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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)

PhD's, Postdocs and Research Assistants

  • Aigars Piruska

    Research Assistant
    Radboud University - PI Wilhelm Huck
  • Alberto Blanch Jover

    PhD
    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.
    Delft University of Technology - PI Cees Dekker
  • Alexander John Foster

    PhD
    University of Groningen - PI Bert Poolman
  • Andreas Biebricher

    Postdoc
    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.
    VU Amsterdam - PI Gijs Wuite
  • Bettina Graupe

    PhD
    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.
    Radboud University - PI Hub Zwart
  • Charlotte Koster

    PhD
    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.
    Delft University of Technology - PI Pascale Daran-Lapujade
  • Daphne Broeks

    PhD
    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.
    Radboud University - PI Hub Zwart
  • Diego Alonso Martinez

    Postdoc
    While cells try to maximize their growth rate, they do not exceed a maximum Gibbs energy dissipation rate to the environment. My project explores biophysical mechanisms at the molecular level that could explain this limit in cellular physiology, therefore linking both scales and providing another level of understanding of cellular functioning.
    University of Groningen - PI Matthias Heinemann
  • Eleonora Bailoni

    PhD
    Within the synthetic cell project, I am interested in coupling metabolic energy conservation with lipid biosynthesis
    University of Groningen - PI Bert Poolman
  • Ernest Yu Liu

    Postdoc
    Does the temporal separation of lipid and protein production automatically facilitate cell division? We will study the effects of the temporal separation of lipid and protein production in budding yeast cell. Now we first focus on the mechanical effects. I will make a model to describe the effects of the separation on the mechanical properties of the cell wall, and then this mechanics may facilitate the cell budding.
    University of Groningen - PI Matthias Heinemann
  • Giulia Bergamaschi

    PhD
    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.
    VU Amsterdam - PI Gijs Wuite
  • Joep Houkes

    PhD
    Building a cellular chassis to test functional modules of a synthetic cell in-vivo.¬¬
    Wageningen University - PI John van der Oost
  • Lennart van Buren

    PhD
    AMOLF - PI Gijsje Koenderink
  • Lucia Baldauf

    PhD
    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.
    AMOLF - PI Gijsje Koenderink
  • Ludo Schoenmakers

    PhD
    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.
    Radboud University - PI Wilhelm Huck
  • Maria Tsanai

    PhD
    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.
    University of Groningen - PI Siewert-Jan Marrink
  • Marten Exterkate

    PhD
    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.
    University of Groningen - PI Arnold Driessen
  • Max den Uijl

    PhD
    The aim of my project is to insert newly synthesized protein into an expanding membrane using the Sec translocon.
    University of Groningen - PI Arnold Driessen
  • Michele Partipilo

    PhD
    My PhD research is focused on the development of an out of equilibrium redox module to integrate within a synthetic cell-like system.
    University of Groningen - PI Bert Poolman and Dirk Jan Slotboom
  • Pauline Lefrançois

    Postdoc
    To achieve the construction of a bottom-up synthetic cell, one of the challenge lies in powering the cell. As a source of energy, an ATP synthesis pathway (arginine deiminase pathway) will be reconstituted in giant unilamellar vesicles (GUVs) together with the osmosregulatory protein OpuA. Because GUVs are micrometre-sized, experiments can be performed using light microscopy (confocal or wide field), providing new technical possibilities.
    University of Groningen - PI Bert Poolman
  • Ramon Creyghton

    PhD
    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.
    AMOLF - PI Bela Mulder
  • Roel Maas

    PhD
    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.
    Radboud University - PI Wilhelm Huck
  • Reza Amini Hounejani

    PhD
    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).
    Delft University of Technology - PI Marileen Dogterom
  • Sandrine D'Haene

    Technical Support
    VU Amsterdam - PI Gijs Wuite
  • Weria Pezeshkian

    Postdoc
    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.
    University of Groningen - PI Siewert-Jan Marrink

Support Office

Publications

Here, we will post the publications produced within the framework of the BaSyC project.