Difference between revisions of "Team:UNebraska-Lincoln"
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| + | <h3 id="header">A Brief Description:</h3> | ||
| + | <p>Deep within the porcupine gut lies a concoction of microorganisms (called a microbiome) and their accompanying enzymes. We believe this fascinating microbiome holds the secret as to why porcupines are capable of digesting tree bark and sap, where as other mammals such as ourselves, are incapable of doing so. The Dalhousie iGEM team is working in close partnership with Schubenacadie Wildlife Park which has provided mammal fecal samples that we can use for microbiome analysis. As much as we are interested in learning about porcupines, we are also interested in learning about the other mammals living at the park. This will allow us to broaden our range, and find more microorganisms of interest. Once the organisms are identified, we can use online search tools like Blast to find enzymes and biosynthetic pathways within the microbiome organisms that are capable of utilizing cellulose or tree sap for the creation of bioplastics, biofuel and many other useful products. The project has developed into three mini-projects that we hope will illuminate not only the porcupine microbiome but also the bacterial population found within the Schubenacadie ecosystem.</p> | ||
| − | + | <p>The first project involves sequencing the porcupine microbiome. A preliminary test was conducted utilizing porcupine fecal samples collected on our first expedition to the park. The samples were prepared via a PowerFecal kit (Mo Bio) and then sent for 16s sequencing at the Integrated Microbiome Resource at Dalhousie University. We are still waiting for our results. On the second expedition to the park, we were provided with twenty fecal samples from mammals such as porcupines, black bears, beavers, deers, otters, and rabbits. These samples have recently been prepared for 16s sequencing using a PowerFecal kit. We hope that once we sequence the microbiome of these twenty mammals that we can produce a microbiome map for the park.</p> | |
| − | + | <p>The second project involves plating the fecal samples on various media and identifying what grows. To begin, cellulose media was prepared as we believe the media to be very selective. Furthermore, identifying bacteria capable of surviving in a cellulose environment will have down steam implications as future teams can study the cellulose degradation properties of these bacteria and their potential biofuel capabilities. Two rounds of plating occurred using porcupine feces from the first trip to the park and from the second. It appears that there is limited growth on the cellulose plates (in comparison to regular LB agar plates) but two colonies have emerged. As the team is interested in identifying the bacteria that allow for digestion of tree bark and sap, sap containing plates were prepared. Any bacteria that grow on the cellulose plates will then be transferred to the sap plates to see if they can survive in these even harsher conditions. We have yet to transfer any bacteria to the sap plates as the first round of cellulose plating was considered preliminary to ensure the selectivity of the media. </p> | |
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| − | + | <p>The third project involves the formation of a genomic DNA library of the environmental DNA collected from the porcupine sample. This stage of the project is very much in its infancy as the team is still working on preparing the vector and the environmental DNA. </p> | |
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| − | + | <p>Dalhousie iGEM hope that these experiments will not only provide immediate insight into the Schubenacadie ecosystem, and porcupine microbiome but will also lay the foundation for exploring biofuel production and cellulose degradation by characterized as well did novel porcupine bacteria.</p> | |
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Revision as of 16:36, 16 September 2016
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Team:UNebraska-Lincoln
A Brief Description:
Deep within the porcupine gut lies a concoction of microorganisms (called a microbiome) and their accompanying enzymes. We believe this fascinating microbiome holds the secret as to why porcupines are capable of digesting tree bark and sap, where as other mammals such as ourselves, are incapable of doing so. The Dalhousie iGEM team is working in close partnership with Schubenacadie Wildlife Park which has provided mammal fecal samples that we can use for microbiome analysis. As much as we are interested in learning about porcupines, we are also interested in learning about the other mammals living at the park. This will allow us to broaden our range, and find more microorganisms of interest. Once the organisms are identified, we can use online search tools like Blast to find enzymes and biosynthetic pathways within the microbiome organisms that are capable of utilizing cellulose or tree sap for the creation of bioplastics, biofuel and many other useful products. The project has developed into three mini-projects that we hope will illuminate not only the porcupine microbiome but also the bacterial population found within the Schubenacadie ecosystem.
The first project involves sequencing the porcupine microbiome. A preliminary test was conducted utilizing porcupine fecal samples collected on our first expedition to the park. The samples were prepared via a PowerFecal kit (Mo Bio) and then sent for 16s sequencing at the Integrated Microbiome Resource at Dalhousie University. We are still waiting for our results. On the second expedition to the park, we were provided with twenty fecal samples from mammals such as porcupines, black bears, beavers, deers, otters, and rabbits. These samples have recently been prepared for 16s sequencing using a PowerFecal kit. We hope that once we sequence the microbiome of these twenty mammals that we can produce a microbiome map for the park.
The second project involves plating the fecal samples on various media and identifying what grows. To begin, cellulose media was prepared as we believe the media to be very selective. Furthermore, identifying bacteria capable of surviving in a cellulose environment will have down steam implications as future teams can study the cellulose degradation properties of these bacteria and their potential biofuel capabilities. Two rounds of plating occurred using porcupine feces from the first trip to the park and from the second. It appears that there is limited growth on the cellulose plates (in comparison to regular LB agar plates) but two colonies have emerged. As the team is interested in identifying the bacteria that allow for digestion of tree bark and sap, sap containing plates were prepared. Any bacteria that grow on the cellulose plates will then be transferred to the sap plates to see if they can survive in these even harsher conditions. We have yet to transfer any bacteria to the sap plates as the first round of cellulose plating was considered preliminary to ensure the selectivity of the media.
The third project involves the formation of a genomic DNA library of the environmental DNA collected from the porcupine sample. This stage of the project is very much in its infancy as the team is still working on preparing the vector and the environmental DNA.
Dalhousie iGEM hope that these experiments will not only provide immediate insight into the Schubenacadie ecosystem, and porcupine microbiome but will also lay the foundation for exploring biofuel production and cellulose degradation by characterized as well did novel porcupine bacteria.
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