Publication: B-cell signaling in dynamic environments

Cells live in constantly changing environments. To truly understand how cells process information in their complex natural environment, it is essential to recreate such dynamic environments in the lab and study cell responses. In our work, we have studied how B-cells respond to dynamic environments by creating gradients of increasing hydrogen peroxide levels over time. This research revealed that B-cells are sensitive to the rate at which hydrogen peroxide is added! We hope this exciting result will spark more research on dynamic environments of cells.

You can read the paper here.

Congratulations to Melde, Emma, Bas, Jessie, and Wilhelm! 🎉🥳

Publication: Iterative design of training data to control intricate enzymatic reaction networks

Congratulations to Bob, Tao and co-authors, who designed training data to control enzymatic reaction networks in flow! The newest article entitled “Iterative design of training data to control intricate enzymatic reaction networks” is now out in Nature Communications! Well done!! 😎🎊🥳

You can read the paper here

Publication: Cell-free expression system based on JCVI-syn3A cells

We are happy to announce that the CFE system derived from JCVI-syn3A cells is functional, after 3 years of unsuccessful attempts. We used a machine learning tool to optimize this novel system. We hope it can serve as a new CFE platform for synthetic biologists. Thanks to all collaborators involved!

Read the paper here.

Congratulations to Andrei, Bob and all the collaborators!

New paper on the role of definitions of life in synthetic biology

The definition of life is a notoriously difficult definition to get right. In response to that difficulty, some philosophers and scientists have argued that definitions of life are useless to the sciences. In this publication, one of our PhD students, Ludo Schoenmakers, argues against this pessimistic conclusion. He argues that if definitions of life are understood pragmatically, they can be, and in fact are, conducive to scientific progress and they are even relevant to our ethical discussions. So no reason for pessimism!

You can find the paper here. 

Congratulations to Ludo!

New publication on Prebiotic reaction networks in a dynamic environment

Before Life arose, the Earth, just as it is now, hosted an ever-changing environment. Our latest work published in JACS investigates what effect such dynamic conditions impose on the formose reaction, a model prebiotic reaction network. By applying random fluctuations to the formose reaction in a flow reactor, we show in detail how its composition responds to varying timescales and magnitudes in these perturbances. Our investigation further led us to discover that the reaction behaves in a modular manner, a remarkable characteristic which it shares with biological reaction networks. These observations demonstrate the importance of understanding the role of environmental dynamics in sculpting the composition, structure and behaviour of the chemical processes destined to form the first Life.

You can find the paper here.

Congratulations to Peer, Lena, Will and Wilhelm!

New publication on uncovering phenotypic characteristics and active signal transduction of human antibody secreting cells

New paper was published by our group members Erik van Buijtenen and Jessie van Buggenum together with collaborators Wout Janssen, Paul Vink, Maurice J.M. Habraken, Laura J.A. Wingens, Andrea van Elsas and Hans van Eenennaam! Here we use integrated multi-omic single-cell sequencing technologies to detect and quantify immunoglobulin subclass-specific surface markers, transcriptional profiles and signaling transduction pathway components. We tested whether human antibody secreting cells (ASCs) that only seem to differ in its ability to secrete different IgM, IgA, or IgG antibodies, exhibit other differences that characterize these different ASCs. Our approach detected differential expression of plasmablast and plasma cell markers, homing receptors and TNF receptors. In addition, differential sensitivity was observed for the different cytokine stimulations that were applied during in vitro differentiation. Taken together, our integrated multi-omics approach allowed high-resolution phenotypic characterization of single cells in a heterogenous sample of in vitro differentiated human ASCs.

Congratulations to Erik, Jessie and Wilhelm!!

Click here to read the paper

New paper published: Computing Arithmetic Functions Using Immobilised Reaction Networks

Nikita, Mathieu, Lía and Wilhelm together with Max Derks from Laboratory of Spectroscopy and Catalysis and Labmate published a new paper on enzyme-based computation! They used proteolytic enzymatic networks immobilised in hydrogel beads and compartmentalised in a CSTR as a novel platform for molecular information processing. They demonstrated robustness of the platform in performing the fundamental arithmetic operations of addition, subtraction and multiplication. This analogue logic approach goes beyond the Boolean gates and has potential applications in future bioelectronic devices. The concept of analogue logic helps to generalize our understanding of computation in catalytic networks.Congratulations!!

You can find the paper here.

New paper on photobiocatalysis in flow conditions

New article on photobiocatalysis in flow was published in ACS Biocatalysis in a collaboration with the group of Wolfgang Kroutil from Graz University!

In this paper immobilised photodecarboxylase from C. variabilis (CvFAP) is taken as an example to demonstrate the methodology development of photobiocatalysis in flow conditions. Various enzyme immobilisation techniques were used to determine the best carrier and conversion.

Congratulations to Stefan, Christoph and Wolfgang from Graz University as well as Miglė and Wilhelm!

You can read the paper here.

New paper on cell-free expression system based on Mycoplasma bacteria

In collaboration with researchers at the J. Craig Venter Institute, University of Minnesota, and Santa Fe Institute, we published a paper describing 2 years of attempts to derive a cell-free expression (CFE) system based on Mycoplasma bacterium. What seemed to be a simple and straightforward project, turned out to be challenging due to unique features of Mycoplasma biology. As a parasite of mammals, mycoplasmas evolved to scavenge its surrounding environment for nutrients. Therefore, surface nucleases are essential for survival. For producing lysates, such nucleases degraded important nucleic acids (e.g. ribosomal RNA), which prevented in vitro transcription-translation reactions.  A series of new methods were designed for testing the quality of lysates and for producing lysates with lower nuclease activity.”

You can find the new article here.

Congratulations Andrei, Wilhelm and all collaborators!

Publication: New methodology for characterization of cell-free genetic networks enables forward engineering

Forward engineering of (cell-free) genetic networks is one of the main goals in the field of synthetic biology. However, despite the vast library of available building blocks for the assembly of these networks, identifying the reaction kinetics to make these building blocks modular for forward engineering remains elusive. In our latest work we established an automated pipeline to produce high-quality time-resolved data through a combination of optimal experimental design, microfluidics and non-linear model identification. We apply this pipeline and progress through a design, characterize test cycle and demonstrate the modularity and predictability of the characterized building blocks in new network configurations. The methodology described in this paper has the potential to enable forward engineering of cell-free genetic networks.

You can find the article here: https://www.nature.com/articles/s41467-022-31306-3

Congratulations Bob, Roel, Wilhelm and collaborators!