1st European Congress on Cell-Free Synthetic Biology

Cell-free synbio community, taken from the eccsb.epfl.ch webpage

Cell-free synbio community, taken from the eccsb.epfl.ch webpage

 

Last March the 1st European Congress on Cell-Free Synthetic Biology took place at the Congressi Stefano Franscini (CSF), a Swiss Federal Institute of Technology of Zurich (ETH, Zurich) division, situated at Monte Verità (south of Switzerland). Top scientists working in the field of cell-free synthetic biology shared their most recent research with a large audience of PhDs, postdocs and PIs. The conference was divided in eight major sessions, four junior researchers’ sessions and a keynote talk, with a broad range of cell-free synbio, from genetic circuits to metabolic engineering.

Richard Murray, opening talk

Richard Murray, opening talk

Richard Murray from Caltech opened the first session, with the inspiring talk ‘Towards genetically-programmed artificial cells in multi-cellular machines’. During his talk he set the basis that will lead us to artificial cells in 10-15 years. He also explained which, he believes, are the main challenges to accomplish such ambitious goal. He mentioned five: i) How artificial should they be?, ii) Which source of power do they require? iii) Can they propagate information? iv) How to integrate multiple systems? v) Which source of motely force could they use? He also highlighted the need of model-based design workflows and more open-source research. Sebastian Maerkl (EPFL) followed the session with his interesting research on microfluidics platforms for the rapid implementation and characterization of genetic circuits. He showed that such an in vitro system resembles quite well the in vivo environment. Finally, Friedrich Simmel (TU Munich) showed that RNA-circuits are capable to perform complicated operations.

After the coffee break, we had the first junior researchers’ session. The talks were given by David Foschepoth (TU Delf), Alice Banks (U. of Newcastle) and Henrike Niderhiltmeyer (UCSD). They presented different systems for the maintenance of genetic networks or minimal genomes, going from platforms fueled solely with PURE systems, to automated platforms for the design and characterization of genetic circuits, and even synthetic shells, with some primordial organelle-like organization.

The second session introduced us to the possibility of generating minimal cells, completely enzyme-free. The first speaker, Erik Winfree (Caltech), with the talk ‘Enzyme-free nucleic acid dynamical systems’ presented the richness of DNA strand displacement for the implementation of basic autonomous and programmable molecular systems, capable to interact with and control their environment. Yannick Rondelez (U.Tokyo), went to the basics and explained the principles of circuits based on DNA strand displacement with his PEN DNA-toolbox. The last talk was given by Georg Seeling (U. Washington), presenting a clear application of DNA strand displacement for disease diagnostic, a fast and reliable technique, cost-efficient when compare with gene expression diagnostic methods. In my opinion, DNA strand displacement seems like a suitable option to program minimal cells, capable of basic tasks with the main advantage that such components are easy to program and characterize.

For the third session, Jørgen Kjems (Aarhus U) presented the versatility of DNA origami. From pores, to compartmentalization, and even direct drug delivery; these were some of the examples of the usefulness of DNA origami towards the assembly of minimal cells. The last talk of the day was given by Paul Freemont (Imperial College). In his talk, he showed that cell-free expression systems (TX-TL) do not only need to rely on E. coli machinery, but it is also possible to get TX-TL systems from other organisms such as Bacillus subtilis or Streptomyces venezuelae, customizing the expression systems upon need.

On the second day, session number 4 covered some recent advances on protein design and the usefulness of cell-free systems for the characterization of such protein entities. Bruno Correia (EPFL) presented his work towards the increase of a structural repertory that later will lead us to the design of functional proteins. Also, Tanja Kortemme, shared her computational pipeline to employ protein-protein interfaces as a scaffold to engineer new functions. On the other hand, Tom de Greef (TU Eidhoven), went back to DNA-based networks and showed how promising are this systems to transform intricate signaling networks into minimalistic circuits.

In the second round of junior talks, Jeo Rollin (NREL) gave us the first example of how cell-free systems are suitable for bioproduction. Nadanai Laohakunakorn (EPFL), gave a great talk on zinc fingers and showed that binding affinity correlates with repression strength. Yong Wu (Caltech) showed TX-TL systems could accelerate the process of design and implementation of novel biosynthetic pathways.

Session 5 was opened by Heiz Koeppl (TU Darmstadt), he gave us a great example of circuits characterization: they characterized a decoupled TX-TL system (TX-only environment), with the purpose to fully understand the dynamics of the implemented circuits. Gašper Tkačik (IST Autria) gave us a great example of how modeling can help understand a biological system. Elisa Franco (UC Riverside) closed the session with a beautiful example on DNA as a way to replace structural functions so far only acquainted by cytoskeletal proteins such as microtubules.

Vincent Noireux, TXTL platform

Vincent Noireux, TXTL platform

After lunch, we had a great talk by one of the pioneers in cell-free synthetic biology, Vincent Noireaux (U. Minnesota). He took us to a tour that covered his first TX-TL system, to the latest version that also includes CRISPR. The session continued with Roy Bar-Ziv (Weizmann) who showed how the combination of different technologies: DNA arrays, microfluidics, and TX-TL systems can be seen as artificial cells capable to be programmable at will. The day ended with Rebecca Schulman’s (Johns Hopkins) talk. There, we got to know that molecular circuits are also capable of some programming chemomechanics. In her research she works with hydrogels in combination of DNA circuits, and such circuits upon stimuli can expand, and this expansion is sequence specific.

On the third day, the first talk of the 7th session was under the charge of Yolanda Schaerli (UNIL). She uses synthetic gene networks to mimic regulatory networks, such as the one present in Drosophila during differentiation. Sven Panke talked about his research done in biocatalysis in cell-free systems: he told us about the beauty of cell-free platforms where all the resources are targeted to the production of a specific compound, rather than to cell maintenance. The session ended with James Bowie (UCLA) who made the point that cell-free biocatalysis can achieve much higher productivity that cell-based. However, there are still some limiting reactions that need to be overcome to get to that point.

In the 3rd junior researchers session, Richar Kelwick (Imperial College) went deeper into the TX-TL system from Bacillus subtilis. Maaruthy Yelleswarapu (Radbound U.) shared his research on cell-free expression platforms, claiming that the main cause of mRNA inactivation is sequence-dependent mRNA secondary structures. Lastly, Alexandar Tayar (Weizmann) gave further details into the programmable artificial cells presented by Roy Bar-Ziv.

On the last day, the 8th session started with Esther Amstad (EPFL), with an interesting talk about on-chip cell-free systems, where, by means of microfluidics devices, screening of different conditions could be tested inside isolated drops in a high throughput manner. Keith Pardee (U. Toronto) was the next on stage, and for me, one of the most exciting talks of the conference. He presented his work on cell-free synbio on paper. He generated paper-based sensors for the rapid and low-cost diagnostic of different diseases, targeting diseases that currently affect humanity, such as Zika. The final talk was delivered by Igor Medintz (US Naval Research). His talk on biocatalysis without cells had an unexpected component, at least for me; the use of quantum dots as a platform to channel reactions and substrate accumulation.

The last junior talks where given by Celine Love (MPI) and Mattheaus Schwarz-Schilling. They talked about cell-like compartments, that could sustain basic cellular functions and capable to even communicate with cells.

Keynote speaker, Petra Schwille

Keynote speaker, Petra Schwille

The final talk was given by my PI, Petra Schwille (MPI). I have to say that she nicely presented the work of many people who have been working towards the reconstitution of a minimal divisome. We are mainly working with components from E. coli division machinery, mainly MinDEC and FtsZ. We expect that a deep characterization of such components will lead us to the primordial division machinery that a minimal cell could use, protein or even DNA based.

The whole conference gave the audience an overview on the state of the art in the field of cell-free synthetic biology. The take home message of this enriching week was that in order to achieve our goal, the generation of a minimal cell, where all the components are known, easy to program and generate, will be achieved by the shared work of numerous research groups. We, as researchers in cell-free synbio need to work together, collaborate, and share our expertise in the different fields where we are currently working on.

Daniela Garcia-Soriano is a 3rd year PhD student working at the Schwille Lab, MPI-Biochemistry. She’s passionate about SynBio and minimal cells. Follow her on Twitter or connect with her on LinkedIn.