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           <td width="235" align="center" valign="middle" bgcolor="#990000"><a href="http://2011.igem.org/Team:Fatih_Turkey"><span class="style3">HOME</span></a></td>
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           <td width="293" align="center" valign="middle" bgcolor="#1D3551"><a href="therainbowgraveyard.html"><span class="style3">THE RAINBOW GRAVEYARD</span></a></td>
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           <td width="235" align="center" valign="middle" bgcolor="#960C47"><a href="notebook.html"><span class="style3">&nbsp;NOTEBOOK</span></a></td>
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         <td width="793"><p class="style3">In our history, our hero is B.subtilis because of capability of catching E.coli, especially  gram-negative bacteria species presenting LPS layer with the help of  synthesized Limulus anti-LPS factor (LALF) onto the biofilm. On the other hand,  in The Canvas Town, all species of our project story including B.subtilis  police squad and E.coli gang can synthesize Reflectin protein transferred from cephalopod. </p>
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         <td width="793" height="140" bgcolor="#FFFFFF"><p align="center"><strong> </strong><strong>FAT</strong><strong>IH UNIVERSITY MEDICAL SCHOOL</strong><br />
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          <p class="style3">Here, we will answer the safety questions to tell how we will take precautions in our lab experiments and in usage of our project in public.</p>
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              <strong>ANSWERS TO NEW SAFETY AND SECURITY QUESTIONS</strong><strong> </strong></p>
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           <p class="style3"><strong>1. Would any of your project ideas raise safety issues in terms of:</strong> <br />
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          <p><strong>1. Would the materials used in your project and/or your final product pose:</strong><br />
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              <a name="Researcher_Safety" id="Researcher_Safety"></a>We have one plan to raise safety issues when studying with B.subtilis. Under stress conditions,&nbsp;<em>B. subtilis</em>&nbsp;will form spores. These spores are highly resistant versions of single cells. While&nbsp;<em>B. subtilis</em>&nbsp;itself isn't pathogenic, its spores can be damaging if inhaled. They are also highly resistant to many conditions that are used to kill cells. Therefore, in other iGEM projects, teams in future may want to kill spores to increase their projects’ safety level. To achieve this, we  optimize a procedure to kill spores in liquid cultures and on solid surfaces with the help of aqueous dissolved Oxygen, Ascorbic Acid, and Copper Ions involving treatment, whose details are given in human practice part. <br />
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              <strong>a. Risks to the safety and health of team members or others in the lab?</strong><br />
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              <strong>Researcher Safety</strong><br />
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            Actually few hazardous  chemicals and solutions 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.  </p>
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            Our all experiments have been performed in the Synthetic Biology lab, opened for following iGEM competitions at Fatih Medical  School. During project, we have made lab meetings in a week to consider safety rules and lab regulations before starting to our project. Also, during lab experiments, lab  technicians and instructors of our team have been helping in handling and safety removing of B.subtilis and E.coli bacteria culture. Also, project advisor  has been participating in all lab executions to perform risk assessments which may rise during experiments and lab usage. In addition, we plan to design a  biofilm containing anti-LPS factor even without B.subtilis and its spores in our project. Because of that reason, we will also kill B.subtilis spores on the  biofilm before testing our biofilm with exposure to E.coli by performing dissolved oxygen procedure. This procedure is optimized to kill the spores which may be infectious to humans when using our designed biofilm on the  surfaces. Thus, we try to maximize safety of our project. Next, we add some general safety issues related with our studies in our lab as follows:</p>
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           <p><strong>b. Risks to the safety and health of the general public if released by design or accident?</strong><br />
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          <p class="style3"><strong>Some safety Issues:</strong><br />
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            When released by accident,  our parts and materials actually cause no negative damage to the general public. B.subtilis is known not to be associated with disease process in humans  in regular conditions and thus are supposed to be benign by nature and present  no danger to anyone. Only under stress conditions,&nbsp;B. subtilis&nbsp;may  form spores and these spores are resistant versions of single cells. While&nbsp;B. subtilis&nbsp;itself isn't pathogenic, its spores may be  infectious if inhaled. But all of our team members are trained for safety of the laboratory rules and use mask and gloves when dealing with bacteria. Besides  all experiments are performed in synthetic laboratory designated by Fatih  University Medical School and no material is carried out of the laboratory. However to increase public safety of our project, in case of accident, our plan is to destroy particles including B.subtilis by cleaning the biofilm from the spores and  treating with Fenton reagent containing dissolved oxygen and other constituents.</p>
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             1. What protective equipment will be used to minimize exposure of laboratory personnel who will be working with the agent?&nbsp;<strong>lab coats and gloves</strong><br />
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          <p><strong>c. Risks to environmental quality if released by design or  accident?</strong></p>
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             2. What will be used for handwashing?&nbsp;<strong>Soap or alcohol gel</strong><br />
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          <p>Bacillus subtilis strain  3610 is a wild type strain that is already widespread in the environment. Bsubtilis strain 168  is a derivative strain of the 3610 and has disabling auxotrophs mutations  that makes it even less likely to colonize or cause harm to human or animal health. Our experiment does not include any modifications, which enhance their ability to survive or disseminate. Thus, there is no specific environmental risk associated with use of the Bacillus subtilis strains except its spore formation. In case of accident, cleaning and treating the spores with Fenton reagent as mentioned above provide environmental safety.  Besides all procedures are performed in a specified laboratory.<br />
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            3. Please state the signs and symptoms of infection.&nbsp;<strong>Ingestion of&nbsp;</strong><em><strong>E. coli</strong></em><strong>&nbsp;may cause diarrhea with or without abdominal crampsSkin infections may be inflammed. Conjunctivitis may occur after inoculation of  the eye.</strong><br />
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             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. <br />
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             4. Please  describe post-exposure therapy to be used in the event of accidental exposure.&nbsp;<strong>Rinse contaminated areas with soap and water. Mucous membranes should be flushed with  water.</strong>&nbsp;<strong>For accidental ingestion rinse mouth  with water, but do not swallow</strong><br />
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             All bacterial waste are kept in 10% bleaching solution for one day, then are autoclaved to be sterilized. </p>
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             Actually, in lab procedures, there were no many  chemical hazards. In gel preparation and electrophoresis, there were some dangerous chemical but these procedures were being performed in the special electrophoresis room and its responsible team members were potentially informed about the hazards. </p>
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          <p><strong>d. Risks to security through malicious misuse by individuals,  groups or states?</strong><br />
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          <p class="style3">On the other hand, in other procedures, we have had  some biological hazards especially related with B.subtilis. Throughout the project, we used the <em>Escherichia coli</em> strain  Top10 and BL1; <em>Bacillus subtilis</em> strain 3610 and <em>Bacillus subtilis</em> strain 168. Wild-type <em>E. coli</em> is classified as a hazard group 2 pathogen by the UK Advisory Committee on the Dangerous Pathogens (ACDP). Wild-type <em>Bacillus  subtilis</em> (i.e. strain 3610) is classified as an ACDP hazard group 1  organism and its derivative <em>B. subtilis</em> strain 168 has disabling  auxotrophs mutations (e.g. conferring a requirement for tryptophan, Zeigler <em>et al</em>, 2008) that makes it even less likely to colonise or cause harm to human or animal health. B.subtilis is at level 1 biosafety according to World Health Organization (WHO). </p>
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            Please explain your  responses (whether yes or no) to these questions. Specifically, are any parts or devices in your project associated with (or known to cause):<br />
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           <p class="style3"><strong>Public Safety</strong></p>
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            - pathogenicity,  infectivity, or toxicity? No <br />
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          <p class="style3">To increase public safety of our project, our first plan is  to kill all infectious particles especially B.subtilis spores on the biofilmTo do this, as we mentioned above, we clean the biofilm from the spores by the  treatment with Fenton reagent containing dissolved oxygen and other  constituents. Thus, our designed biofilm will be safe for public use and its  effectiveness and safety level can be improved in future. </p>
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             - threats to environmental quality? No<br />
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          <p class="style3">B.subtilis is not associated with disease process in humans, however, may prove to be opportunistic pathogens capable of causing infection  in the very young, in the aged and in&nbsp;immunodeficient&nbsp;or&nbsp;immunosuppressed&nbsp;individuals when we regarding public safety. Before using our project in public condition,  especially on food safety and non-pathogenic surface safety via using biofilm,  considerable further research and tests are absolutely necessary as our Fenton  reagent treatment protection. Indeed, production of biofilm from B.subtilis  without B.subtilis bacteria and only including anti-LPS factor is necessary and  should be such a non-pathogenic biofilm. To be able to remove pathogenic effects  of B.subtilis and its waste is necassary before using on surface to be  bacteriacidal for gam-negative bacteria via anti-LPS factor for public safety. </p>
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            - security concerns? No<br />
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           <p class="style3"><strong>Environmental Safety</strong></p>
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            As explained below:<br />
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           <p class="style3"><em>Bacillus subtilis</em> strain 3610 is wild type strain that is already widespread in the environment. It has not been modified to enhance their ability to survive,  disseminate or displace other organisms. Thus, there is no specific  environmental hazards associated with the <em>Bacillus subtilis</em> strain 3610 except its spore formation. Environmental safety is kept to prevent from spores in our synthetic biofilm by Fenton reagent treatment. </p>
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             Nothing could be used  maliciously in our project. The materials we use are commonly used in experimental procedures in various laboratories all over the world and all are harmless and do not pose any threat to environment and public as well as security concerns. <br />
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          <p class="style3"><em>E. coli</em> strain TOP10 and BL1 have very limited ability to survive outside  the laboratory so that it would be unable to survive, disseminate, or displace  other organisms in environment. Therefore, there is no specific environmental  hazards associated with the <em>E. coli</em> strains. </p>
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            Throughout the project, we used the Escherichia coli strains Top10 and BL1, Bacillus subtilis strains 3610 and 168. Wild-type E. coli is classified as a hazard group 2 pathogen by the UK Advisory Committee on the Dangerous Pathogens (ACDP) and Wild-type Bacillus  subtilis (i.e. strain 3610) is classified as hazard group 1 organism by the ACDP and its derivative B. subtilis strain 168 has disabling auxotrophs mutations (e.g. conferring a requirement for tryptophan, Zeigler DR et al, 2008.  J of Bacteriology) that makes it even less likely to colonize or cause harm to  human or animal health. B.subtilis is at level 1 biosafety according to World Health Organization (WHO).</p>
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          <p class="style3">All bacterial waste are kept in 10% bleaching solution for one day then autoclaved to be sterilized</p>
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           <p><strong>2. If your response to any of the questions above is yes:</strong><br />
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          <p class="style3">&nbsp;</p>
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              <strong> a. Explain how you addressed these issues in project design and while conducting laboratory work. </strong><br />
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          <p class="style3">&nbsp;</p>
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              <strong>b. Describe and document safety, security, health and/or  environmental issues as you submit your parts to the Registry</strong></p>
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          <p class="style3">&nbsp;</p>
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           <p><strong>3. Under what biosafety provisions will / do you operate?</strong></p>
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          <p class="style3">&nbsp;</p>
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           <p><strong>a. Does your institution have its own biosafety rules and if so what are they? Provide a link to them online if possible.</strong><br />
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           <p class="style3"><strong>2. Do any of the new BioBrick parts (or devices) that you made this year raise any safety issues?</strong> </p>
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            Yes, our institution 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. The web link is given as (<a href="http://www.fatihmed.edu.tr/icerik/guvenlikkilavuzu.php">http://www.fatihmed.edu.tr/icerik/guvenlikkilavuzu.php</a>). </p>
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           <p class="style3">&nbsp;&nbsp;&nbsp;&nbsp; A.Did you document these issues in the Registry?</p>
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           <p><strong>b. Does your institution have an Institutional Biosafety Committee  or equivalent group? If yes, have you discussed your project with them?  Describe any concerns or changes that were made based on this review</strong> </p>
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          <p class="style3">We have documented our safety issues possessing device with the part ID Bba_K541001. The device which produces and secretes &nbsp;Limulus  anti-LPS factor (LALF)&nbsp; into medium by B. Subtilis, which &nbsp;can bind  LPS on gram negative bacteria and neutralize its biological effects or enhance its clearance could have important clinical applications.&nbsp;Lipopolysaccharide  (LPS), or endotoxin, is the major mediator of septic shock, a serious complication of Gram-negative bacterial infections in humans. Thus, this part can be used to kill infectious gram negative bacteria in iGEM projects if needed like antibiotic. <br />
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           <p>Yes. In Fatih 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 Fatih University Hospital, Prof. Dr. Mehmet Gunduz. Form on safety rules of Fatih  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. (Further questions can be directed to Prof. Gunduz, tel: +90-312-203 5103, mgunduz@fatih.edu.tr).</p>
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            Also we will add alternative devices and parts to raise safety issues in the registry. </p>
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           <p><strong>c.Will / did you receive any biosafety and/or lab training  before beginning your project? If so, describe this training.</strong></p>
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           <p class="style3">&nbsp;&nbsp;&nbsp; B.How did you manage to handle the safety issue?</p>
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           <p>Yes, we did. Our advisor provided us biosafety and lab training before starting of 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.  </p>
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           <p class="style3">In  our Project, we plan to design LALF protein producing system in a specific  bacteria that will not be harmed by this bactericide itself. To do this, we needed a bacteria type that has no lip-A structure which is bound by LALFThus, we decided to use Bacillus subtilis colonies which are the most prefered  gram positive  bacteria in iGEM. In conclusion, our “protector” bacteria affects on E. Coli  mortally, therefore our remaining region is cleared from E.coli. As a future aspect, a special covering material, a biofilm for example, may be used as a cover sheet on surfaces that leads to protection of bacteria.</p>
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           <p><strong>d. Does your country have national biosafety regulations or  guidelines? If so, provide a link to them online if possible.</strong></p>
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           <p class="style3">&nbsp;&nbsp;&nbsp; C.How could other teams learn from your experience?</p>
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           <p>Yes, Turkey has national biosafety regulations and the link is given as (<a href="http://www.tbbdm.gov.tr/Home/BioSafetyCouncilHome/BioSafetyCouncilHomeChoose.aspx">http://www.tbbdm.gov.tr/Home/BioSafetyCouncilHome/BioSafetyCouncilHomeChoose.aspx</a>). </p>
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           <p class="style3">Other teams can have knowledge about our experiences with  anti-LPS factor synthesized from B.subtilis against E.coli via our wiki, especially in project plan site. <br />
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           <p><strong>4. OPTIONAL QUESTION: Do you have other ideas on how to deal with safety or security issues that could be useful for future iGEM competitions? How could parts, devices and systems be made even safer through biosafety engineering?</strong></p>
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            Into iGEM forum system, we have opened  a box for `The safety parts` under `lab’ main box (<a href="http://igem.org/forum/Comment_List?n=322&amp;s=1">http://igem.org/forum/Comment_List?n=322&amp;s=1</a>); thus, teams can learn from the experiences of parts of other  teams. Also, we can add safety issues video via Youtube and integrate into the  forum to inform other teams. </p>
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          <p>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.<br />
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          <p class="style3"><strong>3. Is there a local biosafety group,  committee, or review board at your institution?</strong> </p>
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            Second, a new prize related with security and safety issues may take place in the judging procedure separated from “Best Human Practices” prize. Existence of “Best Safety Part” or “Best Safety Application” can emphasize the importance of the safety issues and  inspire iGEM teams to work on these issues and may give a chance to develop new  ideas, to interrogate current safety and security applications in order to improve them.<br />
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<p class="style3">In Fatih University, Patient and Employee Safety Committee functions as preservation and control of use of chemicals, radiation and infectious medical waste in our laboratory. In addition, the committee performs courses on the safety issues to scientists and workers.</p>
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           Third, 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></td>
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          <p class="style3">&nbsp;</p>
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          <p class="style3"><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 />
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            We think that Synthetic Biology Safety Police Squads can be founded for each continental competitions. This squad may be chosen from an iGEM team from each continent or colloboration of some experienced teams or independent individuals. Firstly, an  iGEM team from a continent wanting to be the safety squad, can control new  established synthetic biology labs and perform meetings via electronic  communication ways (i.e. Skype) to share their safety precautions with new iGEM  teams about their lab needs for security and improvement of project safety of new iGEM teams. For example, experienced iGEM team which may be also experienced with viral Synthetic biology projects can help another iGEM teams which possess to perform synthetic biology projects on viruses. Thus,  experinced teams can collaborate with new teams their experiences while doing such projects. Thus, the Synthetic Biology Safety Police iGEM team can be also regarded as completing their ‘Collaboration option with other teams’  which is required for Gold Award in judgement. </p>
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           <p class="style3">In addition, a safety plan, procedures, prerequisites and meeting how to perform a safe iGEM project in a lab can be gathered in a CD which may be distributed to  each iGEM team with Part Distribution. Thus, each team can update their labs  and their project thinking ways during studying time. </p></td>
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     </table>     

Latest revision as of 05:10, 25 August 2011

 
HOME CANVAS  TOWN THE RAINBOW GRAVEYARD  NOTEBOOK
SAFETY

 FATIH UNIVERSITY MEDICAL SCHOOL
ANSWERS TO NEW SAFETY AND SECURITY QUESTIONS

1. Would the materials used in your project and/or your final product pose:
a. Risks to the safety and health of team members or others in the lab?
Actually few hazardous chemicals and solutions 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.  

b. Risks to the safety and health of the general public if released by design or accident?
When released by accident, our parts and materials actually cause no negative damage to the general public. B.subtilis is known not to be associated with disease process in humans in regular conditions and thus are supposed to be benign by nature and present no danger to anyone. Only under stress conditions, B. subtilis may form spores and these spores are resistant versions of single cells. While B. subtilis itself isn't pathogenic, its spores may be infectious if inhaled. But all of our team members are trained for safety of the laboratory rules and use mask and gloves when dealing with bacteria. Besides all experiments are performed in synthetic laboratory designated by Fatih University Medical School and no material is carried out of the laboratory. However to increase public safety of our project, in case of accident, our plan is to destroy particles including B.subtilis by cleaning the biofilm from the spores and treating with Fenton reagent containing dissolved oxygen and other constituents.

c. Risks to environmental quality if released by design or accident?

Bacillus subtilis strain 3610 is a wild type strain that is already widespread in the environment. B. subtilis strain 168  is a derivative strain of the 3610 and has disabling auxotrophs mutations  that makes it even less likely to colonize or cause harm to human or animal health. Our experiment does not include any modifications, which enhance their ability to survive or disseminate. Thus, there is no specific environmental risk associated with use of the Bacillus subtilis strains except its spore formation. In case of accident, cleaning and treating the spores with Fenton reagent as mentioned above provide environmental safety. Besides all procedures are performed in a specified laboratory.
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 waste are kept in 10% bleaching solution for one day, then are autoclaved to be sterilized.

d. Risks to security through malicious misuse by individuals, groups or states?
Please explain your responses (whether yes or no) to these questions. Specifically, are any parts or devices in your project associated with (or known to cause):
- pathogenicity, infectivity, or toxicity? No
- threats to environmental quality? No
- security concerns? No
As explained below:
Nothing could be used maliciously in our project. The materials we use are commonly used in experimental procedures in various laboratories all over the world and all are harmless and do not pose any threat to environment and public as well as security concerns.
Throughout the project, we used the Escherichia coli strains Top10 and BL1, Bacillus subtilis strains 3610 and 168. Wild-type E. coli is classified as a hazard group 2 pathogen by the UK Advisory Committee on the Dangerous Pathogens (ACDP) and Wild-type Bacillus subtilis (i.e. strain 3610) is classified as hazard group 1 organism by the ACDP and its derivative B. subtilis strain 168 has disabling auxotrophs mutations (e.g. conferring a requirement for tryptophan, Zeigler DR et al, 2008. J of Bacteriology) that makes it even less likely to colonize or cause harm to human or animal health. B.subtilis is at level 1 biosafety according to World Health Organization (WHO).

2. If your response to any of the questions above is yes:
 a. Explain how you addressed these issues in project design and while conducting laboratory work.
b. Describe and document safety, security, health and/or environmental issues as you submit your parts to the Registry

3. Under what biosafety provisions will / do you operate?

a. Does your institution have its own biosafety rules and if so what are they? Provide a link to them online if possible.
Yes, our institution 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. The web link is given as (http://www.fatihmed.edu.tr/icerik/guvenlikkilavuzu.php).

b. Does your institution have an Institutional Biosafety Committee or equivalent group? If yes, have you discussed your project with them? Describe any concerns or changes that were made based on this review

Yes. In Fatih 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 Fatih University Hospital, Prof. Dr. Mehmet Gunduz. Form on safety rules of Fatih 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. (Further questions can be directed to Prof. Gunduz, tel: +90-312-203 5103, mgunduz@fatih.edu.tr).

c.Will / did you receive any biosafety and/or lab training before beginning your project? If so, describe this training.

Yes, we did. Our advisor provided us biosafety and lab training before starting of 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.  

d. Does your country have national biosafety regulations or guidelines? If so, provide a link to them online if possible.

Yes, Turkey has national biosafety regulations and the link is given as (http://www.tbbdm.gov.tr/Home/BioSafetyCouncilHome/BioSafetyCouncilHomeChoose.aspx).

4. OPTIONAL QUESTION: Do you have other ideas on how to deal with safety or security issues that could be useful for future iGEM competitions? How could parts, devices and systems be made even safer through biosafety engineering?

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.
Second, a new prize related with security and safety issues may take place in the judging procedure separated from “Best Human Practices” prize. Existence of “Best Safety Part” or “Best Safety Application” can emphasize the importance of the safety issues and inspire iGEM teams to work on these issues and may give a chance to develop new ideas, to interrogate current safety and security applications in order to improve them.
Third, 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.