Team:UCL/Project/Xenobiology
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<!--- This is the overview section ---> | <!--- This is the overview section ---> | ||
- | <div id="view1"><div class="textTitle"><h4>Xenobiology - The | + | <div id="view1"><div class="textTitle"><h4>Xenobiology - The Ultimate Biosafety Tool</h4></div><br> |
<p>The wide use of genetically modified organisms causes concerns on how they will interact in the natural environment. In particular could the genetically modified microbes escape our constrains, and outcompete the organisms found in the natural ecosystem? Could the DNA we inserted into a specific bacteria be transmitted, with unknown spread of information? | <p>The wide use of genetically modified organisms causes concerns on how they will interact in the natural environment. In particular could the genetically modified microbes escape our constrains, and outcompete the organisms found in the natural ecosystem? Could the DNA we inserted into a specific bacteria be transmitted, with unknown spread of information? | ||
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Xenobiology implements the term "synthetic" by creating organisms that are unable to survive in the natural environment and necessitate an artificial intervention from man to exist. It aims to create a synthetic "man-made" version of Biology, that respects the definition of life, but is based on entirely different mechanisms to function. The biochemistry of a xeno-organism uses new XNAs, genetic codes and cofactors different from the ones explored by Biology and is therefore incompatible with other forms of life. This allows a much higher level of control: a xeno-organism will not be able to find the xenocompounds in the natural environmentnor will be able to use bacterial communication systems. | Xenobiology implements the term "synthetic" by creating organisms that are unable to survive in the natural environment and necessitate an artificial intervention from man to exist. It aims to create a synthetic "man-made" version of Biology, that respects the definition of life, but is based on entirely different mechanisms to function. The biochemistry of a xeno-organism uses new XNAs, genetic codes and cofactors different from the ones explored by Biology and is therefore incompatible with other forms of life. This allows a much higher level of control: a xeno-organism will not be able to find the xenocompounds in the natural environmentnor will be able to use bacterial communication systems. | ||
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+ | <p>We explored this possibility with the longer term vision of creating an <i>X. coli</i> which is metabolically dependent on azo dyes. An alien form of life, different from the one we know, will merge synthetic chemistry with synthetic biology - allowing the remediate the damage that the first one caused and making the remediating agent dependent on the toxic compounds. This system would be completely incompatible and invisible to regular biology, now we can ask: is non-biological life safe enough? | ||
+ | </p></div> | ||
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<!--- This is the first biobrick ---> | <!--- This is the first biobrick ---> | ||
- | <div id="view2"><div class="textTitle"><h4>Biological vs. Xenobiological | + | <div id="view2"><div class="textTitle"><h4>Biological vs. Xenobiological Strategies</h4></div><br> |
<p>Biosafety strategies have so far explored biology to implement clever control mechanisms to control. They investigated various strategies that allow to kill bacteria when needed or that hinder genetic information to spread among different organisms. | <p>Biosafety strategies have so far explored biology to implement clever control mechanisms to control. They investigated various strategies that allow to kill bacteria when needed or that hinder genetic information to spread among different organisms. | ||
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</p> | </p> | ||
- | <h5>Biological | + | <h5>Biological Strategies</h5> |
<p>The biosafety mechanism is added to the system as additional layers of protection, the most explored are: | <p>The biosafety mechanism is added to the system as additional layers of protection, the most explored are: | ||
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</ol> | </ol> | ||
- | <h5>Xenobiological | + | <h5>Xenobiological Strategies</h5> |
<p>The safety mechanism embedded is into the system on three different levels: | <p>The safety mechanism embedded is into the system on three different levels: | ||
<ol> | <ol> | ||
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<!--- This is the second biobrick ---> | <!--- This is the second biobrick ---> | ||
- | <div id="view3"><div class="textTitle"><h4>Choosing an | + | <div id="view3"><div class="textTitle"><h4>Choosing an Essential Co-Factor</h4></div><br> |
<p>In order to create a xenobiological organism with a metabolic firewall we decided to try to design cofactor that would be essential to E-Coli metabolism that could be derived from our Azo Dye waste products. This cofactor would need to be functionally similar to an existing molecule in the E-Coli metabolism. | <p>In order to create a xenobiological organism with a metabolic firewall we decided to try to design cofactor that would be essential to E-Coli metabolism that could be derived from our Azo Dye waste products. This cofactor would need to be functionally similar to an existing molecule in the E-Coli metabolism. | ||
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<!--- This is the third biobrick ---> | <!--- This is the third biobrick ---> | ||
- | <div id="view4"><div class="textTitle"><h4>XenoRank: A | + | <div id="view4"><div class="textTitle"><h4>XenoRank: A Tool for Prioritising Xenobiological Synthesis</h4></div><br> |
- | + | <a name="robPRO"> | |
Our Azodye Night Sky is attractive, but really we want to use these techniques to help us find suitable xenobiological compounds. | Our Azodye Night Sky is attractive, but really we want to use these techniques to help us find suitable xenobiological compounds. | ||
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- | <td width="50%"><img src="https://static.igem.org/mediawiki/2014/4/49/ETC-Detailed-Graphic.png" width="80%"></td> | + | <td width="50%"><img src="https://static.igem.org/mediawiki/2014/4/49/ETC-Detailed-Graphic.png" width="80%"/></td> |
<td width="50%"><img src="https://static.igem.org/mediawiki/2014/0/0d/Properties-of-Ubiquinone-and-Menaquinone.png" width="80%"/></td> | <td width="50%"><img src="https://static.igem.org/mediawiki/2014/0/0d/Properties-of-Ubiquinone-and-Menaquinone.png" width="80%"/></td> | ||
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- | <td width="50%"><img src="https://static.igem.org/mediawiki/2014/8/8a/Sir-Xenoquinone-Pathway-from-Mordant-Brown-33.png" width=" | + | <td width="50%"><img src="https://static.igem.org/mediawiki/2014/8/8a/Sir-Xenoquinone-Pathway-from-Mordant-Brown-33.png" width="95%"/></td> |
- | <td width="50%"><img src="https://static.igem.org/mediawiki/2014/d/de/Sir-Bondiquinone-Pathway-from-Acid-Orange-7.png" width=" | + | <td width="50%"><img src="https://static.igem.org/mediawiki/2014/d/de/Sir-Bondiquinone-Pathway-from-Acid-Orange-7.png" width="95%" style="margin-top:-21px;"/></td> |
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<p>In order for our organism to become an autotroph to our xenobiological quinones it was necessary for us to remove the natural quinones. The best approach it seemed was to do a gene knock out for a biosynthesis step of ubiquinone and menaquinone. The metabolic pathway provided a number of options | <p>In order for our organism to become an autotroph to our xenobiological quinones it was necessary for us to remove the natural quinones. The best approach it seemed was to do a gene knock out for a biosynthesis step of ubiquinone and menaquinone. The metabolic pathway provided a number of options | ||
</p> | </p> | ||
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+ | <img src="https://static.igem.org/mediawiki/2014/c/ca/UCL_2014_Pathway_tube.jpg" width="50%" style="margin-left:25%"/></td> | ||
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- | <p>A search of the literature showed that a knockout of ispB successfully killed e-coli colonies as it is <a href="http://www.ncbi.nlm.nih.gov/pmc/articles/PMC179075/">[1]essential for <i>E. coli's</i></a> . ispB codes for the protein that attaches the hydrophobic side chain on the quinones, allowing them to dock in the membrane. As ispB is used to synthesise all electron buffer quinones, it was the perfect knock out as it meant that only one was required.</p> | + | <p>In order for our organism to become an autotroph to our xenobiological quinones it was necessary for us to remove the natural quinones. The best approach it seemed was to do a gene knock out for a biosynthesis step of ubiquinone and menaquinone. The metabolic pathway provided a number of options. A search of the literature showed that a knockout of ispB successfully killed e-coli colonies as it is <a href="http://www.ncbi.nlm.nih.gov/pmc/articles/PMC179075/">[1]essential for <i>E. coli's</i></a> . ispB codes for the protein that attaches the hydrophobic side chain on the quinones, allowing them to dock in the membrane. As ispB is used to synthesise all electron buffer quinones, it was the perfect knock out as it meant that only one was required.</p> |
<div style="font-size:0.5em;"> | <div style="font-size:0.5em;"> | ||
<p>See paper here: http://goo.gl/MlMY3c | <p>See paper here: http://goo.gl/MlMY3c | ||
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<!--- This is the fifth biobrick ---> | <!--- This is the fifth biobrick ---> | ||
- | <div id="view6"><div class="textTitle"><h4>Antisense RNA | + | <div id="view6"><div class="textTitle"><h4>Antisense RNA Gene Silencing</h4></div><br> |
<p> Our first step was to try a proof of concept knockdown technique: antisense RNA gene silencing. We designed primers to obtain the reverse complement strand of a section of the gene we want to silence. When this section is transcribed it interferes with ispB affecting its translation. | <p> Our first step was to try a proof of concept knockdown technique: antisense RNA gene silencing. We designed primers to obtain the reverse complement strand of a section of the gene we want to silence. When this section is transcribed it interferes with ispB affecting its translation. | ||
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Latest revision as of 02:35, 18 October 2014
Xenobiology - The Ultimate Biosafety Tool
The wide use of genetically modified organisms causes concerns on how they will interact in the natural environment. In particular could the genetically modified microbes escape our constrains, and outcompete the organisms found in the natural ecosystem? Could the DNA we inserted into a specific bacteria be transmitted, with unknown spread of information?
Since the early days of genetic engineering we had to reflect on biosafety strategies to control these risks, and synthetic biology is bringing these concerns to another level: the more we tinker with biology, the more our biosafety needs to be bullet-proof.
Xenobiology implements the term "synthetic" by creating organisms that are unable to survive in the natural environment and necessitate an artificial intervention from man to exist. It aims to create a synthetic "man-made" version of Biology, that respects the definition of life, but is based on entirely different mechanisms to function. The biochemistry of a xeno-organism uses new XNAs, genetic codes and cofactors different from the ones explored by Biology and is therefore incompatible with other forms of life. This allows a much higher level of control: a xeno-organism will not be able to find the xenocompounds in the natural environmentnor will be able to use bacterial communication systems.
We explored this possibility with the longer term vision of creating an X. coli which is metabolically dependent on azo dyes. An alien form of life, different from the one we know, will merge synthetic chemistry with synthetic biology - allowing the remediate the damage that the first one caused and making the remediating agent dependent on the toxic compounds. This system would be completely incompatible and invisible to regular biology, now we can ask: is non-biological life safe enough?