University of Groningen

Deadline: December 1, 2024

Building a synthetic cell is one of the greatest scientific and technological challenges of the 21^st century. In the framework of a huge national Dutch program (EVOLF, https://www.evolf.life) and a European Doctorate network (ComeInCell, https://www.comeincell.org), we have 12 PhD/Postdoc positions available for biophysicists, bioengineers, biochemists, and molecular biologist at the Groningen Biomolecular Sciences and Biotechnology Institute (https://www.rug.nl/research/gbb) of the University of Groningen in the Netherlands.

The positions are available in five different research groups for either computational or experimental research: (i) to experimentally reconstruct reaction networks for metabolic energy and synthesis of cellular building blocks; (ii) to build synthetic cell-like systems for autonomous operation and growth, or (iii) to develop computational models at different levels of complexity to generate designs of synthetic cells.

Positions

Poolman group (https://membraneenzymology.com)

Position 1: Design and construction of reaction networks. We will integrate in bacteria-size vesicles metabolic modules essential for life. Further reading: doi: 10.1038/s41467-024-52085-z
Position 2: Membrane expansion in synthetic cells. We will expand the membrane of cell-like systems through the coupling of lipid transport to lipid synthesis and volume regulation. Further reading: doi: 10.1021/acssynbio.4c00073
Position 3: Evolution and integration of metabolic modules. We will evolve and couple reaction networks through genome design, selection, performance screening and AI. Further reading: doi.org/10.21203/rs.3.rs-3990950/v1
Position 4: Compartmentalization and spatial distribution of reaction networks in synthetic cells. We will exploit the properties of biomolecular condensates to enhance the efficiency of reaction networks for fuel supply and building block synthesis. Further reading: doi: 10.1038/s42003-024-06216-3
Position 5: Membrane expansion with condensates. We will combine active membrane expansion with the expression of synthetic RNA condensates to engineer complex re-structuring events such as engulfment, exocytosis, membrane rupture and/or fission. Further reading: doi: 10.1126/sciadv.abd7697

Heinemann group (www.heinemannlab.eu)

Position 6: To equip synthetic cells with ATP, NADH and amino acids, we will establish a synthetic, bottom-up built glycolysis in vesicles. We will in vitro assemble – in a stepwise manner – a functional glycolytic pathway and optimize it. To this end, high-end mass spectrometric analyses will be used as well as a mathematical model of glycolysis earlier developed by the group.
Position 7: To equip synthetic cells with ATP, NADH and amino acids, we will establish a synthetic, bottom-up built glycolysis in vesicles. We will engineer a synthetic operon for this pathway and optimize it through in vivo evolution. In a stepwise manner, we will build such synthetic operon on a plasmid and delete the respective genes on the E. coli chromosome. We will use evolution and targeted gene mutation strategies to optimize the plasmid-expressed pathway.

Slotboom group (https://membraneenzymology.com)

Position 8: To equip synthetic cells with multiple metabolic pathways, innovative reconstitution and organization methods are needed. We will explore protein scaffolds, membrane-bound and membrane-less compartments, rational and AI-based engineering to obtain efficient fluxes through multiple pathways in the same synthetic cell. https://doi.org/10.1021/acssynbio.3c00062
Position 9: To equip synthetic cells with membrane-associated processes (such as solute transport), a membrane protein insertion machinery is needed. We will identify a minimal insertion machinery and optimize it for efficient insertion of functional transporters, using biochemical and biophysical assays. doi: 10.1093/synbio/ysae007

Kamenz group (kamenzlab.com)

Position 10: For a synthetic cell to continuously divide, cell growth and cell division have to be tightly regulated and temporally separated. We will combine protein biochemistry, directed evolution and mathematical modeling to develop a synthetic oscillator and the necessary control modules to drive periodic cycles of cell growth and division. Further reading: https://www.ncbi.nlm.nih.gov/pmc/articles/PMC2796343/

Marrink group (cgmartini.nl)

Position 11: Multiscale modeling of cell division, probing the interplay between lipids and proteins for the rational design of efficient fission of artificial cells. Further reading: https://doi.org/10.1038/s41467-020-16094-y
Position 12: Molecular dynamics simulations of minimal cells, focusing on the properties and organization of the cell envelope. Further reading: https://doi.org/10.3389/fchem.2023.1106495

Requirements

• Enthusiasm, excellence, commitment to research and team spirit are our key selection criteria.

• Educational backgrounds are preferably in the area of biochemistry, bioengineering, biophysics, molecular biology or comparable.

• Candidates for a PhD position need to have completed a Master’s degree (or equivalent). Postdoctoral candidates need to have completed their PhD.

• Excellent proficiency in English language.

Conditions

Each position can be either filled by a PhD student (with a four-year contract) or a postdoc (with a three-year contract). Salaries will be commensurate with experience and include a generous fringe benefit package. Starting dates are flexible. Yet, a preferred starting date is within the first six months of 2025.

How to apply

To apply for one (or more) of the positions, email a CV including a brief description of your motivation, research interests and accomplishments to EVOLF@RUG.NL, and include two letters of recommendation from former advisors/professors. The recommendation letters can also be sent directly by your former advisors. Please indicate for which position(s) you apply. Application deadline: December 1, 2024.