Latest revision as of 03:24, 4 October 2012

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A Killswitch for Increased Security

The OSCAR component of our project aims to remediate toxins in the oil sands tailings ponds using synthetic bacteria. Despite our belief that the metabolic burden of this system on our bacteria would not allow them to outcompete any native organisms, as we detail in our interviews page, our dialogue with experts really emphasized the need to design such a system so as to minimize any escape of our bacteria regardless. As such, we designed a closed biosensor and a closed bioreactor which incorporated built-in structural design safety mechanisms. In order to implement one more level of control, which industry felt was needed, we wanted an additional genetic-based containment mechanism to kill our bacteria upon escape from our system, thereby lessening the possibility of OSCAR spreading beyond the bioreactor or horizontally transferring genes to other organisms. We implemented novel ribo-killswitch parts. These contain riboswitch regulatory elements and exo/endonuclease kill genes.

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-<h2>Purpose:</h2>
+<p> The OSCAR component of our project aims to remediate toxins in the oil sands tailings ponds using synthetic bacteria.  Despite our belief that the metabolic burden of this system on our bacteria would not allow them to outcompete any native organisms, as we detail in our <a href="https://2012.igem.org/Team:Calgary/Project/HumanPractices/Interviews">interviews</a> page, our dialogue with experts really emphasized the need to design such a system so as to minimize any escape of our bacteria regardless.  As such, we designed a closed <a href=https://2012.igem.org/Team:Calgary/Project/FRED/Prototype>biosensor</a> and a closed <a href=https://2012.igem.org/Team:Calgary/Project/OSCAR/Bioreactor>bioreactor</a> which incorporated built-in structural <a href=https://2012.igem.org/Team:Calgary/Project/HumanPractices/Design> design</a> safety mechanisms.  In order to implement one more level of control, which industry felt was needed, we wanted an additional genetic-based containment mechanism to kill our bacteria upon escape from our system, thereby lessening the possibility of OSCAR spreading beyond the bioreactor or horizontally transferring genes to other organisms.  We implemented novel ribo-killswitch parts.  These contain riboswitch regulatory elements and exo/endonuclease kill genes.</p>
-<p> Synthetic biology entails designing an organism to do a specific task. This involves genetic manipulation and requires scientists to provide the bacteria with a selective advantage such as an antibiotic cassette which forces the bacteria to keep the gene of interest inside the cell. With such manipulation comes a valid “risk of accidental release” (Tucker and Zilinkas, 2006). In order to prevent such a bacteria from becoming rogue a killswitch is designed such that the bacteria is only able to survive in specific environments allowing them to perform the tasks of decarboxylation, denitrification and desulfurization in our bioreactor. However, in case of these bacteria escaping, the lack of a metabolite and or the presence of a particular metabolite will activate the “kill genes” which will cause the bacteria to self destruct. The killswitch mechanism was put in our system as a safety measure in addition to the bioreactor to contain the synthetic bacteria.</p>
-<h2>History: </h2> <p>Scientists have been trying to develop methods to limit bacterial viability and growth outside of the lab environment. One of the most popular methods used to ensure the safety of bacteria used in the lab was the creation of lab strain bacteria such as DH5α and Top10.  These bacteria are metabolically deficient and are unable to survive outside of the lab environment without very specific nutrients. Additionally, The Registry of Biological Parts also has several killswitches readily available that were submitted by previous iGEM teams. </p>
+<h2>Click on either element to learn more about it!</h2>
-<p>The different types of killswitches include:</p>
-	<p><i>Inducible kill genes: </i> Inducible systems generally consist of a regulatory element such as a promoter which is activated in the presence or absence of a metabolite. GIVE EXAMPLES</p>
-	<p><i>Toxin-antitoxin systems: </i> These systems usually insert antitoxin in the plasmid and toxin in the genome. Ideally if the bacteria lose the plasmid then the bacteria dies. This does not address the problem of horizontal gene transfer between species. </p>
+<a style="margin-left: 20px;" href="https://2012.igem.org/Team:Calgary/Project/HumanPractices/Killswitch/Regulation"><img src="https://static.igem.org/mediawiki/2012/d/d5/UCalgary2012_FRED_Killswitch_Regulation.png"></img></a>
-	<p><i>Auxotrophic marker</i>
+<a href="https://2012.igem.org/Team:Calgary/Project/HumanPractices/Killswitch/KillGenes"><img src="https://static.igem.org/mediawiki/2012/f/fd/UCalgary2012_OSCAR_Killswitch_KillGene.png"></img></a>
- <h2>Design considerations:</h2><p> During the first phase of design we considered classic systems such as auxotrophic markers, toxin-antitoxin systems, inducible systems. However, considering the cost of the system if auxotrophic markers were used we did not pursue that route. We have decided to use the inducible systems. We explored four different inducible systems which are induced by inexpensive ligands such as magnesium, manganese, molybate salts and glucose. In order to make sure the systems are controlled well and the kill switch regulation is not leaky, we have added an additional control using the riboswitch. </p>
-<p>A <b>riboswitch </b>provides post-transcriptional control of gene expression. A riboswitch is a small stretch of mRNA which binds to a ligand which increases or decreases the expression of the gene downstream. </p>
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