Events

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.

EUSynBioS Social at Synthetic Biology UK 2017

The Synthetic Biology UK 2017 conference, principally organised by the Biochemical Society, will be held in Manchester 27-28 November 2017. This event aims to showcase recent research and foster community-building across the UK synthetic biology community.

 

EUSynBioS will be there, with a surprise: in collaboration with the conference organizers, we will host a networking event right after the conclusion of the formal conference sessions.

This informal social event brings together early-career researchers with industry representatives and academics in synthetic biology.

Join us for a drink from 15:30 to 17:30 in the Atrium of the Manchester Institute of Biotechnology, next to the Manchester Conference Centre (1 min walk)!

Stay tuned for more updates!

UN CBD COP13: Outcomes relevant to Synthetic Biology

COP13.jpeg
 

Dear Synbio enthusiasts,

three weeks ago, we invited you to follow and contribute to our participation in the 13th Conference of the Parties to the UN Convention on Biological Diversity (COP13) and the parallel Meetings of the Parties to the Cartagena Protocol on Biosafety (CP-MOP8) and the Nagoya Protocol on Access and Benefit-sharing (NP-MOP2). 

Following conclusion of this year's UN CBD events on December 17th, we would like to share with you the below draft outcomes which will have an impact on the future regulation of our discipline.

In case you do not have a particularly keen interest in science policy and governance (yet) or you simply lack the time to read through all of the below bullet points, here is a -considerably simplified- summary:

Synthetic biology may be subject to the same regulatory framework which already exists for classical biotechnology. However, a precautionary approach to synthetic biology has been encouraged, and methodologies for risk assessment of synthetic biology may be updated as new developments emerge.

 

More details are given below:


  • it has been reaffirmed that Parties and other Governments are urged and invited, respectively, to take a precautionary approach when addressing threats of significant reduction or loss of biological diversity posed by organisms, components, and products resulting from synthetic biology.

  • the draft operational definition "synthetic biology is a further development and new dimension of modern biotechnology that combines science, technology and engineering to facilitate and accelerate the understanding, design, redesign, manufacture and/or modification of genetic materials, living organisms and biological systems" has been acknowledged, yet further refinement of this definition has been noted as neccessary.

  • it has been noted that living organisms developed or being developed through current applications of synthetic biology are similar to living modified organisms (LMOs) as defined in the Cartagena Protocol, and that general principles and methodologies for risk assessment under this Protocol and existing biosafety frameworks provide a good basis for risk assessment regarding such LMOs. However, it has also been noted that such methodologies may need to be updated and adapted for current and future developments and applications of synthetic biology.

  • it has been noted that it remains unclear whether or not some organisms created through synthetic biology would fall under the definition of LMOs under the Cartagena Protocol, and whether or not some results of a synthetic biology application are living.

  • Parties have been invited to take into account socio-economic, cultural, and ethical considerations when identifying the potential benefits and potential adverse effects of organisms, components, and products resulting from synthetic biology techniques.

  • Parties, other Governments, relevant organizations, and indigenous peoples have been invited to share experiences and fill knowledge gaps related to potential benefits and potential adverse effects of synthetic biology products as outlined above, to promote public and multi-stakeholder dialogue, and to cooperate in developing guidance and capacity.

  • it has been decided to extend the mandate of the Ad Hoc Technical Expert Group (AHTEG) on Synthetic Biology to make recommendations relevant to the above unresolved issues.

  • it has been decided that, at its next meeting, the Convention will consider any potential implications of the use of digital sequence information on genetic resources for (i) the conservation of biological diversity, (ii) the sustainable use of its components, and (iii) the fair and equitable sharing of the benefits arising out of the utilization of genetic resources. As with potential benefits and potential adverse effects of synthetic biology, relevant information and experiences have been invited from stakeholders, and establishment of a dedicated AHTEG has been decided.


In case you would like to dig deeper into the material, the official meeting documents can be found here.

We, the EUSynBioS Steering Committee, will make an effort to stay involved in this process, and to represent your opinion at future meetings of the UN Convention on Biological Diversity. It is for the sake of a future which allows us to freely and responsibly pursue our scientific careers in an appropriate regulatory environment.

All the best,

-Christian

 

We are an Observer to UN CBD COP13/CP-MOP8/NP-MOP2

 
COP13

Dear SynBio enthusiasts,

in three days' time, the Parties to the UN Convention on Biological Diversity will come together in Cancun, Mexico for their 13th conference (COP13). In parallel,  Meetings of the Parties to the Cartagena Protocol on Biosafety (CP-MOP8) and the Nagoya Protocol on Access and Benefit-sharing (NP-MOP2) will take place.

At this event, an internationally agreed operational definition of synthetic biology shall be finalized, with wide implications for the nascent discipline’s future regulation. Related key decisions to be made include the status of digital DNA sequence information in scope of the Nagoya Protocol’s Access and Benefit-sharing (ABS) rules, and the extent of Socio-Economic, Cultural, and Ethical considerations (SECE) being encouraged as key part of research efforts. We feel that it is imperative for the next generation of young scientists to have a voice in these decisions.

The CBD Secretariat has kindly admitted EUSynBioS as an Observer organization to this event, which gives you, the EUSynBioS community, a unique opportunity to have a voice. Even though Observers have no formal right to vote, the opinion of the next generation of synthetic biology researchers does count, and will on site be communicated in collaboration with partner organizations such as the Public Research & Regulation Initiative.

I would hence like to invite you to share your opinion, your suggestions, and concerns related to the Cancun negotiations with us. You can do so either via our twitter channel @EUSynBioS, or directly by email to sc@eusynbios.org.

You can also follow the official webcast here.

We are looking forward to hearing from you!

Christian, on behalf of the EUSynBioS Steering Committee

 

SynBio Breakout Sessions: what do they tell about our community?

Participants of the first EUSynBioS Symposium in April 2016. Image by Ona Anilionyte.

Participants of the first EUSynBioS Symposium in April 2016. Image by Ona Anilionyte.

Starting from a set of activities pursued by a small number of researchers, the discipline of synthetic biology has taken a remarkable trajectory over the past decade. However, the rapid growth of synthetic biology has also provoked concerns about its prospective impact on society and the environment, which needs to be addressed by future leaders of the field.

Taking a first step towards tackling this challenge, we recently brought together students and postdoctoral researchers from ten different countries at our inaugural EUSynBioS Symposium. Various aspects relevant to building a future vision for the young synthetic biology community were discussed by attendees in scope of our SynBio Breakout Sessions facilitated by experts from ecology, design, and science policy. What have they told about the synthetic biology community of the future?

 
SynBio Breakout Session on Diversity. Image by Christian R. Boehm.

SynBio Breakout Session on Diversity.
Image by Christian R. Boehm.

Embracing diversity is key, so agree participants of the Breakout Session led by Prof. Louise Horsfall (University of Edinburgh). However, the issue of diversity goes beyond gender and ethnic background of researchers. We should make an effort to include people from a variety of age groups, socio-economic backgrounds, and life-styles. Can a non-scientist be a true synthetic biologist? Or someone who only works part of the time because they choose to take time for family? We think yes, because otherwise we may miss out on a lot of different perspectives and potential for creativity. The synthetic biology community needs role models which appeal to various groups in society and can thus encourage both engagement and public acceptance.

 
SynBio Breakout Session on Responsible Innovation. Image by Christian R. Boehm.

SynBio Breakout Session on Responsible Innovation. Image by Christian R. Boehm.

A Breakout Session on the issue of Responsible Innovation led by Dr. Michele Garfinkel (EMBO) surfaced several issues about researchers’ responsibilities, including in what ways the public’s views of them matters. The session participants also discussed what the emerging idea of responsible innovation means and pointed out some possible concerns about the definition of the concept in the broader scientific community. Awareness about both responsible conduct of research and responsible innovation needs to be raised generally, and there was some agreement that it should be introduced as an inherent part of good research, reinforced through the scientific community itself both at the bench and by means of discussion sessions like the ones hosted on this occasion.

 
SynBio Breakout Session on Education&Outreach. Image by Christian R. Boehm.

SynBio Breakout Session on Education&Outreach.
Image by Christian R. Boehm.

Encouragingly, the vast majority of attendees of a Breakout Session led by Prof. Anne Osbourn (John Innes Centre, Norwich) were of the opinion that education and outreach were important, and they moreover felt a responsibility to be proactive in this area. Taking part in outreach and education was seen as a mutually beneficial activity, yet young researchers found it regrettably difficult to identify opportunities to become involved. On a related note, young researchers felt that opportunities for training in how to communicate effectively with an audience of non-scientists were rather scarce. To contribute to closing this gap, we (EUSynBioS) are actively looking for initiatives in the area of science education to work with members of our network.

 

So what is the synthetic biology community going to look like in the future? We do not know for sure yet, but the first SynBio Breakout Sessions revealed its promise: our community embraces a number of young researchers who deeply care about their impact on society and the environment. They are actively looking for opportunities to become better at engaging the public and communicating what they do to a non-specialist audience.

To realize this potential, the organizers of dedicated synthetic biology courses and graduate programs to be established over the years to come are challenged to incorporate relevant training opportunities into their curricula wherever possible. It is bound to pay off.


Written by: Christian R. Boehm

Disclaimer: Views and opinions expressed in EUSynBioS Pulse articles belong solely to the writer(s). They do not reflect the opinion of the Community, the Advisory Board or the Steering Committee.