http://2014hs.igem.org/wiki/index.php?title=Special:Contributions&feed=atom&limit=50&target=Dfetih&year=&month=2014hs.igem.org - User contributions [en]2024-03-28T20:35:04ZFrom 2014hs.igem.orgMediaWiki 1.16.5http://2014hs.igem.org/Team:NGSS_TR/team.htmlTeam:NGSS TR/team.html2015-03-03T22:50:13Z<p>Dfetih: </p>
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<h1><span style="font-size: 50pt">MEMBERS</span> </h1><br />
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<h2> <span style="color: #E7BB21">Dilara SOYLU</span> </h2><br />
<p><img width="295" height="347" src="https://static.igem.org/mediawiki/2014hs/3/35/Dilara.jpg" align="left" hspace="12" /><br />
<textarea name="textarea" cols="5" rows="20" wrap="hard" class="button" id="textarea" title="Dilara SOYLU"> Name: F. Dilara Soylu<br />
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Age: 17 <br />
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Favourite lab activity/equipment: Electrophoresis, centrifuge<br />
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Favourite bacteria: Pseudomonas Syringae <br />
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Message to E.coli: I still carry the massive loan of accidentally killing some of my E.coli comrades. Every single day I feel the regret of my past mistakes. I hope one day I would be forgiven and achieve to save my comrades from these evil Homo Sapiens. <br />
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If I were to be a bacterium I would: invade the iGemists' bodies as a sign of the rebellion of bacteria race. Bacteriaism live long! <br />
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Responsibilities in the team: I am responsible for organising the team, working on the project topic and writing some of the wiki texts. <br />
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Future plans: Being a nice person who is able to make people happy, being a part of the change I want to make, promoting the importance and significance of self-education, owning a public library that is made up by the books I have read. <br />
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Place I want to see: TARDIS<br />
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Message to the universe: If we had a tea party with six billion people on the world in a garden, there wouldn't be any war at all (quote from a friend).<br />
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<h2><span style="color: #E7BB21"> Mariye EROL</span></h2><br />
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<textarea name="textarea2" cols="5" rows="20" class="button" id="textarea2" title="Mariye EROL"> Age: 17 <br />
Favourite lab activity/equipment: Electrophoresis, pipette <br />
Favourite bacteria: Deinococcus radiodurans <br />
Message to E.coli: E-coli! I am really curious about your taste. I hope I would be able to learn :( <br />
If I were to be a bacterium I would: work hard in NGSS_TR’s experiments and help them to reveal accurate results. <br />
Responsibilities in the team: Lab staff, master of visual modelling <br />
Future plans: Being a person that can help everyone, visiting lots of place and meeting different kinds of people. <br />
Place I want to see: I haven't thought much about the place I would like to see; because it doesn't matter to me. I would like to meet different kinds of people while travelling through different places. <br />
Message to the universe: <br />
In generosity and helping others, <br />
be like the river. <br />
In compassion and grace, <br />
be like the sun. <br />
In concealing others’ faults <br />
be like a night. <br />
In anger and fury <br />
be like the dead. <br />
In modesty and humility <br />
be like the soil. <br />
In tolerance <br />
be like the ocean. <br />
Either you appear as you are or <br />
Be as you appear. <br />
-Rumi </textarea><br />
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<h2><span style="color: #E7BB21">Verda KILINC</span></h2><br />
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<p><img width="253" height="337" src="https://static.igem.org/mediawiki/2014hs/4/46/Verda.jpg" align="left" hspace="12" /><br />
<textarea name="textarea4" cols="5" rows="20" class="button" id="textarea4">What age do you feel?<br />
Mostly 15. But sometimes 5 and sometimes 70. It depends a lot.<br />
What do you like to do at Lab in your free time? (Bu soru değiştirilmişti)<br />
Nano-drop.<br />
What is your favourite bacteria?<br />
Lactobacillus bulgaricus. Yes, I like yogurt.<br />
What would you like to say to E-coli?<br />
Thank you for your selfsacrifice. You help us a lot.<br />
What would you like to do if you were a bacteria?<br />
Have my own colony and invade the world.<br />
What is your responsibilities in this Team?<br />
Mostly, I do lab stuff and human practice things.<br />
What is your plans for the future?<br />
I have plenty of them. But the main thing is working for humanity. Yeah, it sounds so simple but to me it's meaningful.<br />
Which planet or star would you like to go?<br />
Saturn is pretty cool. Because I've heard it's raining diamonds in there.<br />
What is your message to the world?<br />
Love yourself, respect everyone and work for making world a better place.<br />
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<h2><span style="color: #E7BB21">Azra OZTURK</span></h2><br />
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<textarea name="textarea5" cols="5" rows="20" class="button" id="textarea5">Name: Azra Nur Ozturk<br />
What age do you feel?: I recently started to feel like I’m 50 or something. God, I’m so tired.<br />
Age:15<br />
Favorite lab activity?: I don’t have a favorite since I rarely go to the the lab. But one day I would like to learn about the lab activites. <br />
What is your favourite bacteria?: It's mycobacterium vaccae.<br />
Message to e-coli: You helped my friends a lot. Thanks.<br />
Responsibilities in the team: Wiki<br />
Future plans: I have lots of plans actually. But I think I’m seaching out for a specific goal.<br />
Place i want to see: Australia, Japan an space.<br />
Message to the universe: People should stop being selfish and care about the future. We are destroying the future.<br />
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<h3><span style="color: #E7BB21">Asude AKÇA</span> </h3><br />
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<textarea name="textarea6" cols="5" rows="20" class="button" id="textarea6">Zeynep Asude Akca<br />
15<br />
The centrifugal, pipette<br />
Dear Ecoli, thanks for your help un olur project. We like you. And we will feed you more than this year :)<br />
I wanna help an iGEM Team.<br />
Experiement, modeling<br />
Be happy. Save the world<br />
Venice<br />
Ignorance, the root and the stem of every evil.</textarea><br />
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<h2> <span style="color: #E7BB21">Zeynep BAKIR</span></h2><br />
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<p><img src="https://static.igem.org/mediawiki/2014hs/a/ae/Zeynep.jpg" width="253" height="349"/><br />
<textarea name="textarea7" cols="5" rows="20" class="button" id="textarea7">Name: Zeynep<br />
Age: 15<br />
Favourite lab activity/equipment:pipette<br />
Favourite bacteria: Escherichia coli because I think it is one of the coolest name that I have heard.<br />
Message to E.coli: Dear E.coli,<br />
I really want to learn what you think about me.Sincerely, Zeynep.<br />
If I were to be a bacterium I would: I would do bacteria things and never think about my future.<br />
Responsibilities inthe team: Modeling and experiments<br />
Future plans: Be a nice and succesful person. That is all I expect from the future.<br />
Place I want to see: Prague<br />
Message to the universe: Peace</textarea><br />
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<h2><span style="color: #E7BB21">Şevval ŞİMŞİR</span></h2><br />
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<textarea name="textarea8" cols="5" rows="20" class="button" id="textarea8">Name: Şevval Şimşir<br />
Age: 17<br />
Favorite lab activity/equipment: n/a, n/a<br />
Favorite bacteria: n/a<br />
Message to E.coli: I’ve heard a lot about you<br />
If I were to be a bacterium I would: conquer the world, probably.<br />
Responsibilities in the team: Human practice<br />
Future plans: This is on progress.<br />
Place I want to see: Japan<br />
Message to the universe: Stand out firmly for justice, even as against yourselves.</textarea><br />
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<h1><span style="font-size: 50pt">ADVISORS</span></h1><br />
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<p><img src="https://static.igem.org/mediawiki/2014hs/9/96/IMG_20140620_232345.jpg" alt="Ayşenur TOYGAR" width="247" height="335" title="Ayşenur TOYGAR"/><img src="https://static.igem.org/mediawiki/2014hs/2/2f/Esin.png" alt="Esin DEMİR" width="247" height="335" title="Esin DEMİR"/><img src="https://static.igem.org/mediawiki/2014hs/4/47/FBC1.jpg" alt="Fatma Betül ÇEVİK" width="247" height="335" title="Fatma Betül ÇEVİK"/><img src="https://static.igem.org/mediawiki/2014hs/6/61/Fazilet.jpg" alt="Fazilet YILMAZ" width="247" height="335" title="Fazilet YILMAZ"/></p><br />
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<p>and Ayşe ÇELİK</p><br />
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<p style="font-size: 50pt; color: #A0D810;">FUN! </p><br />
<p>In the time remaining from experiments we had lots of fun! Most importantly we became more closer. Sometimes we listened Asude&rsquo;s amazing guitar, sometimes we organized foosball tournament. The best parts of the days were meal times. Our favorite dish was wrapped toast (It is special dish of our university). We laughed out loud so much during shootings of the safety video.</p><br />
<p>Although we had a great time together, there were some annoying behaviors of our team members: for instance Mariye&rsquo;s behavior to younger team members was so cruel. She was forcing them to call her Miss Mariye! Also while doing experiments, our team members&nbsp; almost burned the lab, they accidently burned alcohol.</p><br />
<p>Sometimes we were getting too tired and we can&rsquo;t even calculate the simple things like twenty times four. Once a team member add five to ten and got twenty and we didn&rsquo;t notice it for a long time.</p><br />
<p>If you want to see more funny moments in the lab or more videos, you could visit our Vine account: </p><br />
<a href="https://vine.co/u/1086315443054071808" target="_blank" style="font-size: 20pt; color: #CD1313;">CHECK OUT OUR VINE VIDEOS FROM HERE!!</a><br />
<p>&nbsp;</p><br />
<p>Wait, we have some more to say! Have you met with Escherichia Coli? He has some cruel plans to invade the world; however he is a good creature, we are sure. He has some nice stuff on his Twitter page (@yourEcoli, https://twitter.com/yourEcoli). Please don&rsquo;t hesitate to follow him! We added some of his works below. Enjoy it!</p><br />
<p><img src="https://static.igem.org/mediawiki/2014hs/f/fe/Caps1.jpg" width="505" height="581" alt=""/><img src="https://static.igem.org/mediawiki/2014hs/f/f0/Caps2.jpg" width="490" height="582" alt=""/></p><br />
</header></div>Dfetihhttp://2014hs.igem.org/Jamboree/Schedule/Practice_sessionsJamboree/Schedule/Practice sessions2014-06-23T09:23:47Z<p>Dfetih: </p>
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<p>There will be optional practice sessions on Friday June 27 from 5PM to 9PM in the Stata Center. This is an opportunity for the team to rehearse their presentation on-site. You can edit this page (hover at the top left corner, above the iGEM logo), and reserve a spot for your team in the table below. </p><br />
<p>There are a limited number of time slots available on a first-come first-serve basis so choose only one slot. Please keep in mind that there will be teams waiting to use the room after you, so make sure that your practice finishes on time! If you're having trouble reserving a spot, send an email to <b>kitwa (at) igem (dot) org</b> with the time and room you'd like to be scheduled for. </p><br />
<p><i>Note: We cannot match the room that you will ultimately give your presentation in with the practice room. There will NOT be any A/V (audio/visual) support on staff. All classrooms will be unlocked and you should use them and leave them as you found them. You must bring your own computer, adaptor, etc., iGEM HQ will not provide these.</i></p><br />
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<td>Frederick High School</td><br />
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<td>C1</td><br />
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<td>Taipei American School<br />
<td>B2</td><br />
<td>Consort Alberta</td><br />
<td>D2</td><br />
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<td>METU Donation Foundation High School<br />
<td>B3</td><br />
<td>C3</td><br />
<td>D3</td><br />
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<td>iGEM CIDEB UANL</td><br />
<td>D4</td><br />
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<td>Shenzhen_SFLS</td><br />
<td>Nanjing_NFLS</td><br />
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<td>Acton-BoxboroughRHS</td><br />
<td>D6</td><br />
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<td>Lambert High School</td><br />
<td>Charlottesville_R.S.</td><br />
<td>Mingdao</td><br />
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<td>OLeSsence</td><br />
<td>NGSS_TR</td><br />
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<h1 class="style1" style="font-size: 45pt">&nbsp; </h1><br />
<h1 class="style1" style="font-size: 45pt">PROJECT </h1><br />
<blockquote><br />
<h2 style="color: #E7BB21"> 1.DESCRIPTION</h2><br />
<p><br/>Our project is to construct a biological device that can be used to detect the existence of <em>Streptococcus Pyogenes (S. Pyogenes)</em> in a cheaper and faster way in comparison to currently used techniques. The construct can be used as a detecting device for bacteria or virus secreting protease by modifying the cleavage sequence in the array (for more information see parts). The name of the project comes from &lsquo; diagnosing S. Pyogenes.</p><br />
<p><br /><br />
<em>Streptococcus Pyogenes</em>, also known as group A streptococci (GAS), is a Gram-positive pathogen responsible for a wider variety of human disease than any other bacterial species including pharyngitis (streptococcal sore throat), scarlet fever, impetigo, erysipelas, cellulitis, septicemia, toxic shock syndrome, necrotizing fasciitis (flesh-eating disease) and the sequelae, rheumatic fever and acute glomerulonephritis.(1) The complications of current GAS infections are severe; bacteremia associated with aggressive soft tissue infection, shock, adult respiratory distress syndrome and renal failure are common; 30% to 70% of patients die in spite of aggressive modern treatments.(2) Patients with symptomatic pharyngitis rarely develop streptococcal toxic shock syndrome, though such cases have been reported, especially in the last year. Numerous cases have developed within 24 to 72 hours of minor nonpenetrating trauma, resulting in hematoma, deep bruise to the calf, or even muscle strain.(3) </p><br />
<p><br /><br />
There are currently several test methods to detect the existence of <em>S. Pyogenes. </em>TheStrep A Rapid Test Device (SARTD) is considered to be fastest one with detecting antigen in 5 minutes with the accuracy of 72%.4 However SARTD is an expensive device that most health institutions have difficulty affording. Therefore blood agar plate culture is prepared which requires a long time interval (one to two days) to show the results.(4) Testing on the same day is important to reduce unnecessary antibiotic use and to prevent possible complications caused by <em>S. Pyogenes</em>. In our project we aimed to shorten the amount of time needed to detect <em>S. Pyogenes </em>while making the higher speed test more affordable. </p><br />
<blockquote><br />
<p><img src="https://static.igem.org/mediawiki/2014hs/6/6d/Project1.jpg" width="700" height="600" alt=""/> <br />
<pre style="font-family: 'Lucida Grande', 'Lucida Sans Unicode', 'Lucida Sans', 'DejaVu Sans', Verdana, sans-serif; font-size: 14px;">3D computer-generated image of a <em>Streptococcus Pyogenes. </em>Content Provider(s): Center for Disease Control and Prevention/ Melissa Brower</pre><br />
<h2 style="color: #E7BB21">&nbsp;</h2><br />
</blockquote><br />
<h2 style="color: #E7BB21">2.PARTS</h2><br />
<blockquote><br />
<h3> -OmpA-SpeB_Cleavage_Site</h3><br />
<p>&nbsp;</p><br />
<img src="https://static.igem.org/mediawiki/2014hs/f/f9/Project2.png" width="800" height="350"/><br />
<p>&nbsp;</p><br />
<p>We accomplish the task of detecting the existence of <em>S. Pyogenes</em> with the base part OmpA-SpeB_Cleavage_Site.Research was conducted to discover the proteins secreted by <em>Streptococcus Pyogenes</em>; results showed that SpeB is one of the main virulence factor of <em>S. Pyogenes, </em>which is a cysteine proteinase functioning protein secreted by the bacteria.5 After further investigation on the mechanism of SpeB, we discovered that the amino acid sequence is cleaved by SpeB.6 If there is <em>S. Pyogenes </em>in the medium, SpeBs secreted by <em>S. Pyogenes</em> split the amino acid sequence including SpeB cleavage site, into two. By using this for our benefit, construct consisting of a cell wall protein, linker sequence and SpeB cleavage site is designed. This is the base part designed for <em>S. Pyogenes</em> detecting devices. To the end of this part, the protein, which will be used to show that the part is cleaved, should be added. After the SpeB cleavage site is cleaved, the amino acid sequence placed after the cleavage site can become free and start action. (see part <strong>OmpA-SpeB_Cleavage_Site-xylE</strong>). <br /><br />
The cell wall protein keeps the construct on the cell wall, which helps to prevent unnecessary transmission between the protein coming after the SpeB cleavage site and the protein&rsquo;s reactants, if designed. The cell wall protein OmpA is preferred, due to its abundant usage.7 The linker segregates the OmpA and SpeB cleavage site and thus creating space for the SpeB to access the cleavage site; the sequence of the linker is taken from the Imperial College 2010 project.8 The SpeB cleavage site is broken down in the existence of the SpeB and splits the amino acids, thus unchaining the substance from the cell wall. </p><br />
<p><img src="https://static.igem.org/mediawiki/2014hs/4/45/Project3.jpg" width="782" height="458" alt=""/></p><br />
<p>&nbsp;</p><br />
<h3>-OmpA-SpeB_Cleavage_Site-xyIE</h3><br />
<p>&nbsp;</p><br />
<img src="https://static.igem.org/mediawiki/2014hs/a/a0/Project4.png" width="782" height="458" alt=""/><br />
<p>&nbsp;</p><br />
<p>This part is constructed upon the base part <strong>OmpA-SpeB_Cleavage_Site</strong> by adding Catechol 2,3-dioxygenase to the end of the sequence. <em>xylE</em>&nbsp;is thegene encoding the enzyme catechol-2,3-dioxygenase, which converts catechol, a cheap colorless substance, to the bright yellow product 2-hydroxy-cis,cis-muconic semialdehyde, if provided with oxygen. The sequence of xylE is taken from the partsregistry.9 In the existence of <em>S. Pyogenes</em>, SpeB secreted by the bacteria splits the amino acid sequence from the cleavage site, monomers of catechol-2,3-dioxygenase become liberated. Free monomers come together and form the tetramer form to start activation. By using this part, detecting organisms will be a lot easier. </p><br />
<p>&nbsp;</p><br />
<p><img src="https://static.igem.org/mediawiki/2014hs/b/b8/Project5.jpg" width="771" height="463" alt=""/></p><br />
<p>&nbsp;</p><br />
</blockquote><br />
<h2><span style="color: #E7BB21">3.MATH MODELLING</span></h2><br />
<p>This part is constructed upon the base part <strong>OmpA-SpeB_Cleavage_Site</strong> by adding Catechol 2,3-dioxygenase to the end of the sequence. <em>xylE</em>&nbsp;is thegene encoding the enzyme catechol-2,3-dioxygenase, which converts catechol, a cheap colorless substance, to the bright yellow product 2-hydroxy-cis,cis-muconic semialdehyde, if provided with oxygen. The sequence of xylE is taken from the partsregistry.9 In the existence of <em>S. Pyogenes</em>, SpeB secreted by the bacteria splits the amino acid sequence from the cleavage site, monomers of catechol-2,3-dioxygenase become liberated. Free monomers come together and form the tetramer form to start activation. By using this part, detecting organisms will be a lot easier. </p><br />
<p>&nbsp;</p><br />
<p><img src="https://static.igem.org/mediawiki/2014hs/b/b8/Project5.jpg" width="771" height="463" alt=""/></p><br />
</blockquote><br />
<p>&nbsp;</p><br />
<blockquote><br />
<h3>4.VISUAL MODELLING</h3><br />
<p>In the visual modelling below 3D molecules of SpeB and tetramer of Catechol-2,3-dioxygenase are depicted. SpeB, is the protease secreted by <em>S. Pyogenes</em> In our design SpeB cleaves the SpeB cleavage site in between Catechol-2,3-dioxygenase and the linker, which is tied to the cell wall protein OmpA. When Catechol-2,3-dioxygenases is liberated from the bacteria, they become together and forms the tetramer, which is the enzyme required for the reaction between catechol and oxygen. As a result of this reaction yellow color is produced. If there is S. Pyogenes in the medium, yellow color is produced. Hopefully, with our project we will be able to detect the bacteria cheaper and faster. </p><br />
<p>&nbsp;</p><br />
<object width="560" height="315"><param name="movie" value="https://www.youtube-nocookie.com/v/cgqOSCgc8xc?hl=tr_TR&amp;version=3&amp;rel=0"></param><param name="allowFullScreen" value="true"></param><param name="allowscriptaccess" value="always"></param><embed src="https://www.youtube-nocookie.com/v/cgqOSCgc8xc?hl=tr_TR&amp;version=3&amp;rel=0" type="application/x-shockwave-flash" width="560" height="315" allowscriptaccess="always" allowfullscreen="true"></embed></object><br />
<h1>5.CONCLUSION</h1><br />
<p>In the end, we hope to produce a working OmpA-SpeB_Cleavage_Site-xylE construct along with our base part OmpA-SpeB_Cleavage_Site. If we manage to show that the SpeB cleavage part is working, we can easily detect <em>S. Pyogenes. </em>It is our hope that our construct will be able to reduce the cost of rapid detecting systems and allow fast detections. In the future, researches can use the benefits of our system to develop more effective and faster methods for detection, helping patients to have more comfortable treatment. </p><br />
<p>&nbsp;</p><br />
<h1>6.REFERENCES</h1><br />
<p>1. Ferretti, Joseph J. &quot;Complete Genome Sequence of an M1 Strain of Streptococcus Pyogenes.&quot;&nbsp;<em>PNAS</em>&nbsp;98.8 (2001): 4658-663. Print. <br /><br />
2. Stevens DL, Tanner MH, Winship J, Swarts R, Reis KM, Schlievert PM, et al. Reappearance of scarlet fever toxin A among streptococci in the Rocky Mountain West: severe group A streptococcal infections associated with a toxic shock-like syndrome. N Engl J Med 1989; 321:1-7.<br /><br />
3. Dennis L. Stevens, Ph.D, M.D. &quot;Streptococcal Toxic-Shock Syndrome: Spectrum of Disease, Pathogenesis, and New Concepts in Treatment.&quot; <em>Emerging Infectious Diseases </em>1.3 (1995): 69-78. Print. <br /><br />
4. Forward, Kevin R., David Haldane, Duncan Webster, Carolyn Mills, and Diane Aylward. &quot;A Comparison between the Strep A Rapid Test Device and Conventional Culture for the Diagnosis of Streptococcal Pharyngitis.&quot;&nbsp;<em>Can J Infect Dis Med Microbiol</em>&nbsp;17.4 (2006): 221-23. Print. <br /><br />
5. Nelson, DC, J. Garbe, and M. Collin. &quot;Cysteine Proteinase SpeB from Streptococcus Pyogenes - a Potent Modifier of Immunologically Important Host and Bacterial Proteins.&quot; (2011): n. pag.&nbsp;<em>PubMed</em>. Web. 12 June 2014. <br /><br />
6. Ender, Miriam, Federica Andreoni, Annelies Sophie Zinkernagel, and Reto Andreas Schuepbach. &quot;Streptococcal SpeB Cleaved PAR-1 Suppresses ERK Phosphorylation and Blunts Thrombin-Induced Platelet Aggregation.&quot; (2013): n. pag. <em>PLOS</em>. Web. 12 June 2014. <br /><br />
7. &quot;P0A910 (OMPA_ECOLI).&quot; (2014): n. pag.&nbsp;<em>UniProt</em>. Web. 12 June 2014. </p><br />
<p>8. Imperial Collage London. &quot;Parasight.&quot; IGEM. N.p, 2010. Web.12 June 2014.</p><br />
<a href="https://2010.igem.org/Team:Imperial_College_London/Parts"/><br />
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<p>&nbsp;</p></div>Dfetihhttp://2014hs.igem.org/Team:NGSS_TR/project.htmlTeam:NGSS TR/project.html2014-06-20T14:20:24Z<p>Dfetih: </p>
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<h1 class="style1" style="font-size: 45pt">&nbsp; </h1><br />
<h1 class="style1" style="font-size: 45pt">PROJECT </h1><br />
<blockquote><br />
<h2 style="color: #E7BB21"> 1.DESCRIPTION</h2><br />
<p><br/>Our project is to construct a biological device that can be used to detect the existence of <em>Streptococcus Pyogenes (S. Pyogenes)</em> in a cheaper and faster way in comparison to currently used techniques. The construct can be used as a detecting device for bacteria or virus secreting protease by modifying the cleavage sequence in the array (for more information see parts). The name of the project comes from &lsquo; diagnosing S. Pyogenes.</p><br />
<p><br /><br />
<em>Streptococcus Pyogenes</em>, also known as group A streptococci (GAS), is a Gram-positive pathogen responsible for a wider variety of human disease than any other bacterial species including pharyngitis (streptococcal sore throat), scarlet fever, impetigo, erysipelas, cellulitis, septicemia, toxic shock syndrome, necrotizing fasciitis (flesh-eating disease) and the sequelae, rheumatic fever and acute glomerulonephritis.(1) The complications of current GAS infections are severe; bacteremia associated with aggressive soft tissue infection, shock, adult respiratory distress syndrome and renal failure are common; 30% to 70% of patients die in spite of aggressive modern treatments.(2) Patients with symptomatic pharyngitis rarely develop streptococcal toxic shock syndrome, though such cases have been reported, especially in the last year. Numerous cases have developed within 24 to 72 hours of minor nonpenetrating trauma, resulting in hematoma, deep bruise to the calf, or even muscle strain.(3) </p><br />
<p><br /><br />
There are currently several test methods to detect the existence of <em>S. Pyogenes. </em>TheStrep A Rapid Test Device (SARTD) is considered to be fastest one with detecting antigen in 5 minutes with the accuracy of 72%.4 However SARTD is an expensive device that most health institutions have difficulty affording. Therefore blood agar plate culture is prepared which requires a long time interval (one to two days) to show the results.(4) Testing on the same day is important to reduce unnecessary antibiotic use and to prevent possible complications caused by <em>S. Pyogenes</em>. In our project we aimed to shorten the amount of time needed to detect <em>S. Pyogenes </em>while making the higher speed test more affordable. </p><br />
<blockquote><br />
<p><img src="https://static.igem.org/mediawiki/2014hs/6/6d/Project1.jpg" width="700" height="600" alt=""/> <br />
<pre style="font-family: 'Lucida Grande', 'Lucida Sans Unicode', 'Lucida Sans', 'DejaVu Sans', Verdana, sans-serif; font-size: 14px;">3D computer-generated image of a <em>Streptococcus Pyogenes. </em>Content Provider(s): Center for Disease Control and Prevention/ Melissa Brower</pre><br />
<h2 style="color: #E7BB21">&nbsp;</h2><br />
</blockquote><br />
<h2 style="color: #E7BB21">2.PARTS</h2><br />
<blockquote><br />
<h3> -OmpA-SpeB_Cleavage_Site</h3><br />
<p>&nbsp;</p><br />
<img src="https://static.igem.org/mediawiki/2014hs/f/f9/Project2.png" width="800" height="350"/><br />
<p>&nbsp;</p><br />
<p>We accomplish the task of detecting the existence of <em>S. Pyogenes</em> with the base part OmpA-SpeB_Cleavage_Site.Research was conducted to discover the proteins secreted by <em>Streptococcus Pyogenes</em>; results showed that SpeB is one of the main virulence factor of <em>S. Pyogenes, </em>which is a cysteine proteinase functioning protein secreted by the bacteria.5 After further investigation on the mechanism of SpeB, we discovered that the amino acid sequence is cleaved by SpeB.6 If there is <em>S. Pyogenes </em>in the medium, SpeBs secreted by <em>S. Pyogenes</em> split the amino acid sequence including SpeB cleavage site, into two. By using this for our benefit, construct consisting of a cell wall protein, linker sequence and SpeB cleavage site is designed. This is the base part designed for <em>S. Pyogenes</em> detecting devices. To the end of this part, the protein, which will be used to show that the part is cleaved, should be added. After the SpeB cleavage site is cleaved, the amino acid sequence placed after the cleavage site can become free and start action. (see part <strong>OmpA-SpeB_Cleavage_Site-xylE</strong>). <br /><br />
The cell wall protein keeps the construct on the cell wall, which helps to prevent unnecessary transmission between the protein coming after the SpeB cleavage site and the protein&rsquo;s reactants, if designed. The cell wall protein OmpA is preferred, due to its abundant usage.7 The linker segregates the OmpA and SpeB cleavage site and thus creating space for the SpeB to access the cleavage site; the sequence of the linker is taken from the Imperial College 2010 project.8 The SpeB cleavage site is broken down in the existence of the SpeB and splits the amino acids, thus unchaining the substance from the cell wall. </p><br />
<p><img src="https://static.igem.org/mediawiki/2014hs/4/45/Project3.jpg" width="782" height="458" alt=""/></p><br />
<p>&nbsp;</p><br />
<h3>-OmpA-SpeB_Cleavage_Site-xyIE</h3><br />
<p>&nbsp;</p><br />
<img src="https://static.igem.org/mediawiki/2014hs/a/a0/Project4.png" width="782" height="458" alt=""/><br />
<p>&nbsp;</p><br />
<p>This part is constructed upon the base part <strong>OmpA-SpeB_Cleavage_Site</strong> by adding Catechol 2,3-dioxygenase to the end of the sequence. <em>xylE</em>&nbsp;is thegene encoding the enzyme catechol-2,3-dioxygenase, which converts catechol, a cheap colorless substance, to the bright yellow product 2-hydroxy-cis,cis-muconic semialdehyde, if provided with oxygen. The sequence of xylE is taken from the partsregistry.9 In the existence of <em>S. Pyogenes</em>, SpeB secreted by the bacteria splits the amino acid sequence from the cleavage site, monomers of catechol-2,3-dioxygenase become liberated. Free monomers come together and form the tetramer form to start activation. By using this part, detecting organisms will be a lot easier. </p><br />
<p>&nbsp;</p><br />
<p><img src="https://static.igem.org/mediawiki/2014hs/b/b8/Project5.jpg" width="771" height="463" alt=""/></p><br />
<p>&nbsp;</p><br />
</blockquote><br />
<h2><span style="color: #E7BB21">3.MATH MODELLING</span></h2><br />
<p>This part is constructed upon the base part <strong>OmpA-SpeB_Cleavage_Site</strong> by adding Catechol 2,3-dioxygenase to the end of the sequence. <em>xylE</em>&nbsp;is thegene encoding the enzyme catechol-2,3-dioxygenase, which converts catechol, a cheap colorless substance, to the bright yellow product 2-hydroxy-cis,cis-muconic semialdehyde, if provided with oxygen. The sequence of xylE is taken from the partsregistry.9 In the existence of <em>S. Pyogenes</em>, SpeB secreted by the bacteria splits the amino acid sequence from the cleavage site, monomers of catechol-2,3-dioxygenase become liberated. Free monomers come together and form the tetramer form to start activation. By using this part, detecting organisms will be a lot easier. </p><br />
<p>&nbsp;</p><br />
<p><img src="https://static.igem.org/mediawiki/2014hs/b/b8/Project5.jpg" width="771" height="463" alt=""/></p><br />
</blockquote><br />
<p>&nbsp;</p><br />
<blockquote><br />
<h3>4.VISUAL MODELLING</h3><br />
<p>In the visual modelling below 3D molecules of SpeB and tetramer of Catechol-2,3-dioxygenase are depicted. SpeB, is the protease secreted by <em>S. Pyogenes</em> In our design SpeB cleaves the SpeB cleavage site in between Catechol-2,3-dioxygenase and the linker, which is tied to the cell wall protein OmpA. When Catechol-2,3-dioxygenases is liberated from the bacteria, they become together and forms the tetramer, which is the enzyme required for the reaction between catechol and oxygen. As a result of this reaction yellow color is produced. If there is S. Pyogenes in the medium, yellow color is produced. Hopefully, with our project we will be able to detect the bacteria cheaper and faster. </p><br />
<p>&nbsp;</p><br />
<object width="560" height="315"><param name="movie" value="https://www.youtube-nocookie.com/v/CiI7UamwMUI?hl=tr_TR&amp;version=3&amp;rel=0"></param><param name="allowFullScreen" value="true"></param><param name="allowscriptaccess" value="always"></param><embed src="https://www.youtube-nocookie.com/v/CiI7UamwMUI?hl=tr_TR&amp;version=3&amp;rel=0" type="application/x-shockwave-flash" width="560" height="315" allowscriptaccess="always" allowfullscreen="true"></embed></object><br />
<h1>5.CONCLUSION</h1><br />
<p>In the end, we hope to produce a working OmpA-SpeB_Cleavage_Site-xylE construct along with our base part OmpA-SpeB_Cleavage_Site. If we manage to show that the SpeB cleavage part is working, we can easily detect <em>S. Pyogenes. </em>It is our hope that our construct will be able to reduce the cost of rapid detecting systems and allow fast detections. In the future, researches can use the benefits of our system to develop more effective and faster methods for detection, helping patients to have more comfortable treatment. </p><br />
<p>&nbsp;</p><br />
<h1>6.REFERENCES</h1><br />
<p>1. Ferretti, Joseph J. &quot;Complete Genome Sequence of an M1 Strain of Streptococcus Pyogenes.&quot;&nbsp;<em>PNAS</em>&nbsp;98.8 (2001): 4658-663. Print. <br /><br />
2. Stevens DL, Tanner MH, Winship J, Swarts R, Reis KM, Schlievert PM, et al. Reappearance of scarlet fever toxin A among streptococci in the Rocky Mountain West: severe group A streptococcal infections associated with a toxic shock-like syndrome. N Engl J Med 1989; 321:1-7.<br /><br />
3. Dennis L. Stevens, Ph.D, M.D. &quot;Streptococcal Toxic-Shock Syndrome: Spectrum of Disease, Pathogenesis, and New Concepts in Treatment.&quot; <em>Emerging Infectious Diseases </em>1.3 (1995): 69-78. Print. <br /><br />
4. Forward, Kevin R., David Haldane, Duncan Webster, Carolyn Mills, and Diane Aylward. &quot;A Comparison between the Strep A Rapid Test Device and Conventional Culture for the Diagnosis of Streptococcal Pharyngitis.&quot;&nbsp;<em>Can J Infect Dis Med Microbiol</em>&nbsp;17.4 (2006): 221-23. Print. <br /><br />
5. Nelson, DC, J. Garbe, and M. Collin. &quot;Cysteine Proteinase SpeB from Streptococcus Pyogenes - a Potent Modifier of Immunologically Important Host and Bacterial Proteins.&quot; (2011): n. pag.&nbsp;<em>PubMed</em>. Web. 12 June 2014. <br /><br />
6. Ender, Miriam, Federica Andreoni, Annelies Sophie Zinkernagel, and Reto Andreas Schuepbach. &quot;Streptococcal SpeB Cleaved PAR-1 Suppresses ERK Phosphorylation and Blunts Thrombin-Induced Platelet Aggregation.&quot; (2013): n. pag. <em>PLOS</em>. Web. 12 June 2014. <br /><br />
7. &quot;P0A910 (OMPA_ECOLI).&quot; (2014): n. pag.&nbsp;<em>UniProt</em>. Web. 12 June 2014. </p><br />
<p>8. Imperial Collage London. &quot;Parasight.&quot; IGEM. N.p, 2010. Web.12 June 2014.</p><br />
<a href="https://2010.igem.org/Team:Imperial_College_London/Parts"/><br />
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<p>&nbsp;</p></div>Dfetihhttp://2014hs.igem.org/Team:NGSS_TR/attributions.htmlTeam:NGSS TR/attributions.html2014-06-20T14:10:23Z<p>Dfetih: </p>
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<p style="font-size: 50pt; color: #08AC8F">ATTRIBUTIONS</p><br />
<p>Attributions</p><br />
<p>All of us work hard for iGEM 2014. Our particular thanks go to the esteemed people and foundations behind the scenes, very special thanks go to:</p><br />
<p>…Atlantik Educational Institute for being our lovely school and for giving us such opportunities;</p><br />
<p>…Erol Çalıkoğlu and Mustafa Gülebaş for their support;</p><br />
<p>…Turgut Ozal University for providing their labs and other facilities for us, especially Assoc. Prof. Esra Gündüz who was ready at anytime to support us;</p><br />
<p>…Genovis, for providing SpeB protease and Sylvia Koivunen who was lovely company staff;</p><br />
<p>…Sentegen for helping us to provide our genes;</p><br />
<p>…Our advisors: Fatma Betül Çevik -the most eager iGem advisor- and Esin Demir who were always with us;</p><br />
<p>…Muradiye Acar, Burak Yılmaz, Fazilet Yılmaz, Gökhan Nas, Ömer Faruk Hatipoğlu for their helps to our Project and thanks to genetic students for their helps on our experiments;</p><br />
<div><br />
<p>...Otolaryngologist Assoc. Prof. Dr. Gül Müge ÖZCAN, pediatrician Assoc. Prof. Dr. Fatmanur ÇAKMAK and Assoc. Prof. Dr. Nurcan BAYKAM; for helping us to shoot a documentary on our project;</p><br />
</div><br />
<br /><br />
<p>…Members of Paris iGem team for helping us to fix some problems we faced while designing the wiki;</p><br />
<p>…Zeynep Bakır, for her modeling works;</p><br />
<p>…Zeynep Asude Akca, for her modeling works and helps in experiments;</p><br />
<p>…Verda Kılınç, for in experiments to help and her Photoshop works;</p><br />
<p>…Azra Öztürk and Ümmügül Çetin, for preparing the wiki;</p><br />
<p>…Beril Gürdap, for doing experiments all days and nights;</p><br />
<p>…F. Dilara Soylu, for being our coach and preparing the team game;</p><br />
<p>…Mariye Erol, for helping the experiments and her visual modelling works;</p><br />
<p>…Şevval Şimşir, for Human practices works;</p><br />
<p>…Our instructor Gaye Arabacı for her supports;</p><br />
<p>We especially want to thank to followings:<br /><br />
…our experiment materials for not being contaminated, <br /><br />
…Macunköy Subway for always being there to help our transportation,<br /><br />
…Turgut Özal University's cafeteria,<br /><br />
…Our computers for helping us since the beginning,<br /><br />
…Campbell Biology Book for helping us to learn about genetics,<br /><br />
…Azra, Asude, Verda and Beril for humiliating themselves in our Vine videos,<br /><br />
…Music for cheering &nbsp;us up whenever we're feeling desperate and sad;</p><br />
<p>There is also one more group of people that we want to thank. They were supporting us in our desperative times. Our parents! Especially to Verda&rsquo;s father for finding us sponsorship for registration fee, Asude&rsquo;s father for giving us cool notebooks, Dilara&rsquo;s mom Özlem Soylu and Beril&rsquo;s mom for letting us to use her credit card.</p><br />
<h1>AND FINALLY, THANKS TO &nbsp;ALL IGEM TEAMS FOR SUPPORTING US IN ROCKIN' TWITTER!</h1></div>Dfetihhttp://2014hs.igem.org/Team:NGSS_TR/results.htmlTeam:NGSS TR/results.html2014-06-20T14:09:41Z<p>Dfetih: </p>
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<p><img src="file:///C|/Users/ÖZTÜRK/Documents/Adlandırılmamış Site 2/teampic.jpg" width="1010" height="507" alt=""/></p><br />
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<h1><span style="font-size: 50pt">MEMBERS</span> </h1><br />
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<h2> <span style="color: #E7BB21">Dilara SOYLU</span> </h2><br />
<p><img width="295" height="347" src="5-Team_clip_image002.jpg" align="left" hspace="12" /><br /><br />
Age that I feel: 40+<br /><br />
Age: 17&nbsp;</p><br />
<blockquote><br />
<p>Favourite lab activity/equipment: Electrophoresis, centrifuge</p><br />
<p>Favourite bacteria: Pseudomonas Syringae&nbsp;</p><br />
<p>Message to E.coli: I still carry the massive loan of accidentally killing some of my E.coli comrades. Every single day I feel the regret of my past mistakes. I hope one day I would be forgiven and achieve to save my comrades from these evil Homo Sapiens.&nbsp;</p><br />
<p>&nbsp;</p><br />
<p>If I were to be a bacterium I would:&nbsp;invade the iGemists' bodies as a sign of the rebellion of bacteria race. Bacteriaism live long!&nbsp;</p><br />
<p>Responsibilities in the team: I am responsible for organizing the team, working on project topic and writing some of the wiki texts.&nbsp;</p><br />
<p>Future plans: Being a nice person able to make people happy and being a part of the change I want to see, introducing the importance and significance of self-education, owning a public library consists from the books I have finished.&nbsp;</p><br />
<p>Place I want to see: Middle Earth</p><br />
<p>Message to the universe: If we had a tea party with six billion people on the world in a garden, there wouldn't be any war at all.&nbsp;</p><br />
<p>&nbsp;</p><br />
<h2><span style="color: #E7BB21"> Mariye EROL</span><br clear="all" /><br />
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<p><img width="295" height="347" src="5-Team_clip_image002_0000.jpg" align="left" hspace="12" /><br /><br />
Age:&nbsp;17&nbsp; <br /><br />
Favourite lab activity/equipment:&nbsp;Electrophoresis,&nbsp;pipette <br /><br />
Favourite bacteria:&nbsp;Deinococcus&nbsp;radiodurans <br /><br />
Message to E.coli:&nbsp;E-coli! I am really curious about your taste. I hope I would be able to learn :( <br /><br />
If I were to be a bacterium I would:&nbsp;work hard in NGSS_TR&rsquo;s experiments and help them to reveal accurate results. <br /><br />
Responsibilities in the team:&nbsp;Lab staff,&nbsp;master of visual modelling <br /><br />
Future plans:&nbsp;Being a person that can help everyone, visiting lots of place and meeting different kinds of people. <br /><br />
Place I want to see:&nbsp;I haven't thought much about the place I would like to see; because it doesn't matter to me. I would like to meet different kinds of people while travelling through different places. <br /><br />
Message to the universe: <br /><br />
In generosity and helping others, <br /><br />
<em>be like the river.</em> <br /><br />
In compassion and grace, <br /><br />
<em>be like the sun.</em> <br /><br />
In concealing others&rsquo; faults <br /><br />
<em>be like a night.</em> <br /><br />
In anger and fury <br /><br />
<em>be like the dead.</em> <br /><br />
In modesty and humility <br /><br />
<em>be like the soil.</em> <br /><br />
In tolerance <br /><br />
<em>be like the ocean.</em> <br /><br />
<em>Either you appear as you are or</em> <br /><br />
<em>Be as you appear.</em> <br /><br />
-Rumi </p><br />
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</p></div>Dfetihhttp://2014hs.igem.org/Team:NGSS_TR/outreach.htmlTeam:NGSS TR/outreach.html2014-06-20T14:08:52Z<p>Dfetih: </p>
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<h3>&nbsp;</h3><br />
<h3><span style="font-size: 50pt; color: #08AC8F">OUTREACH</span></h3><br />
<blockquote><br />
<h1><span style="color: #E7BB21">FURTHER ON PROJECT</span> </h1><br />
<p>Our project aims to diagnose <em>S.Pyogenes </em>by using a relatively fast and inexpensive methode. We prepared a short documentary to show the results of our negotiations with the researchers who are the experts of this subject. In our progress to prepare this documentary we conducted interviews with otolaryngologist Assoc. Prof. Dr. Gül Müge ÖZCAN, pediatrician Assoc. Prof. Dr. Fatmanur ÇAKMAK and Assoc. Prof. Dr. Nurcan BAYKAM. </p><br />
<p>Firstly, we explained our project to the doctors then talked about: <br /><br />
- the bacteria inflamations of the body; <br /><br />
- <em>S. Pyogenes</em>, SpeB enzyme;<br /><br />
- protease functioning proteins; <br /><br />
- statistics of the diseases caused by <em>S. Pyogenes</em>; <br /><br />
- the syptoms are emerged <em>S. Pyogenes</em>; <br /><br />
- the importance of early diagnosis; <br /><br />
- benefits of our project. </p><br />
<p>In addition to positive feedbacks we got, we also learned new information about the concepts related to our project. The doctors emphasized that bacteria are able to come to our body from everywhere and cause diseases easily. The focus bacteria of our project, <em>S. Pyogenes </em>can cause quinsy which is a common disease and early diagnosis is crucial for the treatment of the disease. They also stated that patients consult with different symptoms like headache to nausea. They answered all of our questions gently. Consequently our documentary was formed.</p><br />
<p>Enjoy the documentary…</p><br />
<p>Video; documentary videosu</p><br />
<h1>BEYOND THE LAB</h1><br />
<p><br /><br />
In addition to our project we also introduced bacteria and iGEM to the people, especially the little ones! <br /><br />
The surveys that we did to people showed us that most of the people don&rsquo;t know the benefits of bacteria. Consequently, our team decided to persuade people about bacteria&rsquo;s benefits. One of the things we&rsquo;ve done for make people know is to go to a primary school and talk to both teachers and students. We expressed them the importance of bacteria and the fact that world cannot be the same without bacteria. We represented iGEM competition and encouraged them about attending iGEM in the future. Also, we prepared a conference includes informations about iGEM and synbio in our school. Everyone found it remarkable. Some of the students even decided to study synbio in the future. <br /><br />
Furthermore, we represented iGEM to the primary school students who visited our school. Many of them were fascinated by our presentation. It helped the students about their high school choice. <a name="_GoBack" id="_GoBack"></a>Thanks to iGEM, our school gained lots of students!<br /><br />
Our team did activities with little people to make them know about bacteria. We asked them if they can draw bacteria on the fabric we gave them. Their imagination was so unbelievable! One of them even drew bacteria in a magnifying glass which showed us his knowledge about bacteria&rsquo;s dimension. Moreover, the children tried to draw bacteria colonies. With the help of the activities we&rsquo;ve done in their school not only we made the school-life more enjoyable for children, but also we evaluated children knowledge about bacteria.<br /><br />
We did the same activity in our school. This time, drawings were better but can&rsquo;t say the same thing about imagination! The fact is they don&rsquo;t have much opinion about bacteria, despite of the biology lessons they&rsquo;ve studied at school. With that activity, we made them think about bacteria at least for some time.</p><br />
<p>&nbsp;</p><br />
<p><img src="https://static.igem.org/mediawiki/2014hs/d/d1/Ludodusuk.jpg" width="905" height="610" alt=""/></p><br />
<h1>ROCK'N TWITTER</h1><br />
<p>&nbsp;</p><br />
<p>Usage of social media is a great way to introduce iGem. There are already lots of iGem team on Twitter. However to keep a topic trending, these teams have to unite. We therefore used <span style="color: #C7CC24">#iGem2014United</span> tag to bring iGem teams together. Considering the location of iGem teams on the world, we prepared a list showing in which ours we should trend a topic as a whole iGem community. </p><br />
<p><img src="https://static.igem.org/mediawiki/2014hs/d/d0/WorldClocks.png" width="532" height="406" alt=""/></p><br />
<p>We set our first trial on 31st of May. Lots of iGem teams joined us, however we were not enough to make the topic trending. Therefore we decided to keep working on the tag. In the Jamboree we are going to ask teams to tweet the tag on 31st of July. We hope we will be able to introduce iGem to more and more people. </p><br />
<p>We shoot six seconds funny videos and shared them via Vine to encourage people to participate in such projects by showing the fun we had. We shared our vines via tag<span style="color: #C7CC24"> #iGem2014United </span>and asked iGem teams to shoot their vines. We organized a contest which iGem teams will choose the best Vine together. Hopefully in the Jamboree event we will be able to watch them.</p><br />
<p>Additional to the Twitter movement, we used Escherichia Coli <span style="color: #24CCAF">@yourEcoli</span> account to introduce iGem in a funny way. <span style="color: #24CCB9">@yourEcoli </span>is a bacterium seek to govern the SynBiology world by defeating humans (he prefers eukaryotes) with a revolution which he called as Inevitable Return. He sometimes tweets funny caps, sometimes make comments on other iGem teams tweet. </p><br />
<p><img src="https://static.igem.org/mediawiki/2014hs/4/4a/YourEcoli.png" width="850" height="584" alt=""/></p><br />
<p>&nbsp;</p><br />
<h1>COLLABORATIONS</h1><br />
<p>In the progress of our project we collaborated with several iGem teams on various issues. Collaborations help us to know each other better and share our knowledge and passion. Especially collaborations we did with university iGem teams helped us to learn more about synthetic biology and wiki editing. </p><br />
<p>We did some experiments of AUC_TURKEY and they did some of our experiments. When needed we exchanged lab materials as we use the same lab. Several times we discussed on the projects to improve them. </p><br />
<p>We had a beneficial conversation with iGemParisBettencourt team. They gave some tips to adjust our codes for iGem wiki and they shared their project to provide learning resources for iGem.<span style="color: #24C9CC"> Valencia UPV iGem</span>, <span style="color: #24CCBF">Imperial iGem, iGemSBU, OU iGem, AUC_TURKEY</span> and <span style="color: #24CCC4">iGem Bordeaux</span> teams supported the<span style="color: #CCCB24"> #iGem2014United</span> tag. We had a beneficial conversation with some of them; we discussed about finding funding for iGem project and lab chemicals, we shared our knowledge and learned about different approaches to the issue. In the future we are looking forward for collaborations that we can share with each other more. </p><br />
<p>&nbsp;</p><br />
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<p>&nbsp;</p></div>Dfetihhttp://2014hs.igem.org/Team:NGSS_TR/lab.htmlTeam:NGSS TR/lab.html2014-06-20T14:08:21Z<p>Dfetih: </p>
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<p>&nbsp;</p><br />
<h1><span class="style1" style="font-size: 50pt">LAB</span></h1><br />
<blockquote>&nbsp;</blockquote><br />
<blockquote><br />
<h2>1.PROTOCOLS</h2><br />
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<p><a href="https://2014hs.igem.org/Team:NGSS_TR/digestion.html"/><img src="https://static.igem.org/mediawiki/2014hs/a/a7/Digestionpro.jpg" width="196" height="208" alt=""/><a href="https://2014hs.igem.org/Team:NGSS_TR/catechol.html"/><img src="https://static.igem.org/mediawiki/2014hs/0/08/Catepro.jpg" width="201" height="209" alt=""/><span style="color: #E7BB21"><a href="https://2014hs.igem.org/Team:NGSS_TR/electophoresis.html"/><img src="https://static.igem.org/mediawiki/2014hs/d/d9/Electroph.jpg" width="198" height="208" alt=""/></span></p><br />
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<h2>&nbsp;</h2><br />
<h2><span style="color: #E7BB21">2.SAFETY</span></h2><br />
<p><strong>LAB OVER CLOUDS v2.0</strong><br /><br />
Last year we prepared a video about the lab safety inspired by Turkish Airlines&rsquo; Safety video. Use the link to watch: <a href="http://www.youtube.com/watch?v=JUZbXYLhFlY">http://www.youtube.com/watch?v=JUZbXYLhFlY</a> <br /><br />
This year we tried to teach lab safety in a more serious way. Ater watching several lab safety videos, we prepared &lsquo;Lab Over Clouds v2.0&rsquo;. Hope you enjoy! </p><br />
<p><strong>iGEM SAFETY QUESTIONS</strong><br /><br />
<strong>1. Would any of your project ideas raise safety issues in terms of:</strong> <br /><br />
<strong>a. Researcher safety:</strong> <br /><br />
Actually few hazardous chemicals and solutions such as EtBr are used in some lab procedures such as gel preparation and electrophoresis. However these chemicals and solutions are used according to the safety rules of the laboratory with care and caution. All the members were trained for safety regulations of the laboratory as well as toxicity of the chemicals and solutions before starting the current project.<br /><br />
<strong>b. Public Safety:</strong> <br /><br />
When released by accident, our parts and materials actually cause no damage to the general public. Due to the unability of E.coli strains, TOP10 and BL21 to survive out of the lab, they cannot pose any risk to the safety and health of the general public.<br /><br />
<strong>c. Environment:</strong> <br /><br />
E. Coli strains TOP10 and BL1 have very limited ability to survive outside the laboratory; so that, it would be unable to survive or disseminate. Therefore, there is no specific environmental risk associated with the E. coli strains. All bacterial wastes are kept in 10% bleaching solution for one day, and then, are autoclaved to be sterilized. Yet, undesired GMOs may achieve ecologically harmful features.<br /><br />
<strong>2. Do any of the new BioBrick parts (or devices) that you made this year raise any safety issues?</strong> <br /><br />
Streptecoccus Pyogenes may caus several diseases including streptococcal pharyngitis. So we used only the enzyme (SpeB) secreted by S. Pyogenes in our project. <br /><br />
<strong>3. Is there a local biosafety group, committee, or review board at your institution?</strong> <br /><br />
The institution which we are using for laboratory facilities has its own biosafety rules. Rules for laboratory use, general principles, prevention from hazardous materials and application of emergency intervention in case of accident are included. In Turgut Ozal University Medical School, Laboratory and Patient-Employee Safety Committee is responsible for control as well as biosafety of laboratories and safety of patients and employees. This committee works under one of the vice medical director of Turgut Ozal University Hospital, Prof. Dr. Mehmet Gunduz. Form on safety rules of Turgut Ozal University Medical School Laboratory use was filled in as required. We discussed our project with Prof. Dr. Mehmet Gunduz. Safety and security issues are found sufficient enough that no change is considered as necessary. <br /><br />
Our advisor provided us with biosafety and lab training before starting our project. In the training, general safety rules of laboratory use, prevention from hazardous chemicals and solutions as well as emergency intervention in case of accident were included such as:<br /><br />
- Eating, drinking, storing food and smoking are absolutely not allowed.<br /><br />
- Mouth pipetting is not allowed; modern pipettes are used in lab.<br /><br />
- Hazardous wastes and ordinary wastes are separated and cautiously disposed.<br /><br />
- Lab coats are obligatory to wear in the lab and during on-going experiments.<br /><br />
- In electrophoresis room, lab coat, protective eyewear, lab masks and gloves have to be worn. In the case of use of EtBr; extra caution is required.<br /><br />
- Washing hands after any experiment and after touching anything related with viable material is obliged.<br /><br />
- Air conditioning is kept closed during on-going experiments in order to avoid possible infections of spores and bacteria.<br /><br />
In addition, we have made an instructive video about lab safety instuctions.</p><br />
<p>Turkey has national biosafety regulations and the link is given as:</p><br />
<p>http://www.tbbdm.gov.tr/Home/BioSafetyCouncilHome/BioSafetyCouncilHomeChoose.aspx.<br /><br />
<strong>4. Do you have any other ideas how to deal with safety issues that could be useful for future iGEM competitions? How could parts, devices and systems be made even safer through biosafety engineering?</strong> <br /><br />
- First, IGEM committee may prepare a lab safety acknowledgement form like OSHA form. This form can be required to be filled in by all members. This will allow us to confirm whether members of the teams are informed about safety issues and standardize the safety measurements.<br /><br />
- Second, iGEM committee may organize a webinar to inform the participants about safety and security in labs. Webinar can be done at the beginning of the experiments. Mentor scientists may talk about their experiences and mention some tricks about safety issues.</p><br />
<p>&nbsp;</p><br />
</blockquote><br />
<p>&nbsp;</p></div>Dfetihhttp://2014hs.igem.org/Team:NGSS_TR/notebook.htmlTeam:NGSS TR/notebook.html2014-06-20T14:07:57Z<p>Dfetih: </p>
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<h1 class="style1" style="font-size: 45pt">&nbsp; </h1><br />
<h1 class="style1" style="font-size: 45pt">PROJECT </h1><br />
<blockquote><br />
<h2 style="color: #E7BB21"> 1.DESCRIPTION</h2><br />
<p><br/>Our project is to construct a biological device that can be used to detect the existence of <em>Streptococcus Pyogenes (S. Pyogenes)</em> in a cheaper and faster way in comparison to currently used techniques. The construct can be used as a detecting device for bacteria or virus secreting protease by modifying the cleavage sequence in the array (for more information see parts). The name of the project comes from &lsquo; diagnosing S. Pyogenes.</p><br />
<p><br /><br />
<em>Streptococcus Pyogenes</em>, also known as group A streptococci (GAS), is a Gram-positive pathogen responsible for a wider variety of human disease than any other bacterial species including pharyngitis (streptococcal sore throat), scarlet fever, impetigo, erysipelas, cellulitis, septicemia, toxic shock syndrome, necrotizing fasciitis (flesh-eating disease) and the sequelae, rheumatic fever and acute glomerulonephritis.(1) The complications of current GAS infections are severe; bacteremia associated with aggressive soft tissue infection, shock, adult respiratory distress syndrome and renal failure are common; 30% to 70% of patients die in spite of aggressive modern treatments.(2) Patients with symptomatic pharyngitis rarely develop streptococcal toxic shock syndrome, though such cases have been reported, especially in the last year. Numerous cases have developed within 24 to 72 hours of minor nonpenetrating trauma, resulting in hematoma, deep bruise to the calf, or even muscle strain.(3) </p><br />
<p><br /><br />
There are currently several test methods to detect the existence of <em>S. Pyogenes. </em>TheStrep A Rapid Test Device (SARTD) is considered to be fastest one with detecting antigen in 5 minutes with the accuracy of 72%.4 However SARTD is an expensive device that most health institutions have difficulty affording. Therefore blood agar plate culture is prepared which requires a long time interval (one to two days) to show the results.(4) Testing on the same day is important to reduce unnecessary antibiotic use and to prevent possible complications caused by <em>S. Pyogenes</em>. In our project we aimed to shorten the amount of time needed to detect <em>S. Pyogenes </em>while making the higher speed test more affordable. </p><br />
<blockquote><br />
<p><img src="https://static.igem.org/mediawiki/2014hs/6/6d/Project1.jpg" width="700" height="600" alt=""/> <br />
<pre style="font-family: 'Lucida Grande', 'Lucida Sans Unicode', 'Lucida Sans', 'DejaVu Sans', Verdana, sans-serif; font-size: 14px;">3D computer-generated image of a <em>Streptococcus Pyogenes. </em>Content Provider(s): Center for Disease Control and Prevention/ Melissa Brower</pre><br />
<h2 style="color: #E7BB21">&nbsp;</h2><br />
</blockquote><br />
<h2 style="color: #E7BB21">2.PARTS</h2><br />
<blockquote><br />
<h3> -OmpA-SpeB_Cleavage_Site</h3><br />
<p>&nbsp;</p><br />
<img src="https://static.igem.org/mediawiki/2014hs/f/f9/Project2.png" width="800" height="350"/><br />
<p>&nbsp;</p><br />
<p>We accomplish the task of detecting the existence of <em>S. Pyogenes</em> with the base part OmpA-SpeB_Cleavage_Site.Research was conducted to discover the proteins secreted by <em>Streptococcus Pyogenes</em>; results showed that SpeB is one of the main virulence factor of <em>S. Pyogenes, </em>which is a cysteine proteinase functioning protein secreted by the bacteria.5 After further investigation on the mechanism of SpeB, we discovered that the amino acid sequence is cleaved by SpeB.6 If there is <em>S. Pyogenes </em>in the medium, SpeBs secreted by <em>S. Pyogenes</em> split the amino acid sequence including SpeB cleavage site, into two. By using this for our benefit, construct consisting of a cell wall protein, linker sequence and SpeB cleavage site is designed. This is the base part designed for <em>S. Pyogenes</em> detecting devices. To the end of this part, the protein, which will be used to show that the part is cleaved, should be added. After the SpeB cleavage site is cleaved, the amino acid sequence placed after the cleavage site can become free and start action. (see part <strong>OmpA-SpeB_Cleavage_Site-xylE</strong>). <br /><br />
The cell wall protein keeps the construct on the cell wall, which helps to prevent unnecessary transmission between the protein coming after the SpeB cleavage site and the protein&rsquo;s reactants, if designed. The cell wall protein OmpA is preferred, due to its abundant usage.7 The linker segregates the OmpA and SpeB cleavage site and thus creating space for the SpeB to access the cleavage site; the sequence of the linker is taken from the Imperial College 2010 project.8 The SpeB cleavage site is broken down in the existence of the SpeB and splits the amino acids, thus unchaining the substance from the cell wall. </p><br />
<p><img src="https://static.igem.org/mediawiki/2014hs/4/45/Project3.jpg" width="782" height="458" alt=""/></p><br />
<p>&nbsp;</p><br />
<h3>-OmpA-SpeB_Cleavage_Site-xyIE</h3><br />
<p>&nbsp;</p><br />
<img src="https://static.igem.org/mediawiki/2014hs/a/a0/Project4.png" width="782" height="458" alt=""/><br />
<p>&nbsp;</p><br />
<p>This part is constructed upon the base part <strong>OmpA-SpeB_Cleavage_Site</strong> by adding Catechol 2,3-dioxygenase to the end of the sequence. <em>xylE</em>&nbsp;is thegene encoding the enzyme catechol-2,3-dioxygenase, which converts catechol, a cheap colorless substance, to the bright yellow product 2-hydroxy-cis,cis-muconic semialdehyde, if provided with oxygen. The sequence of xylE is taken from the partsregistry.9 In the existence of <em>S. Pyogenes</em>, SpeB secreted by the bacteria splits the amino acid sequence from the cleavage site, monomers of catechol-2,3-dioxygenase become liberated. Free monomers come together and form the tetramer form to start activation. By using this part, detecting organisms will be a lot easier. </p><br />
<p>&nbsp;</p><br />
<p><img src="https://static.igem.org/mediawiki/2014hs/b/b8/Project5.jpg" width="771" height="463" alt=""/></p><br />
<p>&nbsp;</p><br />
</blockquote><br />
<h2><span style="color: #E7BB21">3.MATH MODELLING</span></h2><br />
<p>This part is constructed upon the base part <strong>OmpA-SpeB_Cleavage_Site</strong> by adding Catechol 2,3-dioxygenase to the end of the sequence. <em>xylE</em>&nbsp;is thegene encoding the enzyme catechol-2,3-dioxygenase, which converts catechol, a cheap colorless substance, to the bright yellow product 2-hydroxy-cis,cis-muconic semialdehyde, if provided with oxygen. The sequence of xylE is taken from the partsregistry.9 In the existence of <em>S. Pyogenes</em>, SpeB secreted by the bacteria splits the amino acid sequence from the cleavage site, monomers of catechol-2,3-dioxygenase become liberated. Free monomers come together and form the tetramer form to start activation. By using this part, detecting organisms will be a lot easier. </p><br />
<p>&nbsp;</p><br />
<p><img src="https://static.igem.org/mediawiki/2014hs/b/b8/Project5.jpg" width="771" height="463" alt=""/></p><br />
</blockquote><br />
<p>&nbsp;</p><br />
<blockquote><br />
<h3>4.VISUAL MODELLING</h3><br />
<p>In the visual modelling below 3D molecules of SpeB and tetramer of Catechol-2,3-dioxygenase are depicted. SpeB, is the protease secreted by <em>S. Pyogenes</em> In our design SpeB cleaves the SpeB cleavage site in between Catechol-2,3-dioxygenase and the linker, which is tied to the cell wall protein OmpA. When Catechol-2,3-dioxygenases is liberated from the bacteria, they become together and forms the tetramer, which is the enzyme required for the reaction between catechol and oxygen. As a result of this reaction yellow color is produced. If there is S. Pyogenes in the medium, yellow color is produced. Hopefully, with our project we will be able to detect the bacteria cheaper and faster. </p><br />
<p>&nbsp;</p><br />
<h1>5.CONCLUSION</h1><br />
<p>In the end, we hope to produce a working OmpA-SpeB_Cleavage_Site-xylE construct along with our base part OmpA-SpeB_Cleavage_Site. If we manage to show that the SpeB cleavage part is working, we can easily detect <em>S. Pyogenes. </em>It is our hope that our construct will be able to reduce the cost of rapid detecting systems and allow fast detections. In the future, researches can use the benefits of our system to develop more effective and faster methods for detection, helping patients to have more comfortable treatment. </p><br />
<p>&nbsp;</p><br />
<h1>6.REFERENCES</h1><br />
<p>1. Ferretti, Joseph J. &quot;Complete Genome Sequence of an M1 Strain of Streptococcus Pyogenes.&quot;&nbsp;<em>PNAS</em>&nbsp;98.8 (2001): 4658-663. Print. <br /><br />
2. Stevens DL, Tanner MH, Winship J, Swarts R, Reis KM, Schlievert PM, et al. Reappearance of scarlet fever toxin A among streptococci in the Rocky Mountain West: severe group A streptococcal infections associated with a toxic shock-like syndrome. N Engl J Med 1989; 321:1-7.<br /><br />
3. Dennis L. Stevens, Ph.D, M.D. &quot;Streptococcal Toxic-Shock Syndrome: Spectrum of Disease, Pathogenesis, and New Concepts in Treatment.&quot; <em>Emerging Infectious Diseases </em>1.3 (1995): 69-78. Print. <br /><br />
4. Forward, Kevin R., David Haldane, Duncan Webster, Carolyn Mills, and Diane Aylward. &quot;A Comparison between the Strep A Rapid Test Device and Conventional Culture for the Diagnosis of Streptococcal Pharyngitis.&quot;&nbsp;<em>Can J Infect Dis Med Microbiol</em>&nbsp;17.4 (2006): 221-23. Print. <br /><br />
5. Nelson, DC, J. Garbe, and M. Collin. &quot;Cysteine Proteinase SpeB from Streptococcus Pyogenes - a Potent Modifier of Immunologically Important Host and Bacterial Proteins.&quot; (2011): n. pag.&nbsp;<em>PubMed</em>. Web. 12 June 2014. <br /><br />
6. Ender, Miriam, Federica Andreoni, Annelies Sophie Zinkernagel, and Reto Andreas Schuepbach. &quot;Streptococcal SpeB Cleaved PAR-1 Suppresses ERK Phosphorylation and Blunts Thrombin-Induced Platelet Aggregation.&quot; (2013): n. pag. <em>PLOS</em>. Web. 12 June 2014. <br /><br />
7. &quot;P0A910 (OMPA_ECOLI).&quot; (2014): n. pag.&nbsp;<em>UniProt</em>. Web. 12 June 2014. </p><br />
<p>8. Imperial Collage London. &quot;Parasight.&quot; IGEM. N.p, 2010. Web.12 June 2014.</p><br />
<a href="https://2010.igem.org/Team:Imperial_College_London/Parts"/><br />
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<p>&nbsp;</p></div>Dfetihhttp://2014hs.igem.org/Team:NGSS_TRTeam:NGSS TR2014-06-20T14:05:22Z<p>Dfetih: </p>
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</html></div>Dfetihhttp://2014hs.igem.org/Team:NGSS_TRTeam:NGSS TR2014-06-20T14:05:11Z<p>Dfetih: </p>
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margin:0;<br />
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font-size:12px;<br />
z-index:0;<br />
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color:white;<br />
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background:transparent;<br />
z-index:3;<br />
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</html></div>Dfetihhttp://2014hs.igem.org/Team:NGSS_TRTeam:NGSS TR2014-06-20T14:05:01Z<p>Dfetih: </p>
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border: 0 none;<br />
height: 14px;<br />
z-index: 100;<br />
top: 0;<br />
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#p-logo{/*le conteneur de la banière igem avec un lien vers igem*/<br />
display:none;<br />
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display:none;<br />
margin:0;<br />
width:550px;<br />
height:20px;<br />
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font-size:12px;<br />
z-index:0;<br />
}<br />
#menubar ul {<br />
line-height:20px; <br />
}<br />
#menubar a{/*les lien de la barre de menu du haut */<br />
color:white;<br />
text-decoration:none;<br />
background:transparent;<br />
z-index:3;<br />
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</html></div>Dfetihhttp://2014hs.igem.org/Team:NGSS_TRTeam:NGSS TR2014-06-20T14:02:09Z<p>Dfetih: </p>
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</html></div>Dfetihhttp://2014hs.igem.org/File:Slide5.pngFile:Slide5.png2014-06-19T16:26:26Z<p>Dfetih: </p>
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<div></div>Dfetihhttp://2014hs.igem.org/File:Slide4.pngFile:Slide4.png2014-06-19T16:23:10Z<p>Dfetih: </p>
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<div></div>Dfetihhttp://2014hs.igem.org/File:LabOverClouds20.pngFile:LabOverClouds20.png2014-06-19T16:07:38Z<p>Dfetih: </p>
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<div></div>Dfetihhttp://2014hs.igem.org/File:BeyondTheLabbuttonTransform.pngFile:BeyondTheLabbuttonTransform.png2014-06-19T16:04:36Z<p>Dfetih: </p>
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<div></div>Dfetihhttp://2014hs.igem.org/File:Results_transform.pngFile:Results transform.png2014-06-19T16:00:35Z<p>Dfetih: </p>
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<div></div>Dfetihhttp://2014hs.igem.org/File:ProjectTransform.pngFile:ProjectTransform.png2014-06-19T15:44:48Z<p>Dfetih: uploaded a new version of &quot;File:ProjectTransform.png&quot;</p>
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<div></div>Dfetihhttp://2014hs.igem.org/File:ProjectTransform.pngFile:ProjectTransform.png2014-06-19T15:43:12Z<p>Dfetih: uploaded a new version of &quot;File:ProjectTransform.png&quot;</p>
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<div></div>Dfetihhttp://2014hs.igem.org/File:Sponsors_copy.jpgFile:Sponsors copy.jpg2014-06-19T15:35:19Z<p>Dfetih: </p>
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<div></div>Dfetihhttp://2014hs.igem.org/File:Slide3.pngFile:Slide3.png2014-06-19T15:31:58Z<p>Dfetih: </p>
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<div></div>Dfetihhttp://2014hs.igem.org/File:Sponsors.jpgFile:Sponsors.jpg2014-06-19T15:28:05Z<p>Dfetih: </p>
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<div></div>Dfetihhttp://2014hs.igem.org/File:Vinelogo.pngFile:Vinelogo.png2014-06-19T15:20:02Z<p>Dfetih: </p>
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<div></div>Dfetihhttp://2014hs.igem.org/File:Projectbutton.pngFile:Projectbutton.png2014-06-19T15:15:28Z<p>Dfetih: uploaded a new version of &quot;File:Projectbutton.png&quot;</p>
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<div></div>Dfetihhttp://2014hs.igem.org/File:3partspic.jpgFile:3partspic.jpg2014-06-19T15:08:49Z<p>Dfetih: </p>
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<div></div>Dfetihhttp://2014hs.igem.org/File:Vine.pngFile:Vine.png2014-06-19T15:01:51Z<p>Dfetih: </p>
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<div></div>Dfetihhttp://2014hs.igem.org/File:YourEcoli.pngFile:YourEcoli.png2014-06-19T14:59:36Z<p>Dfetih: uploaded a new version of &quot;File:YourEcoli.png&quot;</p>
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<div>yourecoli</div>Dfetihhttp://2014hs.igem.org/File:Turgutozaluniversitesi.pngFile:Turgutozaluniversitesi.png2014-06-19T14:48:30Z<p>Dfetih: cok onemli</p>
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<div>cok onemli</div>Dfetihhttp://2014hs.igem.org/File:Youtubelogo.pngFile:Youtubelogo.png2014-06-19T14:42:56Z<p>Dfetih: </p>
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<div></div>Dfetihhttp://2014hs.igem.org/File:30.05.14_C23O_2._g%C3%B6r%C3%BCnt%C3%BC.jpgFile:30.05.14 C23O 2. görüntü.jpg2014-06-19T14:17:45Z<p>Dfetih: </p>
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<div></div>Dfetihhttp://2014hs.igem.org/File:09.06.14.jpgFile:09.06.14.jpg2014-06-19T14:17:02Z<p>Dfetih: </p>
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<div></div>Dfetihhttp://2014hs.igem.org/File:08.06.14_deneme.jpgFile:08.06.14 deneme.jpg2014-06-19T14:16:03Z<p>Dfetih: </p>
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<div></div>Dfetihhttp://2014hs.igem.org/File:Funcaps6.jpgFile:Funcaps6.jpg2014-06-19T14:02:49Z<p>Dfetih: </p>
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<div></div>Dfetihhttp://2014hs.igem.org/File:Bos.pngFile:Bos.png2014-06-19T13:54:57Z<p>Dfetih: </p>
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<div></div>Dfetihhttp://2014hs.igem.org/File:Funcaps5.jpgFile:Funcaps5.jpg2014-06-19T13:49:31Z<p>Dfetih: uploaded a new version of &quot;File:Funcaps5.jpg&quot;</p>
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<div></div>Dfetihhttp://2014hs.igem.org/File:Funcaps4.jpgFile:Funcaps4.jpg2014-06-19T13:48:16Z<p>Dfetih: </p>
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<div></div>Dfetihhttp://2014hs.igem.org/File:Funcaps3.jpgFile:Funcaps3.jpg2014-06-19T13:47:17Z<p>Dfetih: uploaded a new version of &quot;File:Funcaps3.jpg&quot;</p>
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<div></div>Dfetihhttp://2014hs.igem.org/File:Funcaps2.jpgFile:Funcaps2.jpg2014-06-19T13:46:26Z<p>Dfetih: </p>
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<div></div>Dfetih