iGEM

iGEM Marburg 2018: establishing Vibrio natriegens as a chassis for synthetic biology

Imagine a lab where you need twelve hours for a cloning cycle instead of three days. Imagine a lab where you start your culture in the morning and harvest your cells after lunch. Imagine a lab where the time lost waiting for cells to grow is reduced to the absolute minimum.

In the past years almost all processes (e.g. DNA synthesis or sequencing) have become faster, but one aspect is still unchanged: The organism that is used as chassis in the majority of Synbio projects remains Escherichia coli. The iGEM Team Marburg 2018 attempts to shake the fundaments of biological engineering by replacing E. coli with Vibrio natriegens, the fastest growing organism known to date, with a demonstrated doubling time of seven minutes.

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The iGEM Team Marburg and their project “Vibrigens - Accelerating Synbio“ aim for the establishment of V. natriegens as the new go-to organism for everyday lab work in both academic and industrial applications. This could improve production output of valuable chemicals and pharmaceuticals and pave the way for a brighter future of research. V. natriegens is very easy for labs to adapt to. It is a non-pathogenic S1 organism, which grows on salt rich standard LB-Medium.

The team is organized in three subgroups: First the strain engineering subgroup will adapt the genome to create the perfect chassis for molecular biology, as has been done with E. coli over the past decades. Strains without nucleases for ideal cloning, others with T7 expression systems and no proteases to express proteins as desired, and many more. These changes shall be done through genome engineering, recombineering and V. natrigens’s exceptional natural competence.

The part-collection subgroup will build the “Vibrigens MoClo toolbox” which will consist of a large number of precisely characterized parts. First experiments showed already, most parts commonly used in E. coli are also functional in V. natriegens. Still, plenty of work is required for the exact characterization of these parts in V. natriegens to achieve the same degree of predictability which is needed for the construction of synthetic regulatory networks or metabolic pathways.

Finally, the Metabolic Engineering subgroup will implement the first heterologous pathway into Vibrio natriegens, producing 3-Hydroxypropionic acid (3-HPA) one of the twelve most important bio-based chemicals needed to reduce dependence on fossil fuel. There is also another, theoretical pathway, which is the most efficient 3HPA-pathway. Because there is no known enzyme for the last reaction, it has never been tested in vivo, but that can be changed. The team will try to build multiple suitable enzymes by calculating the binding pocket for the substrate and subsequently expanding the protein structure until the whole enzyme is built. After testing these enzymes, the pathway can be perfected at a fast pace because biosensors will be established to translate product concentration into a measurable fluorescent output.

In their project “Vibrigens - Accelerating Synbio“ , Marburg's iGEM team is going to combine the fastest cloning methods available with the fastest growing organism Vibrio natriegens optimized for the needs of the community and to show its usefulness by producing 3-Hydroxypropionic acid.

In addition to their ambitious scientific project, iGEM Marburg will be hosting the German iGEM Meetup (22nd - 24th) in collaboration with iGEM Bielefeld and the GASB. This meetup will give all german iGEM teams a platform to reach out for collaborations and to present preliminary results of their projects.

 

You can join iGEM Marburg 2018 on social media to stay informed about their project:

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iGEM Montpellier 2018 : A New Non-Hormonal Contraception

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This year, and for the very first time, a Montpellier (France) iGEM team has been created, composed of nine passionate undergraduate students from different schools. iGEM is the world’s biggest competition of synthetic biology. They have decided to study the vaginal microbiome.

 

Microbiome. This word has been everywhere in the scientific community for the last decade. Although this is a very complex system, scientists are discovering new findings every day, and even if there are a lot of different microbiomes to study, one of the most represented is the gut microbiome. Did you know that another microbiome below is just as important and interesting than the gut microbiome for half of the population? The vaginal flora is part of every woman’s life, it is protecting every single one of them from a lot of inconveniences such as discomfort and even diseases. It is made from specific bacteria living together in balance to make the vagina a safe and healthy place. Unfortunately, this microbiome is sometimes damaged due to everyday life (for instance vaginal wash, bad hygiene or the membrane surfactant nonoxynol-9 (N-9) from vaginal contraceptive products). Once the balance is lost, the flora can be surrounded by pathogenic microorganisms. This can go from an itchy vagina to mycosis or increasing chances of having a sexually transmitted disease. Moreover, women have suffered from invasive and expensive methods for contraception, such as the pill and the IUDs (intrauterine devices). Based upon these facts, the Montpellier team wanted to tackle an iGEM project that would address those issues.

 

The team decided to focus on making a new kind of contraceptive using Lactobacillus jensenii, which is one of the most represented bacteria in the vaginal flora. This hormone-free contraception uses a designed Lactobacillus jensenii that has the ability to immobilize spermatozoa in the vagina. How does it really work? Their goal is to create bacteria capable of having a “light switch effect”. When a woman decides to turn it on, bacteria will have a spermicidal effect and will allow in situ contraception. Otherwise, bacteria will be in “off mode”, and spermatozoa will be able to pass. Several studies have demonstrated that Nisin - an antimicrobial peptide - has spermicidal activity. Nisin is a bacteriocin produced by Lactococcus lactis, which is nontoxic to humans. The idea is to introduce the gene that is coding for Nisin into Lactobacillus jensenii and then to apply a colony of these designed bacteria into the vagina for long-term contraception. When a woman wants to remove this contraceptive device, the team must find a way to stop the spermicidal effect of the bacteria.

 

Microbicide can allow a new way of contraception: safe and affordable, where women don’t have to negotiate with their partners.

Why is it crucial to find a new approach to contraception?

Hormonal contraception has a lot of side effects for women (such as weight gain or acne), a pill is easy to forget, and there is the environmental aspect of water contamination by hormones.

Moreover, it has been shown that it’s difficult for women to negotiate the use of condoms with their partners (which is the only method to prevent STD infections and another common method to avoid unwanted pregnancies). Microbicide can allow a new way of contraception: safe and affordable, where women don’t have to negotiate with their partners.

 

This project is generously supported by their university (Université de Montpellier), and the CBS research center (Center of Structural Biochemistry), which they are proud to represent on their visit to the USA. The team wants to take part in this science program by characterizing and sharing new parts of L. jensenii as well as to present their project to the scientific community.

 

You can join us on social media to follow our adventure:

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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

 

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

 

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