Team:Queens Canada/Project/Intro

Oil sands operations in Northern Alberta bring economic prosperity to Canada. But, they also produce contaminated air, water and soil. We are in the process of transforming the nematode worm Caenorhabditis elegans into a soil bioremediation toolkit with a specific focus on naphthalene.

Wild-type C. elegans have a weak chemotaxis response to naphthalene. However, we will enhance this chemotaxis response using G-protein coupled receptors (GPCRs) found in H. sapiens, M. musculus, and R. norvegicus. Our goal is to import these foreign GPCRs into the worm under control of C. elegans neuron-specific promoters. This should produce a transgenic worm with enhanced capacity to seek out naphthalene.

We will then design a field bioassay based on our C. elegans chemotaxis system. We envision an agar plate with two populations of worms expressing different types of fluorescent protein. One population will chemotax toward naphthalene, and the other will be repulsed by naphthalene.The presence of naphthalene in a soil sample in the middle of the plate would be indicated by concentric rings of fluorescence forming around the sample.

We will also equip C. elegans with the capacity to degrade naphthalene. The NAH7 plasmid in Pseudomonas putida encodes all of the enzymes necessary break naphthalene down to pyruvate. Our ultimate goal is to bring each NAH7 gene into C. elegans under control of one of the worm’s constitutive promoters. For our project this summer, we will focus on the first enzyme in the pathway, encoded by the gene nahA. If we can demonstrate the working of this enzyme in C. elegans cells, it will provide a proof of concept that encourages further work on this pathway.

Safety Proposal

We feel confident that our project does not pose a risk to ourselves, to the public, or to the environment. C. elegans, our chassis, is not a human pathogen. Working with C. elegans carries very little risk to researchers, and BSL-1 level laboratory clearance is satisfactory for work with this organism1. Furthermore, microinjection of extrachromosomal arrays reduces the worm’s fitness. So, if a transgenic worm were to escape into the outside environment, it would be unlikely to have a selective advantage over wild-type worms. Our biobricks do not provide the worm with any selective advantages. In fact, they may reduce fitness by forcing the worm to chemotax toward naphthalene, a toxic chemical. In addition, there are a number of germline mortal C. elegans mutants. If our transgenic worm were to be used in the field, we would ensure that it contained a germline mortal mutation.

As a machine designed to chemotax toward toxic compounds, our organism poses little threat to the environment. By contrast, our organism could prove beneficial to the environment if we succeed in getting it to degrade naphthalene. By extension, our organism could also prove beneficial to human health. We feel it is unlikely that a mutation in any of our biobricks would result in harm to humans or the environment. Mutations in our biobricks would lead to deactivation of our imported GPCRs, and we would not expect this to alter the ability of the worm to survive and out-compete other organisms. Overall, C. elegans can be considered safer than E. coli, the standard synthetic biology chassis, because the worm is not capable of horizontal gene transfer.

As a machine designed to chemotax toward toxic compounds, our organism poses little threat to the environment. By contrast, our organism could prove beneficial to the environment, and by extension, human health. All our biobricks target intracelluar pathways within C. elegans. We judge it unlikely that a mutation in this kind of biobrick would result in harm to humans or the environment. Mutations in our biobricks would lead to deactivation of our imported GPCRs, and we would not expect this to alter the ability of the worm to survive and out-compete other organisms. Overall, C. elegans can be considered safer than E. coli, the standard synthetic biology chassis, because the worm is not capable of horizontal gene transfer.

Dr. Ian Chin-Sang and Kenton Ko are two of the team’s Faculty Advisors this year, and have provided the team with lab space in which we conduct all of our wet work. They are both members of the Queen’s Biohazards Committee and have ensured that we work within the appropriate biosafety regulations. Furthermore, all of our team members have undergone WHMIS and radiation safety training. Safety is one of our top priorities.

@@ Line 25: / Line 25: @@
 <h3red>Project Description</h3red> <p>
-<regulartext>The nematode worm C. elegans does not normally chemotax toward environmental pollutants like naphthalene, toluene, phenol, and DDT. However, certain G-protein coupled receptors found in H. sapiens, M. musculus, and R. norvegicus are agonized by these compounds. Our main goal is to import these foreign GPCRs into the worm in the hopes of observing novel chemotaxis behaviour. Secondarily, we will design a field bioassay based on our C. elegans chemotaxis system. We envision two populations of worms expressing different types of fluorescent protein. One population will be repulsed by toxic compounds, and one will chemotax toward those compounds. The presence of toxicity in a soil sample would be indicated by a ring of one type of fluorescence forming around the sample. <p> </regulartext>
+<regulartext>Oil sands operations in Northern Alberta bring economic prosperity to Canada. But, they also produce contaminated air, water and soil. We are in the process of transforming the nematode worm Caenorhabditis elegans into a soil bioremediation toolkit with a specific focus on naphthalene. <p> </regulartext>
+<regulartext> Wild-type C. elegans have a weak chemotaxis response to naphthalene. However, we will enhance this chemotaxis response using G-protein coupled receptors (GPCRs) found in H. sapiens, M. musculus, and R. norvegicus. Our goal is to import these foreign GPCRs into the worm under control of C. elegans neuron-specific promoters. This should produce a transgenic worm with enhanced capacity to seek out naphthalene. <p> </regulartext>
+<regulartext>We will then design a field bioassay based on our C. elegans chemotaxis system. We envision an agar plate with two populations of worms expressing different types of fluorescent protein. One population will chemotax toward naphthalene, and the other will be repulsed by naphthalene.The presence of naphthalene in a soil sample in the middle of the plate would be indicated by concentric rings of fluorescence forming around the sample. <p></regulartext>
+<regulartext>We will also equip C. elegans with the capacity to degrade naphthalene. The NAH7 plasmid in Pseudomonas putida encodes all of the enzymes necessary break naphthalene down to pyruvate. Our ultimate goal is to bring each NAH7 gene into C. elegans under control of one of the worm’s constitutive promoters. For our project this summer, we will focus on the first enzyme in the pathway, encoded by the gene nahA. If we can demonstrate the working of this enzyme in C. elegans cells, it will provide a proof of concept that encourages further work on this pathway. </regulartext>
-<regulartext> Finally, we will experiment with the natural relationship between C. elegans and the bacterium E. faecium. This bacterium is known to colonize the intestine of C. elegans without causing mortality. E. faecium can also degrade polycyclic aromatic hydrocarbons (such as naphthalene). We predict that coupling E. faecium to our transgenic worm will increase the tolerance of the worm to oil contaminants and provide it with a way to biodegrade those contaminants. </regulartext>
 </div>
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 <h3red>Safety Proposal</h3red> <p>
 <regulartext>
-The QGEM 2011 project is a safe endeavour in many respects. The nematode worm C. elegans, our chassis organism,  is non-pathogenic. Working with C. elegans carries very little risk to researchers, and BSL-1 level laboratory clearance is satisfactory for work with this organism1. Furthermore, microinjection of extrachromosomal arrays reduces the worm’s fitness. So, if a transgenic worm were to escape into the outside environment, it would be unlikely to have a selective advantage over wild-type worms. Our biobricks do not provide the worm with any selective advantages. In fact, they reduce fitness by forcing the worm to chemotax toward toxic chemicals. We are also designing an RNAi-based kill switch to ensure the worm does not live to reproductive age. </regulartext>
+We feel confident that our project does not pose a risk to ourselves, to the public, or to the environment. C. elegans, our chassis, is not a human pathogen. Working with C. elegans carries very little risk to researchers, and BSL-1 level laboratory clearance is satisfactory for work with this organism1. Furthermore, microinjection of extrachromosomal arrays reduces the worm’s fitness. So, if a transgenic worm were to escape into the outside environment, it would be unlikely to have a selective advantage over wild-type worms. Our biobricks do not provide the worm with any selective advantages. In fact, they may reduce fitness by forcing the worm to chemotax toward naphthalene, a toxic chemical. In addition, there are a number of germline mortal C. elegans mutants. If our transgenic worm were to be used in the field, we would ensure that it contained a germline mortal mutation.</regulartext>
 <p>
-<regulartext> A component of this year’s project involves working with the organism E. faecium. This bacterium is capable of colonizing the intestine of C. elegans and breaking down polycyclic aromatic hydrocarbons. E. faecium is a natural component of the human gut microflora. However, this organism can also act as a human pathogen and requires BSL-2 level laboratory clearance2. MSDS guidelines will be strictly observed when working with this bacterium in the appropriate laboratory. All work done with E. faecium will be for proof of concept purposes, to investigate the potential of manipulating the natural relationship between E. faecium and C. elegans. We have no intention of releasing a worm loaded with bacteria into the environment. </regulartext>
+<regulartext> As a machine designed to chemotax toward toxic compounds, our organism poses little threat to the environment. By contrast, our organism could prove beneficial to the environment if we succeed in getting it to degrade naphthalene. By extension, our organism could also prove beneficial to human health. We feel it is unlikely that a mutation in any of our biobricks would result in harm to humans or the environment. Mutations in our biobricks would lead to deactivation of our imported GPCRs, and  we would not expect this to alter the ability of the worm to survive and out-compete other organisms. Overall, C. elegans can be considered safer than E. coli, the standard synthetic biology chassis, because the worm is not capable of horizontal gene transfer. </regulartext>
 <p>
 <regulartext> As a machine designed to chemotax toward toxic compounds, our organism poses little threat to the environment. By contrast, our organism could prove beneficial to the environment, and by extension, human health. All our biobricks target intracelluar pathways within C. elegans. We judge it unlikely that a mutation in this kind of biobrick would result in harm to humans or the environment. Mutations in our biobricks would lead to deactivation of our imported GPCRs, and  we would not expect this to alter the ability of the worm to survive and out-compete other organisms. Overall, C. elegans can be considered safer than E. coli, the standard synthetic biology chassis, because the worm is not capable of horizontal gene transfer. </regulartext>
 <p>
-<regulartext> Dr. Ian Chin-Sang and Kenton Ko are two of the team’s Faculty Advisors this year, and have provided the team with lab space in which we conduct all of our wet work. They are all members of the Queen’s Biohazards Committee and have ensured that we work within the appropriate biosafety regulations. Furthermore, all of our team members have undergone WHMIS and radiation  safety training, as safety is one of our top priorities.
+<regulartext> Dr. Ian Chin-Sang and Kenton Ko are two of the team’s Faculty Advisors this year, and have provided the team with lab space in which we conduct all of our wet work. They are both members of the Queen’s Biohazards Committee and have ensured that we work within the appropriate biosafety regulations. Furthermore, all of our team members have undergone WHMIS and radiation  safety training. Safety is one of our top priorities.
 </regulartext>