Difference between revisions of "Team:METU Turkey"

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            <a class="one" href="https://2015.igem.org/Team:METU_Turkey/Attributions">Attributions</a>
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            <a class="one" href="https://2015.igem.org/Team:METU_Turkey/Collaborations">Collaborations</a>
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            <a class="one" href="https://2015.igem.org/Team:METU_Turkey/Safety">Safety</a>
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            <a class="one" href="https://2015.igem.org/Team:METU_Turkey/Gallery">Gallery</a>
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            <a class="one" href="https://2015.igem.org/Team:METU_Turkey/Sponsors">Sponsors</a>
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<h3>Welcome!  <br> We are Team METU Turkey! </h3>
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<h3>Welcome!  <br> We are Team METU_Turkey! </h3>
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<p>Scroll down to find more about our project! </p>
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<a class="twitter-timeline" href="https://twitter.com/iGEM_METU2014" data-widget-id="499378473245229057">@iGEM_METU2014 kullanıcısından Tweetler</a>
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<h1>Degredo PETronum!</h1>
 
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<p> Introduction:</p>
 
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<p> This year's METU iGEM Team is composed of eight undergraduates, two advisors, and two graduate students. We come from different areas of study, but we're all working together on this year's synthetic biology project for the iGEM competition. Due to the global impact of plastic pollution, we have decided to focus on biodegradation of polyethylene terephthalate (PET). PET is a widely used material, commonly found in plastic bottles, textiles, and other consumer goods. However, only a small percentage of it ends up being recycled, it became a  global issue, and achieving our goal would have a big impact on the issue of plastic degradation. </p>
 
  
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<h2 align=center>Project Description</h2>
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<p align=center>As an autoimmune disease, celiac disease is sensitivity to grains such as wheat rye and barley that have gliadin which is a glycoprotein complex rich in proline and glutamine, especially alpha-2-gliadin. Alfa-2-glaidin basically binds to a specific receptor called HLA-DQ2 or HLA-DQ8. This is because tTG alter the alfa-2-gliadin’s charge density which results in highly negative charges. This negative charge density creates significant binding effect to alfa-2-gliadin to HLA-DQ2 OR HLA-DQ8. This receptor is an important key component of the  immune system, which has loci at chromosome 6. Epitopes of that receptor create cellular signaling pathway which results in increase of T and B-cells. These important immune cells eventually kill the specific antigens presented cells. Thus, in order to prevent  this autoimmune disorder, our project aims to destroy these specific subunits of gluten before the intake of food. This will be accomplished by adding specific enzymes’ genes to E.coli’s genome. Then, E.coli will be added into dough while it is in fermentation process. So during the process of fermentation, specific enzymes’ genes will be transcribed and they will break down the gluten. To sum up, with the specific enzyme, which is expressed by E.coli, will alter and brake down the specific protein subunit which is a key component of celiac disease, .  In addition, we would like to improve the consistency of gluten-free bread by letting bacteria secrete additives. For the efficiency of the gluten destruction process, the homogenization of dough will also be improved by the bacteria secretion of additives. Last but not least, receptor complex within E.coli is going to be designed and this  will enable the bacteria to express a receptor which is like HLA-DQ; in order to detect whether there is a gluten or not.
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<h2 align=center>Lets eat some Gluten-Free Biscuits</h2>
  
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<h3> </h3>
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<p> "Nature doesn't make things like that," said Kenneth Peters, an organic geochemist at Stanford University, "so organisms have never seen that before." </p>
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<h1 align="center">A Journey Against BalroGluten: The Epic Story of Gandalf the Grey Yeast</h1>
  
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"Good day to you, hobbits! Today is Frodo's 73. birthday. Why don't we celebrate this wonderful day with cakes and pies and bread that I brought along?" said Aragorn, then he immediately noticed the grim in the Hobbits' faces. "What troubles you?" he asked. "Why are you all so upset?"</br>
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"We can't eat them anymore." said Sam in a bitter voice. "A darkness cursed us. We cannot enjoy these delicacies anymore because of the Balrogluten, they poison us!"</br>
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"A darkness, you say." said Aragorn. "I must inform the others. You hobbits go see Gandalf the Grey Yeast. Only he can help you lift the curse." </br>
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As Aragorn was riding his horse far from the sight, the hobbits were already prepared for the journey ahead when Gandalf the Grey Yeast appeared out of nowhere.
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"Woah, Gandalf. I didn't see you there. Where did you come from?" said Frodo, suprised. Gandalf ignored the question. "We must make haste!" he said. "There is smoke on Mordor. Never a good sign..." </br>
 +
"Also, is that a blazing eye?" Sam tried to point out to the smoke. Something about Gandalf interrupted him. There was hatred in the Grey Yeast's eyes. Is it possible that Gandalf the Grey Yeast found his archenemy, he thought. Is Balrogluten the reason Gandalf became a magical yeast? To fight against him?</br>
 +
Sam shook his head as he got on his ponny. These thoughts are nonsense, he thought. </br>Then Sam saw Gandalf smiling at him on his horse, nodding his head as if he knew what Sam was thinking about.
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<h3> How our project will be helpful?</h3>
+
Frodo, one morning, saw that Gandalf put a bottle of elixir in his robe, but Frodo didn't ask any questions. As the group was getting closer and closer to Mordor, Gandalf the Grey Yeast started to act even stranger. He was moving in a weird way now, trying to hide something in his robe from the hobbits. </br>
−
<p> With increasing global consumption and their natural resistance to degradation, plastic materials and their accumulation in the environment is becoming of increasing concern.PET used for carbonated soft drink bottles, processed meat packages peanut butter jars pillow and sleeping bag filling, textile fibers. The issue of plastic pollution has evolved to become a threat to global ecology. Plastic pollution arises from both terrestrial and marine (like bags,pots and bottles). Of course, plastic buried in a landfill rarely sees the light of day. But in the ocean, which is where a lot of discarded grocery bags, soft drink bottles and six-pack rings end up, plastic is bathed in as much light as water. In 2009, researchers from Nihon University in Chiba, Japan, found that plastic in warm ocean water can degrade in as little as a year. This doesn't sound so bad until you realize those small bits of plastic are toxic chemicals such as bisphenol A (BPA) and PS oligomer. These end up in the guts of animals or wash up on shorelines, where humans are most likely to come into direct contact with the toxins.
+
They reached to Mordor. As the heat and hunger rises, they saw the monstrosity. The Balrogluten, 5 meters long, greeted them with a laugh.</br>
−
  With our project we aim to clean environment from waste PET(like bags,pots and bottles) by biodegradation with E.coli. With this project, PET would reduced to pyruvate, the world will be cleaned from PET and our bacteria could use PET as a food-energy source. All universe is happy!
+
"Hello, weaklings... I see you brought my archenemy. I wonder what's in your robes, Gandalf the Grey Yeast! I wonder what you can do to defeat me." said Balrogluten, spitting fire.
−
References
+
</p>
−
    Ahmed, S. , Haamed, A., Hasan, F., Shah A.A., (2008)Biological degradation of plastics: A comprehensive review. Biotechnology Advances. 26(3).246-265. Retrieved from http://www.sciencedirect.com/science/article/pii/S0734975008000141
+
</td>
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  Harris, W. (2014). How long does it take for plastics to biodegrade? Retrieved from http://science.howstuffworks.com/science-vs-myth/everyday-myths/how-long-does-it-take-for-plastics-to-biodegrade.htm
+
</tr>
−
  Webb, H.K., Arnott, J., Crawford, R., Ivanova, E. (28 December 2012 )Plastic Degradation and Its Environmental Implications with Special Reference to Poly(ethylene terephthalate). Polymers 2013, 5, 1-18. Retrieved from http://marinedebris.info/sites/default/files/literature/Plastic%20Degradation%20and%20Its%20Environmental%20Implications%20with%20Special%20Reference%20to%20Poly(ethylene%20terephthalate).pdf</p>
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 +
"I need to defeat you Balrogluten." shouted Gandalf the Yeast. "I feel like this is the reason of my life! I will kill you even if it means my end!"</br>
 +
"You can only try, you old Yeast." replied Balrogluten. "As long as I curse these breads and cakes, these hobbits cannot eat them! I will curse them forever and ever! You can't even catch me!" As he was fusing in the fire and smoke, Gandalf the Grey Yeast hit his staff to the ground: </br>
 +
"YOU SHALL NOT PASS!"
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 +
"Is that what you want you filthy Yeast?" asked Balrogluten, "I cannot fuse in the air because of your pathetic magic! We will fight then, I will crush you like the bug you are." "Dude, I'm a Yeast." replied Gandalf. "And oh boy, you are going down." </br>
 +
"So are you!" replied Balrogluten as he hurled his whip, catching Gandalf.
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<h3>Why did we choose this project?</h3>
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<p> All over the world, pollution is a huge problem. People are so reckless and unconcious about pollution and recycling, precautions of governments are usually insufficient. For example, Americans generate abo¬ut 210 million tons (231 million short tons) of trash, or solid waste, each year. Most of this trash (57 percent) gets placed in municipal landfills. About 56 million tons (27 percent) is recovered through either recycling, (such as glass, paper products, plastic or metals) or through composting.
+
As Balrogluten was falling deeper and deeper into the fire pit, he began to pull Gandalf along with it. He took out his robe in no time, exposing all the elixirs he prepared along the road. There were hundreds of them. As he was about to fall, he looked at the hobbits for the last time, saying:</br>
−
So we wanted to make people conscious of pollution and importance of recycling, also tried to give a solution for cleaning enviroment from this toxic waste because it is known that plastics contain toxic chemicals such as bisphenol A (BPA) and PS oligomers.
+
"EAT, YOU FOOLS."</br>
−
References
+
The hobbits heard the explosions and saw the magic coming from the hundreds of elixirs exposed to the flames and onto Balrog. As they heard the scream of the monster, the pit collapsed.
−
Freudenrich,C., (2014) How Composting Works. Retrieved from
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"Do you feel any different?" asked Frodo to the other hobbits. "Not really," replied Pippin. "I don't feel any different. Did Gandalf lift the curse?" "Let's try and see." said Sam, as he reached to the cake basket and grabbed a cake. He bit it, then he swallowed whole. "So?" asked Frodo. "I don't know. I should try another one." </b>
 +
"THE CURSE IS GONE! WE CAN EAT NOW!" shouted Pippin, grabbing another cake. In a short time, the basket was empty. Gandalf the Grey Yeast was gone, but so was the curse. There was a bitter happiness in their eyes.</br>
 +
Frodo laughed all of a sudden, saying "I don't even like cake."
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<td align="center" width="162px"><a href="http://odtuteknokent.com.tr/"> <img src="https://static.igem.org/mediawiki/2014/4/47/Odtuteknokent.jpg" width="175px"></a></td>
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<td align="center" width="162px"><a href="http://www.kardiosis.com.tr/"> <img src="https://static.igem.org/mediawiki/2014/d/d4/Kardiosis.jpg" width="175px"></a></td>
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<td align="center"><a href="http://www.taa-ankara.org.tr/eng/index-eng.php"> <img src="https://static.igem.org/mediawiki/2014/0/00/Turkamerikan.jpg" width="175px"></a></td>
 
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<td align="center" width="162px"><a href="http://odtuteknokent.com.tr/" target="_blank"> <img src="https://static.igem.org/mediawiki/2014/4/47/Odtuteknokent.jpg" width="175px"></a></td>
  
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<td align="center"><a href="http://biyoakademi.org/"> <img src="https://static.igem.org/mediawiki/2014/b/b1/Biyoakademi.png" width="175px"></a></td>
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<td align="center" width="162px"><a href="http://www.kardiosis.com.tr/" target="_blank"> <img src="https://static.igem.org/mediawiki/2014/d/d4/Kardiosis.jpg" width="175px"></a></td>
  
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<td align="center" width="162px"><a href="http://www.tr-idea.com/" target="_blank"> <img src="https://static.igem.org/mediawiki/2015/c/c6/METU_Turkey_Idea.PNG" width="350px"></a></td>
  
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<td align="center"><a href="http://www.sentegen.com/" target="_blank"> <img src="https://static.igem.org/mediawiki/2014/d/dd/Sentegenlogoder.PNG" width="175px"></a></td>
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Latest revision as of 13:28, 4 October 2015

Welcome!
We are Team METU_Turkey!

Project Description

As an autoimmune disease, celiac disease is sensitivity to grains such as wheat rye and barley that have gliadin which is a glycoprotein complex rich in proline and glutamine, especially alpha-2-gliadin. Alfa-2-glaidin basically binds to a specific receptor called HLA-DQ2 or HLA-DQ8. This is because tTG alter the alfa-2-gliadin’s charge density which results in highly negative charges. This negative charge density creates significant binding effect to alfa-2-gliadin to HLA-DQ2 OR HLA-DQ8. This receptor is an important key component of the immune system, which has loci at chromosome 6. Epitopes of that receptor create cellular signaling pathway which results in increase of T and B-cells. These important immune cells eventually kill the specific antigens presented cells. Thus, in order to prevent this autoimmune disorder, our project aims to destroy these specific subunits of gluten before the intake of food. This will be accomplished by adding specific enzymes’ genes to E.coli’s genome. Then, E.coli will be added into dough while it is in fermentation process. So during the process of fermentation, specific enzymes’ genes will be transcribed and they will break down the gluten. To sum up, with the specific enzyme, which is expressed by E.coli, will alter and brake down the specific protein subunit which is a key component of celiac disease, . In addition, we would like to improve the consistency of gluten-free bread by letting bacteria secrete additives. For the efficiency of the gluten destruction process, the homogenization of dough will also be improved by the bacteria secretion of additives. Last but not least, receptor complex within E.coli is going to be designed and this will enable the bacteria to express a receptor which is like HLA-DQ; in order to detect whether there is a gluten or not.

Lets eat some Gluten-Free Biscuits

A Journey Against BalroGluten: The Epic Story of Gandalf the Grey Yeast

"Good day to you, hobbits! Today is Frodo's 73. birthday. Why don't we celebrate this wonderful day with cakes and pies and bread that I brought along?" said Aragorn, then he immediately noticed the grim in the Hobbits' faces. "What troubles you?" he asked. "Why are you all so upset?"
"We can't eat them anymore." said Sam in a bitter voice. "A darkness cursed us. We cannot enjoy these delicacies anymore because of the Balrogluten, they poison us!"
"A darkness, you say." said Aragorn. "I must inform the others. You hobbits go see Gandalf the Grey Yeast. Only he can help you lift the curse."
As Aragorn was riding his horse far from the sight, the hobbits were already prepared for the journey ahead when Gandalf the Grey Yeast appeared out of nowhere.

"Woah, Gandalf. I didn't see you there. Where did you come from?" said Frodo, suprised. Gandalf ignored the question. "We must make haste!" he said. "There is smoke on Mordor. Never a good sign..."
"Also, is that a blazing eye?" Sam tried to point out to the smoke. Something about Gandalf interrupted him. There was hatred in the Grey Yeast's eyes. Is it possible that Gandalf the Grey Yeast found his archenemy, he thought. Is Balrogluten the reason Gandalf became a magical yeast? To fight against him?
Sam shook his head as he got on his ponny. These thoughts are nonsense, he thought.
Then Sam saw Gandalf smiling at him on his horse, nodding his head as if he knew what Sam was thinking about.

Frodo, one morning, saw that Gandalf put a bottle of elixir in his robe, but Frodo didn't ask any questions. As the group was getting closer and closer to Mordor, Gandalf the Grey Yeast started to act even stranger. He was moving in a weird way now, trying to hide something in his robe from the hobbits.
They reached to Mordor. As the heat and hunger rises, they saw the monstrosity. The Balrogluten, 5 meters long, greeted them with a laugh.
"Hello, weaklings... I see you brought my archenemy. I wonder what's in your robes, Gandalf the Grey Yeast! I wonder what you can do to defeat me." said Balrogluten, spitting fire.

"I need to defeat you Balrogluten." shouted Gandalf the Yeast. "I feel like this is the reason of my life! I will kill you even if it means my end!"
"You can only try, you old Yeast." replied Balrogluten. "As long as I curse these breads and cakes, these hobbits cannot eat them! I will curse them forever and ever! You can't even catch me!" As he was fusing in the fire and smoke, Gandalf the Grey Yeast hit his staff to the ground:
"YOU SHALL NOT PASS!"

"Is that what you want you filthy Yeast?" asked Balrogluten, "I cannot fuse in the air because of your pathetic magic! We will fight then, I will crush you like the bug you are." "Dude, I'm a Yeast." replied Gandalf. "And oh boy, you are going down."
"So are you!" replied Balrogluten as he hurled his whip, catching Gandalf.

As Balrogluten was falling deeper and deeper into the fire pit, he began to pull Gandalf along with it. He took out his robe in no time, exposing all the elixirs he prepared along the road. There were hundreds of them. As he was about to fall, he looked at the hobbits for the last time, saying:
"EAT, YOU FOOLS."
The hobbits heard the explosions and saw the magic coming from the hundreds of elixirs exposed to the flames and onto Balrog. As they heard the scream of the monster, the pit collapsed.

"Do you feel any different?" asked Frodo to the other hobbits. "Not really," replied Pippin. "I don't feel any different. Did Gandalf lift the curse?" "Let's try and see." said Sam, as he reached to the cake basket and grabbed a cake. He bit it, then he swallowed whole. "So?" asked Frodo. "I don't know. I should try another one." "THE CURSE IS GONE! WE CAN EAT NOW!" shouted Pippin, grabbing another cake. In a short time, the basket was empty. Gandalf the Grey Yeast was gone, but so was the curse. There was a bitter happiness in their eyes.
Frodo laughed all of a sudden, saying "I don't even like cake."