The availability of new technologies has facilitated the exchanges worldwide and so promoted multidisciplinarity and collaboration in science. Collaboration is a key part among iGEMers. Indeed, collaborations help to achieve goals that would not be fulfilled alone. This year the Sorbonne U Paris 2018 team has been collaborating with 9 iGEM teams from all over the world. Herein, we detail the nature of all of our collaborations with these awesome teams with whom we shared great moments for which thank them a lot!
By clicking on our collaborators' logos, you will have access to the abstract of their project.
Cytotoxic anticancer drugs are among the harmful chemicals found in hospital wastewater at high concentrations. Degradation processes 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. Modelling of this system highlights the interest of a division of labor between “cleaning” and “stem” bacterial cells.
The iGEM Go Paris Saclay team and us have built a very strong relationship and have faced various challenges together. Their mathematicians introduced us to the bio-modeling bases. We could implement our essential retrotransposons' biological data into the model created together. Indeed, this model aimed to simulate the behavior of our retrotransposons. So, we are able to generate a data bank to select the best parts for our system.
For more information about our modelling visit our modelling page.
On our side, Céline, our former wiki manager, taught some members of the iGEM Paris Saclay team to code, in order to realize their wiki page and Saniya has been an advisor.
Marie-Charlotte realized several sketches of their logo for a submission to a design agency.
They also took part in the organization of the conference untitled “What will synthetic biology bring to the future?” hosted on the Campus Pierre et Marie Curie of Sorbonne Université. They helped us contact experts and purchase food and materials for the buffet through a communal fund.
Further information about this conference are available on the 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.
“Friendship is born at that moment when one person says to another: “What! You too? I thought I was the only one.” (C.S Lewis). It is the perfect quote to sum up our collaboration with the iGEM Bordeaux team. We first met at the Parisian meetup in Paris (7th July 2018). As we share the same conception of an iGEM project, our partnership was obvious.
We invited them to participate to the organization of the conference “What will synthetic biology bring to the future?”. They helped us a lot to contact experts.
Alternative Roots: Engineering Microbial Communities
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.
One of our team member, Charlotte Bellamy, went to Newcastle University to meet the iGEM Newcastle team and discuss about a collaboration. The team worked on the 3D prototype of our initial photobioreactor. Furthermore, after meetings with experts, they kept supporting us in the improvement of our photobioreactor design.
Vagineering : A New Non Hormonal Contraception
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.
Léa Meneu and Léo Carillo, two students from the iGEM 2018 Montpellier team are pursuing their master’s degree at Sorbonne Université in Paris. So we invited them to help us introduce synthetic biology and the iGEM experience to high school students. To do so, practical sessions were organized. Several meetings between our teams were set to prepare the slides and purchase the equipments. Teaching students was a very nice opportunity to learn how to explain our project with simple words.
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
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. Through several emails, we helped each other to write the guide “Accessible webdesign”. We tried to write the guide with easy words and bring examples so that beginners can easily apprehend this wiki concept. The long-term goal is for all iGEM teams to design their wiki without difficulties. We also helped each other improve various parts of our respective wikis. They made a logo to indicate that our wiki is accessible and we put it in the footer of our wiki.
To read the “accessible webdesign-guide navigation”, visit the Human practices page of iGEM Marburg.
ADaPtat1on : Expanding Toolkit for Acinetobacter baylyi
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 asked us for a collaboration to translate educational synthetic biology videos into our native languages. So we translated some of their video scripts to French, Italian and Persian. We also recorded the audio of some videos: the “DNA and RNA” video in French and Italian and the “introduction of synthetic biology” video in Persian. It was a real pleasure to help them in this fantastic initiative!
Stronger Together: An efficient, generalizable approach to design biosensors for small molecules
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.
iGEM Washington team has created a Synthetic Biology Activity Booklet. This Booklet contains outreach activities for children. They wanted it to be accessible to the entire iGEM community. Therefore, they asked us to translate their booklet in French. This aims to allow the future French teams to improve their public engagement part by explaining synthetic biology to children with fun.
Trinity - towards an engineered co-culture toolbox
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 using self-designed postcards. Every participating team designed a postcard related to synthetic biology or their respective project topic. To spread the iGEM team’s innovative ideas, different teams exchanged their postcards. The postcards were then received and collected all over the world and could be shared with the general public during events...
The postcard we made reinvented the famous painting of the Liberty guiding the people: "La liberté guidant le peuple" by Eugène Delacroix. Our microalgae, Claude, is there leading the way to the Sugar Revolution.
NeuronArch: the novel connecting and protecting biofilm based system for prostheses
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 collaborated with the iGEM Pasteur team on the InterLab measurement study. We gave them the E. coli DH5 alpha strain they needed for the InterLab. In return, they answered some questions concerning the InterLab.