Difference between revisions of "Team:METU Turkey/Safety"

 
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            <a class="one" href="https://2015.igem.org/Team:METU_Turkey">Home</a>
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<td id="rcorners1" align=center > <a class="one" href="https://2015.igem.org/Team:METU_Turkey">HOME</a></td>
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<td id="rcorners1" align=center> <a class="one" href="https://2015.igem.org/Team:METU_Turkey/Team">TEAM</a> </td>
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<td id="rcorners1" align=center><a class="one" href="https://2015.igem.org/Team:METU_Turkey/Project">PROJECT</a></td>
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<td id="rcorners1" align=center><a class="one" href="https://2015.igem.org/Team:METU_Turkey/Parts">PARTS</a></td>
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<td id="rcorners1" align=center><a class="one" href="https://2015.igem.org/Team:METU_Turkey/Notebook">NOTEBOOK</a></td>
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<td id="rcorners1" align=center><a class="one" href="https://2015.igem.org/Team:METU_Turkey/Attributions">ATTRIBUTIONS</a></td>
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<td id="rcorners1" align=center><a class="one" href="https://2015.igem.org/Team:METU_Turkey/interlab">INTERLAB</a></td>
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            <a class="one" href="https://2015.igem.org/Team:METU_Turkey/Description">Project</a>
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            <ul>
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                <li><a href="https://2015.igem.org/Team:METU_Turkey/Experiments">Experiments</a></li>
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                <li><a href="https://2015.igem.org/Team:METU_Turkey/Results">Results</a></li>
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                <li><a href="https://2015.igem.org/Team:METU_Turkey/Design">Design</a></li>
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            <a class="one" href="https://2015.igem.org/Team:METU_Turkey/Parts">Parts</a>
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            <ul>
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                <li><a href="https://2015.igem.org/Team:METU_Turkey/Basic_Part">Basic Part</a></li>
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                <li><a href="https://2015.igem.org/Team:METU_Turkey/Composite_Part">Composite Part</a></li>
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                <li><a href="https://2015.igem.org/Team:METU_Turkey/Part_Collection">Part Collection</a></li>
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            </ul>
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            </li>
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        <li>
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            <a class="one" href="https://2015.igem.org/Team:METU_Turkey/Notebook">Notebook</a>
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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/interlab">Interlab</a>
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        </li>
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        <li>
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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/Practices">Human Practices</a>
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        </li>
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        <li>
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            <a class="one" href="https://2015.igem.org/Team:METU_Turkey/Safety">Safety</a>
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        </li>
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            <a class="one" href="https://2015.igem.org/Team:METU_Turkey/Gallery">Gallery</a>
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        </li>
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        <li>
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            <a class="one" href="https://2015.igem.org/Team:METU_Turkey/Sponsors">Sponsors</a>
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        </li>
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        </li>
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<td align="center" width="350px"><a href="https://igem.org/Main_Page" target="_blank"> <img src="https://static.igem.org/mediawiki/igem.org/6/60/Igemlogo_300px.png" width="150px"></a></td>
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<img src="https://static.igem.org/mediawiki/2014/c/cc/Metuigem_logo.png" width="120px">
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<h3>Welcome!  <br> We are Team METU_Turkey! </h3>
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</td>
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<td align="center" width="162px"><a href="http://www.metu.edu.tr"color:#FFFFFF" target="_blank"><img src="https://static.igem.org/mediawiki/2014/9/91/Metulogo.jpg" width="300px"></a></td>
 
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<td id="rcorners1" align=center><a class="one" href="https://2015.igem.org/Team:METU_Turkey/Collaborations">COLLABORATIONS</a></td>
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<td id="rcorners1" align=center><a class="one" href="https://2015.igem.org/Team:METU_Turkey/Practices">HUMAN PRACTICES</a></td>
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<td id="rcorners1" align=center><a class="one" href="https://2015.igem.org/Team:METU_Turkey/Safety">SAFETY</a></td>
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<h1> An importat issue: Safety!</h1>
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<td id="rcorners1" align=center><a class="one" href="https://2015.igem.org/Team:METU_Turkey/Modeling">MODELING</a></td>
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<p> All projects are being conducted in lab-safe strains of E.coli(dh5A) and Saccharomyces cerevisiae. All researchers have been trained in applicable lab safety to insure that no bacteria are inadvertently released into the environment. We have also been trained in proper handling of chemicals. In plastics projects, the actual organisms being engineered were maintained in lab conditions (cultures, bioreactors, etc.).
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<td id="rcorners1" align=center><a class="one" href="https://2015.igem.org/Team:METU_Turkey/Measurement">MEASUREMENT</a></td>
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None of the parts we made this year raise any particular safety issues that we can foresee. All of our major parts were either taken from pre-registered biobricks, None of our new parts would provide any foreseeable selective advantage in the wild. Thus, these parts would not increase bacterial survival in the case of accidental release.</p>
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<td id="rcorners1" align=center><a class="one" href="https://2015.igem.org/Team:METU_Turkey/Galery">GALERY</a></td>
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<td id="rcorners1" align=center><a class="one" href="https://2015.igem.org/Team:METU_Turkey/Sponsors">SPONSORS</a></td>
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<h3>Is there any possible situation against to our kill-switch mechanism?</h3>
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</tr>
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<p>Our kill switch mechanism is dependent to a cheap thickener (Xanthan gum), so our organism would die absence of it. Its basic logic is to addict the organism our wanted enviromental conditions, so it can be controlled.</p>
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<img align=center src="https://static.igem.org/mediawiki/2015/f/f9/LO_ODTU_METU_ACIK_RENKLI_ZEMIN.png" width="1140" hspace="100">
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<h1> Safety Questions & Answers</h1>
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<h1>An Interview with Prof. Doctor H. Canan Sümer</h1>
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<h3>1.Would any of your project ideas raise safety issues in terms of:</h3>  
 +
<p>RESEARCHER SAFETY? </p>
 +
<p>There are no hazardous chemicals that we used in the laboratory except for EtBr that we used in a special room for gel visualization and some buffers used in commercially available kits.
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<p>PUBLIC SAFETY?</p>
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Since all the organisms used in the wetlab are destroyed after they are done working with they pose no danger for public safety. We use E.coli strain DH5alpha which is easy to kill and all the student members who work in the wetlab are very well trained to make sure there is no unwanted contamination. This year we are also working on a kill switch which, if works properly, will eliminate any bacteria whereas they will not be able to survive without Xanthan gum present.
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<p>ENVIRONMENTAL SAFETY?</p>
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As mentioned above a kill switch will be available in the organism which will initiate cell death when the cell is in an environment that does not contain enough Xanthan gum.
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<h3>2. Do any of the new BioBrick parts (or devices) that you made this year raise any safety issues?</h3>
 +
<p>We have followed all the safety procedures during the isolation process from the cells we had and we successfully isolated the DNA without any problems that will raise safety issues.</p>
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<h3>3.Is there a local biosafety group, committee, or review board at your institution?
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If yes, what does your local biosafety group think about your project?
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If no, which specific biosafety rules or guidelines do you have to consider in your country?</h3>
 +
<p>In our university we have a biosafety and ethical research center which monitors the safety of our projects. http://www.ueam.metu.edu.tr The members of METU Biology department are also members of National Biosafety Coordinating Committee. We are able to consult to them whenever it is necessary. Also biosafety is a very important subject for METU Department of Biology, whereas the student members are very well trained in the subject. Also the projects that we decided to work on are presented to many people in the area in order to see if they are of any concern for the biosafety regulations. All the procedures that are used in the lab are also approved procedures that are used by these people mentioned above.</p>
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<h3>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?</h3>
 +
We believe using specific strains designed specifically for labwork will be safer. It is possible to genetically modify the organisms so that, they are not able to grow outside the lab environment. There probably is not a way to build some biobricks that can be modified in order to make them safer since their function will be the cause of safety issues. </p>
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<h1>More Safety Information!</h1>
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<p> Our organisms (Saccharomyces cerevisiae) are meant to live and die in foodstuffs so we will be testing them on food such as bread and cookies. Also, after cooking them in a 300 degree celsius oven, the yeast will die. Also, we are creating a kill switch mechanism which depends on a thickener (Xanthan gum, http://parts.igem.org/Part:BBa_K1606020 ).</p>
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<p>We are using E. coli for all lab procedures. But our future prospective/future aim is to use it directly by Yeast.</p>
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<p>Since we are using E.coli (DH5alpha), there are no extreme risks we should cope with. (We are also considering a kill switch mechanism.) However, we are using Safety Class II Cabinets, we work appropriate for aseptic conditions. We are using autoclave frequently. We are always sterilizing our waste and we give our waste to well equipped/trained biological waste assistants. We are wearing rubber gloves while we are not using flame.</p>
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<p>Safe Shipment: Our DNA submissions always wait for the government inspections in USA. The inspections will be speed up by sending them a letterhead for multiple times by our principle investigator.</p>
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<h1>Kill Switch Mechanism</h1>
 
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<p>Prof. Doctor H. Canan Sümer graduated from METU department of psychology. After that, she got her phd from Kansas State University. Then, she started to work at METU department of psychology and she is still working there. </br> We asked her some questions about celiac disease because she has been diagnosed with celiac disease quite recently. We wanted to know how she deals with this disease and what can she suggest to other people who also have celiac disease. This interview shows us what patients go through before and after celiac disease diagnosis. Therefore, this interview helps us understand what celiac disease patients need, which helps us improve our project.</p>
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<h4 align=center>Kill Switch Circuit</h4>
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<img hspace="375px" align=center src="https://static.igem.org/mediawiki/2015/7/7d/K1606014.PNG" width="600px">
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<p align=center>Strong promoter without thickener of LuxR and antiholin sequence:
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For our kill switch model first we design a circuit that secrete antiholin LuxR gene to supress the activity of holin and endolysin enzymes for working under normal conditions by digesting gluten into its small particles. After this composite part we design a new circuit that our composite gene part secrete a thickener that dough doesn't lose its stability and viscose structure type for consumers' choice.
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</p>
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<img hspace="375px" align=center src="https://static.igem.org/mediawiki/2015/5/56/K1606020.PNG" width="600px">
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<p align=center>Lux promoter activated by thickener(Xanthan Gum) gene part of LuxR and it start to lyse the cell with holin and endolysin activity.
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</p>
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<h2 align=center>Xanthan Gum Structure</h2>
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<img hspace="375px" align=center src="https://static.igem.org/mediawiki/2015/0/06/2000px-Xanthan.svg.png" width="600px">
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<img hspace="375px" align=center src="https://static.igem.org/mediawiki/2015/c/c2/123456.PNG" width="600px">
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<h1>300°C Oven</h1>
  
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<img align=center src="https://static.igem.org/mediawiki/2015/4/44/Ovenfireigem.jpg" width="365px">
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<p>After dough fermentation, dough is ready to bake under 300 °C, which
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kills all of the microorganism inside it(except sporulated bacteria). And also the enzyme will be denaturated.
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</p>
  
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<img align=center src="https://static.igem.org/mediawiki/2015/2/2b/Metu_2015_interview_1.png">
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<hr>
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<p><h4>When were you diagnosed with celiac disease?</h4>
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About year ago, actually eleven months to be perfect.. </br> </br>
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<h4>Could you please tell what happened after diagnosis process?</h4>
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<img align=center src="https://static.igem.org/mediawiki/2015/a/a8/5665safetyaspect.PNG" width="365px">
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They performed blood test, endoscopy and colonoscopy to diagnose me with the disease. Following the diagnosis, my doctor directed me to dietitian where I received some important information concerning my diet, but I was already prepared at time as I had already searched a number of pages and a number of groups that are available in the Internet. </br></br>
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<h4>What were your symptoms and signs of your diseases before diagnosis?</h4>
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I felt horrible after eating certain foodstuffs. I was not able to digest them. Even if I had little to eat, I felt a fullness in my stomach. Most of the time, I felt bad after meals.</br></br>
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<h4>Is there any treatment of your disease?</h4>
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<a href="http://www.metu.edu.tr" target="_blank"> <img src="https://static.igem.org/mediawiki/2014/9/91/Metulogo.jpg" width="350px" align="center"></a>
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A completely gluten free diet helps you feel much better and this is what I am doing. My diet is 100% gluten free and I pay strict attention to possibility of contamination.</br></br>
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<table  id="firstblock" width="60%"  cellspacing="10px" height="200px" align="center">
  
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<h4>What sort of replacements do you use regarding the products that contain gluten?</h4>
 
  
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There are a number of products available. There are things like gluten free flour, breads, cookies, crackers, pasta. Most of these are available from Turkish brands. Also, I use corn and corn flour and quinoa. </br></br>
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<tr>
  
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<h4>In Turkey, people usually prefer products including gluten such as bread, pie, and cookies. What do you do when you go to the restaurants? Is there any place which you prefer the most?</h4>
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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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When I go to a new restaurant, I talk to the head waiter or the cook  if possible, and I explain my situation. I usually check which dishes might contain gluten. Moreover, I sometimes carry my own bread. Plus, there are gluten free restaurant in the town that I live. There is place that I like to go. They have an excellent selection of gluten free meals. </br></br>
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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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<h4>How do you prevent gluten contamination for foods that you prepared?</h4>
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It is not a big deal for me, because I physically separated my kitchen. One part of my kitchen contains the gluten free food while the other part contains food that has gluten. </br></br>
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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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<h4>Before and after diagnosis, which changes happened in your body?</h4>
 
  
  
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Compared to the time before my diagnosis, I feel much more energetic. My skin is not as dry as it used to be. I regained my appetite, so I am not losing weight anymore. Also, my hair loss stopped. </br></br>
 
  
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<td align="center"><a href="http://www.mathworks.com/" target="_blank"> <img src="https://static.igem.org/mediawiki/2015/a/ab/METU_Turkey_mathworks.png" width="175px"></a></td>
  
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<h4>Is there any suggestions to celiac patients?</h4>
 
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100% gluten free diet and nothing else. If you do that, there will not be any problems.
 
  
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Latest revision as of 13:31, 4 October 2015

Welcome!
We are Team METU_Turkey!

An importat issue: Safety!

All projects are being conducted in lab-safe strains of E.coli(dh5A) and Saccharomyces cerevisiae. All researchers have been trained in applicable lab safety to insure that no bacteria are inadvertently released into the environment. We have also been trained in proper handling of chemicals. In plastics projects, the actual organisms being engineered were maintained in lab conditions (cultures, bioreactors, etc.). None of the parts we made this year raise any particular safety issues that we can foresee. All of our major parts were either taken from pre-registered biobricks, None of our new parts would provide any foreseeable selective advantage in the wild. Thus, these parts would not increase bacterial survival in the case of accidental release.

Is there any possible situation against to our kill-switch mechanism?

Our kill switch mechanism is dependent to a cheap thickener (Xanthan gum), so our organism would die absence of it. Its basic logic is to addict the organism our wanted enviromental conditions, so it can be controlled.

Safety Questions & Answers

1.Would any of your project ideas raise safety issues in terms of:

RESEARCHER SAFETY?

There are no hazardous chemicals that we used in the laboratory except for EtBr that we used in a special room for gel visualization and some buffers used in commercially available kits.

PUBLIC SAFETY?

Since all the organisms used in the wetlab are destroyed after they are done working with they pose no danger for public safety. We use E.coli strain DH5alpha which is easy to kill and all the student members who work in the wetlab are very well trained to make sure there is no unwanted contamination. This year we are also working on a kill switch which, if works properly, will eliminate any bacteria whereas they will not be able to survive without Xanthan gum present.

ENVIRONMENTAL SAFETY?

As mentioned above a kill switch will be available in the organism which will initiate cell death when the cell is in an environment that does not contain enough Xanthan gum.

2. Do any of the new BioBrick parts (or devices) that you made this year raise any safety issues?

We have followed all the safety procedures during the isolation process from the cells we had and we successfully isolated the DNA without any problems that will raise safety issues.

3.Is there a local biosafety group, committee, or review board at your institution? If yes, what does your local biosafety group think about your project? If no, which specific biosafety rules or guidelines do you have to consider in your country?

In our university we have a biosafety and ethical research center which monitors the safety of our projects. http://www.ueam.metu.edu.tr The members of METU Biology department are also members of National Biosafety Coordinating Committee. We are able to consult to them whenever it is necessary. Also biosafety is a very important subject for METU Department of Biology, whereas the student members are very well trained in the subject. Also the projects that we decided to work on are presented to many people in the area in order to see if they are of any concern for the biosafety regulations. All the procedures that are used in the lab are also approved procedures that are used by these people mentioned above.

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?

We believe using specific strains designed specifically for labwork will be safer. It is possible to genetically modify the organisms so that, they are not able to grow outside the lab environment. There probably is not a way to build some biobricks that can be modified in order to make them safer since their function will be the cause of safety issues.

More Safety Information!

Our organisms (Saccharomyces cerevisiae) are meant to live and die in foodstuffs so we will be testing them on food such as bread and cookies. Also, after cooking them in a 300 degree celsius oven, the yeast will die. Also, we are creating a kill switch mechanism which depends on a thickener (Xanthan gum, http://parts.igem.org/Part:BBa_K1606020 ).

We are using E. coli for all lab procedures. But our future prospective/future aim is to use it directly by Yeast.

Since we are using E.coli (DH5alpha), there are no extreme risks we should cope with. (We are also considering a kill switch mechanism.) However, we are using Safety Class II Cabinets, we work appropriate for aseptic conditions. We are using autoclave frequently. We are always sterilizing our waste and we give our waste to well equipped/trained biological waste assistants. We are wearing rubber gloves while we are not using flame.

Safe Shipment: Our DNA submissions always wait for the government inspections in USA. The inspections will be speed up by sending them a letterhead for multiple times by our principle investigator.

Kill Switch Mechanism

Kill Switch Circuit

Strong promoter without thickener of LuxR and antiholin sequence: For our kill switch model first we design a circuit that secrete antiholin LuxR gene to supress the activity of holin and endolysin enzymes for working under normal conditions by digesting gluten into its small particles. After this composite part we design a new circuit that our composite gene part secrete a thickener that dough doesn't lose its stability and viscose structure type for consumers' choice.

Lux promoter activated by thickener(Xanthan Gum) gene part of LuxR and it start to lyse the cell with holin and endolysin activity.

Xanthan Gum Structure

300°C Oven

After dough fermentation, dough is ready to bake under 300 °C, which kills all of the microorganism inside it(except sporulated bacteria). And also the enzyme will be denaturated.