni Karinou, Pedro Almada, Yann Cesbron, Ricardo Henriques, Cees Dekker and Séamus Holden
FtsZ treadmilling is essential for Z-ring condensation and septal constriction initiation in Bacillus ubtilis cell division
27 April 2021, Nature Communications, 12:2448
https://doi.org/10.1038/s41467-021-22526-0
Marten Exterkate, Niels A. W. de Kok, Ruben L. H. Andringa, Niels H. J. Wolbert, Adriaan J. Minnaard and Arnold J. M. Driessen
A promiscuous archaeal cardiolipin synthase enables construction of diverse natural and unnatural phospholipids
22 April 2021, Journal of Biological Chemistry, 296, 100691
https://doi.org/10.1016/j.jbc.2021.100691
Christoffer Aberg, and Bert Poolman
Glass-like characteristics of intracellular motion in human cells
19 April 2021, Biophysical Journal, 120, 2355–2366
https://doi.org/10.1016/j.bpj.2021.04.011
Agata Szuba, Fouzia Bano, Gerard Castro-Linares, Francois, Manos Mavrakis, Ralf P Richter, Aurelie Bertin and Gijsje H Koenderink
Membrane binding controls ordered self assembly of animal septins
13 April 2021, eLife, 10:e63349
https://doi.org/10.7554/eLife.63349
Siddharth Deshpande and Cees Dekker
Studying phase separation in confinement
April 2021, Colloid & Interface Science, 52:101419
https://doi.org/10.1016/j.cocis.2021.1014191359-0294
Alessio Fragasso, Hendrik W. de Vries, John Andersson, Eli O. van der Sluis, Erik van der Giessen, Andreas Dahlin, Patrick R. Onck and Cees Dekker
A designer FG-Nup that reconstitutes the selective transport barrier of the nuclear pore complex
31 March 2021, Nature Communications, 12:2010
https://doi.org/10.1038/s41467-021-22293-y
Je-Kyung Ryu, Céline Bouchoux, Hon Wing Liu, Eugene Kim, Masashi Minamino, Ralph deGroot, Allard J. Katan, Andrea Bonato, Davide Marenduzzo, Davide Michieletto, Frank Uhlmann and Cees Dekker
Bridging-induced phase separation induced by cohesin SMC protein complexes
10 February 2021, Science Advances, 7:eabe5905
https://doi.org/10.1126/sciadv.abe5905
Wayne Yang, Boya Radha, Adnan Choudhary, Yi You, Gangaiah Mettela, Andre K. Geim, Aleksei Aksimentiev, Ashok Keerthi and Cees Dekker
Translocation of DNA through Ultrathin Nanoslits
1 February 2021, Advanced Materials, 2007682
https://doi.org/10.1002/adma.202007682
Anne Doerr, David Foschepoth, Anthony C. Forster and Christophe Danelon
In vitro synthesis of 32 translation‑factor proteins from a single template reveals impaired ribosomal processivity
21 January 2021, Nature.com, Scientific Reports, 11:1898
https://doi.org/10.1038/s41598-020-80827-8
Anthony Birnie and Cees Dekker
Genome-in-a-Box: Building a Chromosome from the Bottom Up
21 December 2020, ACS Nano, 15, 111−124
https://dx.doi.org/10.1021/acsnano.0c07397
Michelle G.J.L. Habets, Hub A.E. Zwart and Rinie van Est
Why the Synthetic Cell Needs Democratic Governance
1 December 2020, Trends in Biotechnology
https://doi.org/10.1016/j.tibtech.2020.11.006
Thijs Nieuwkoop, Max Finger-Bou, John van der Oost and Nico J. Claassens
The Ongoing Quest to Crack the Genetic Code for Protein Production
15 October 2020, Molecular Cell, 80, 2, 193-209
https://doi.org/10.1016/j.molcel.2020.09.014
Elisa Godino, Jonas Noguera Lopez, Ilias Zarguit, Anne Doerr, Mercedes Jimenez, German Rivas and Christophe Danelon
Cell-free biogenesis of bacterial division proto-rings that can constrict liposomes
30 September 2020, Communications Biology, 3, article number: 539
https://doi.org/10.1038/s42003-020-01258-9
Mahesh A. Vibhute, Mark H. Schaap, Roel J.M. Maas, Frank H. T. Nelissen, Evan Spruijt, Hans A. Heus, Maike M. K. Hansen and Wilhelm T. S. Huck
Transcription and translation in Cytomimetic Protocells Perform Most Efficiently at Distinct Macromolecular Crowding Conditions
25 September 2020, ACS Synthetic Biology, 10, 2797-2807
https://doi.org/10.1021/acssynbio.0c00330
Duco Blanken, David Foschepoth, Adriana Calaça Serrão and Christophe Danelon
Genetically controlled membrane synthesis in liposomes
28 August 2020, Nature Communications, 11, 4317
https://doi.org/10.1038/s41467-020-17863-5
Zhanar Abil and Christophe Danelon
Roadmap to Building a Cell: An Evolutionary Approach
19 August 2020, Front. Bioeng. Biotechnol, Volume 8, Article 927
https://doi.org/10.3389/fbioe.2020.00927
Max Finger-Bou, Enrico Orsi, John van der Oost and Raymond H. J. Staals
CRISPR with a Happy Ending: Non-Templated DNA Repair for Prokaryotic Genome Engineering
17 June 2020, Biotechnology Journal, 1900404
https://doi.org/10.1002/biot.201900404
Weria Pezeshkian, Melanie König, Tsjerk A. Wassenaar and Siewert J. Marrink
Backmapping triangulated surfaces to coarsegrained membrane models
8 May 2020, Nature Communications, 11, 2296
https://doi.org/10.1038/s41467-020-16094-y
Eugene Kim, Jacob Kerssemakers, Indra A. Shaltiel, Christian H. Haering and Cees Dekker
DNA-loop extruding condensin complexes can traverse one another
4 March 2020, Nature, 579, 438-442
https://doi.org/10.1038/s41586-020-2067-5
Carsten F.E. Schroer, Lucia Baldauf, Lennard van Buren, Tsjerk A. Wassenaar, Manuel N. Melo, Gijsje H. Koenderink and Sieuwert J. Marrink
Charge-dependant interactions of monomeric and filamentous actin with lipid bilayers
4 February 2020, PNAS, 117, 5861-5872
https://doi.org/10.1073/pnas.1914884117
Elisa Godino, Jonás Noguera López, David Foschepoth, Céline Cleij, Anne Doerr,
Clara Ferrer Castellà and Christophe Danelon
De novo synthesized Min proteins drive oscillatory liposome deformation and regulate FtsA-FtsZ cytoskeletal patterns
31 October 2019, Nature Communications, 10, 4969
https://doi.org/10.1038/s41467-019-12932-w
Laura Restrepo-Pérez, Gang Huang, Peggy R. Bohländer, Nathalie Worp, Rienk Eelkema, Giovanni Maglia, Chirlmin Joo and Cees Dekker
Resolving Chemical Modifications to a Single Amino Acid within a Peptide Using a Biological Nanopore
19 October 2019, ACS Nano, 13, 12, 13668-13676
https://doi.org/10.1021/acsnano.9b05156
Tjeerd Pols, Hendrik R. Sikkema, Bauke F. Gaastra, Jacopo Frallicciardi, Wojciech M. Śmigiel, Shubham Singh and Bert Poolman
A synthetic metabolic network for physicochemical homeostasis
18 September 2019, Nature Communications, volume 10, Article number 4239
https://doi.org/10.1038/s41467-019-12287-2
Wojciech Mikołaj Śmigiel, Pauline Lefrançois and Bert Poolman
Physicochemical considerations for bottom-up synthetic biology
28 August 2019, Emerging Topics in Life Sciences, 3, 445–458
https://doi.org/10.1042/ETLS20190017
Siddharth Deshpande and Cees Dekker
Synthetic life on a chip
20 August 2019, Emerging Topics in Life Sciences, 3 (5) 559–566
https://doi.org/10.1042/ETLS20190097
Hendrik R. Sikkema, Bauke F. Gaastra, Tjeerd Pols and Bert Poolman
Cell Fuelling and Metabolic Energy Conservation in Synthetic Cells
05 August 2019, ChemBioChem, 20, 2581 – 2592
https://doi.org/10.1002/cbic.201900398
Siddharth Deshpande, Sreekar Wunnava, David Hueting and Cees Dekker
Membrane Tension–Mediated Growth of Liposomes
31 July 2019, Small, Volume15, Issue 38
https://doi.org/10.1002/smll.201902898
Weria Pezeshkian, Melanie König, Siewert J. Marrink and John H. Ipsen
A Multi-Scale Approach to Membrane Remodeling Processes
23 July 2019, Frontiers in Molecular Biosciences, Volume 6, Article 59
https://doi.org/10.3389/fmolb.2019.00059
Marten Exterkate and Arnold J. M. Driessen
Continuous expansion of a synthetic minimal cellular membrane
23 July 2019, Emerging Topics in Life Sciences, 3 (5) 543–549
https://doi.org/10.1042/ETLS20190020
Fabai Wu, Pinaki Swain, Louis Kuijpers, Xuan Zheng, Kevin Felter, Margot Guurink, Jacopo Solari, Suckjoon Jun, Thomas S. Shimizu, Debasish Chaudhuri, Bela Mulder and Cees Dekker
Cell Boundary Confinement Sets the Size and Position of the E. coli Chromosome
8 July 2019, Current Biology, 29, 13, 2131-2144
https://doi.org/10.1016/j.cub.2019.05.015
Hub Zwart
What is Mimicked by Biomimicry? Synthetic Cells as Exemplifications of the Threefold Biomimicry Paradox
July 2019, Environmental Values, 28 (5), 527-549
https://doi.org/10.3197/096327119X15579936382356
Alessio Fragasso, Sergii Pud and Cees Dekker
1/f noise in solid-state nanopores is governed by access and surface regions
27 June 2019, Nanotechnology, 30, 395202
https://doi.org/10.1088/1361-6528/ab2d35
Nico J. Claassens, Max Finger-Bou, Bart Scholten, Frederieke Muis, Jonas J. de Groot, Jan-Willem de Gier, Willem M. de Vos and John van der Oost
Bicistronic Design-Based Continuous and High-Level Membrane Protein Production in Escherichia coli
17 June 2019, ACS Synthetic Biology, 8, 7, 1685−1690
https://doi.org/10.1021/acssynbio.9b00101
Federico Fanalista, Anthony Birnie, Renu Maan, Federica Burla, Kevin Charles, Grzegorz Pawlik, Siddharth Deshpande, Gijsje H. Koenderink, Marileen Dogterom and Cees Dekker
Shape and Size Control of Artificial Cells for Bottom-Up Biology
10 may 2019, ACS Nano, 13, 5, 5439-5450
https://doi.org/10.1021/acsnano.9b00220
Siddharth Deshpande, Frank Brandenburg, Anson Lau, Mart G.F. Last, Willem Kasper Spoelstra, Louis Reese, Sreekar Wunnava, Marileen Dogterom and Cees Dekker
Spatiotemporal control of coacervate formation within liposomes
17 April 2019, Nature Communications, 10, 1800
https://doi.org/10.1038/s41467-019-09855-x
Marten Exterkate and Arnold J. M. Driessen
Synthetic Minimal Cell: Self-Reproduction of the Boundary Layer
13 March 2019, ACS Omega, 4, 3, 5293-5303
https://doi.org/10.1021/acsomega.8b02955
Hub Zwart
From primal scenes to synthetic cells
13 March 2019, eLife, 8:e46518
https://doi.org/10.7554/eLife.46518
Anne Doerr, Elise de Reus, Pauline van Nies, Mischa van der Haar, Katy Wei, Johannes Kattan, Aljoscha Wahl and Christophe Danelon
Modelling cell-free RNA and protein synthesis with minimal systems
9 January 2019, Physical Biology, 16, 2
https://doi.org/10.1088/1478-3975/aaf33d
Hub Zwart
Scientific iconoclasm and active imagination: synthetic cells as technoscientific mandalas
14 May 2018, Life Sciences, Society and Policy, 14, 10
https://doi.org/10.1186/s40504-018-0075-0