Project

Overview

Very often, the risks related to the safety of a genetically modified organism (GEO), except for a possible toxicity or pathogenicity of the organism, correspond to the spread of GEO. Most laws, "guidelines" and associations related to the Biosafety agree in trying to prevent the spread of any living modified organism. They suggest a precautionary approach whose main purpose is the protection of the environment and human health. This is clearly stipulated in the Cartagena protocol on Biosafety (international Convention on Biological Diversity): "The Protocol seeks to protect biological diversity from the potential Risks Posed by living modified organisms (LMOs) resulting and from modern biotechnology". Synthetic biology fits especially into the definition of "modern biotechnology". Indeed, biological machines designed in the iGEM competition, and more generally in synthetic biology, do not exist in nature and can be randomly introduced into existing natural biomass through undesired cross interactions.

This is why the scientific community is unanimous in saying that the "biosafety mechanisms" are essential and will ensure the neutralization of the living device created outside the laboratory conditions under which it was generated. Thus, any alleged dissemination would be impossible.

These mechanisms can be of several types, the most famous examples are the suicide genes (encoding RNAse, DNase https://2012.igem.org/Team:Paris_Bettencourt) and/or the establishment of a nutrient dependency, where the selected nutrient does not exist in the external environment.

We reviewed previous iGEM projects over the last decade and found that despite the crucial aspect of biosafety in synthetic biology and iGEM, especially for projects registered in "Environment" and "Health / Medicine" track, it happens that no biosafety mechanism is designed, or even considered. This may be due to lack of time or resources on the part of teams preferring to focus on developing their basic idea by putting safety into the background. This reason is understandable given the complexity of the challenge of Biosafety.

Our solution

In this context, the 2015 iGEM Paris Saclay team has decided to focus its project entirely on Biosafety. The goal is to provide the community with an original system able to prevent or at least significantly reduce the main danger: the spread of GEO. This system will include a chassis called SafetE.coli and can be used by all future iGEM teams, which will be a great time-saver and will give an easy access to requirements in terms of safety to all iGEMERS. In addition to this system, our project also includes a brand new encapsulation device also intended to prevent the escape of Genetically Engineered Coli.

Environment Contamination Evaluation

We decided to experimentally simulate a GEO spreading in the environment in order to evaluate the survival rate of genetically modified E. coli strains. To achieve such purpose, we collected different natural media such as soil, sea and fresh water in which we introduced growth culture of different E. coli strains. Then, each day, samples from these contaminated environments were withdrawn and plated on a selective medium to observe the evolution of the strains’ survival.

Physical containment

Considering the non-negligible risk of escape of a GEO, we wanted to add an extra layer of safety in our project. Therefore, we devised a way to physically contain E. coli and other bacteria without hindering it to perform its main function. Indeed, the system we designed is a porous glass beam in which bacteria can grow, survive and carry out their function. The nutrients of the external medium, like sugars, amino acids, etc. can penetrate inside the devise but the bacteria cannot escape from it.

Thus, the SafetE.coli chassis can be in a safer manner in contact with natural environments, which is an important aspect when the project competes in iGEM competition tracks such as Environment (lien) or Health and Medicine.

Some teams include in their project a devise, more or less sophisticated, in which the GEO or their products will perform its function. Here we can cite the 2014 project of NCTU Formosa where we can found an example of such devise: The pyramid trap (lien) containing PBAN (Pheromone Biosynthesis Activating Neuropeptide) produced by a Genetically Engineered Escherichia coli. However, other teams do not have the time or means to do as well.

Thus, the 2015 Paris Saclay team project offers to all iGEM teams a fast, efficient and inexpensive way to build an impenetrable shelter for bacteria.

The system principle

The aim of the containment is to create a physical barrier which should prevent accidental spreading of bacterial culture. The idea is to make a containment where bacteria can grow but which does not allow them to be in contact with the environment. Bacteria will be contained inside silica monoliths. To enable cell growth, we found a protocol which describes how to make cavities inside silica monoliths possible.

First, cells are encapsulated in an alginate gel. The alginic acid polysaccharide is a linear copolymer of β-D-mannuronic and α-L-guluronic acid extracted from brown algae or bacteria.

The bacterial culture is mixed with sodium alginate and the solution is dropped in a chloride calcium solution. At neutral pH, carboxylic acid functions are deprotonated so that the polymer bears a global negative charge, usually compensated by sodium ions. Addition of divalent cations such as Ca²⁺ induces cross-linking of the polymer, and therefore gel formation.

Then, silica monoliths are created around the beads obtained by a sol-gel process. The formation of silica gels at room temperature from aqueous precursors was rendered possible by the development of sol-gel chemistry (Brinker and Scherrer 1990 ). The most popular precursors are silicon alkoxides Si(OR)₄ with R being an organic group (-CH₃, -C₂H₅,...). When put in contact with water , they undergo hydrolysis, creating water-soluble species bearing Si-OH silanol groups and releasing ROH alcohol molecules. A suspension of silica is mixed with sodium silicate to make a polymerization.

Finally, the gel is dissolved by using an acid which chelates Ca²⁺ so that cells have a cavity where they can grow and which can be filled with a defined growth medium.

Protocol

The first one is performed by dropwise addition of a 1.5% (w/w) sodium alginate cells suspension in a 0.1 M CaCl₂ solution. After 10 min stirring, about 3 mm diameter beads are easily collected by filtration. The calcium alginate polymer prevents cell contact with synthesis precursors. The second step consists of silicate polymerization in the presence of commercial silica nanoparticles (Ludox HS40 from Aldrich), leading to a nanoporous monolithic structure. Monoliths are prepared at room temperature by mixing 2 volumes of 1.25 M sodium silicate with 1 volume of colloidal silica and 1 volume of succinic acid (5 wt %) into a recipient containing the alginate-cells bead. Once the sol-gel polymerization reaction is completed, the stiff monolith obtained is left in contact with 0.05% potassium citrate 3h. To provide necessary nutrients to the immobilized cells, potassium citrate solution is further replaced by LB medium according to encapsulated cell strain requirements.

Results

We obtained nice beads which are properly jellified and measure about 3 mm as expected:

The silica monolith was obtained only when we let it in contact with air:

We did not have the time to test our system.

The Temperature-Based System for E. coli: SafetE.coli

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Suspendisse potenti. Aenean ac gravida leo, eget ultrices eros. Nunc quis turpis nec purus aliquam porttitor. Mauris vitae elementum lorem. Praesent molestie congue molestie. Vivamus nec mi sed neque volutpat consectetur. Sed vitae elementum dolor. Aenean quis faucibus sapien, ac tristique magna. Curabitur augue elit, vulputate ut massa at, posuere tempus mi. Vestibulum ullamcorper, augue eget vehicula consectetur, elit ex fringilla justo, eu scelerisque arcu ante sed risus.

Sed ac nulla sit amet urna hendrerit ornare ut id odio. Nam euismod consectetur pharetra. Donec facilisis egestas tincidunt. Mauris ut libero nec sapien maximus consequat non varius magna. Donec interdum bibendum urna, vel vehicula sem fermentum vel. Vivamus a semper justo, in porttitor eros. Ut tempus tempus facilisis. Morbi pretium augue ut leo volutpat laoreet. Mauris rhoncus dui non nisl gravida aliquet. Integer a leo ut mi molestie pellentesque id eu orci. Fusce lobortis justo metus, a facilisis orci congue eget. Nunc accumsan eget nunc lacinia eleifend. Nullam mi neque, sodales ac sagittis quis, pellentesque porta orci. Vestibulum ultricies tortor ante, vulputate convallis felis lobortis ornare.

Morbi vehicula, lacus a sollicitudin porta, lectus arcu tristique tortor, ut tincidunt sem metus et arcu. Duis non tellus facilisis dui convallis sagittis in in arcu. Proin dictum ligula diam, sit amet ullamcorper diam facilisis sed. Fusce tortor eros, tempus vel dignissim rhoncus, placerat ac lacus. Sed aliquam felis ut lacus aliquet, vel dapibus nisl eleifend. Curabitur sodales justo eget lectus commodo convallis. Fusce eu nibh facilisis, posuere diam a, congue neque. Cras sapien urna, aliquam fringilla ex vel, aliquam porttitor erat. Class aptent taciti sociosqu ad litora torquent per conubia nostra, per inceptos himenaeos. Nunc imperdiet mi placerat enim cursus lacinia. Vivamus interdum a sapien sed convallis. Sed et elementum tellus, non accumsan turpis. Duis consequat dolor eros, at posuere libero ultricies id.

Perspectives

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Etiam neque lectus, scelerisque vitae justo at, molestie gravida est. Quisque in nulla tincidunt, maximus nisi sit amet, fringilla velit. Donec id massa diam. Curabitur posuere mi tellus, ut vulputate ligula auctor a. Integer molestie eu metus vitae auctor. Maecenas id suscipit ligula. Vestibulum auctor eget velit at bibendum. Quisque congue sed sapien eget pharetra. Morbi euismod sagittis tortor, cursus commodo augue placerat id. Aliquam erat volutpat.

Suspendisse potenti. Aenean ac gravida leo, eget ultrices eros. Nunc quis turpis nec purus aliquam porttitor. Mauris vitae elementum lorem. Praesent molestie congue molestie. Vivamus nec mi sed neque volutpat consectetur. Sed vitae elementum dolor. Aenean quis faucibus sapien, ac tristique magna. Curabitur augue elit, vulputate ut massa at, posuere tempus mi. Vestibulum ullamcorper, augue eget vehicula consectetur, elit ex fringilla justo, eu scelerisque arcu ante sed risus.

Sed ac nulla sit amet urna hendrerit ornare ut id odio. Nam euismod consectetur pharetra. Donec facilisis egestas tincidunt. Mauris ut libero nec sapien maximus consequat non varius magna. Donec interdum bibendum urna, vel vehicula sem fermentum vel. Vivamus a semper justo, in porttitor eros. Ut tempus tempus facilisis. Morbi pretium augue ut leo volutpat laoreet. Mauris rhoncus dui non nisl gravida aliquet. Integer a leo ut mi molestie pellentesque id eu orci. Fusce lobortis justo metus, a facilisis orci congue eget. Nunc accumsan eget nunc lacinia eleifend. Nullam mi neque, sodales ac sagittis quis, pellentesque porta orci. Vestibulum ultricies tortor ante, vulputate convallis felis lobortis ornare.

Morbi vehicula, lacus a sollicitudin porta, lectus arcu tristique tortor, ut tincidunt sem metus et arcu. Duis non tellus facilisis dui convallis sagittis in in arcu. Proin dictum ligula diam, sit amet ullamcorper diam facilisis sed. Fusce tortor eros, tempus vel dignissim rhoncus, placerat ac lacus. Sed aliquam felis ut lacus aliquet, vel dapibus nisl eleifend. Curabitur sodales justo eget lectus commodo convallis. Fusce eu nibh facilisis, posuere diam a, congue neque. Cras sapien urna, aliquam fringilla ex vel, aliquam porttitor erat. Class aptent taciti sociosqu ad litora torquent per conubia nostra, per inceptos himenaeos. Nunc imperdiet mi placerat enim cursus lacinia. Vivamus interdum a sapien sed convallis. Sed et elementum tellus, non accumsan turpis. Duis consequat dolor eros, at posuere libero ultricies id.

Modeling

Lorem ipsum dolor sit amet, consectetur adipiscing elit. Proin sit amet lacus vestibulum, cursus nisl non, volutpat nulla. Integer quis nulla nisl. Etiam sagittis sagittis dolor quis sagittis. Proin velit eros, porttitor quis dictum in, blandit eu nulla. Nam eu nibh consectetur, laoreet felis at, consectetur est. Aenean ornare, nisl in tincidunt consequat, arcu justo volutpat lacus, vel placerat orci dolor eu enim. Vivamus vitae mollis dui, sed ultrices sem.

Etiam neque lectus, scelerisque vitae justo at, molestie gravida est. Quisque in nulla tincidunt, maximus nisi sit amet, fringilla velit. Donec id massa diam. Curabitur posuere mi tellus, ut vulputate ligula auctor a. Integer molestie eu metus vitae auctor. Maecenas id suscipit ligula. Vestibulum auctor eget velit at bibendum. Quisque congue sed sapien eget pharetra. Morbi euismod sagittis tortor, cursus commodo augue placerat id. Aliquam erat volutpat.

Suspendisse potenti. Aenean ac gravida leo, eget ultrices eros. Nunc quis turpis nec purus aliquam porttitor. Mauris vitae elementum lorem. Praesent molestie congue molestie. Vivamus nec mi sed neque volutpat consectetur. Sed vitae elementum dolor. Aenean quis faucibus sapien, ac tristique magna. Curabitur augue elit, vulputate ut massa at, posuere tempus mi. Vestibulum ullamcorper, augue eget vehicula consectetur, elit ex fringilla justo, eu scelerisque arcu ante sed risus.

Sed ac nulla sit amet urna hendrerit ornare ut id odio. Nam euismod consectetur pharetra. Donec facilisis egestas tincidunt. Mauris ut libero nec sapien maximus consequat non varius magna. Donec interdum bibendum urna, vel vehicula sem fermentum vel. Vivamus a semper justo, in porttitor eros. Ut tempus tempus facilisis. Morbi pretium augue ut leo volutpat laoreet. Mauris rhoncus dui non nisl gravida aliquet. Integer a leo ut mi molestie pellentesque id eu orci. Fusce lobortis justo metus, a facilisis orci congue eget. Nunc accumsan eget nunc lacinia eleifend. Nullam mi neque, sodales ac sagittis quis, pellentesque porta orci. Vestibulum ultricies tortor ante, vulputate convallis felis lobortis ornare.

Morbi vehicula, lacus a sollicitudin porta, lectus arcu tristique tortor, ut tincidunt sem metus et arcu. Duis non tellus facilisis dui convallis sagittis in in arcu. Proin dictum ligula diam, sit amet ullamcorper diam facilisis sed. Fusce tortor eros, tempus vel dignissim rhoncus, placerat ac lacus. Sed aliquam felis ut lacus aliquet, vel dapibus nisl eleifend. Curabitur sodales justo eget lectus commodo convallis. Fusce eu nibh facilisis, posuere diam a, congue neque. Cras sapien urna, aliquam fringilla ex vel, aliquam porttitor erat. Class aptent taciti sociosqu ad litora torquent per conubia nostra, per inceptos himenaeos. Nunc imperdiet mi placerat enim cursus lacinia. Vivamus interdum a sapien sed convallis. Sed et elementum tellus, non accumsan turpis. Duis consequat dolor eros, at posuere libero ultricies id.