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<img src="https://static.igem.org/mediawiki/2016/e/e6/T--Edinburgh_OG--Matin_CARE_LOGO_orange.png" width= "90%"> | <img src="https://static.igem.org/mediawiki/2016/e/e6/T--Edinburgh_OG--Matin_CARE_LOGO_orange.png" width= "90%"> | ||
− | <br><a href="https://static.igem.org/mediawiki/2016/2/29/T--Edinburgh_OG--Anette_CARE_CODE.zip" class="page-scroll btn btn-default btn-xl sr-button"> | + | <br><a href="https://static.igem.org/mediawiki/2016/2/29/T--Edinburgh_OG--Anette_CARE_CODE.zip" class="page-scroll btn btn-default btn-xl sr-button">CARE tool's updated code</a> |
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− | <h3>This tool, named “CARE” | + | <h3>This tool, named “CARE” – Chassis Assessment & Risk Evaluation <br> includes information about 30 microorganisms: </h3> |
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<p style="font-size: 14px"> <br><b>● The microorganisms from the Edinburgh OG 2016 iGEM team: the cyanobacterium <i>Synechosistis sp.</i> PCC 6803, the bacterium <i>Rhodococcus jostii</i> RHA1 and the fungus <i>Penicillium roquefortii</i>. | <p style="font-size: 14px"> <br><b>● The microorganisms from the Edinburgh OG 2016 iGEM team: the cyanobacterium <i>Synechosistis sp.</i> PCC 6803, the bacterium <i>Rhodococcus jostii</i> RHA1 and the fungus <i>Penicillium roquefortii</i>. | ||
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<img src="https://static.igem.org/mediawiki/2016/3/34/T--Edinburgh_OG--Matin_CARE_criteria.png" width="100%"> | <img src="https://static.igem.org/mediawiki/2016/3/34/T--Edinburgh_OG--Matin_CARE_criteria.png" width="100%"> | ||
− | <br><br><a href="https://static.igem.org/mediawiki/2016/ | + | <br><br><a href="https://static.igem.org/mediawiki/2016/f/fb/T--Edinburgh_OG--Anette_List.xlsx" class="page-scroll btn btn-default btn-xl sr-button">Download List</a> |
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− | <p> According to the toxic effect of these compounds on human health, animal health and the environment, a quantitative criterion for clear toxicity scores was created using a scale from 1 to 5 and a “traffic light” colour scheme. If the reviewed information showed that the secondary metabolite did not affect in a negative manner any of the three parameters, it was considered non-toxic and categorised as a “1” (green). If the data showed that the compound exhibited some degree of toxicity but nothing considerably serious or untreatable, it was considered slightly to moderately toxic and scored as a “3” (yellow). And if it showed that the secondary metabolite was extremely toxic, it was considered as highly toxic and classified as a “5” (red). However, considering there were three parameters to be | + | <p>According to the toxic effect of these compounds on human health, animal health and the environment, a quantitative criterion for clear toxicity scores was created using a scale from 1 to 5 and a “traffic light” colour scheme. If the reviewed information showed that the secondary metabolite did not affect in a negative manner any of the three parameters, it was considered non-toxic and categorised as a “1” (green). If the data showed that the compound exhibited some degree of toxicity but nothing considerably serious or untreatable, it was considered slightly to moderately toxic and scored as a “3” (yellow). And if it showed that the secondary metabolite was extremely toxic, it was considered as highly toxic and classified as a “5” (red). However, considering there were three parameters to be considered, combinations of those three scores could occur (e.g., a secondary metabolite being considered non-toxic for humans but slightly to moderately toxic to animals). Therefore, if a compound was non-toxic according to one |
− | <br><br>As a proof of concept, the 30 organisms were screened using the CARE tool and the results showed that, although some secondary metabolites were considered as toxic (e.g. roquefortine, PR-toxin, isofumigaclavine and mycophenolic acid for P. roqueforti), their amounts do not affect human health, meaning that these organisms were safe to work with in laboratory settings and we could proceed with the experimentation with them. | + | parameter and slightly to moderately toxic for the others, it was categorised as a “2” (green-yellow). On the other hand, if it was slightly to moderately toxic according to some parameter and highly toxic for others, it was classified as a “4” (yellow-red). Finally, if the secondary metabolite had no documented toxicity information, or if there was no specific BGC exposed by antiSMASH and just the general class of secondary metabolite or microorganism, the compound was categorised as “?” (black) with the note to consider if, according to the precautionary principle, one should pursue the use of the given microorganism in the laboratory. |
+ | <br><br>As a proof of concept, the 30 organisms were screened using the CARE tool and the results showed that, although some secondary metabolites were considered as toxic (e.g. roquefortine, PR-toxin, isofumigaclavine and mycophenolic acid for P. roqueforti), their amounts do not affect human health, meaning that these organisms were safe to work with in laboratory settings and we could proceed with the experimentation with them. | ||
<br><br>When a laboratory works on a non-model organism with the objective of harnessing its industrial potential, genome editing processes may be involved (e.g., CRISPR-Cas9 tool). Therefore, this tool could additionally be used in order to determine differences in toxicity between native and genetically modified organisms. | <br><br>When a laboratory works on a non-model organism with the objective of harnessing its industrial potential, genome editing processes may be involved (e.g., CRISPR-Cas9 tool). Therefore, this tool could additionally be used in order to determine differences in toxicity between native and genetically modified organisms. | ||
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<h2>Outreach</h2> | <h2>Outreach</h2> | ||
− | <p>In order to test the tool’s functionality, we contacted via social media this year’s iGEM teams and the following 25 teams engaged on our conversation: Vilnius, Dundee, Cardiff, Exeter, Imperial, Valencia UPV, UPO Sevilla, BIOSINT México, TEC Costa Rica, Tec Chihuahua, Emory, MQ, BGU, IIT Kharagpur, Technion, Barcelona, Leiden, TU Darmstadt, Queens, Evry Genopole, MSU, EPFL, Georgia State, DTU Denmark and LMU & TU Munich. | + | <p style="font-size: 16px">In order to test the tool’s functionality, we contacted via social media this year’s iGEM teams and the following 25 teams engaged on our conversation: Vilnius, Dundee, Cardiff, Exeter, Imperial, Valencia UPV, UPO Sevilla, BIOSINT México, TEC Costa Rica, Tec Chihuahua, Emory, MQ, BGU, IIT Kharagpur, Technion, Barcelona, Leiden, TU Darmstadt, Queens, Evry Genopole, MSU, EPFL, Georgia State, DTU Denmark and LMU & TU Munich. |
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Special thanks go to the Tec Chihuahua, Tec Costa Rica and EPFL teams for being “CARE ambassadors” and helping us spread the word of our tool. | Special thanks go to the Tec Chihuahua, Tec Costa Rica and EPFL teams for being “CARE ambassadors” and helping us spread the word of our tool. | ||
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<p>It is important, however, to establish the limitations of our program so that they can be addressed properly in the future. One limitation of the CARE tool is that it requires any microorganism to have an annotated genome for it to be screened, as the accession number is needed to build the database from antiSMASH. | <p>It is important, however, to establish the limitations of our program so that they can be addressed properly in the future. One limitation of the CARE tool is that it requires any microorganism to have an annotated genome for it to be screened, as the accession number is needed to build the database from antiSMASH. | ||
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− | Moreover, when performing the data mining for each secondary metabolite, we found that a significant number of the assessed secondary metabolites did not have clear data on their toxic effect on the surrounding environment, humans and animals (i.e. classified as “?” – unknown – to be managed according to the precautionary principle). These kind of results could spur further investigation into these compounds and corresponding biological functions and effects by the scientific community. | + | Moreover, when performing the data mining for each secondary metabolite, we found that a significant number of the assessed secondary metabolites did not have clear data on their toxic effect on the surrounding environment, humans and animals (i.e. classified as “?” – unknown – to be managed according to the precautionary principle). These kind of results could spur further investigation into these compounds and corresponding biological functions and effects by the scientific community. Further, the utility of the tool is limited by the great number of as yet unknown secondary metabolites. In filamentous fungi alone the number of unknown mycotoxins is expected to be in the range of several hundred thousand (Barlow et al., 2007). |
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− | + | Furthermore, the program could be further refined by completing the missing front-ends and including a risk matrix for every secondary metabolite in which the risks are directly related to the probability of them happening. Furthermore, since the extent of the assessments on non-model organisms is not limited to their secondary metabolites, tools to screen for recombinases, virulent factors and CRISPR-Cas9 systems could be developed for them to be incorporated in the CARE program. | |
</p> | </p> | ||
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Latest revision as of 01:46, 20 October 2016
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