Team:Toulouse France/HP/Silver

iGEM Toulouse 2016

Why we deserve the Silver Medal

The Human Practices are an integral and fundamental part of our project. It was mandatory for us to question what we were doing outside from laboratory manipulations and all the consequences of our commitment. We have so thought important issues related to very different questions such as Ethics, Safety, or the place of women in nowadays science.

This year, chance has brought together 8 girls and only girls to create the 2016 IGEM Toulouse team. This peculiar and quite funny situation has somehow triggered our thinking about the actual position of women in Science, specially taking into account that our principal supervisors are only men…

Results of a vast survey on the role of women in scientific research conducted by the Boston Consulting Group were published in March 2014 in the European Union, show that only 11% of the highest academic posts are occupied by women in science subjects. The percentage of women heads of scientific institutions varies from one country to another: only 6% in Japan, 27% in the US, 29% in France or 34% in Spain. Clearly, women are underrepresented in scientific professions.

Nevertheless, these percentages are slowly increasing, mainly because women are fighting for to reach the goal that the parity would be respected in all levels of society. Regarding specifically the scientific area, many women have raised the flag of parity such as Caroline Herschel, the first woman recognized as scientist but also the first one to publish a scientific paper in 1786 about the discovery of a comet, or such as Marie Curie who obtained two Nobel prizes in physics and chemistry. However, efforts are still needed for a much fair treatment of women in order to grant full equality in all countries around the world.

In the left: Caroline Herschel , in the right: Marie Curie

Thus today, what is happening is that only 8 young women are involved in the iGEM adventure in Toulouse. Actually the selection to be part of the team was made based on the skill and motivation of the student and not on his gender. At the end of the selection process, it turned out that the most appropriate candidates were all women! Not to say, we are quite proud of the results!

We are of course aware of the statistical study from the 2013 iGEM Paris-Bettencourt team showing that parity inside a team positively influences its success. Against this statistic and for modestly contribute to the fight for men-women parity, we would like to demonstrate that only complementary skills are the secret ingredient to the success in this competition, beyond the gender.

Art is a paradox in itself. Indeed, at the time of the Renaissance, an interesting definition of art appeared: it is a disinterested and free activity, pleasant in itself, having no utility for production. But if art is aimless, why of all times, men made art and attempted to protect it?
In other words, is it really necessary to save art? Indeed, one may think that science is useful only when it is in the service of health or the environment. But why limit oneself? Combining science and disciplines based on beauty and aesthetics for example is an interesting combination. Art has existed for as long as we did, and has always seemed to be associated with what makes us humans.
However, isn’t a work of art destined to disappear? In the Tibetan Buddhist tradition, Buddhist conceived mandalas (support for meditation and visualization, symbol of the universe) in the sand (very sensitive material overtime). These disappear with the tide and weather. For Buddhists, a work of art made of sand, then destroyed, allows the artist to understand and accept the transience of material things and to detach oneself. Even today, ephemeral art is practiced for example in the Landart. This is a trend of contemporary art that uses the framework and materials of nature (wood, earth, stones, sand, water, rock, etc.). Thus, at any time, ephemeral art persists. Does it really make sense to save these frescoes? Moreover, despite all our efforts, the world tends toward entropy (second law of thermodynamics), which means that the universe tends toward disorder and disintegration. Will we actually counteract this law of nature by saving the frescoes in the cave? Or maybe, we could be satisfied with the survival to transmit this work as long as possible to the future generations? Humans have used art to fight oblivion and leave a trace of their passages on earth. Therefore, Art is an important part of our humanity. It is a proof of our intelligence and our necessity of expression. It is through the power and intelligence of men that we can organize the formless and chaos of the real world in a style, an expression. Thus, Nietzsche promotes art as the purest of spiritual entertainment. Although it is not directly useful, art can be engaged, be a witness and memory. Some works also have a decorative goal. They exist for their beauty, even though beauty is subjective. For the artist, art is also used to escape and to express themselves. Generally, art is a means of timeless communication. Thus, the Lascaux cave is a work of art, it deserves to exist, to be maintained and protected. It carries a message and a memory of the Paleolithic man.

Some philosophers of aesthetics, defined art as "sensitive knowledge": an autonomous knowledge which is opposed to knowledge through concepts. In this case, art is not for art, it has no goals but is a means of knowledge, and is necessarily a role in men’s evolution; it goes beyond the individual. It belongs to no one and is not the object of desire: it is there for contemplation of a generation, and then transmitted to the next.

These frescoes show the representation that men had of their world 18,000 years ago. Notwithstanding, wildlife depicted on walls of the cave does not match the species hunted and consumed at the time. It includes mainly horses, buffalos and goats, and rare and often dangerous animals, such as bears, rhinos and big felines. A single reindeer engraved was found when it seems that it was very consumed at the time. This art does not represent the time of the hunting scenes as one might imagine. Still, the frescoes are extremely realistic in terms of morphology and attitudes of animals. For many prehistorians, the cave is actually a sanctuary, a sort of religious monument. Other theories circulated on the significance of the frescoes compared with the celestial constellations, shamanic worship, magic destruction of these terrifying animals, etc. Anyway, these frescoes carry the message of men 18,000 years ago, and they show us how they lived and what they believed in. They carry a page of humanity. Is it not necessary to keep this message alive as long as possible?

Ethics issues

At the heart of the synthetic biology iGEM competition is the modification of microorganisms and therefore the creation of genetically modified microorganisms (GMM), a sub- category of the genetically modified organisms (OGM) that also include higher organisms such as animals and plants. Although the issues raised by OGM in the public mainly concern plants (GMP) and more recently also animals (GMA) including Human because of the ease of manipulate organisms with the powerful CRISPR-Cas9 tools, we need to think about the ethics of our iGEM project and share our thinking with the public. To fuel our thinking, beside reading few publications, we were lucky enough to be able to regularly discuss with Dr Vincent Grégoire-Delory, Head of the “Ecole Supérieure d’Ethique des Sciences” in Toulouse. We have also participated to a workshop on Genetically Modified Microorganism organized by the “Plateforme Génétique & Société” whose guest stars were Pr Bernadette Bensaude-Vincent from Paris, members of ethics committees and Pr. Thierry Magnin from Lyon, Head of the « groupe d’épistémologie et d’éthique des sciences et technologies ». We have also attended a seminar on genome editing given by the Pr. Père Puigdomenech from Barcelona, member of European ethics committees, co-organized by the “Académie des Sciences, Inscriptions et Belles Lettres” of Toulouse. While participating to an exhibition on genetics at the “Museum d’Histoire Naturelle” in Toulouse, we also have had the opportunity to discuss with Dr Anne Cambon-Thomsen, Head of the “Plateforme Génétique & Société” of Toulouse and member of European ethics committees. From all these readings and discussions, we realized that as far as ethics issues are concerned, there are two main point of views, anthropocentrism vs biocentrism, that would deeply impact on the outcome of any debate.

Photo 1: GMA, Photo2: GMP, Photo3: GMM

Our project is very interesting for us in terms of the connexion between the art and science. But it has leaded us to ask different questions about the role of the synthetic biology in art. We have known, at the beginning, it is essential to save the Lascaux cave belonging to the World Heritage of UNESCO and containing an artistic treasure for the Humanity. But different questions have surfaced: why save art? It is destined to disappear? Why Human need art? Moreover, the Lascaux cave is a particular piece of art, because is alive: it contain a very complex and dynamic ecosystem. We think synthetic biology can be a solution to regulate this disturbed ecosystem. Thus, the Lascaux cave is an alive work of art, it deserves to protected. It carries a memory of the Palaeolithic man.

The first step in the project of preserving the Lascaux caves was to get in touch with the scientists and managers who are taking of the cave. The last information we had about the condition of the cave was from 2011 and we needed to know the current issues regarding the cave. We have really appreciated the discussion with Muriel Mauriac, who as a Lascaux cave conservator, guided us at the beginning of our project about the Lascaux historic, with Yvan Moënne-Loccose, microbiologist of the Lascaux cave, who helped us analyzing the state of the cave and gave us precious scientific remarks concerning our project and with Jean-Jacques Cleyet-Merle, director of the national prehistory museum who encouraged us in our activity. They were pleased by our initiative and agreed that our project was an original way to conserve the frescoes, but worried on the probiotic design of our project, that was to modify the microbiota of the caves. They made us realized that the ecosystem as it is, is important for the integrity of the caves and of the frescoes. Thanks to these feedbacks, we therefore modified the design of our scientific project.

At our first meeting with the public during this spring, at a time where we had just chosen the topic of our project, we felt that the public was concerned, not by the objective itself but by the means to reach it. Interestingly the kind of reactions was age-dependent, the younger ones were rather enthusiastic whereas the older ones much reserved. It also appeared clearly that there were some misconceptions about the OGMs, a lack of concrete knowledge about what DNA manipulations and Synthetic Biology mean. So from these feedbacks we felt that we had to involve the general public in the design of our project and that we also needed to explain it in the more general context of GMOs and Synthetic Biology. In order to do so, we planned to participate in various scientific exhibitions for the public, to broadcast our project in medias, to create educative videos translated in different languages and to create a theater play, as an innovative mean, to educate and to trigger debates with the public about the OGMs and synthetic biology.

We were aware that we were manipulating toxic chemicals as well as GMOs that could endanger the environment and people’s health. Therefore, we were willing to take all the precautionary measures. The first was to complete a formation about safety in the laboratory supervised by Nathalie Doubrovine who was in charge of the safety procedures in the laboratory.

Abstract: In the lab, we have to respect numerous safety regulations for the security and health of others and the environment.

Presence of safety department in INSA

During summer, our team worked in the engineering school INSA, which has a safety department. Their goal is to ensure the well-being of the employees, regarding safety rules and risk prevention. In our laboratory, the LISBP, safety is supervised by Nathalie Doubrovine who was the one instructing us regarding safety procedures. Thanks to her, we have completed a formation (with the NEO software) to learn the different risks related to our work in the laboratory and how to react in case of danger. The formation contained four parts: prevention, fire risk, biological risk and chemical risk. At the end, we had a test to make sure that we comprehended everything.

--> Autoclave training: Our team has taken an autoclave training, which showed us the explosive and implosive dangers of the dispositive and the security measures to take in order to protect oneself. A lab coat, heat resistant gloves and glasses were required for the manipulation of the autoclave.

--> Legislation and French Labor Law: We work in a public school for engineers (INSA Toulouse), thus we have to respect the French national regulations about working conditions and the manipulation of genetically modified organisms. As we work with microorganisms and cell cultures, we are concerned by the regulation on workers’ protection against risks resulting from their exposure to pathogenic biological agents (Decree No. 94-352 of 4 May 1994). It also includes human endoparasites which may cause infections, allergies or toxicity. This Decree is the French transposition of the Directive 90/679 / EEC and is also transcribed in the Labour Code (Articles L4421-1 R4421-1 to R4427-5). This Decree of the 16th July 2007 describes the technical preventive measures that are to be followed in research laboratories, where workers are likely to be exposed to biological pathogens. We have to obey to the rules of health, safety, and preventive medicine applied in public services in France (Decree No. 82-453). This decree refers to the Labour Code, Public Health Code and Environmental Code.

Basic rules in a lab

We have to apply the basic safety principles in all laboratory rooms:
- It is forbidden to smoke in all rooms.
- It is forbidden to drink and eat in the laboratory rooms.
- It is compulsory to wear a closed lab coat in cotton.
- It is compulsory to wear closed shoes.
- Long hair must be tied back.
- Oral pipetting of any substance is prohibited in any laboratory.

There are also others precautions when working with biological organisms:
- We need to wash our hands regularly.
- It is compulsory to wear gloves except for the use of an electric burner.
- In some cases (UV light, projection risk), it is compulsory to wear protection glasses.

Safety in the Lab

- Equipments: As soon as we manipulate in the lab, we have to wear the following personal protective equipments (a conventional lab coat, closed with long sleeves, closed shoes, gloves, glasses if needed).

- Storage: 3 cup-boards for different kinds of chemical products: flammable, acids, bases.

- Waste: Different trash containers are available in the lab:
- One for biological waste. This waste will be autoclaved before being thrown out.
- One for common waste.
- Special waste for chemicals.
- Special waste for waste in contact with ethidium bromide.

- Biological safety cabinet: To work into a sterile area and thus avoid external contamination by unwanted microorganisms, we have used a biological safety cabinet (FASTER – Ultrasafe). This BSC was cleaned with ethanol before and after each manipulation. A control of maintenance is done each year. The last control was executed on October 25th 2015.

- Water-bathes: We often used the water-bathes for transformation or digestion, etc. They can be dangerous because of the exposition to hot or even boiling water. To protect us, wearing a lab coat and special gloves was indispensable. The same equipment is necessary for the microwave.

- Ethidium Bromide: For some manipulations (to reveal gel electrophoresis), we have used ethidium bromide and UV light. Thus, a dark room is dedicated for that. This room is key-closed and the wearing of a lab coat, gloves and glasses is mandatory. Everything in direct contact with something in this room has to stay there. Wastes are treated specifically. A specific trash can is dedicated to gloves or paper and another is dedicated to the agarose gels that were contaminated.

- Chemical hood: We used the chemical hood when we had to manipulate dangerous and volatile chemicals (for example: the usage of alcohol 96°)

Safety for our project

We have described above the relevant security measures taken all through summer to minimize the risk of incidents in the lab. However, when working in the field of synthetic biology, one of the main concerns is the dissemination of our engineered strain, which could be a threat to the public and the environment.

We have used E. coli and B. subtilis chassis, since their genomes are very well characterized and, of course, since these bacteria are non-pathogenic. E. coli was used for genetic manipulations, moreover the genes that were inserted (BioBricks) into this bacterium, did not increase its pathogenicity. B. subtilis was the final therapeutic agent because of its natural presence in the cave’s microbiote. Therefore, the main threat is the dissemination of our bacteria in the external environment where gene transfer could occur between microorganisms.

This is the reason why, to prevent any risk of dissemination, all our waste was autoclaved before being appropriately disposed. Moreover, the French regulation does not allow any genetically modified microorganisms to be taken outside the lab. We are therefore aware that it won’t be possible to test our genetically modified bacteria in real conditions. In fact, it is unthinkable to release our bacteria in the environment without being confident enough that there won’t be any disturbances of the ecosystems of the Lascaux caves and the surrounding environment.

That’s why, to minimize both the risk of dissemination and of gene transfer, several solutions were planned. First of all, we have designed a physical device that would confine our engineered bacteria to the area to be treated (see the device part).

Apart from this physical containment, we also planned of adding two toxin/anti-toxin systems that would considerably decrease the probability of gene transfer (see project section). We also thought of including a biological clock that would limit the lifespan of our therapeutic bacterium. Moreover, we planned to use a spo- B. subtilis strain to prevent the bacterium to form spores that would allow it to resist to any competitors and to poor nutriment conditions.

Chassis organisms


Risk group

Risk Group Source

Disease risk for humans ?

Escherichia coli DH5 alpha



No. These organisms do not cause diseases in healthy adult humans. (However, they might cause diseases in young children, elderly people, or people with immune system deficiencies.)

Bacillus subtilis 168



No. These organisms do not cause diseases in healthy adult humans. (However, they might cause diseases in young children, elderly people, or people with immune system deficiencies.)


Risk group

Risk Group Source

Disease risk for humans ?

Aspergillus niger 246.65 CBS



No. These organisms do not cause diseases in healthy adult humans. (However, they might cause diseases in young children, elderly people, or people with immune system deficiencies.)

Talaromyces funiculosum CBS 235.94



No. These organisms do not cause diseases in healthy adult humans. (However, they might cause diseases in young children, elderly people, or people with immune system deficiencies.)

Chaetomium globosum CBS 148.51



No. These organisms do not cause diseases in healthy adult humans. (However, they might cause diseases in young children, elderly people, or people with immune system deficiencies.)

Because our project was based on a play between a predator (our modified bacteria) and a prey (fungi and bacteria), in order to rationalize our strategy, we have developed a modeling software that would give the optimum ratio between the two players to get the most efficient rate of killing of the prey. This software is in open source, therefore available to any scientist (or not) confronted to this kind of issue.