Difference between revisions of "Team:HebrewU/Description"

 
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             <li><a href="https://2018.igem.org/Team:HebrewU/Description">Description</a></li>
 
             <li><a href="https://2018.igem.org/Team:HebrewU/Description">Description</a></li>
 
             <li><a href="https://2018.igem.org/Team:HebrewU/Model">Model</a></li>
 
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             <li><a href="https://2018.igem.org/Team:HebrewU/Results">Results</a></li>
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             <li><a href="https://2018.igem.org/Team:HebrewU/Parts">Parts</a></li>
 
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             <li><a href="https://2018.igem.org/Team:HebrewU/Software">Moolti</a></li>
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       <h1 class="w3-center" style="color:#e4e4e4;">The Problem</h1> <br /><br />
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       <h1 class="w3-center" style="color:#e4e4e4;">The Problem</h1>  
 
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       <p class="w3-justify" style="padding-right:100px;color:#e4e4e4;"> <b>For over a century , dioxins – and specifically chlorinated dioxins </b> – have been notorious as some of the most toxic and persistent environmental pollutants. This means that these man-made chemicals don’t easily break-down, remaining stable in our ecosystems for many decades. Among a large family of dioxin compounds, a chemical known as TCDD is by far the most toxic. <br /> </p>
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       <p class="w3-justify" style="padding-right:100px;color:#e4e4e4;"> <b> For over a century, dioxins – and specifically chlorinated dioxins – have been notorious as some of the most toxic and persistent environmental pollutants.</b> Though some dioxins occur naturally, 2,3,7,8-tetrachlorodibenzodioxin (TCDD), the most toxic chemical of this family, is entirely synthetic. These compounds are extremely stable and, due to their synthetic nature, many are not easily broken down by living organisms. Dioxins remain in our ecosystems for decades, transferring from soil to plant, to animal, and back to the soil again in an unending cycle. <br /> </p>
 
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       <p class="w3-justify" style="padding-right:100px;padding-left:30px;color:#e4e4e4;"> <br /><br /> The toxicity of TCDD is such that varying doses of the toxin had caused cancer in all animals tested and had affected nearly all of their organs. Severe developmental and birth defects are observed in exposed animals and humans as well. TCDD is more toxic than cyanide, ricin and even plutonium. A dose as small as a peanut can kill several adult elephants.
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       <p class="w3-justify" style="padding-right:100px;padding-left:30px;color:#e4e4e4;"> <br /><br /> The toxicity of TCDD is such that varying doses of the toxin had caused cancer in all animals tested<sup>1</sup>. TCDD’s effect is widespread, reaching almost all of the internal organs, depending on the type of animal that is exposed. Birth defects, as well as severe developmental issues have been observed in humans as well as other animals<sup>2</sup>. TCDD is more toxic than cyanide, ricin and even plutonium.  <br /> <br /> <br /> </p>
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       <p class="w3-justify" style="padding-left:30px;padding-right:100px;color:#e4e4e4;"> Now, TCDD’s extreme toxicity is only one of the reasons we decided to address this issue. Another reason involves its chemical features. TCDD is both a dioxin and a poly-chlorinated compound, which are two distinct types of ubiquitous pollutants. By creating a degradation pathway for TCDD, we, in turn, create a solution for both types of pollutants.
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       <p class="w3-justify" style="padding-left:30px;padding-right:100px;color:#e4e4e4;">  
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      <b>How is TCDD created? </b> <br /><br />
 +
      TCDD is not, and has never been produced commercially except as a pure chemical for scientific research. It is, however, a byproduct of chlorophenols or chlorophenoxy acids which are produced as herbicides and fungicides. It may also be formed along with other polychlorinated dibenzodioxins (PCDD’s) and dibenzofuranes (PCDF’s) during incineration, especially if certain metal catalysts such as copper are present<sup>3</sup>. Generally, small amounts of PCDD/Fs are formed whenever organic materials such as oxygen and chlorine are available at suitable temperatures. As a result of this, when organic material is burned in less-than-optimal conditions- open or building fires, domestic fireplaces, and poorly operated and designed solid waste incinerators- these chemicals are synthesized at the highest high rates.  Historically, municipal and medical waste incineration was a central source of PCDD/Fs.
 
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<br />  <br />
  
  
<b> If, despite TCDD's extreme toxicity and its pervasiveness, there existed solutions practical enough to truly address TCDD pollution on the global scale that it is found, we would not have devoted ourselves to this issue. However, to date, the existing solutions are astoundingly impractical and inefficient. </b><br />  
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Other sources of PCDD/F include: <br />
<br />  
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&nbsp;&nbsp;·Metal smelting and refining. <br />
 +
&nbsp;&nbsp;·Chlorine bleaching of pulp and paper - historically important source of PCDD/Fs to waterways.<br />
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&nbsp;&nbsp;·Synthesis side products of several chemicals, especially PCBs, chlorophenols, chlorophenoxy acid herbicides, and hexachlorophene. <br />
 +
&nbsp;&nbsp;·Uncontrolled combustion, particularly the open burning of waste ("backyard barrel burning"), accidental fires, wildfires.<br />
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&nbsp;&nbsp;·Engines using leaded fuel, which contained the additives 1,2-Dichloroethane and 1,2-Dibromoethane, (a practice no longer used).<br />
  
 
For example, during the Vietnam war in the 60’s, tens of thousands of kilometers of land were heavily sprayed with an herbicide called Agent Orange, which was used to clear heavily forested areas for combat purposes. But TCDD was an unintended byproduct of Agent Orange production; thus, the military had unknowingly contaminated all of that land with this toxin. Even today, over 50 years after the events took place, the United States is spending hundreds of millions of dollars to reclaim that land.
 
 
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            <p class="w3-justify" style="padding-left:30px;padding-right:100px;color:#e4e4e4;">  
      <p class="w3-justify" style="padding-left:30px;color:#e4e4e4;"> <br />The method currently being used to decontaminating soils in Vietnam involves the transport of only the most heavily contaminated soils to a castle-sized, makeshift “oven” that burns the soil at temperatures of about 350°C. Although this method successfully rids soils of their dioxin contaminants, they can only gather so much soil for purification. It doesn’t even begin to address the thousands of kilometers of forests, rivers and lakes that stretch beyond the reach of this clean-up project… And yet, it is the only method of TCDD purification being used today.  
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<b>Mode of action </b> <br /><br />TCDD and dioxin-like compounds act via a specific receptor<sup>4</sup> present in all mammalian cells: the aryl hydrocarbon (AH) receptor. This receptor is a transcription factor which is involved in the expression of genes; in fact, it has been shown that high doses of TCDD affect the expression of several hundred genes in rats, increase some while decreasing others. Research shows a particularly strong effect on the transcription of  enzymes activating the breakdown of foreign and toxic compounds.
 +
<br /> <br />
 +
Polycyclic hydrocarbons also activate the AH receptor, but less than TCDD and only temporarily. Even many natural compounds (present in certain vegetables, for instance) cause some activation of the AH receptor. This phenomenon can be viewed as adaptive and beneficial because it protects the organism from toxic and carcinogenic substances. Despite this, excessive and persistent stimulation of AH receptor leads to a number of adverse effects.
 +
<br /> <br />
 +
While the mutagenic and genotoxic effects of TCDD are sometimes disputed, it has been confirmed that it does foster the development of cancer<sup>5</sup>. Its main action in causing cancer is promoting the carcinogenicity initiated by other compounds. Very high doses may, in addition, cause cancer indirectly; one of the proposed mechanisms is oxidative stress and the subsequent oxygen damage to DNA. There are other explanations such as endocrine disruption or altered signal transduction.
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 +
<b>We devoted ourselves to this issue because to date, the existing solutions are astoundingly impractical and inefficient. The solutions being employed address only local-scale pollution, and are not sustainable.
 +
  </b><br /><br />
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 +
The biggest TCDD remediation project today is happening in Vietnam. During the American-Vietnam war in the 1960’s, tens of thousands of kilometers of land were heavily sprayed with an herbicide called Agent Orange. But TCDD was an unintended byproduct of Agent Orange production; thus, the military had unknowingly contaminated all of that land with this toxin. Today, over 50 years after the events took place, the United States is spending hundreds of millions of dollars to reclaim this land.
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       <p class="w3-justify" style="padding-left:30px;padding-right:100px;color:#e4e4e4;"> <br /> It is important to note that dioxin pollution is found in small amounts nearly everywhere in the world – soil-burning is far too inefficient and expensive to deal with these types of contaminations. Furthermore, this solution is detrimental to the ecosystem, killing essential microbial communities [in the soil] and destroying the soil’s structure.
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       <p class="w3-justify" style="padding-left:30px;padding-right:100px;color:#e4e4e4;"> <br /> Today, soils in Vietnam are being decontaminated by transporting only the most heavily contaminated soils to a castle-sized, makeshift “oven”. Once there, the soil is incinerated 350°C for months. Although this method successfully rids soils of their dioxin contaminants it is impractical for a number of reasons. <br /><br />
  
<b> Our motivation for addressing the issue of global TCDD pollution is that this problem can and should be solved through synthetic biology in an efficient and ecologically safe manner. We wanted to find a solution that treats ubiquitous contamination on a global, not local, scale. As many of us are students of Agroecology and Plant Sciences, it quickly became clear that our teams’ passion for the environment would guide our decision, eventually leading us to a this project in bioremediation. </b>
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1. Only so much soil can be gathered for purification.<br />
 +
2. The process is detrimental to the soil, damaging both microbial communities and soil structure.<br />
 +
3. This method is unsustainable, and cannot be used for large-scale pollution over large areas.<br /><br />
  
 +
Additionally, is important to note that dioxin pollution is found in small amounts nearly everywhere in the world. Soil-burning would be far too inefficient and expensive to deal with these types of contaminations.
  
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       <h1 class="w3-center" style="color:#e4e4e4;">Our Solution</h1> <br /><br />
 
       <h1 class="w3-center" style="color:#e4e4e4;">Our Solution</h1> <br /><br />
 
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       <p class="w3-justify" style="padding-right:100px;color:#e4e4e4;"> <b>The biological solution we have designed is a novel enzymatic pathway capable of converting TCDD into harmless metabolites. </b> We have identified a group of enzymes derived from different microorganisms that, when combined, create this pathway.  
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       <p class="w3-justify" style="padding-right:100px;color:#e4e4e4;"> <b> The biological solution we have designed is a novel enzymatic pathway capable of breaking down TCDD into harmless metabolites. </b> We have identified a group of enzymes derived from different organisms that, when combined, completely degrade TCDD. We incorporated these enzymes into a single transgenic plant that can breakdown TCDD and dioxins, as well as detoxify chlorinated pollutants.  
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      <p class="w3-justify" style="padding-right:100px;padding-left:30px;color:#e4e4e4;""> We incorporated these enzymes into a singular transgenic plant that can breakdown TCDD and dioxins, as well as detoxify chlorinated pollutants. We chose plants as the host for this pathway for several reasons. First and foremost, plants are easy to track and control. Through various genetic and molecular methods, we can sterilize the plants to ensure our GMO’s don’t invade the ecosystem. By contrast, microbes require more intricate and complicated control mechanisms that hinder efficiency and flexibility regarding the implementation of our research. Secondly, plants possess specific attributes that are critical to our project’s success. Plant root systems are relatively efficient at accumulating materials such as dioxins from soils and waters. This means that our plants will do the work for us, collecting even minute amounts of TCDD from vast areas of contaminated land that cannot be remedied by soil-burning. Also, plants naturally contain some useful enzymes, that actually aid in the breakdown of TCDD.
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       <p class="w3-justify" style="padding-left:30px;color:#e4e4e4;">Lastly, by treating soils and water sources through plants, which sit at the lowest rung of the food chain,
+
     
we can protect the animals in infected areas, not only humans. When we began our project, we considered two possible courses of action. One was to deal with TCDD poisoning through RNA and gene therapy for human liver cells to assist in the breakdown of the molecules. This would have solved the problem of poisoning in humans, but would not have addressed the environmental aspect. Our second option was, of course, creating a plant that can breakdown the toxin in soil and water sources. TCDD is  very stable and moves up the food chain via bioaccumulation, until it reaches humans in potentially toxic  concentrations.
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       <p class="w3-justify" style="padding-right:30px;padding-left:30px;color:#e4e4e4;"> We chose plants as the host for this pathway for several reasons:<br /><br />
<br /><br /><br /><br /> </p>
+
1. Plants are easy to track and control. Through various genetic and molecular methods, we can sterilize the plants to ensure our GMO’s don’t invade the ecosystem. <br /></p>
 +
<p class="w3-justify" style="padding-right:45px;padding-left:45px;color:#e4e4e4;">
 +
-By contrast, microbes require more intricate and complicated control mechanisms that hinder efficiency and flexibility regarding the implementation of our research. </p><br /><br />
 +
<p class="w3-justify" style="padding-right:30px;padding-left:30px;color:#e4e4e4;">
 +
2. Plants possess specific attributes that are critical to our project’s success. </p>
 +
<p class="w3-justify" style="padding-right:45px;padding-left:45px;color:#e4e4e4;">
 +
-Plant root systems are efficient at accumulating dioxins from soil and water. <br />
 +
-Plants naturally contain useful enzymes, that aid in the breakdown of TCDD. <br />
 +
</p><br />
 +
<p class="w3-justify" style="padding-right:30px;padding-left:30px;color:#e4e4e4;">
 +
3. Utilizing plants, which sit at the bottom of the food chain, we can keep animals in polluted areas safe, and decrease the bioaccumulation of TCDD.  <br />
  
 +
<br />  </p>
  
 
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<p class="w3-justify" style="padding-right:100px;padding-left:30px;color:#e4e4e4;""> By implementing our solution at the base of the food chain, not only can we protect humans from TCDD, but also the animals that live in contaminated environments, many of which are highly sensitive to TCDD poisoning.   </p>
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  <h2 align="left"> References: </h2>
 +
        <p align="left" style="text-align:justify;line-height:1.5;padding-left:30px;">
 +
           
 +
                1. <a href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3154583/">"TCDD and cancer: A critical review of epidemiologic studies"; P. Boffetta, Crit. Rev. Toxicology. 41(7): 622–636; 2011</a><br />
 +
             
 +
               
 +
                2. <a href="https://embryo.asu.edu/pages/agent-orange-birth-defects">"Agent Orange Birth Defects"; J. King, The Embryo Project Encyclopedia; 2017 </a><br />
 +
               
 +
            3. <a href="https://pubs.acs.org/doi/abs/10.1021/es00003a015">"Polychlorinated Dibenzo-p-dioxin and Dibenzofuran Contamination at Metal Recovery Facilities, Open Burn Sites, and a Railroad Car Incineration Facility"; M. Harnly, Environ. Sci. Tech;
 +
29 (3), pp 677–68; 1995.</a><br />
 +
           
 +
              4. <a href="https://pubs.acs.org/doi/abs/10.1021/es00003a015">"Mechanism of dioxin action: Ah receptor-mediated increase in promoter accessibility in vivo"; L. Wu, Proc. Natl. Acad. Sci. U. S. A. Vol. 89, pp. 4811-4815; 1992</a><br />
 +
     
 +
      5. <a href="https://www.sciencedirect.com/science/article/pii/0165111086900229?via%3Dihub">"Mutagenic and genotoxic effects of 2,3,7,8-tetrachlorodibenzo-p-dioxin, a review"; A. Giri, Mutation Research/Reviews in Genetic Toxicology.Vol. 186, Issue 3, pp. 241-248; 1986</a><br />
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Latest revision as of 17:29, 12 December 2018

HebrewU HujiGEM 2018



The Problem

For over a century, dioxins – and specifically chlorinated dioxins – have been notorious as some of the most toxic and persistent environmental pollutants. Though some dioxins occur naturally, 2,3,7,8-tetrachlorodibenzodioxin (TCDD), the most toxic chemical of this family, is entirely synthetic. These compounds are extremely stable and, due to their synthetic nature, many are not easily broken down by living organisms. Dioxins remain in our ecosystems for decades, transferring from soil to plant, to animal, and back to the soil again in an unending cycle.






The toxicity of TCDD is such that varying doses of the toxin had caused cancer in all animals tested1. TCDD’s effect is widespread, reaching almost all of the internal organs, depending on the type of animal that is exposed. Birth defects, as well as severe developmental issues have been observed in humans as well as other animals2. TCDD is more toxic than cyanide, ricin and even plutonium.




How is TCDD created?

TCDD is not, and has never been produced commercially except as a pure chemical for scientific research. It is, however, a byproduct of chlorophenols or chlorophenoxy acids which are produced as herbicides and fungicides. It may also be formed along with other polychlorinated dibenzodioxins (PCDD’s) and dibenzofuranes (PCDF’s) during incineration, especially if certain metal catalysts such as copper are present3. Generally, small amounts of PCDD/Fs are formed whenever organic materials such as oxygen and chlorine are available at suitable temperatures. As a result of this, when organic material is burned in less-than-optimal conditions- open or building fires, domestic fireplaces, and poorly operated and designed solid waste incinerators- these chemicals are synthesized at the highest high rates. Historically, municipal and medical waste incineration was a central source of PCDD/Fs.

Other sources of PCDD/F include:
  ·Metal smelting and refining.
  ·Chlorine bleaching of pulp and paper - historically important source of PCDD/Fs to waterways.
  ·Synthesis side products of several chemicals, especially PCBs, chlorophenols, chlorophenoxy acid herbicides, and hexachlorophene.
  ·Uncontrolled combustion, particularly the open burning of waste ("backyard barrel burning"), accidental fires, wildfires.
  ·Engines using leaded fuel, which contained the additives 1,2-Dichloroethane and 1,2-Dibromoethane, (a practice no longer used).





Mode of action

TCDD and dioxin-like compounds act via a specific receptor4 present in all mammalian cells: the aryl hydrocarbon (AH) receptor. This receptor is a transcription factor which is involved in the expression of genes; in fact, it has been shown that high doses of TCDD affect the expression of several hundred genes in rats, increase some while decreasing others. Research shows a particularly strong effect on the transcription of enzymes activating the breakdown of foreign and toxic compounds.

Polycyclic hydrocarbons also activate the AH receptor, but less than TCDD and only temporarily. Even many natural compounds (present in certain vegetables, for instance) cause some activation of the AH receptor. This phenomenon can be viewed as adaptive and beneficial because it protects the organism from toxic and carcinogenic substances. Despite this, excessive and persistent stimulation of AH receptor leads to a number of adverse effects.

While the mutagenic and genotoxic effects of TCDD are sometimes disputed, it has been confirmed that it does foster the development of cancer5. Its main action in causing cancer is promoting the carcinogenicity initiated by other compounds. Very high doses may, in addition, cause cancer indirectly; one of the proposed mechanisms is oxidative stress and the subsequent oxygen damage to DNA. There are other explanations such as endocrine disruption or altered signal transduction.

We devoted ourselves to this issue because to date, the existing solutions are astoundingly impractical and inefficient. The solutions being employed address only local-scale pollution, and are not sustainable.

The biggest TCDD remediation project today is happening in Vietnam. During the American-Vietnam war in the 1960’s, tens of thousands of kilometers of land were heavily sprayed with an herbicide called Agent Orange. But TCDD was an unintended byproduct of Agent Orange production; thus, the military had unknowingly contaminated all of that land with this toxin. Today, over 50 years after the events took place, the United States is spending hundreds of millions of dollars to reclaim this land.



Today, soils in Vietnam are being decontaminated by transporting only the most heavily contaminated soils to a castle-sized, makeshift “oven”. Once there, the soil is incinerated 350°C for months. Although this method successfully rids soils of their dioxin contaminants it is impractical for a number of reasons.

1. Only so much soil can be gathered for purification.
2. The process is detrimental to the soil, damaging both microbial communities and soil structure.
3. This method is unsustainable, and cannot be used for large-scale pollution over large areas.

Additionally, is important to note that dioxin pollution is found in small amounts nearly everywhere in the world. Soil-burning would be far too inefficient and expensive to deal with these types of contaminations.

Our Solution



The biological solution we have designed is a novel enzymatic pathway capable of breaking down TCDD into harmless metabolites. We have identified a group of enzymes derived from different organisms that, when combined, completely degrade TCDD. We incorporated these enzymes into a single transgenic plant that can breakdown TCDD and dioxins, as well as detoxify chlorinated pollutants.

We chose plants as the host for this pathway for several reasons:

1. Plants are easy to track and control. Through various genetic and molecular methods, we can sterilize the plants to ensure our GMO’s don’t invade the ecosystem.

-By contrast, microbes require more intricate and complicated control mechanisms that hinder efficiency and flexibility regarding the implementation of our research.



2. Plants possess specific attributes that are critical to our project’s success.

-Plant root systems are efficient at accumulating dioxins from soil and water.
-Plants naturally contain useful enzymes, that aid in the breakdown of TCDD.


3. Utilizing plants, which sit at the bottom of the food chain, we can keep animals in polluted areas safe, and decrease the bioaccumulation of TCDD.

References:

1. "TCDD and cancer: A critical review of epidemiologic studies"; P. Boffetta, Crit. Rev. Toxicology. 41(7): 622–636; 2011
2. "Agent Orange Birth Defects"; J. King, The Embryo Project Encyclopedia; 2017
3. "Polychlorinated Dibenzo-p-dioxin and Dibenzofuran Contamination at Metal Recovery Facilities, Open Burn Sites, and a Railroad Car Incineration Facility"; M. Harnly, Environ. Sci. Tech; 29 (3), pp 677–68; 1995.
4. "Mechanism of dioxin action: Ah receptor-mediated increase in promoter accessibility in vivo"; L. Wu, Proc. Natl. Acad. Sci. U. S. A. Vol. 89, pp. 4811-4815; 1992
5. "Mutagenic and genotoxic effects of 2,3,7,8-tetrachlorodibenzo-p-dioxin, a review"; A. Giri, Mutation Research/Reviews in Genetic Toxicology.Vol. 186, Issue 3, pp. 241-248; 1986