Synthetic Cell a new frontier in science and technology for Europe

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Read about the initiative

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What people say about the initiative

This is an excellent project. The economic impact of the work will be huge. This program would lay the foundation for Europe to lead the world in Synthetic Biology.

Brian Jester - iSSB, CNRS

By its groundbreaking nature, this project will place European Science at the forefront of this important field. It will bring together scientists from various disciplines, foster technological developments, focus the ethical discussion and breach conversation with policy makers.

Sophie Martin - Universite' de Lausanne

Now is a perfect time to launch such an ambitious programme, because advances in the life sciences and in physics have converged on a detailed understanding of the component parts of life while chemistry has at the same time come to a point where (supra)molecular systems can be synthesized that are able to mimic key functions of biomolecules such as self-recognition and mechanochemical activity.

Gijsje Koenderink - Amolf & VU Amsterdam

This new initiative could revolutionarize our ways of understanding cells, organisms, and living matter, and I think that Europe should have a leading role in this endeavor.

Daniel Riveline - Strasbourg University, CNRS

The people behind the initiative

My project aims to modularize and group genes related to the core metabolism of E. coli, starting with genes of the glycolytic pathway enzymes. This will lead to a gain of insight about the possibilities and rules for synthetic genome design

Henrique da Costa Oliveira

Postdoc
Wageningen University - PI John van der Oost
During my post-doc in the groups of Prof. Gijsje Koenderink and Prof. Cees Dekker, I aim to achieve robust synthetic cell division which requires constriction of the synthetic cells into dumbbells followed by their neck abscission to split the cell into two daughter cells.

Charu Sharma

Postdoc
Delft University of Technology - PI Gijsje Koenderink & Cees Dekker
Melike Uysal

PhD
University of Groningen - PI Bert Poolman
I am optimizing yeast strains and protocols for assembling synthetic chromosomes compatible with cell-free expression systems.

Elynor Moore

Postdoc
Delft University of Technology - PI Pascale Daran-Lapujade & John van der Oost
In this project, we are constructing a model to gain insights into the dynamic changes in the internal pH and membrane potential of the synthetic cell. We have obtained the pertinent parameters through fitting procedures based on experimental data collected on-site, and our findings demonstrate that pH-dependent proton permeability is essential for a comprehensive depiction of the system's temporal evolution.

Yan Borges Barreto

Postdoc
University of Groningen - PI Matthias Heinemann
Pietro Sillano

PhD
Delft University of Technology - Associate PI Timon Idema & PI Siewert-Jan Marrink
Federico Ramirez Gomez

PhD
Delft University of Technology - PI Gijsje Koenderink
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 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 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
I am basically a Liquid chromatography and mass spectrometry specialist for the Bionanosience department.

Adja Zoumaro-Djayoon

Technical support
Delft University of Technology
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
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
Evolutionary optimization of synthetic genomes for module integration in PURE

Marijn van den Brink

PhD
Delft University of Technology - PI Christophe Danelon
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
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
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
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
Timon Idema

Delft University of Technology
Nico Claassens

Wageningen University
Kristina Ganzinger

AMOLF
Evan Spruijt

Radboud University
Dirk Jan Slotboom

University of Groningen
Jose P. Vila Cha Losa

PhD
University of Groningen - PI Matthias Heinemann
Pim America

PhD
Vrije Universiteit Amsterdam - PI David Dulin
Zhanar Abil

Postdoc
Delft University of Technology
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
David Dulin

VU Amsterdam
David Foschepoth

Postdoc
Delft University of Technology
Manuel Reinhardt

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

Marco van den Noort

PhD
University of Groningen - PI Bert Poolman
In-vitro reconstitution of the actin-microtubule cross-talk during cell division

Ilina Bareja

Postdoc
Delft University of Technology - PI Marileen Dogterom
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
Alex Cumberworth

Postdoc
AMOLF - PI Pieter Rein ten Wolde
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
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
Federico Fanalista

Postdoc
Delft University of Technology
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
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
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
Douwe Grundel

PhD
University of Groningen - PI Matthias Heinemann
Thijs Ettema

University of Groningen
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
Andrei Sakai

Postdoc
Radboud University - PI Wilhelm Huck
Nicola de Franceschi

Postdoc
Delft University of Technology - PI Cees Dekker
George Dadunashvili

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

Postdoc
AMOLF
Gerard Castro Linnares

PhD
Delft University of Technology - PI Gijsje Koenderink
Rob Joosten

Research Assistant
Wageningen University - PI John van der Oost
Sandrine D'Haene

Technical Support
VU Amsterdam - PI Gijs Wuite
Aigars Piruska

Research Assistant
Radboud University - PI Wilhelm Huck
Anne Schwabe

Research Technician
Delft University of Technology
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
Mattia Rovetta

PhD
University of Groningen - PI Matthias Heinemann
Melanie Konig

PhD
University of Groningen - PI Siewert-Jan Marrink
Thijs Nieuwkoop

PhD
Wageningen University - PI John van der Oost
Mareike Berger

PhD
AMOLF - PI Pieter Rein ten Wolde
Lennard van Buren

PhD
Delft University of Technology - PI Gijsje Koenderink
Elisa Godino

PhD
Delft University of Technology - PI Christophe Danelon
Michele Partipilo

Postdoc
University of Groningen - PI Bert Poolman and Dirk Jan Slotboom
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
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
Pauline Lefrançois

Postdoc
University of Groningen
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
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
Diego Alonso Martinez

Postdoc
University of Groningen
Ernest Yu Liu

Postdoc
University of Groningen
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
Previously, we engineered a phospholipid biosynthesis pathway based on a cascade of eight purified (membrane) proteins reconstituted into pre-existing liposomes. It starts with simple building blocks, fatty acids and glycerol-3-phosphate, to finally yield the two essential phospholipids phosphatidylethanolamine (PE) and phosphatidylglycerol (PG). Currently, we are further developing and optimizing the pathway.

Marten Exterkate

Postdoc
University of Groningen - PI Arnold Driessen
For the theoretical phase of the BaSyC (Building a Synthetic Cell) project, we are going to use this multi-scale simulation approach to decipher conditions of spontaneous membrane fission. Our aim is to find a minimal system, in which a vesicle spontaneously transform into a dumbbell-like shape. Then, an active process can split this structure into two vesicles, reminiscent of the cell division.

Weria Pezeshkian

Postdoc
University of Groningen - PI Siewert-Jan Marrink
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
Eleonora Bailoni

Postdoc
University of Groningen - PI Bert Poolman
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
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
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
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
Charlotte Koster

Postdoc
Wageningen University
Building a cellular chassis to test functional modules of a synthetic cell in-vivo.¬¬

Joep Houkes

PhD
Wageningen University - PI John van der Oost
Max Finger

PhD
Wageningen University - PI John van der Oost
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
Reza Amini Hounejani

Postdoc
Delft University of Technology - PI Marileen Dogterom
Drew Endy

Stanford University
Allen Liu

University of Michigan
Mohan Balasubramanian

University of Warwick
Kate Adamala

University of Minnesota
Petra Schwille

Max-Planck-Institute of Biochemistry
Carla Rita Palmerino

Radboud University
Tom de Greef

Eindhoven University of Technology
Michael Jewett

Northwestern University
Eörs Szathmáry

Eötvös University
Eugene Koonin

NCBI/NIH
Yannick Rondelez

CNRS
Tobias Erb

MPI for Terrestrial Microbiology
Hagan Bayley

University of Oxford
Joachim Spatz

MPI for Medical Research
John Sutherland

Laboratory of Molecular Biology
Siewert-Jan Marrink

University of Groningen
Sander Tans

AMOLF/Delft University of Technology
Pieter Rein ten Wolde

VU Amsterdam/AMOLF
Pascale Daran-Lapujade

Delft University of Technology
Nynke Dekker

Delft University of Technology
Matthias Heinemann

University of Groningen
Gijs Wuite

VU Amsterdam
Christophe Danelon

Delft University of Technology
Bela Mulder

AMOLF/Wageningen University
Arnold Driessen

University of Groningen
Bert Poolman

University of Groningen
John van der Oost

Wageningen University
Gijsje Koenderink

Delft University of Technology
Wilhelm Huck

Radboud University
Hub Zwart

Erasmus School of Philosophy - ESPhil
Heleen van Rooijen-Bosscha

Communications Officer
Delft University of Technology
Ava Nievaart

Management Assistant
Delft University of Technology
Stefania Usai

Program Manager
Delft University of Technology
Marileen Dogterom

Delft University of Technology
Cees Dekker

Delft University of Technology

What are our targets
What is the impact

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Name	Institute	Country	Comment
Felix Campelo	ICFO-Institut de Ciencies Fotoniques	Spain	-
Friedrich Simmel	TU Munich	Germany	-
Petra Schwille	Max Planck Institute of Biochemistry	Germany	-
Gijs Wuite	VU Amsterdam	The Netherlands	-
Christophe Danelon	Delft University of Technology	The Netherlands	-
John van der Oost	Wageningen University	The Netherlands	-
Gijsje Koenderink	AMOLF/ VU Amsterdam	The Netherlands	-
Bert Poolman	Groningen University	The Netherlands	-
Wilhelm Huck	Radboud University Nijmegen	The Netherlands	-
Marileen Dogterom	Delft University of Technology	The Netherlands	-
Cees Dekker	Delft University of Technology	The Netherlands	-

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Synthetic Cell a new frontier in science and technology for Europe

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What people say about the initiative

The people behind the initiative

Zhanar Abil

David Foschepoth

Federico Fanalista

Nicola de Franceschi

George Dadunashvili

Gitta Buskermolen

Gerard Castro Linnares

Rob Joosten

Sandrine D'Haene

Anne Schwabe

Mattia Rovetta

Melanie Konig

Thijs Nieuwkoop

Lennard van Buren

Elisa Godino

Pauline Lefrançois

Diego Alonso Martinez

Ernest Yu Liu

Drew Endy

Allen Liu

Mohan Balasubramanian

Kate Adamala

Petra Schwille

Carla Rita Palmerino

Tom de Greef

Michael Jewett

Eörs Szathmáry

Eugene Koonin

Yannick Rondelez

Tobias Erb

Hagan Bayley

Joachim Spatz

John Sutherland

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