Team:Sorbonne U Paris/Collaborations

Our collaborations

The availability fo new teachnologies, scientific or not, have facilitate the exchanges worldwild and so promoted multidisciplinarity and collaboration in science. Collaboration is a key part among iGEMers. Indeed, collaborations help to achieve goals that we will not be fulfilled alone. This year Sorbonne U Paris 2018 has been collaboring with 8 iGEM teams from all over the world. Here, we detailled the nature of all of our collaborations with iGEM teams. We shared a great moments with all of these teams and we thank them a lot for that!

By clicking on our collaborators logos, you will have access to the abstract of their project.

• Index
• iGEM Paris Saclay
• iGEM Bordeaux
• iGEM NewCastle
• iGEM Montpellier
• iGEM Marburg
• iGEM IIT Madras
• iGEM Washington
• iGEM Duesseldorf
• iGEM Pasteur

iGEM Go Paris Saclay

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iGEM Go Paris Saclay

MethotrExit: a HeteroGenious Cleaning Factory

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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.

https://2018.igem.org/Team:GO_Paris-Saclay

The Paris Saclay team and us built a very strong link. We have built a very strong relationship and have faced various challenges together. Our team, mainly composed of biologists was helped by the the mathematicians of the Paris Saclay team. Their mathematicians introduced us to biomodeling bases. They helped to write the bases of our bio-modeling and we added the biological data. Our modeling simulates the behavior of our retrotransposons. So, we were able to create a system allowing the generation of a data bank on the most advantageous transfers.

For more information about our modeling visit our modeling part.

Modeling 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.

Finally, we invited them to join us in the preparation of a conference untitled “What will synthetic biology bring in the future” hosted in the Campus Pierre et Marie Curie at Sorbonne Université together with the iGEM Bordeaux team. They helped us contacting experts and we made a communal fund to purchase food and materials. The conference ended with a friendly cocktail reception with our invited speakers, the attending audience and the members of the three co-organizing iGEM teams.

The video of the conference is available on our Facebook page.Further informations about this conference are available on the Human practices pages section “Public engagement and education”.

Human practices

Meeting 9th June 2018

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Meeting 9th June 2018

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Meeting 9th June 2018

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Meeting 9th June 2018

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iGEM Bordeaux

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iGEM Bordeaux

Far Waste in the Landes Forest

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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. .

https://2018.igem.org/Team:Bordeaux

“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 the iGEM Bordeaux team. We first met at the Parisian meetup in Paris (7th July 2018). As we have We share the same idea of the same conception of a iGEM project, our partnership was obvious. As mentionned before, we organized a conference with them and the Paris Saclay team. And we would like to organize another conference adressing the potential benefits of synthetic biology in environmental issues.

iGEM Newcastle

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iGEM Newcastle

Alternative Roots: Engineering Microbial Communities

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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.

https://2018.igem.org/Team:Newcastle

One of our team member, Charlotte Bellamy is originate from England and she optimized a travel back home to met the iGEM Newcastle team in July to potentially initiate 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.

iGEM Montpellier

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iGEM Montpellier

Vagineering : A New Non Hormonal Contraception

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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.

https://2018.igem.org/Team:Montpellier

This year, 3 students from the iGEM Montpellier team 2017 came to Sorbonne Université to complete a master degree. So we invited 2 of them (Léa Meneu and Léo Carillo) to join us to share their knowledge, lab skills and vision of the iGEM competition. To do so, a practical work was organized. Several meetings between our teams were set before end to organize it and purchase the equipment. Teaching at students is a good experience and a good 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”.

Human practices

iGEM Marburg

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iGEM Marburg

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..

https://2018.igem.org/Team:Marburg

As a part of their Human Practices project, they would like to make the iGEM competition accessible to everyone. The iGEM Marburg team sent us a message to participate in the designing of accessible wiki to everyone. We helped them to write a guide navigation “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.

To read the “accessible webdesign-guide navigation”, visit the Human practices page of iGEM Marburg.

Human practices

iGEM IIT Madras

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iGEM IIT Madras

ADaPtat1on : Expanding Toolkit for Acinetobacter baylyi

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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.

https://2018.igem.org/Team:IIT-Madras

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 record the “DNA and RNA” video in french and italian, and the “introduction of synthetic biology” in persian.

iGEM Washington

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iGEM Washington

Stronger Together: An efficient, generalizable approach to design biosensors for small molecules

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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.

https://2018.igem.org/Team:Washington

The Washington team create 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 there booklet in french. This aims to allow the future french teams to improve there public engagement part by explaining synthetic biology to children with fun

iGEM Duesseldorf

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iGEM Duesseldorf

Trinity - towards an engineered co-culture toolbox

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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.

https://2018.igem.org/Team:Duesseldorf

The Duesseldorf team 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 or their respective project topic. To spread the iGEM teams innovative ideas to everyone, teams exchanged their postcards between them. The postcards were then received and collected all over the world and could be shared with the general public during events etc... We made a postal card recreating the famous painting of "La liberté guidant le people" by Eugène Delacroix, with Claude the microalgae leading the way to the Sugar Revolution.

iGEM Pasteur

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iGEM Pasteur

NeuronArch:
the novel connecting and protecting biofilm based system for prostheses

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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.

https://2018.igem.org/Team:Pasteur_Paris

We collaborate on the interlab interlab measurement study.part, by sharing a E. coli DH5 alpha strain and they helped us when we had some question on the interlab.

Judges gave you a feedback about our presentation and how to improve our project. To learn more about this event visit our meetup page.

Meetups

Figure Meeting with the iGEM Pasteur team 24th May 2018
From top to bottom and left to right : Ellyn Redheuil, Dounia Chater, Sarah Porte, Antoine Ehret, Victor Sayous, Emma Picaud-Lucet (1st row), Léa Guerassimoff, Alice Dejoux, Samuel Jaoui, Sarah khalilian and Saniya Kari (2nd row)

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4 place Jussieu
75005 Paris France

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Made in Paris with love © iGEM Sorbonne U Paris 2018