iGEM 2017 UCL: Light Induced Technologies (LIT)

Using light in the future will mean more than illuminating rooms and flash photography. This year, a team of 9 undergraduates from UCL, with academic backgrounds ranging from Biochemical Engineering to Psychology, are shaping this vision. The members, coming from anywhere between Mexico and Luxembourg, will use the world’s largest synthetic biology competition at MIT, iGEM (international Genetically Engineered Machines), as a platform to develop light induced technologies.

The goal is to make synthetic biology more accessible to the general public by providing standardised and easy-to-use light control systems

LIT (Light Induced Technologies) - and no, it’s not Elon Musk’s new company - came out of a two-day project hackathon back in June. Ideas ranged from bio-robots to improve survival chances and collect data on Mars, to using optogenetics to control gene circuits. “The goal is to make synthetic biology more accessible to the general public by providing standardised and easy-to-use light control systems” – the team`s stated vision. The potential applications range from medicine to fabrication. The cells are engineered to respond to light in a tightly controlled manner. This switch can then be coupled to a wide variety of biological processes.

In essence, organs are made out of complex networks of different mammalian cells. To gain control over that complexity, LIT will use light to induce cell adhesion and trigger genetic networks in specific parts of the cell population. This work will be done in pluripotent stem cells. Their work is the first steps towards building organs from digital blueprints and tissue regeneration.

Stereolithography is an important technique in engineering and prototyping. The team aims to produce an organic version of this 3D printing method by allowing bacteria to form 3D structures through cell adhesion. Once this is implemented, specific wavelengths will be tested to produce biopolymers that are UV-resistant and environmentally friendly. Light induced technologies are also trying to optimise a bioluminescence system to create an efficient bacterial lightbulb.

This interdisciplinary project is based on research and mathematical modelling. However, other components such as entrepreneurship and public engagement will also contribute to its success. Research and engineering doesn’t happen in a bubble, so one must acknowledge and involve a wide variety of actors. The team has been working with different non-academic stakeholders in the project. For example, talking to architects has shaped the vision of what can be done with biopolymers in the field and inspired design. The planned activities over the summer aim to get people excited about synthetic biology, communicate science effectively and assimilate the ethical and societal implications of the projects.

There is an easy answer to the ‘so… what happens next?’ question. The website and social media pages (see below) are platforms for both communication and feedback on the project. Until November, you can get in touch, offer suggestions and collaborate.

Facebook: UCL iGEM

Instagram: ucl_igem17

Twitter: @ucligem

Website: http://2017.igem.org/Team:UCL

 

YEBN'S 2nd Round Table

Our friends at the Young European Biotechnology Network hold their second round table event this September, join them!

YEBN'S 2nd Round Table is going to take place in Frankfurt, Germany. When? Saturday 9th of September.

Here you could find an exciting one day program to exchange between different local and national life sciences organization within Europe in terms of activities and structure (sponsoring, working groups etc). We will also inform you about European supporting programs such as Erasmus +.

Are you a member of a life science organization within Europe? We are looking forward to your application: eb@yebn.eu

iGEM 2017 INSA-UPS Toulouse: Detecting and killing V. cholerae in contaminated water

This year the iGEM Toulouse team and the INSA Lyon team have merged, leading to a single team of students from the National Institute of Applied Sciences (INSA) Toulouse, University Paul Sabatier and the INSA Lyon.

The project of the team INSA-UPS Toulouse is to purify water contaminated by the pathogenic bacteria Vibrio cholerae. Cholera is still a disease that millions of people have to deal with every day.

The INSA-UPS Toulouse iGEM team

The INSA-UPS Toulouse iGEM team

Our team intends to treat small to medium volumes of contaminated water in countries impacted by cholera. For example, this year, an outbreak of cholera occurred in Yemen with already more than
250 000 people affected. Current treatments have limitations and people are still dying from cholera, either because it is hard to detect before cases are declared, or because patients live in remote areas not easily reachable by aid services. Thus, two solutions need to be found: one to detect V. cholerae before epidemic bursts occur and one to treat water in remote areas.

We want our final device to be able to combine detection and treatment of contaminated water. Furthermore, to have a greater impact, we aim for our device to be easily used by non-qualified people so everyone can contribute to improving the quality of water. We found a solution fulfilling all these criteria using synthetic biology.

Our system relies on the following biological facts: Vibrio species, hence V. cholerae, use a specific method of intra-species communication through quorum sensing. Vibrios have a specific one, using the CAI-1 molecule which binds to its specific membrane receptor CqsS. More interestingly, each Vibrio has its own CAI-1/CqsS system. That’s why, by inserting a punctual mutation on Vibrio harveyi –a nonpathogenic Vibrio- CqsS, this bacteria becomes able to detect the V. cholerae CAI-1. Using a system of communication close to the natural one will allow a strong and reliable detection of the V. cholerae in water.

The final goal is to kill the bacteria V. cholerae. We decided to focus on newly described peptides from the immune system of crocodiles. They showed a promising effect on V. cholerae. A secretion system for this peptide is needed in order to have a specific and efficient response to V. cholerae in water. Obviously, the peptide specific to V. cholerae will also kill V. harveyi.

It was thus essential to find a fast growing, large producer able to survive the antimicrobial peptides. Our team chose Pichia pastoris as it met these criteria, with a lot of publications supporting its ability to produce a great amount of antimicrobial peptide. Therefore P. pastoris has the role of cholera killer.

Summary of the iGEM team's strategy to kill Vibrio cholerae by using synthetic biology

Summary of the iGEM team's strategy to kill Vibrio cholerae by using synthetic biology

The link between the two previous entities is to kill V. cholerae only upon its detection. The challenge was to find a way of communication between the prokaryotic detector and the eukaryotic killer. A previously described engineered ligand/receptor system was found in the iGEM registry. This diacetyl/ODR-10 system meets perfectly our needs. Upon detection of V. cholerae, diacetyl is produced by V. harveyi. Diacetyl is then detected by the Odr10 receptor present on P. pastoris. This cell signalling induces the activation of the pFUS promoter. Behind this promoter, the peptides can be produced by reception of the signal of presence of V. cholerae.

For more information: http://2017.igem.org/Team:INSA-UPS_France

 

Introducing Synthetic Biology: A New Journal for the SynBio Community

Last year saw the launch of Synthetic Biology - a new open access journal from Oxford University Press. Aiming to serve the whole synthetic biology community, it has an extensive scope including everything from viral, protein and metabolic engineering through to mathematical modelling and engineering processes. It will provide a platform for original research papers, reviews, commentaries, project reports and discussions around the theme of synthetic biology to those working in academia, education and industry.

Professor Jean Peccoud

Professor Jean Peccoud

We got in touch with Editor-in-Chief Jean Peccoud to get more of an insight into what Synthetic Biology will bring to our community and find out where he thinks synthetic biology is heading over the next few years.

Q: What will Synthetic Biology bring to the SynBio community - how does it differ from other synthetic biology journals?

Jean Peccoud: Most of synthetic papers are still published in non-specialized journals that span a broad spectrum of scientific specialties from bioinformatics to molecular biology and biotechnology. It can be difficult for readers to notice synthetic biology papers among all the other papers that these journals publish. For authors, this dispersion can also be problematic as editors of well-established journals sometimes struggle to see how a synthetic biology submission fits within the scope of their journal.

The first journal dedicated to synthetic biology was IET Synthetic Biology. For some reason the journal was short-lived. It took five years after this early experiment to see the launch of a new journal dedicated to serving the needs of our community. Since 2012, ACS Synthetic Biology has been extremely successful. It now provides the community with a well-respected venue to publish synthetic biology research.

Its success is also a sign that the growing synthetic biology community needs channels to disseminate its research. Oxford University Press (OUP) identified this need when they decided to launch this new journal. Many synthetic biology authors are familiar with OUP, the world’s largest university press. They also publish Nucleic Acids Research and Bioinformatics, two journals that have been publishing synthetic biology papers for many years. This creates opportunities. For instance, we have developed a process to streamline the transfer of manuscripts from one journal to another. If a paper is rejected by Nucleic Acids Research because of its perceived limited significance, authors will be offered the possibility of transferring the submission and the reviews to Synthetic Biology. OUP is also known for the quality of its production process. Accepted manuscripts are formatted very quickly and only published in their final form. Authors benefit from a rigorous proofreading and typesetting that, I think, greatly contribute to the value provided by the journal.

Prior to working with OUP, I spent several years working with PloS. I became an academic editor of PloS One in 2009 and then I was instrumental in launching the PloS Synthetic Biology Collection. The editorial policies for Synthetic Biology are partly inspired by PloS ONE editorial policies. In particular, the significance of a submission is not considered when making editorial decisions. We are not chasing the Impact Factor. I think the editor’s role is to ensure that the results that are published are scientifically sound. It is for the readers to decide which papers are important by citing them over the years.

We also offer to publish categories of articles that may be difficult to publish in other journals. This includes reviews, papers describing educational programs, datasets, and even conference papers that summarize results previously presented in conference proceedings.

However, we chose not to publish any Comments or Policy papers as we think less specialized journals are probably better venues to discuss these issues.

Q: What do you think is the biggest challenge facing synthetic biology?

JP: My main concern is the security implications of the technology and its possible dual use. I think we are greatly benefiting from a fairly permissive regulatory environment. I am afraid that if a security incident were to happen, something isolated like the Amerithrax in 2001, we could end up operating in a more constraining environment that could dramatically hamper the development of the technology and its economic impact.

Q: What do you think the most exciting opportunities for synthetic biology are over the next 10 years?

JP: In the journal editorial, I explained that synthetic biology is catalyzing the next industrial revolution. I don’t think that many people could have anticipated in the 60s how the semiconductor industry is shaping our world today. We can only anticipate a revolution of a similar magnitude. It will be very interesting to see how this technology will shape the world of our children.

Although it’s still very early days for Synthetic Biology, it has already started to publish some great research, with four articles having been published this year. Two of these are experimental articles. One paper describes a biosensor for high throughput screening in metabolic engineering of yeast whilst the other paper describes a method to quickly assemble BioBrick parts.

Synthetic Biology also published two computational articles. A theoretical article proposes a network of chemical reactions capable of computing logarithms and a software paper describes an application to analyse the robustness of regulatory networks.

Submission process

On the submission process, Prof. Peccoud commented “I am very grateful to the editorial board who has set very rigorous peer-review standards. This policy translates in a fairly low acceptance rate. None of this would be possible without the efforts of the hundreds of anonymous reviewers who have generously volunteered their time to help us evaluate the submissions. The number of submissions is increasing steadily but now that our processes are running smoothly, we are certainly able to handle a larger volume of submissions.”

Ready to publish your research? Synthetic Biology currently has an open call for papers for a special issue on cell-free expression systems. This includes gene circuits, metabolic engineering, synthetic cell systems, self-assembly and TXTL and material science.

Synthetic Biology are kind sponsors of our annual Symposium at the Spanish National Centre for Biotechnology in Madrid from the 31st of August to the 1st of September. For more information about Synthetic Biology, to sign up for new content alerts, or to submit an article for publication, visit their website.


 


 

iGEM 2017 Manchester: On the Mission to Save Phosphorus Reserves and Clean Water

iGEM Manchester 2017 is a team of nine students participating in iGEM, the biggest synthetic biology competition in the world. In their project, iGEM Manchester aims to solve two imminent environmental dangers, which threaten our ecosystem: eutrophication and rapid depletion of phosphorus reserves. Their solution involves designing phosphate-accumulating bacteria in order to recycle phosphorus from waste-water and polluted eutrophic rivers and lakes, thus killing two birds with one stone.

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iGEM Manchester 2017 started their work in early February, by analysing assorted environmental, energetic, and medical problems to be solved in society. This is a standard procedure for each of over 300 teams participating in the competition. “We considered projects ranging from fungal bricks to synthetic amino acids, from directed evolution to plastic degradation. In the end, however, we decided to focus on phosphorus exhaustion. Phosphorus is the main ingredient of agricultural fertilizers, forming the backbone of 21st-century food supply methods,” says Maciej Słowiński, a member of the team.

In fact, phosphorus is a finite resource, 99% of the reserves of which can only be found in four countries. Its reserves are predicted to be exhausted in 50–100 years. This will deliver a serious blow to the rising world population: meeting increasing demand for food might become an impossible task. At the same time, significant amounts of phosphorus end up in rivers and lakes as agricultural waste-water, giving rise to a major environmental problem: eutrophication. New recycling methods could mitigate this issue, and soaring food needs coupled with depleting phosphorus reserves create a huge incentive to develop such methods.

iGEM Manchester Team saw it as a chance to design and engineer phosphate-accumulating bacteria, thereby potentially solving two problems with one environmentally friendly and sustainable approach. The team intends to mutate the enzyme Polyphosphate Kinase (PPK) and encapsulate it in a synthetic microcompartment within E.coli. This would allow for significantly increased accumulation and storage of phosphorus inside the engineered cell compared to existing methods. Phosphate gathered in this process could be used as an organic fertilizer on farmland.

As part of the iGEM Competition, the Manchester Team will be building a business model based on the bacteria designed. To this end, the team is speaking to experts in the water industry to determine the relevance of their project and feasibility of implementation on a large scale, as well as to understand the GMO legislation framework affecting this work. In order to reach a wider public, the team also started illustrating their project on a Wiki page.

The finals of the iGEM Competition, the Giant Jamboree, take place in Boston in November. The Giant Jamboree gathers students, academia, researchers and company representatives to celebrate synthetic biology accomplishments, feature team presentations, and hold workshops as well as social events. This is where iGEM Manchester Team will compete against other universities. “We would love to receive the gold medal at the competition. For now, however, let us focus on carrying out our experiments… and on finding sponsors. After all, without them, we will not be able to complete our project,” concluded Jessica Burns, one of the team’s members.

For more information: http://2017.igem.org/Team:Manchester