Team:Grenoble

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Diaporama
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<h1>Safety</h1>
 
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<a href="https://2011.igem.org/Team:Grenoble/Projet/Intro" title="Introduction"><img src="https://static.igem.org/mediawiki/2011/d/d3/Slide_home2.png"></img></a>
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<a href="https://2011.igem.org/Team:Grenoble/Projet/regulation" title="RsmA: post-transcriptional regulation system"><img src="https://static.igem.org/mediawiki/2011/1/1a/Slide_home4.png"/></a>
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<a href="https://2011.igem.org/Team:Grenoble/Projet/Modelling" title="Model"><img src="https://static.igem.org/mediawiki/2011/1/19/Slide_home5.png"></img></a>
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<a href="https://2011.igem.org/Team:Grenoble/Projet/Device" title="Device prototype"><img src="https://static.igem.org/mediawiki/2011/5/51/Slide_home6.png"></img></a>
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<a href="https://2011.igem.org/Team:Grenoble/HumanPractice" title="Human Practice"><img src="https://static.igem.org/mediawiki/2011/8/85/Slide_home7.png"/></a>
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<li><a href="#lab">Lab work safety.</a></li>
 
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<li><a href="#general">General consderations.</a></li>
 
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<h2>Ready for take-off !<span>By the Team</span></h2>
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<p>We are proud to say we obtained our pass for the iGEM World Championship at the MIT (Boston) and got a gold medal !
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<li>Would the materials used in your project and/or your final product pose:</li>
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We will double our efforts to acomplish our goals until Boston in early November. Many thanks to all our
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supports.</p>
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<li>Risks to the safety and health of team members or others in the lab?</li>
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<li>Risks to the safety and health of the general public if released by design or accident?</li>
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<li>Describe and document safety, security, health and/or environmental issues as you submit your parts to the Registry.</li>
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<li>Under what biosafety provisions will / do you operate?</li>
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<li>Does your institution have its own biosafety rules and if so what are they? Provide a link to them online if possible.</li>
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<li>Does your institution have an Institutional Biosafety Committee or equivalent group? If yes, have you discussed your project with them?</li>
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<li>Describe any concerns or changes that were made based on this review.</li>
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<li>Will / did you receive any biosafety and/or lab training before beginning your project? If so, describe this training.</li>
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<li>OPTIONAL QUESTION: Do you have other ideas on how to deal with safety or security issues that could be useful for future iGEM competitions? How could parts, devices and systems be made even safer through biosafety engineering?</li>
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<h2>Mercuro-Coli: A new way to quantify heavy metals.<span>By JB</span></h2>
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<h2 id="lab">Lab work safety.</h2>
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<h2>Mercuro-Coli: A new way to quantify heavy metals.</h2>
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Laboratory work requires the using of complex equipment or performing delicate operations, it also involves the use of toxic, flammable or explosive. The execution of this work may cause accidents or serious poisoning; the effects can be immediate or insidious. For this all reasons there are safety rules to follow.
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Our project aims at constructing an easy to use, transportable sensor capable of quantifying the concentration of mercury, in an aqueous sample.  
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During our project, we have seek much information about products and materiel employed in our experiments and the risks associated with these latter. The litterature, the material safety datasheet and moreover the safety engineers of our labs.
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Our system is based on a comparison between an unknown mercury concentration and a known IPTG concentration. A linear IPTG gradient is present on a test-strip containing the engineered bacteria. When the mercury solution is added, the regulatory network will switch to one of two states depending on the IPTG/mercury ratio.  
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At the CEA there is a special section of people in charge of the security and the safety. It is called FLS: Formation locale de sécurité, we may translate: Local Group of Security and Safety. They ensure the safety of the people who are working in the center and the visitors and also of the goods and the material. Six members of our team have assists to safety conferences organised by CEA. All team members have met the safety engineer of the labs where we conduct the experiments. He explained the safety rules to be followed.
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Bacteria become either “sender” or “receiver”. The bacteria sensing a predominance of mercury over IPTG, the “senders”, will release a quorum sensing molecule which is detected by the nearby “receivers”. The reception of quorum sensing molecules will induce the expression of a red dye in the “receivers”. In this way, a red line emerges at a position in the IPTG gradient from which the unknown mercury concentration can be deduced.
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At CEA some researchers worked on microsystems devices to detect and quantify these pollutants. They will share their experience and knowledge with us about the way to conduct safe experiments with very toxic chemicals like mercury and also about technical aspects of existing measurement device. We would like to compare our work, our biosystem to “technological only” system that already exist, in terms of precision, sensitivity, reliability, speed and costs.
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We plan to present our work and the synthetic biology to a larger public: companies which fund us, school in our villages and town, a conference at “Midi Minatec”, ... 
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<h3 id="instru">Instruments.</h3>
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The experiences of our project did not require the use of sophisticated equipment. We have used basic devices that we find in molecular biological laboratory:
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Now booming, synthetic biology is a scientific field that divides the world into 2 parts. On the one hand, people who believe it will  science and our life. On the over hand, people who believe that synthetic biology is dangerous and it simply means playing God.
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<dt>Ultra violet lamp: </dt>
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There is a risk for the eyes and in case of long exposure for the skin, but the UV lamp are only used to take a picture of our gel after electrophoresis, so we are never directly exposed, and it is always for very short period.
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<dt>Centrifuge:</dt>
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The main risk is for the material. The centrifuge have to be perfectly balance otherwise the rotor could break. The majority of the centrifuge in our lab have detector that warns the operator in case of bad balance.
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The risks might be contamination if bacterial suspension is spillt, a burn risks might exists in some case (high temperature of water)
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<h3 id="chemical">Chemical risk-assessment.</h3>
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We aim to design a detector and measurement device for a pollutant in water, like heavy metals. We are actualy working on two versions of this quantification device. One of them involves the use of the MerR sensor for the mercury, and the second one, TetR for the tetracycline. We therefore need to use mercury to test this system. That raises questions about security for the researcher but also for the public and the environment.
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Like all new domains of science, many questions may be raised about synthetic biology. Albert Einstein said: “It is strange that science which before seemed to be inoffensive will be turned into a nightmare that frightens everyone”. The goal of iGEM competition is to promote synthetic biology in the scientific community, but also to inform the public about this new science. Synthetic biology is a very controlled science to prevent side-effects and many countries such as France move to a strong legislative supervision in order to respect the ethical issues related to the modification of life.
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the environmental issue of the toxic waste management. Liquid having Mercury or tips and dishes that are in contact with this toxic are kept in specials bins. This rubbish bin is then given to a society specialized into toxic waste treatment. A slip monitoring is sign up by every organism that is involved into the production, transportation and treatment of the toxic waste. When the later is cremated, the producer of the waste receive and attestation that must be kept as a proof of the appropriate treatment.
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According to the <a href="http://www.bulletins-electroniques.com/actualites/66814.htm">newsletter of the French Embassy to the United States</a>, the international scientific community recognizes the dangers of synthetic biology and it must identify them precisely. It has especially given to the competition iGEM an important educational role for the scientific community of tomorrow.
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Our project is based on the utilization of mercury, which raises  Mercury is an element that has toxic effects on brain and renal function. The other source of important chemical risks is BET. To avoid these latters, experiments are performed under chemical hoods and used contaminated materials are sterilized.
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During our project, mercury is conserved in the laboratory and is subjected to special treatment for elimination of heavy metals.  
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However, synthetic biology is a science with an extraordinary potential. Technological advances it could bring are huge. The fields of application are vast, from agriculture to medicine through the environment and energy, synthetic biology offers new possibilities and new alternatives to current technologies. The iGEM competition directly contributes to advance research in all these fields by enabling student teams to contribute in <a href="http://ung.igem.org/Team_Tracks?year=2011">these categories</a>.
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Concerning the reprocessing of toxic chemicals or biological wastes, we follow the standard protocols of our lab. The main  toxic wastes we have to deal with in our experiments is BET, the other very dangerous chemical is the mercury. Each one of this product is collected in a special barrel (one for each dangerous chemical) that are recovered by a company specialized in the reprocessing of hazardous wastes. The biological wastes are sterilized in an autoclave by heat and pressure before reprocessing by another company.
 
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<h3 id="bio">Biological risks, biosafety rules.</h3>
 
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We work with a strain of E.Coli designed for lab works : BW25113. This strain is commonly used by students and researchers. It has no virulence gene, and is therefore a riskless chassis. Furthermore, it has got several genetic modifications that avoid its development if ever it was to make it out of the lab. Those modifications are :
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"Open source" policy conveyed by iGEM allows the world to take advantage of advances in this field and thus to improve every year the level of competition and projects. And we can say that the objective is on track, because the number of teams participating in this competition is <a href="http://ung.igem.org/Previous_iGEM_Competitions">constantly increasing</a>.
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<li>An inactivated LacZ and rha genes : the bacteria can use neither the lactose or the rhamnose as a source of energy.</li>
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<li>A deletion into a gene coding for an enzyme (pyr E) that produce a matrice required for DNA fabrication (Thymine and Cytosine bases).</li>
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<li>A deletion into the gene that code for an enzyme involved in the fabrication of arabinose, an amino acid component of most protein.</li>
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So this bacteria has limited source of energy, needs to be supplied into DNA and protein constituents. Those are such disadvantages that this strain can only grow on highly supplemented medium. We also apply the national lab biohazard policy to each experiment : all the biological waste are collected on a special bin and autoclaved before leaving the lab.
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The system we develop needs to be kept off until we want to induce it. In order to achieve that, we extract a post-transcriptional switch mechanism. This system comes from Pseudomonas aeruginosa, a similar one exists in E. coli.
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The rsma system of P.aeruginosa controls numerous genes including some virulence factors expressed in some oportunist condition. When activated, it allows the transcription of some genes involved in the creation of a syringe. The later is used to inject some proteins into a targeted cell. E.Coli has not this kind of pathogenic mechanism at all.
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The rsma system could somehow interfere with the Csra system of E. coli, which is highly similar and also involved in global regulation mechanism. This has not been tested so far. So what would happen if our strain was to make it out of the lab ?  Could our genetic device activate some gene of a wild E.coli strain, or other bacteria ? We have no experimental data to argue for any response. Considering the worst case - the mechanism we use can be effective in wild bacteria - this event would require several extremely low probability events to occur :
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<li>Harmless lab bacteria containing the device should be out of the lab. So far the project is experimental and no bacteria should get out, as describe above.</li>
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If incorporated into a wild strain, the risk would be to activate some virulence gene.
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<li>First, it implies that the wild strain has a similar mechanism of global gene regulation.</li>
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<li>Even if there is a similar mechanism, the wild one and the one extracted from pseudomonas would need to be made of similar DNA sequence to interact. A  good compatibility of two mechanisms is quite unlikely.</li>
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<li>To become pathogenic, the wild bacteria should also have virulence genes to human, which is not that common. Otherwise its metabolism would be modified without any consequences to human.</li>
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<li>The system we use is originally activated in some specific conditions : when pseudomonas is in contact with a target cell. In which environment would be the lucky bacteria that could have got the sequence ? A rubbish bin, a dump, a river ?... In most of the situations, it would not be an environment on that gives an advantage to the cell that produce virulence factor.</li>
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<li>Given that it is a global mechanism control system, there are always numerous other check point into the cell before modifying its expression. So even if integrated, the rsma system would certainly be either a disadvantage or would get inhibited.</li>
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An other system used in our device can modify expression of numerous genes : the CinI quorum sensing. The later is shared by many species of legume-nodulating rhizobia : a genus of soil bacteria that fix nitrogen. The cin quorum regulates growth inhibition, expression of some genes that influence nodulation, but no harmful response have been notice so far. It is quite a Rhizobium specific communication system. This bacteria colonises plant cells within root nodules and has never shown any pathogenic sign to human.
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<h2> A great human adventure </h2>
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Manipulation of living organism allows producing artificial form of life and metabolism. These modifications, although well controlled, require application of the precautionary principle.  
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iGEM competition includes about 160 teams (more or less 2000 students) over the world. There will be a first regional jamboree in different regions such as Europe, Asia, America,… and then a third of us will go to Boston for the last jamboree. This will be the first opportunities for most of students to meet people from so many universities at once ! We ‘ll be hosting at the same places, sharing breakfast and even partying together !... We ‘ll be able to discuss abouts many topics related to our fields, share ideas, and to see how others managed their work by watching their presentations.
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Even if in our project we don't plan to take our work out of the lab, so this can not be a cause of safety issue, engineered bacteria might be accidentally or on purpose released in the environment. So, caution involves the implementation of different blocking to limit the propagation of these organisms in the nature:
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iGEM competition is not just about doing scientific work in order to get a medal, but is also about doing all of what an engineer or researcher needs to do ! Each team needs to set up contacts and collaboration with other groups. Sharing bricks or helping others is a criteria for winning a gold medal! We also need to get funds in order to finance our work…. So we  must make a project that fits some challenge of our society ! As every one knows, new technologies rise up new ethical issues. This aspect has to be considered on every single project !
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<dt>Nutritional blocking:</dt>
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<dd>Organisms could survive only with artificial substances. In this way, in case of release into the nature such organisms would die.</dd>
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<dt>Evolutionary blocking:</dt>
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<dd>Organisms couldn’t adapt themselves and evolve alone in the nature. This blocking prevents mutations of the organisms that allow them to survive.</dd>
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<dt>Preprogrammed cellular death:</dt>
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<dd>implementation of a suicide gene which is inhibited during wet work. In this way, organisms couldn’t survive outside the laboratory.</dd>
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Now that we have found an interesting  project and can be useful for the society, we are on the way for 4 month of intense work ! Our group is made of 12 people with very different education , that have to understand and synchronise each other. Since we are spread out in multiple places, we already meet once a week in order to coordinate or work. This need of an efficient communication within the team is an exiting part of the project !
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<strong>Do you have other ideas on how to deal with safety or security issues that could be useful for future iGEM competitions? How could parts, devices and systems be made even safer through biosafety engineering?</strong>
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From the environmental point of view, simple and efficiency methods can be used like bacteria not able to survive outside by use Amino Acids which not existing in nature. It’s too possible to use rare carbon source for the bacteria. We can also use a suicide gene repress by a chemical molecule not found out of a laboratory. Another ways is to make bacteria weak face to the micro-organisms natural selection. For the researcher’s safety in lab, the work in sterile middle, overall and gloves wearing and all other standard protections things are evidently recommended.
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To increase the safety off iGEM competition, we think about bacteria which have an inducible essential gene for binary division by a chemical not existing or rare in nature, by this way the bacteria can’t be divide itself so it will be not selected and going to disappear nearly.
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The system of P.aeruginosa controls numerous genes including some virulence factors implied in the development of a syringe mechanism to inject toxic compounds to a targeted cell.
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Latest revision as of 22:11, 28 October 2011

Grenoble 2011, Mercuro-Coli iGEM

Mercuro-Coli: A new way to quantify heavy metals.

Our project aims at constructing an easy to use, transportable sensor capable of quantifying the concentration of mercury, in an aqueous sample.

Our system is based on a comparison between an unknown mercury concentration and a known IPTG concentration. A linear IPTG gradient is present on a test-strip containing the engineered bacteria. When the mercury solution is added, the regulatory network will switch to one of two states depending on the IPTG/mercury ratio.

Bacteria become either “sender” or “receiver”. The bacteria sensing a predominance of mercury over IPTG, the “senders”, will release a quorum sensing molecule which is detected by the nearby “receivers”. The reception of quorum sensing molecules will induce the expression of a red dye in the “receivers”. In this way, a red line emerges at a position in the IPTG gradient from which the unknown mercury concentration can be deduced.

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