Difference between revisions of "Team:Edinburgh OG/Human Practices"

 
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                     <h3> Summary <h3>
 
                     <h3> Summary <h3>
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                     <p class="text-faded" style="font-size: 18px">Our project encompasses the characterisation of standardized biological parts that could potentially allow non-model microorganisms to be used as novel chassis. Domestication of non-model strains with high potential for industrial applications, could accelerate their understanding and increase the list of strains that are suitable for bioproduction. However, the domestication of strains of non-model organisms raises both biosafety and biosecurity challenges (e.g. unknown pathogenicity and toxicity), which are enhanced by the fast development of SynBIo and DIYBio fields. Such issues, if are not properly addressed, can be a risk for both users and their surroundings. In order to contribute to current risk assessment procedures, and as a precautionary step for both experienced and non-experienced users, the Edinburgh OG team worked on an accessible, easy-to-use program to evaluate the toxicity of curated secondary metabolites of both model and non-model organisms.</p>
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                     <p class="text-faded" style="font-size: 18px">Our project encompasses the characterisation of standardized biological parts that facilitate the use of non-model microorganisms as novel chassis. The domestication of non-model strains with high potential for industrial applications could accelerate their understanding and increase the list of strains that are suitable for bioproduction of relevant products (Check out the team’s essay “Masses of Chassis” for more information).
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                      <br></p>
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                      <a href="https://static.igem.org/mediawiki/2016/0/08/T--Edinburgh_OG--Tom_Essay_WhyNeedMoreChassis.pdf" class="page-scroll btn btn-default btn-xl sr-button">Essay</a>
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<p class="text-faded" style="font-size: 18px">However, we recognise that the integration of uncommon or new strains into the laboratory raises both biosafety and biosecurity questions (e.g. unknown pathogenicity and toxicity), which are heightened by the fast development of SynBIo and DIYBio fields. Such issues, if not properly addressed, can constitute a risk for both users and their surroundings (i.e. unwanted health and environmental problems).
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<br><br>
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In order to contribute to current risk assessment procedures, and as a precautionary step for both experienced and non-experienced users, the Edinburgh OG team has worked on an accessible, easy-to-use program to evaluate the toxicity of curated secondary metabolites of both model and non-model organisms.
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<br><br>
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In the Silver section, the biosafety and biosecurity issues regarding our project are exposed along the description of current risk assessment practice.
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<br><br>
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In the Gold section, our “CARE” program is presented  along with its characteristics, feedback from other iGEM teams, limitations and further improvements.
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<br><br>
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Finally, in the Integrated Human Practices section, the main characteristics of the human practices’ of our project are highlighted. 
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                    <a href="https://2016.igem.org/Team:Edinburgh_OG/HP/Silver" class="page-scroll btn btn-default btn-xl sr-button">Silver</a>
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                    <a href="https://2016.igem.org/Team:Edinburgh_OG/HP/Gold" class="page-scroll btn btn-default btn-xl sr-button">Gold</a>
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                      <a href="https://2016.igem.org/Team:Edinburgh_OG/Integrated_Practices" class="page-scroll btn btn-default btn-xl sr-button">Integrated Practices</a>
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         <h2>SILVER REQUIREMENT</h2>
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         <br><br><h2>SILVER REQUIREMENT</h2>
 
         <h3>How we have identified, investigated and addressed <br> the biosafety issue in the context of the ExpandED project. </h3>
 
         <h3>How we have identified, investigated and addressed <br> the biosafety issue in the context of the ExpandED project. </h3>
 
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              <h2>GOLD REQUIREMENT</h2>
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        <br><br><h2>GOLD REQUIREMENT</h2>
 
         <h3>How the investigation of biosafety issues have been integrated <br> into the design and execution of the ExpandED project.</h3>
 
         <h3>How the investigation of biosafety issues have been integrated <br> into the design and execution of the ExpandED project.</h3>
 
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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%">
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          <br><a href="https://2016.igem.org/Team:Edinburgh_OG/Human_Practices#HP_Gold" class="page-scroll btn btn-default btn-xl sr-button">Download CARE</a>
 
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        <h3>This tool, named “CARE” - Chassis Assessment & Risk Evaluation <br> includes information of more than 20+ microorganisms:</h3>
 
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        <p style="font-size: 14px"> This tool, named “CARE” – Chassis Assessment & Risk Evaluation – includes information about of more than 20+ microorganisms:
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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>.
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<br><br>● The microorganisms from the Edinburgh OG 2016 iGEM team: the cyanobacterium Synechosistis sp. PCC 6803, the bacterium Rhodococcus jostii RHA1 and the fungus Penicillium roquefortii.
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            <br><br>● The non-model organisms used by iGEM teams based in North America in 2014 and 2015 (as documented by the Yale 2015 iGEM team): <i>Chlamydomonas reinhardtii, Chlorella kessleri, Chlorella vulgaris, Flavobacterium psychrophilum, Gilliamella apicola, Lactococcus lactis, Rhizobium tropici</i> CIAT 899, <i>Snodgrassella alvi</i> and <i>Synechococcus sp.</i> PCC 7002.
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<br><br>● The non-model organisms used by iGEM teams based in North America in 2014 and 2015 (as documented by the Yale 2015 iGEM team): Chlamydomonas reinhardtii, Chlorella kessleri, Chlorella vulgaris, Flavobacterium psychrophilum, Gilliamella apicola, Lactococcus lactis, Rhizobium tropici CIAT 899, Snodgrassella alvi and Synechococcus sp. PCC 7002.
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            <br><br>● The industrially relevant <i>Shewanella oneidensis, Saccharopolyspora erythraea, Myxococcus xanthus, Cupriavidus necator, Chromobacterium violaceum, Carnobacterium maltaromaticum, Sorangium cellulosum</i> and <i>Pseudomonas fluorescens</i>.
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<br><br>● The industrially relevant Shewanella oneidensis, Saccharopolyspora erythraea, Myxococcus xanthus, Cupriavidus necator, Chromobacterium violaceum, Carnobacterium maltaromaticum, Sorangium cellulosum and Pseudomonas fluorescens.
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          <p style="font-size: 16px"><br> Along with these microorganisms, a database with the related secondary metabolites information (the general class of secondary metabolite, the most similar biosynthetic gene cluster (BGC) related to the secondary metabolite, its location in the genome and the percentage of gene similarity for each annotated microorganism) was constructed using the Antibiotics & Secondary Metabolite Analysis Shell (antiSMASH) software.  
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          <br><br>It is worth mentioning that the databases can be updated by integrating new microorganisms or editing existing ones simply by logging-in and waiting for the validation of the data by the program administrators.
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        <p> Along with these microorganisms, a database with the related secondary metabolites information (the general class of secondary metabolite, the most similar biosynthetic gene cluster (BGC) related to the secondary metabolite, its location in the genome and the percentage of gene similarity for each annotated microorganism) was constructed using the Antibiotics & Secondary Metabolite Analysis Shell (antiSMASH) software.  
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<br><br>It is worth mentioning that the databases can be updated by integrating new microorganisms or editing existing ones simply by logging-in and waiting for the validation of the data by the program administrators.
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<br><br>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 contemplated, 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  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  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 prusue with the use of the given microorganism in the laboratory.
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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 contemplated, 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  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  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 prusue with the use of the given microorganism in the laboratory.
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Latest revision as of 01:02, 20 October 2016

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Human Practices

Summary

Our project encompasses the characterisation of standardized biological parts that facilitate the use of non-model microorganisms as novel chassis. The domestication of non-model strains with high potential for industrial applications could accelerate their understanding and increase the list of strains that are suitable for bioproduction of relevant products (Check out the team’s essay “Masses of Chassis” for more information).

Essay

However, we recognise that the integration of uncommon or new strains into the laboratory raises both biosafety and biosecurity questions (e.g. unknown pathogenicity and toxicity), which are heightened by the fast development of SynBIo and DIYBio fields. Such issues, if not properly addressed, can constitute a risk for both users and their surroundings (i.e. unwanted health and environmental problems).

In order to contribute to current risk assessment procedures, and as a precautionary step for both experienced and non-experienced users, the Edinburgh OG team has worked on an accessible, easy-to-use program to evaluate the toxicity of curated secondary metabolites of both model and non-model organisms.

In the Silver section, the biosafety and biosecurity issues regarding our project are exposed along the description of current risk assessment practice.

In the Gold section, our “CARE” program is presented along with its characteristics, feedback from other iGEM teams, limitations and further improvements.

Finally, in the Integrated Human Practices section, the main characteristics of the human practices’ of our project are highlighted.

Silver Gold Integrated Practices