iGEM project 2023

Team Paris Bettencourt 2023

Former teams

2022

A synthetic biology toolkit to interface genetic circuits with electronics

Language originating from the field of electronics is often employed in synthetic biology to describe genetic logic circuits, meanwhile, the real intersection of electronics with genetics remains largely unexplored. Our iGEM team is developing a toolkit of genetic parts with the concomitant open-source hardware to enable synthetic biologists to interface bacterial gene expression with electronics. Our toolkit incorporates a multitude of genetic parts from previous research in electro-microbiology that have been standardised to allow for a wide variety of applications. We are conversely researching new means of bioelectronic control using hyperpolarization of bacterial membranes for gene induction. Our toolkit will open doors for foundational research in gene expression and control while finding applications in manufacturing, robotics, arts and new media.

Florence Heng
Taylor Rayne
Daria Fedorova
Advisors : Juliette Bellengier, Clement Galan, Alexis Casas

2021

Mini.ink: think big, go with minicells

Biosafety is central when manipulating GMOs. We aim to participate in increasing biosafety by using minicells, nanosized and chromosome-free bacterial cells formed by abnormal division of rod-shaped bacteria. We observed their behaviour and hypothesized their use as chassis for local production of desired proteins, without purification expenses. This project is centered around the production of compounds through minicells of E.coli MG1655 containing a plasmid of interest. Minicells are produced using two approaches: overexpression of the FtsZ ring and deletion of the min operon. In parallel, a bioreactor for cultivation and isolation of minicells from parental cells was designed to guarantee a final genomic DNA-free sample. Filtration and introduction of an infection-defective lambda phage into the genome of parental cells was implemented to achieve higher separation yield. We focused the project on production of indigo pigment and found a method to safely dye textile without purification or addition of chemicals.

Camila Ballenghien
Karolina Guzauskaite
Nathalia Raquel de Souza Fernandes
Daria Fedorova
Etienne LEMIERE
Advisors : Alexis Casas

2020

SynDerma : a foundational advance toward synthetic dermatology

In SynDerma we envisioned therapeutics being administered by engineered microbes integrated into the skin microbiome. First, to understand the perturbaility of the skin microbiome by individual habits such as hygiene, social interaction and exercise, which are all affected by this current unprecedented context of COVID-19 pandemia, we developed a community science project called Quaranskin. In Quaranskin we developed an at-home sampling kit, protocol and survey, where participants swabbed four body sites for metagenomic analysis. We correlated the diversity and composition of these collected microbiome data to behaviours noted in the surveys to uncover any trends. In parallel, we chose the skin commensal microbe Staphylococcus epidermidis to be a chassis for our future vision of microbial therapeutics enabled by synthetic biology. In projects EpiFlex, EpiGlow, and EpiGrow, we built a MoClo kit, expressed fluorescent proteins as a proof of concept, and optimised growth conditions, respectively.

Nicolas Levrier
Anu Susan kurian
Subham Choudhury

Advisors : Radoslaw Kamil Ejsmont, Darshak Bhatt, Alexis Casas

2018

STAR CORES: Protein scaffolds for star-shaped antimicrobial peptides

Antibiotic overuse in livestock industry is one of the major drivers to the antibiotic resistance evolution; motivating calls to reduce, replace, and re-think the antibiotic usage in animals. Antimicrobial peptides (AMPs) are a promising alternative to conventional antibiotics. Recently, a class of chemically-synthesized, star-shaped AMPs has been shown to exhibit broad-spectrum antimicrobial activity while maintaining biocompatibility with mammalian cells. In this project, we combinatorially fused a set of known AMPs to structurally diverse, self-assembling protein cores to produce star-shaped complexes. Over 200 fusions were designed and expressed in a cell-free system, then screened for activity, biocompatibility, and membrane selectivity. In addition, we selected 4 AMPs for rational mutagenesis (~12000 variants), and a subset of fusions for molecular dynamic modeling, to identify features of surface charge and star geometry that impact AMP performance. Overall, we aim to create a novel class of selective, non-toxic AMPs which are biologically-produced.

Santino NANINI
Antoine LEVRIER
Maksim Bakovic

Advisors : Oleksandra Sorokina

2017

Medusa: Bringing control to the 3rd dimension

Accurate spatial-temporal response is fundamental to synthetic biology. Optogenetics has emerged as a powerful tool for genetic control and Medusa brings optogenetics to the next level. By engineering E. coli to respond to multiple light inputs, creating a logical AND gate, we aim to achieve both spatial and temporal control of gene expression. Photosensory transmembrane proteins as well as photoswitchable protein caging were investigated to further expand the existing library of optogenetic tools. For spatial control at the subcellular level, we explored the use of a novel synthetic RNA organelles to manipulate enzymatic activity. Finally, in an effort to promote synthetic biology, we sought the input of the DIY community and chose to illustrate the power of our system by 3D-printing biomaterials.

Alicia Graham
Oleksandra Sorokina
Paul Cachera
Aya Gomaa

Advisors : Sophie Gontier, Prateek Garg

2016

Frank&Stain: Enzymetic alternatives to perchloroethylene for stain removal from fabrics

Dry cleaning is the removal of stains from delicate fabrics using solvents other than water. The most widely used solvent in dry cleaning is perchloroethylene (PERC), a volatile carcinogen that is increasingly banned and restricted for environmental and safety reasons. Our team is using synthetic biology to replace PERC with a biological alternative. To do so we are screening samples from all around the world to look for stain-digesting microbes, we are characterising candidate enzymes with putative stain digesting activity, and we are searching for fabric binding domains to enhance their stain fighting power! With some microbiology, synthetic biology, metabolic engineering and a lot of creativity we will find a green technology to make dry cleaners forget all about PERC.

Shruthi Narayanan
Mislav Acman
Sébastien Gaultier
Mani Sai Suryateja Jammalamadaka
Thomas Meiller-Legrand

Advisors : Nadine Bongaerts

2015

Ferment It Yourself

Food fermentation is practiced by every culture in the world, and is especially widespread throughout the Indian subcontinent. Although fermentation enriches foods with some essential vitamins and amino acids, many regions of the subcontinent still suffer from high malnutrition. We are addressing this problem by engineering S. cerevisiae and lactobacilli, commonly found in Indian fermented rice dishes, to enrich foods with vitamins A, B2, and B12, and bioavailable iron.
We also implemented a differentiation system for reducing the fitness cost of over-expression of multiple pathways, and an easy E. coli sensor for measuring vitamin concentration using a riboswitch.
Our user-centered approach incorporates a low-cost and open hardware framework, both for growing and distributing starter cultures, and for quality control. This will give local affected populations power over their own food, as opposed to other GMO nutritional enrichment strategies, by allowing them to grow their own source of vitamins.

Ferrando Jérémy
Célia Foulon
Amaury Monmeyran
Constant Bourdeloux
EMILIE TAVAN
Cloé Pierson

Advisors : Ihab Boulas, Juan Manuel GARCIA ARCOS

2014

The smell of us

Body odors are complex phenomena observed among mammalian species. Corynebacterium striatum and Bacillus subtilis are among the main contributors to body odors. One of the objectives of our project is identifying and isolating natural mutants that have non-functional odor-producing enzymes using CRISPRs. We’re also engineering bacteria to degrade smelly molecules: TMA (trimethylamine) and 2-nonenal. The old people smell is mainly due to 2-nonenal. To degrade it, we want to perform directed evolution on skin bacteria. TMA has a fish odor and it appears in people suffering from trimethylaminuria. We will clone the enzyme trimethylamine monooxygenase, which degrades TMA, in E.coli and skin bacteria. Parallelly, we intend to develop a set of primordial odors by cloning enzymes known to catalyze reactions yielding volatile compounds. We’re also focusing on scientific communication, for that, we are developing an online course developed on the Education Genius platform about iGEM high school.

Judith Boldt
Marguerite Benony
marianne cardon
Mégane Matysiak
Naresh Rambabu
Pierre-Luc Satin
Shuyi(Sylvia) Yang
Urszula Czerwinska

Advisors : Clovis Basier, Ian Marcus, Jake Wintermute, Matthew Deyell, Zoran Marinkovic

2013

Fight Tuberculosis with Modern Weapons!

We are testing new weapons for the global war against Mycobacterium tuberculosis (MTb), a pathogen that infects nearly 2 billion people. Our 4 synergistic projects aim to help in the prevention, diagnosis, and treatment of tuberculosis. 1) We are reproducing an essential MTb metabolic pathway in E. coli, where it can be easily and safely targeted in a drug screen. 2) We are building a phage-based biosensor to allow the rapid diagnosis specifically drug-resistant MTb strains. 3) We are constructing a mycobacteriophage to detect and counterselect drug-resistant Mtb in the environment. 4) We are programming E. coli to follow MTb into human macrophages and saturate it with bacteriolytic enzymes. We want to vanquish tuberculosis and build a TB-free world.

Sarah ZAHRA
Sebastian Jaramillo-Riveri
Vincent Libis
Yonatan Zegman

Advisors : Mathias Toulouze, Zoran Marinkovic

2012

bWARE

Many synthetic biology projects propose the application of Genetically Engineered Organisms (GEOs) in natural environments. However, issues of biosafety and ethics constrain the use of GEOs outside the lab. A primary concern is the Horizontal Gene Transfer (HGT) of synthetic genes to natural populations. Strategies developed to address this problem provide varying levels of containment, however, the substantial elimination of HGT remains difficult or perhaps impossible. We have developed a new containment system to expand the range of environments where GEOs can be used safely. To do so, we rely on three levels of containment: physical containment with alginate capsules, semantic containment using an amber suppressor system, and an improved killswitch featuring delayed population-level suicide through complete genome degradation. We aim to raise the issue of biosafety by engaging the general public and scientific community through debate, and to advocate the discerning use of biosafety circuits in future iGEM projects. 

Guillaume VILLAIN
Jean Cury
Julianne Rieders
Zoran Marinkovic

Advisors : Aleksandra Nivina, Babak Nichabouri, Yang Yifan

2011

TuBe or not TuBe? Toward a new bacterial cell-to-cell communication

Bacterial communication and resource sharing hitherto thought to be mediated through the medium has been challenged by a recent paper (G.P.Dubey et al.) suggesting an extraordinary new form of communication between B.subtilis cells and even exchanges with E.coli through nanotubes. We set to provide new evidence for this cell-to-cell communication and to allow the synthetic biology community to harness its potential for amorphous computing and metabolic engineering. We developed and characterized new B.subtilis BioBricks designed to validate this finding by testing a wide range of molecules that could potentially travel through the nanotubes and be detected via signal amplification. We worked on molecules of different size and nature to best characterize the transfer. Modeling suggests that we will be able to follow the diffusion through the nanotube network by fluorescence microscopy. TuBe or not TuBe? Our ongoing experiments will shed light on this elusive question.

Danyel Lee
Edward Owusu Kwarteng
Kévin Yauy
Laura da Silva
Mathias Toulouze
Oleg MIKHAJLOV
Ouriel Caen

Advisors : Aleksandra Nivina, Antoine Decrulle, Raphael Pantier, Thomas Lombes

2010

Every bacteria counts!

Counting is the action of finding the number of elements in a set. Past attempts at developing counters in cells have mostly attempted to mimic the binary methods that computers use to count.Our first counter takes a new approach to counting in cells, essentially a mechanical rotary counter implemented on a micro scale. Each time the counter detects an input, it performs an excision and integration directly down-stream of the active site, turning on a reporter and rotating over one ‘notch’ on the counter.Our second counter operates on the wholly different principle that the statistical occurrence of a rare event in a large population can be modeled. Each cell in our population harbors a construct that when stimulated has a small chance of excising a terminator and expressing a resistance gene. The number of resistant cells is thus an accurate count of the number of input stimuli.

Raphael Pantier
Stéphane PINHAL
Théotime Calandra
Xavier Duportet

Advisors : Coquel anne-sophie, David Bikard, Thomas Lombes