In Pasteur's day, the scientific disciplines were compartmentalized from each other. Today, scientific research promotes multidisciplinarity and collaboration to answer a problem. Collaboration plays an important role among iGEMers. Indeed, collaborations achieve goals that we will not achieve alone. This year Sorbonne U Paris 2018 has been collaboring with 9 iGEM teams from all over the world! A deeply connection between iGEM Go Paris Saclay and iGEM Bordeaux were born during the Parisian meetup (Paris, France). This page details the nature of our collaborations with another iGEM teams.
After, clicking on our collaborators logos, you can read the name and the abstract of their project.
Cytotoxic anticancer drugs are among the harmful chemicals found in hospital wastewater at high concentrations. Degradation through physical and chemical methods exist but are often inefficient, unsustainable or expensive. We propose MethotrExit, a bioreactor-based approach to tackle this problem. We focused on the biotransformation of methotrexate (MTX), a widely used anticancer drug. We designed synthetic cassettes encoding a new biotransformation pathway using a heterologous carboxypeptidase in Escherichia coli. In only five hours, MethotrExit drastically removes MTX from the media. However, anticancer drug degradation products and/or the biotransformation pathway itself might be toxic for E. coli. To overcome this issue, biobricks generating heterogeneity in enzyme expression were built to ensure survival of a subpopulation. Modeling of this system highlights the interest of a division of labor between “cleaning” and “stem” bacterial cells.
iGEM Go Paris Saclay team is our fellow traveller. We share a very strong link between our two teams and together we confronted the obstacles. Due to the lack of mathematician in our team, the mathematicians of their team written the bases of our biomodelling, which we complete with the essential biological data, bound to the retrotransposon. Our modeling simulate the behavior of our retrotransposons. So, we were able to create a system allowing generating a data bank on the most advantageous transfers on the work, which allows targeting one or several transfers of interests. They were kind to help us and they enjoy to conceive this modelisation.
For more information about our modeling visit our modeling part.
On our side, Céline, our former wiki manager, taught few members of iGEM Saclay team to code, so that they can realize their wiki page. After that, Saniya gave them advice about the wiki.
Furthermore, Marie-Charlotte realized several sketches of their logo so that they can submit most appreciated sketches to a design agency.
Finally, we invited them to join the preparation of conference “What will synthetic biology bring in the future” with iGEM Bordeaux. They helped us to contact experts and we made a communal fund to purchase food and materials for the buffet. Indeed, the conference ended with a friendly buffet. They lent a hand to organize the conference. They were present with us during the conference.
The video of the conference “What will synthetic biology bring in the future?” is published on our Facebook page. This conference did not have a geographical barrier. We can have more information about this conference on Human practices pages section “Public engagement and education”.
This year IGEM Bordeaux Team would like to find an alternative to an entire segment of the traditional petrobased chemistry by a new green biobased chemistry. Indeed, we would like to focus on the biocatalysis of the hydroxymethylfurfural (HMF) in 2,5-furandicarboxylic acid (FDCA). Don’t worry, it is not as complicated as it appears. HMF is a by-product of the lignocellulosic biomass treatment. Its toxicity toward microorganisms leads to big issue for many companies which want to use these microorganisms to produce molecules of interest from lignocellulosic biomass. Our project consists in HMF detoxification by using it as a substrate to produce FDCA through bacteria .FDCA was identify as one of most promising biobased molecules which can replace many polymers such as PET (and other petrobased molecules). We suggest a sustainable alternative, eco-friendly and independent from fossil resource.
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“Friendship is born at that moment when one person say to another: “What! You too? I thought I was the only one.” (C.S Lewis). It is the perfect quotation to sum up our collaboration with iGEM Bordeaux. We first met at the Parisian meetup at Paris. We share the same idea of the conception of a iGEM project. We don’t have any budget at the beginning of the iGEM season and we have built our project from A to Z. We rely only on our fundraising to achieve our project.
We discussed to make a potential conference for our collaboration. We also invited the team of GO Paris Saclay to join us to participate in the preparation of the conference. We tried to tackle the same problematic with our project but with different vision : environmental issues. The purpose of this collaboration is to set up a conference open to all. The theme would be: "What can synthetic biology contribute to sustainable development?". They helped us to contact experts. Then , we broadcast a Facebook live during the conference. They shared this video and broadcast in direct in the University of Bordeaux, so that the students and professors of Bordeaux can take advantage of the conference.
The video of the conference “What will synthetic biology bring in the future?” is published on our Facebook page. This conference did not have a geographical barrier. We can have more information about this conference on Human practices pages section “Public engagement and education”.
Alternative Roots: Engineering Microbial Communities
Abtract
The demand for food, fuel and materials is placing unprecedented pressure on agricultural production. To secure higher productivity, the sector relies upon synthetic fertilisers derived from energy intensive manufacturing methods. Here, we propose an alternative approach to support plant productivity. The Alternative Roots project investigated Pseudomonas fluorescens as a chassis organism. Development of a plant-colonising chassis provides novel mechanisms for soil microbiome manipulation without genetically modified crops. As proof of concept, we focus on improving nitrogen supply via naringenin biosynthesis - a potential chemoattractant of free-living, nitrogen-fixing bacteria. Legal and social considerations of the project drove the development of NH-1, a low-cost, small-scale and programmable hydroponic system. Tailored to overcome experimental limitations faced by many plant scientists, NH-1 provides improved reproducibility, coupled with high-throughput experimentation. This system enabled exploration of future deployment techniques within contained environments that may result in enhanced, sustainable crop productivity at a local and accessible level.
Charlotte come from England and for the summer holidays, she came back at home. In July, Charlotte met the Newcastle team for a probable collaboration. Newcastle worked on an initial visual of our photobioreactor. We discussed with them for a collaboration in Human Practices part. We thought about to make a survey with them on the society’s opinion GMO and our projects. Unfortunately, we aborted this idea because of lack of time and we only work on the design of our photobioreactor. They help us to improve our photobioreactor after we met experts during the summer. They were really helpful and kind enough to help us.
iGEM Montpellier
iGEM Montpellier
Vagineering : A New Non Hormonal Contraception
Abtract
Modern hormonal contraceptive methods have been revolutionary for women in developed countries; however, they still exhibit a variety of challenges. Developing countries lack consistent access, hormonal contraceptives can produce harmful environmental effects, and some women are unable use them due to health problems. The Vagineering project looks to solve these issues with a novel, non-hormonal method. Our team aims to engineer Lactobacillus jensenii, a bacterium from the vaginal flora, to produce two proteins to prevent unintentional pregnancy: antisperm antibodies that inhibit sperm motility and anti-microbial peptides (AMPs) that produce spermicidal effects. The goal is to create a lasting contraceptive using only bacteria, which can later be reversed by engineering the strain with a kill-switch. Additionally, our studies of this strain have produced a toolbox that will help other teams to further engineer this less-characterized bacterium.
This year 3 students from the iGEM Montpellier team 2018 came to Sorbonne Universite to pursue their master’s degree at Paris. So we invited 2 of them to join us to share with the pupils their knowledge, their lab skills and their vision of iGEM experience. Thus, we collaborated with two members of their team : Lea Meneu and Léo Carillo. They were in charge of the slides. We bought the material for the practical labs :Saccharomyces cerevisiae Ade- strain and lab equipments .We participated together in organization of the practical work. We met several times before the practical work for the organization of the TP and the purchase of equipment. We were glad to organize this practical work with Léa and Léo.
Teaching at students is a good experience and a good opportunity to learn how to explain our project with easy words. We shared a great moment with them.
To learn more about this practical work at High school Maurice Genevoix (city of Montrouge),go to our Human practices page section “Public engagement and education”.
Vibrigens - Accelerating Synbio : Establishing Vibrio natriegens as the new chassis organism for synthetic biology
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Waiting for cells to grow is an enormous time sink for synthetic biologists. Cloning cycles with the current standard, Escherichia coli, typically take up to three days. In our project Vibrigens - Accelerating Synbio, we established the tools to turn Vibrio natriegens into the next generation chassis for synthetic biology, ready to be used reliably. By taking advantage of its unbeaten doubling time of 7 minutes, we substantially reduced waiting time and made one-day-cloning a reality. We built and characterized a flexible golden-gate-based part collection, consisting of more than 100 parts, which enables the creation of complex pathways in a short amount of time. Our engineered V. natriegens strains VibriClone and VibriExpress are designed for cloning and protein expression applications, respectively. Moreover, we established the first synthetic metabolic pathway in this organism by producing the platform chemical 3-Hydroxypropionate and along the way developed an accelerated workflow for metabolic engineering..
As a part of their Human Practices project, they aim to make the iGEM competition accessible to everyone. The iGEM Marburg team sent us a message to participate in the design of an accessible wiki to everyone. After several emails, we helped each other to write the guide“Accessible webdesign”. We try to explain with easy words and examples so that, the beginner wiki manager can understand this concept. We really enjoyed to participate in this project. The long time goal would be that every iGEM team would design their wiki barrier-free. They made a logo to indicate that our wiki is accessible. We put it in the footer of our wiki. Moreover, we have them some tips to improve their wiki. We explained them that it is possible to add a language tag so that the browsers can recognise the language of the website and it is also possible to translate in a given language. They helped us to make an accessible wiki. It was a real pleasure to collaborate with iGEM Marburg team.
To read the “accessible webdesign-guide navigation”, visit the Human practices page of iGEM Marburg.
ADaPtat1on : Expanding Toolkit for Acinetobacter baylyi
Abtract
Acinetobacter baylyi is a gram-negative, soil-dwelling, non-pathogenic, naturally competent and nutritionally versatile organism especially known for its ability to degrade aromatic compounds. However, only a few tools are available for its gene manipulation. This year, we plan to expand the toolkit for A. baylyi ADP1 by making a synthetic promoter library along with codon optimized fluorescent reporter proteins to achieve better control over its expression rates. The codon table is not available for this organism. So we obtained sequence data of well-characterised proteins of this organism by filtering manually putative and hypothetical sequences and used this data to generate the codon table using CUTE - a tool of ChassiDex. The codon optimisation is done manually by replacing the less frequent codons with high-frequency codons based on the generated table. This can potentially open up various new exciting synthetic biology opportunities with this unexplored organism.
IIT Madras shared their wish to collaborate with iGEM Team on the iGEM team collaborations. The goal of this collaboration is to translate in our native language educational synthetic biology videos. We are helping IIT Madras team in translating the script of some synthetic biology video in french, italian, persian and arabic. We are also recording the audio of some videos. We translate and recording the “DNA and RNA” video in french and italian, and the “introduction of synthetic biology” in persian. It was be a really pleasure to help in this fantastic initiatives!
iGEM Washington
iGEM Washington
Stronger Together: An efficient, generalizable approach to design biosensors for small molecules
Abtract
Chemically induced dimerization (CID), in which two proteins dimerize only in the presence of a small molecule, has been widely used to control cell signaling, regulatory, and metabolic pathways, and used as logic gates for biological computation in living mammalian cells. However, few naturally occuring CID systems and their derivatives are currently available. Creating a CID system with desired affinity and specificity for any given small molecule remains an unsolved problem for computational design and other protein engineering approaches. To address this challenge, we have used a novel strategy to select CID binders from a vastly diverse combinatorial nanobody library. We have created new CID systems that can sense cholecalciferol and artemisinin. We are validating CID biosensors by a yeast three-hybrid system and built structural models to understand the small molecule-induced dimerization. Our work is a proof-of-concept that can be generalized to create CID systems for many applications.
Washington create a Synthetic Biology Activity Booklet. This contain outreach activities for school children which they are hoping to make accessible to the entire iGEM community. They offered us to translate there booklet in a french version. This will allow the future french team to use this booklet to improve there public engagement part and permit to explain with fun that is synthetic biology.
iGEM Duesseldorf
iGEM Duesseldorf
Trinity - towards an engineered co-culture toolbox
Abtract
Co-cultures are found in all conceivable entities, such as the human gut, cheese or plants, but good tools to study those communities are currently not given. Indeed we created a modularly built toolbox using not only three different dependencies but also three different organisms: With Escherichia coli, Saccharomyces cerevisiae and Synechococcus elongatus our team engineered a system based on nutrient exchange. Here phosphate is provided through oxidation of phosphite, nitrogen source produced by melamine breakdown, whilst carbon source is provided by Synechococcus elongatus. Two additional independent approaches are designed, too. The first includes regulation via cross-feeding by amino acid auxotrophies and production: lysine by Escherichia coli and leucine by Saccharomyces cerevisiae. The other utilizes regulated self-lysis via quorum sensing molecules, to control cell density by a phage lysis gene. This engineered toolbox opens a wide range of possibilities to create microbial communities for different purposes, such as synthetic probiotics.
Duesseldorf created a project to promote synthetic biology in public using self-designed postcards. Every participating team designs a postcard which shows an image related to synthetic biology on the front and a small informational text on the back. Afterwards each team’s postcards are exchanged with other iGEM-teams so that every team can collect postcards from all over the world. The received postcards can then be shared with people in the neighborhood, during public events etc.
We participate in the postal card collaboration which is organized by the team. We have made a postcard that it recreated the famous painting of the Liberty guiding the people: "La liberté guidant le people" by Eugène Delacroix, but instead with microalgae leading the way to the Sugar Revolution. You can admire our postal card.
iGEM Pasteur
iGEM Pasteur
NeuronArch: the novel connecting and protecting biofilm based system for prostheses
Abtract
In the future, a long due consideration and an easier access to healthcare will be given to people with disabilities. Presently, some prostheses allow amputees to perform simple actions but without a direct connection between the nerves and the prosthesis. Furthermore, a major health risk is the development of pathogenic communities of microorganisms in structures called biofilms. Strong treatments with antibiotics, or even surgical reinterventions are then required. They represent a heavy burden for both the patient and the healthcare system. We imagined NeuronArch as a novel application that subverts potential pathogenic biofilms using an engineered one. This interface produces substances called neurotrophins (NGF), for directed and controlled growth of nerves. Using a conductive membrane, it will also allow passing of information and enhancement of the electrical properties. Altogether, these improvements would enable patients to regain natural perceptions and prevent the formation of Staphylococcus aureus biofilms by blocking quorum sensing.
We have met iGEM Pasteur team in May for a potential collaboration with them. However, our projects are too different. So we have chosen to collaborate only on the interlab measurement study. We offered, to Pasteur team, the strain of E. coli DH5 alpha that they need for the interlab. They answered our questions about interlab and gave you some tips.
Moreover, we have participated to the 4th Parisian meetup. So, we introduced our Suga[R]evolution project and stimulated our presentation before the Giant Jamboree at Boston
Judges gave you a feedback about our presentation and how to improve our project. To learn more about this event visit our meetup page.
