Research

Directly to people

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

  • I am basically a Liquid chromatography and mass spectrometry specialist for the Bionanosience department.

    Adja Zoumaro-Djayoon

    Technical support
    Delft University of Technology

  • Aigars Piruska

    Research Assistant
    Radboud University - PI Wilhelm Huck
  • The division of a cell is a key factor for the development of life. In my project, I study how the cell division mechanism present in many archaea (Cdv system) works in vitro. Understanding this system will allow us to reconstitute it inside of liposomes, to make them divide, and develop like this a cell division mechanism for the synthetic cell.

    Alberto Blanch Jover

    PhD
    Delft University of Technology - PI Cees Dekker

  • Alex Cumberworth

    Postdoc
    AMOLF - PI Pieter Rein ten Wolde
  • I am currently working on the genetic characterization of tetraether lipids in the archaeal strain Sulfolobus acidocaldarius. Not much is known about the lipid biosynthesis of tetraether membranes which confer extremophilic characteristics to archaea. Unravelling this information could help in engineering more robust membranes in other organisms and in synthetic cells.

    Alka Rao

    PhD
    University of Groningen - PI Arnold Driessen

  • Andrei Sakai

    PhD
    Radboud University - PI Wilhelm Huck
  • Optical tweezers in combination with fluorescence provides a powerful tool to quantify nucleic acid processing by enzymes such as polymerases and helicases. Our aim is to be able to catch and manipulate a single nucleic acid strand between two trapped beads and to immerse this construct inside a GUV. This method would allow us to later measure and control nucleic acid processing activities of, e.g., a fully reconstituted replisome inside an artificial cell.

    Andreas Biebricher

    Postdoc
    VU Amsterdam - PI Gijs Wuite
  • A successful minimal cell model requires an optimized cell-like enclosed compartment which can efficiently perform fundamental living processes such as the ability to grow, replicate, and evolve. With this in mind, we aim to explore the development of a synthetic cell from an evolutionary perspective. We propose to use an in vitro directed evolution approach to recreate natural selection and introduce the ability to evolve as a must for building a minimal synthetic cell. Specifically, this project aims to establish the methodologies for i) genetic diversification ii) gene expression in liposomes iii) liposome screening/selection iv) DNA recovery and re-amplification. Moreover, directed evolution will be applied to improve the performance of fundamental biological modules such as Phi29 based DNA amplification and phospholipid synthesis enzymes as primary targets.

    Ana Restrepo Sierra

    PhD
    Delft University of Technology - PI Christophe Danelon
  • DNA must be spatially segregated in a synthetic cell after its replication to ensure that, upon cell division, each daughter cell contains enough copies of it. The cytoskeleton is a crucial player in this process as it is composed of protein filaments that can elongate, shrink, and treadmill to pull the genetic material. Using bacteria cytoskeleton proteins that can be cell-free expressed, in this project, we aim to construct a hybrid DNA segregation system that can be encapsulated in liposomes and can be externally controlled, for instance, using light-induced dimers.

    Beatriz Orozco Monroy

    PhD
    Delft University of Technology - PI Marileen Dogterom
  • I’m a PhD candidate in the groups of Professor Cees Dekker and Professor Gijsje Koenderink, and I will focus on the development and use of an integrated lab-on-chip system for the generation and manipulation of synthetic cells. The aim is to engineer the entire life cycle of synthetic cells on-chip.

    Bert van Herck

    PhD
    Delft University of Technology - PI Gijsje Koenderink & Cees Dekker
  • The aim of this project is to develop criteria for a productive dialogue on the synthetic cell between technoscience and civil society, and to analyse the views, expectations and concerns resulting from this. Special attention shall be given to the genres of imagination and the use of metaphors as structuring elements, as ways of highlighting promising or uncanny capacities of new technologies.

    Bettina Graupe

    PhD
    Radboud University - PI Hub Zwart
  • We aim to construct synthetic genomes for the minimal cell, using baker’s yeast. To achieve functional integration of the cellular modules encoded on these genomes, we will encapsulate genome libraries into liposomes and select for the desired phenotype in multiple rounds of directed evolution.

    Céline Cleij

    PhD
    Delft University of Technology - PI Pascale Daran-Lapujade and Christophe Danelon
  • I work on the ‘in yeasto’ assembly of synthetic chromosomes, which means I investigate the use of the recombination machinery of baker’s yeast to construct synthetic chromosomes for a minimal cell. Additionally, I study mitochondria as models for minimal living systems.

    Charlotte Koster

    PhD
    Delft University of Technology - PI Pascale Daran-Lapujade
  • The aim of my research will be to investigate how a fully functioning synthetic cell will impact our understanding of life, technology and nature. Specifically I will assess both the epistemological commitments and the ontological dimensions underlying the concept of ‘life’ within synthetic biology. Finally I will also question where and if there is a divide between technology and nature in a time when both are assuming characteristics of the other.

    Daphne Broeks

    PhD
    Radboud University - PI Hub Zwart

  • Douwe Grundel

    PhD
    University of Groningen - PI Matthias Heinemann
  • Within the synthetic cell project, I am interested in coupling metabolic energy conservation with lipid biosynthesis

    Eleonora Bailoni

    PhD
    University of Groningen - PI Bert Poolman

  • Elisa Godino

    PhD
    Delft University of Technology - PI Christophe Danelon

  • George Dadunashvili

    PhD
    Delft University of Technology - PI Cees Dekker & Timon Idema

  • Gerard Castro Linnares

    PhD
    Delft University of Technology - PI Gijsje Koenderink
  • The creation of a self-sustaining synthetic cell is intimately linked to the presence of an internal protein network and DNA, both participating in its mechanical response to loads. By means of optical tweezers and Acoustic Force Spectroscopy we are investigating the mechanics of isolated nuclei as simple biological systems which will help us to understand the mechanical contributions of such components to force response.

    Giulia Bergamaschi

    PhD
    VU Amsterdam - PI Gijs Wuite
  • In-vitro reconstitution of the actin-microtubule cross-talk during cell division

    Ilina Bareja

    Postdoc
    Delft University of Technology - PI Marileen Dogterom
  • Optical Tweezers for Studying The Dynamics of Disome Co-Translation: During protein synthesis in the cell, it is possible for ribosomes to 'pair up' and work together to assemble multimeric proteins directly. This so-called 'co-co' assembly mechanism is ubiquitous in humans; but the mechanism which allows these ribosomes to choose to 'pair up' is entirely unknown. I use optical tweezers to track the movements of ribosomes in vitro, to elucidate the mechanicsms underlying the formation of ribosome pairs and their co-ordinated translation of mRNA messages.

    Jack Tait

    PhD
    AMOLF - PI Sander Tans
  • I am working on the development of a sustainable phospholipid biosynthesis pathway and the development of giant-unilamellar vesicles for the compartmentalization of metabolic modules.

    Jelmer Coenradij

    PhD
    University of Groningen - PI Bert Poolman
  • Building a cellular chassis to test functional modules of a synthetic cell in-vivo.¬¬

    Joep Houkes

    PhD
    Wageningen University - PI John van der Oost

  • Jose P. Vila Cha Losa

    PhD
    University of Groningen - PI Matthias Heinemann

  • Lennard van Buren

    PhD
    Delft University of Technology - PI Gijsje Koenderink
  • In my research project, I will investigate gene expression from isolated genomes in synthetic compartments, such as emulsion droplets and liposomes. By combining top-down and bottom-up approaches, this system will serve both as a model for fundamental research and as a tool for synthetic biology.

    Leonardo Morini

    PhD
    Radboud University - PI Wilhelm Huck
  • Control over chromosomal replication initiation is essential for a synthetic cell. In its absence, the copy number of the genome would constantly increase, leading to the redirection of all the available energy in the form of nucleoside triphosphates towards this process. However, due to the same essentiality that leads this research, testing modules to control this process is an hard task. In my project, I am looking to establish an in vivo platform allowing for an easy screening of different modules controlling this fundamental process

    Lorenzo Olivi

    PhD
    Wageningen University - PI John van der Oost
  • The project revolves around investigation of transcription-translation coupling in PURE System. The aim is to define NusG and RfaH role in this process and possible improvement in ribosome processivity through magnetic tweezers and optical tweezers/fluorescence.

    Luca Buccolieri

    PhD
    VU Amsterdam - PI David Dulin
  • The assembly and folding of proteins is highly complex and guided by proteins which help other proteins to evolve into their final conformation, called chaperones. We use optical tweezers as a single molecule technique to learn more about this process, which is essential for a miminum organism to be self-sustainable.

    Luca Gross

    PhD
    AMOLF - PI Sander Tans
  • A synthetic cell, just like any other cells, must be able to grow and divide. In living cells division is mediated by a complex protein machinery which attaches to the cell membrane and actively exerts forces on it to deform the cell body. I aim to construct a minimal version of such a cell division machinery in vitro, taking inspiration from the actin cytoskeleton, a crucial player in eukaryotic cell division.

    Lucia Baldauf

    PhD
    Delft University of Technology - PI Gijsje Koenderink
  • An important hurdle in creating a synthetic cell is the incorporation of membrane transporters into the synthetic cell membrane. Without these transporters, key physico-chemical conditions cannot be controlled and any complex reaction network on the inside of a synthetic cell will eventually run out of fuel. Using microfluidics and cell-free transcription-translation, we hope to reconstitute the bacterial Sec translocase - which is responsible for membrane transporter insertion into the bacterial inner membrane - inside a synthetic cell membrane. This would not just be an important step towards an autonomous self-reproducing synthetic cell, but it would also provide a powerful new tool for the reconstitution and study of complex enzymatic pathways in vitro.

    Ludo Schoenmakers

    PhD
    Radboud University - PI Wilhelm Huck

  • Manuel Reinhardt

    PhD
    AMOLF - PI Pieter Rein ten Wolde
  • My project concerns cell volume regulation through transport of compatible solutes

    Marco van den Noort

    PhD
    University of Groningen - PI Bert Poolman
  • Influence of the membrane geometry on the assembly and functionality of minimal actomyosin rings reconstituted within synthetic cells

    Marcos Arribas Perez

    Postdoc
    Delft University of Technology - PI Gijsje Koenderink
  • We will focus on two important aspects of the computational framework underlying the synthetic cell project: To provide fundamental insight in the use of coacervates as a means to drive compartementalization of the cell, based on high-throughput coarse-grain molecular dynamics simulations. And to combine coarse-grain molecular dynamics models with Green's function reaction dynamics to bridge the molecular level to the system's level.

    Maria Tsanai

    PhD
    University of Groningen - PI Siewert-Jan Marrink
  • Evolutionary optimization of synthetic genomes for module integration in PURE

    Marijn van den Brink

    PhD
    Delft University of Technology - PI Christophe Danelon

  • Mareike Berger

    PhD
    AMOLF - PI Pieter Rein ten Wolde
  • The aim of my project is to insert newly synthesized protein into an expanding membrane using the Sec translocon.

    Max den Uijl

    PhD
    University of Groningen - PI Arnold Driessen

  • Max Finger

    PhD
    Wageningen University - PI John van der Oost

  • Melanie Konig

    PhD
    University of Groningen - PI Siewert-Jan Marrink
  • My PhD research is focused on the development of an out of equilibrium redox module to integrate within a synthetic cell-like system.

    Michele Partipilo

    PhD
    University of Groningen - PI Bert Poolman and Dirk Jan Slotboom
  • The aim of my PhD research is to investigate entropy-driven chromosome segregation and its potential implications for the development of synthetic cells.

    Minco Polinder

    PhD
    Delft University of Technology - PI Cees Dekker & Marileen Dogterom
  • My current research project is focused on the generation of an artificial pH regulatory system in a reconstituted environment. Such system may guarantee optimal conditions for the performance of the metabolic pathways that constitute a synthetic cell.

    Miyer Fabian Patino Ruiz

    Postdoc
    University of Groningen - PI Bert Poolman
  • My project deals with synthetic cells and sustainability, from a philosophy of science perspective. Important aspects include biomimicry and Open Science. I plan to collect and analyse empirical data related to public, expert and stakeholders’ views on the topic, using mixed research methods.

    Olga Rook

    PhD
    Delft University of Technology - PI Marileen Dogterom & Hub Zwart

  • Pim America

    PhD
    Vrije Universiteit Amsterdam - PI David Dulin
  • The project aims to develop and implement a reliable method for spatially segregating genetic material after replication in a synthetic cell, in order to allow division. Starting point is the observation that the entropy of DNA-strands, which can be understood as polymers, can provide a force for segregation. The dependence of this process on the structure and the spatial organisation of the DNA in the cell will be investigated.

    Ramon Creyghton

    PhD
    AMOLF - PI Bela Mulder

  • Rob Joosten

    Research Assistant
    Wageningen University - PI John van der Oost
  • To construct synthetic cells from the bottom-up we need to build and study the complex genetic networks required to regulate them. Mathematical models serve as blueprints, used by experimentalist to engineer a regulatory network with a specific behavior in mind e.g. oscillations. We built a library of biological parts to be used by an evolutionary algorithm that can evolve mathematical models of large genetic networks towards any desired behavior. We test these networks in vitro and aim to use this design pipeline as a rapid prototyping tool for regulatory networks and as a stepping stone towards building a synthetic cell.

    Roel Maas

    PhD
    Radboud University - PI Wilhelm Huck
  • During my PhD project, I will probe the interaction of SMC proteins and transcription in vitro at the single molecule level and investigate if and how SMC proteins may regulate transcription.

    Roman Barth

    PhD
    Delft University of Technology - PI Cees Dekker
  • In one line of research, we’ll investigate the biophysical features of bacterial microtubules. In a second line of research, we will explore their potential functional role in an artificial cell; to do so, we need to explore the behavior of bacterial microtubules by investigating them in artificial cell-like containers (in vesicles and/or droplets).

    Reza Amini Hounejani

    PhD
    Delft University of Technology - PI Marileen Dogterom
  • My project focuses on the Min protein system, a pattern-forming system in E. coli. Min proteins perform pole-to-pole oscillations, exhibiting a concentration minimum at mid cell. This leads to the correct positioning of the Z-ring, which then initiates cell division. In our lab, we study Min proteins in a number of in vitro environments, which gives us control over critical parameters. Our goal is to gain a better understanding of the mechanisms underlying Min protein pattern formation.

    Sabrina Meindlhumer

    PhD
    Delft University of Technology - PI Cees Dekker

  • Sandrine D'Haene

    Technical Support
    VU Amsterdam - PI Gijs Wuite
  • My project focuses on development of synthetic metabolic pathways in E. coli for assimilation of one-carbon compounds, which can provide crucial insights for engineering core metabolism in a synthetic cell.

    Suzan Yilmaz

    PhD
    Wageningen University - PI John van der Oost

  • Thijs Ettema

    University of Groningen

  • Thijs Nieuwkoop

    PhD
    Wageningen University - PI John van der Oost
  • The goal of my project to develop giant unilamelar vesicles (GUVs) with reconstituted Sec-translocons as an ignitor of assisted membrane protein insertion to increase the fidelity of the synthetic cell. The ultimate goal is to generate synthetic cells that efficiently insert membrane proteins and that are capable of protein secretion through the Sec-translocon, providing a productive shell supporting the aforementioned critical processes in a synthetic cell.

    Tim van den Akker

    PhD
    University of Groningen
  • Creating an artificial cell, we strive to characterize and understand it as deeply as possible. Utilizing optical tweezers integrated with fluorescence spectroscopy and microfluidic techniques, I aim to build a system for in vivo manipulation of DNA. It will allow for a quantitative description of protein-DNA interaction inside the artificial cell during such fundamental processes of molecular biology as replication and transcription.

    Vadim Bogatyr

    PhD
    VU Amsterdam - PI Gijs Wuite
  • The goal is to reconstitute the asymmetric cell division process and acquire insights into the design of cytoskeleton-based strategies for DNA segregation in synthetic cells.

    Yash Jawale

    PhD
    Delft University of Technology - PI Marileen Dogterom

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		 Mattia Rovetta
PhD
University of Groningen		 Nicola de Franceschi
Postdoc
Delft University of Technology		 Pauline Lefrançois
Postdoc
Delft University of Technology
Weria Pezeshkian
Postdoc
University of Groningen		 Zhanar Abil
Postdoc
Delft University of Technology

Publications

2023

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

2022

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

2021

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

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