Projects

BaSyC consists of 7 interacting work packages (WPs):

WP0 – System Design In this WP, theoretical and computational models are developed on all levels of complexity. The aim is to converge on a feasible overall design of the system with continuous feedback from the experiments.

WP1 – Cell Fuelling The aim of this WP is to engineer a minimal metabolism in a sealed system that can supply the vesicle with energy, and building blocks to operate replication, transcription and translation, that can accomplish energy, redox, volume, and pH homeostasis, and that can synthesize lipids allowing the synthetic cell to grow and divide.

WP2 – DNA Processing In this WP, an information processing machinery will be built that can replicate its own genetic information, that can transcribe the DNA in order to generate the flow of mRNA for protein production, and that can synthesize/assemble ribosomes, which in turn produce the proteins allowing the synthetic cell to grow and divide

WP3 – Cell Division In this WP, we will engineer a force generating machinery for constriction and fission of a vesicle, which will be responsible for the division of the BaSyC cell.

WP4 – Spatio-Temporal Integration WP4 will be devoted to integrating the base modules from WP1-3. In addition, strategies and machineries will be devised for the spatio-temporal control of the three base modules.

WP5 – Towards Autonomy In this WP, we will synthesize a whole genome supporting the functional modules as explored in WP1-4. We will apply an iterative cycle of genome design, assembly and testing.

WP6 – Philosophy, Ethics, and Public Debate 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.

Each Work package is subdivided in a number of projects, as shown in this table.

Project Title
 WP0  System Design
 WP0.1  Identification of global variables and constraints
WP0.2  Development of models for subsystems
 WP0.3  Integrating models ultimately leading to an in silico synthetic cell
 WP1  Cell Fuelling 
 WP1.1  A system for ATP and redox homeostasis
 WP1.2  Modules to provide the cell with essential nutrients
 WP1.3  Synthesizing a functional, expanding membrane
 WP2  DNA Processing 
 WP2.1  Replication
 WP2.2  Transcription
 WP2.3  Translation
 WP3  Cell Division
 WP3.1  Vesicle constriction
 WP3.2  Vesicle fission
 WP4  Spatio-Temporal Integration
 WP4.1  Integrating different modules
 WP4.2  Container control
 WP4.3  Temporal control
 WP4.4  Spatial control
 WP5  Towards Autonomy
 WP5.1  Genome design & assembly
 WP5.2  In vitro analysis of operon functionality
 WP5.3  A cellular chassis for module optimization
 WP5.4  Towards an autonomous synthetic cell
 WP6  Philosophy, Ethics, and Public Debate
 WP6.1  Philosophical assessment
 WP6.2  Bridging the science – humanities divide
 WP6.3  Proactively exploring societal potentials and concerns

People

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.

Principal investigators (PI's)

Associate PI's

PhD's, Postdocs and Research Assistants

Support Office

Former staff

Anne Schwabe
Research Technician
Delft University of Technology

David Foschepoth
Postdoc
Delft University of Technology

Diego Alonso Martinez
Postdoc
University of Groningen

Ernest Yu Liu
Postdoc
University of Groningen

Federico Fanalista
Postdoc
Delft University of Technology

Gitta Buskermolen
Postdoc
AMOLF

Marten Exterkate
Postdoc
University of Groningen

Pauline Lefrançois
Postdoc
University of Groningen

Weria Pezeshkian
Postdoc
University of Groningen

Zhanar Abil
Postdoc
Delft University of Technology

Publications

2021

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

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

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

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

2020

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

2019

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

2018

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