Team:USTC/Project/safe

From 2010.igem.org

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== overview ==
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== Overview ==
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<p ><span class="firstletter">T</span>hanks to the study of synthetic biology ,more efficient ways to produce medical treatments, to solve pollution problems.etc. have been available.But it may also lead to synthesis or redesign of harmful pathogens (e.g., smallpox) by malicious actors.So it is necessary that we make sure we conduct experiment  with a non-infectious host organism and estimate the potential risks before and when doing the experiment.Besides,strictly following some standards on synthetic biology concerning the safety is also required.</p>
 +
== Experimental Safety ==
 +
*Just like any other practical activities in school science, all microbiology investigations require the user to adopt good laboratory practice. The [[Team:USTC/Notebook| preliminary experiment training]] made sure that every one of us get familiar with the whole system of basic microbiology investigations and get adroit skills especially for those in related majors.
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*'''Several regulations has been set to guarantee personal protection.''' <br />
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<!--[http://www.microbiologyonline.org.uk/safety.html| refer to messages online]
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-->
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[[Image:poison.jpg]]
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**Food or drink should not be stored or consumed in a laboratory or prep room that is used for microbiology. <br />
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**No-one should lick labels, apply cosmetics, chew gum, suck pens or pencils or smoke in a laboratory or prep room. <br />
 +
**Facilities should be provided within the laboratory or prep room for hands to be washed with soap after handling microbial cultures and whenever leaving the lab. <br />
 +
**Paper towels or some other hygienic method should be used for drying hands. If contamination of the hands is suspected, then they should be washed immediately with soap and water. <br />
 +
**Cuts or abrasions should be protected by the use of waterproof dressings or by wearing disposable gloves. <br />
 +
**Safety glasses should be worn in some certain circumstances,eg. when using a UV lamp.<br />
 +
*'''Work Safety in our lab is categorized into two levels as follows:'''
 +
**Level 1: ''organisms we work with have little known risk and are observed in the closed containers in which they are grown.'' Microbes ('''K12''') we growing is tested as non-risk and harmless, furthermore, by culturing closed containers which are taped before examination and remain unopened unless the cultures inside have been killed by the autoclave sterilizer. We made every effort to exclude any possibility of unsafety.
 +
**Level 2: ''biological reagents we use are considered on environmental and human safety.'' We choose '''GelRed''' instead of EB as our nuleic acid stains.
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== experimental safety ==
+
==Safety Issues in China==
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*From Feb.4th to Feb.13th, a collective training is held targeting to the practice of basic experiment. Setting GFP protein expression system as an example, we learn from the program how to construct standard components and then an expression system. Also,it`s the time we get to know each other and become a team as a whole.
+
<p>On the June 24, 2010， a symposium was held in Suzhou by CAST new ideas new doctrine Academic Salon, discussing  biological safety issues in China.</p>
 +
<p>The issues includes</p>
 +
<p>***how to limit the abuse of synthetic biology technology and prevent bio-hacking, biological terrorists, in order to protect public safety.</p>
 +
<p>***What the influence of synthetic life may be on the ecosystem</p>
 +
<p> how to control the polution manipulated genes may do to the environment</p>
 +
etc.
 +
For more information>>[http://www.biols.cas.cn/xwdt/zhxw/201007/t20100701_2890628.html]
 +
<p></p>
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<p></p>
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**The contents of the training are listed as followed:
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==Security==
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***1. outlines
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<p>
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***2. E.coli culture (Medium preparation, Inoculation, Aseptic operation)
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We held a discussion on this open-security delima and generated some suggestions for this issue.
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***3. plasmid extraction
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*'''Precaution'''
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***4. PCR
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**'''A declaration is extremely necessary:''' The declaration should include not only the authorship but also the committement not to misuse the project.Obviously, a general declaration for all the iGEM projects is needed.
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***5. DNA Electrophoresis
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**'''The registration information for OpenWetWare should be audited under a strict standard:''' Although an extensvie group of users means a large influence, the armory of synthetic biology world without any fence would be a threat to our society since none can guarantee all the prospective users are research-oriented.
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***6. Double Digest
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*'''Sanction: '''Given the unpredictability and severity of crimes in biology field, the levels of punishment are hard to define. However, any possible damage should have a punishment level in the scope of legal regulations.
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***7. reclaim and appraise of the product of enzyme cutting
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</p>
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***8. Ligation
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***9. preparation of competent cell
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***10. genomic screening of masculine clone
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***11.  DNA sequencing
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== asking the experts ==
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==Consulting with Experts==
 +
In case we may neglect some potential risks of the Bacterial Microcompartment (BMC) encoded by pdu operon from Salmonella enterica,we also wrote a letter consulting the safety issues of BMC to Prof. Martin Warren (one of the writers of ''Synthesis of Empty Bacterial Microcompartments, Directed Organelle Protein Incorporation, and Evidence of Filament-Associated Organelle Movement'' [http://www.sciencedirect.com/science?_ob=ArticleURL&_udi=B6WSR-4YX6M74-H&_user=1555926&_coverDate=04%2F23%2F2010&_rdoc=1&_fmt=high&_orig=search&_origin=search&_sort=d&_docanchor=&view=c&_searchStrId=1507901721&_rerunOrigin=scholar.google&_acct=C000053683&_version=1&_urlVersion=0&_userid=1555926&md5=7792f360749d8fdb12d3e537c5df4ce5&searchtype=a]
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<p></p>
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<p>Below are the qustions and his answers.</P>
 +
<p>1)  Some people think the E.coli we are engineering could evolve into some superbug with the help of the BMC.What do you think the chances of that may be? What measure do you think we should take to prevent that?</p>
 +
<p><em>'You are probably doing the engineering in an E. coli laboratory strain - which is quite safe and unlikely to survive if released. Moreover, there is no evidence that the BMC confers any great advantage - E. coli has already lost the pdu operon so it cannot be that important.'</em></p>
 +
<p></p>
 +
<p>2) Beside doing the experiment,we have already organized a campus-wide talk to extend awareness on synthetic biology as well as to instill a scientific and responsible attitude towards it.To what extent do you think that can help eliminate people's panic over our work? Have you ever done something similar?</p>
 +
<p><em>'The important thing is not to be arrogant with science - take on people's concerns and answer each question they raise. Synthetic biology is an amalgamation of genetic and metabolic engineering. As such, Nature has been doing this for 3.5 billion years. We still have a lot to learn and we do have to be careful. Nonetheless, synthetic biology offers genuine hope for the enhanced production of biofuels, vitamins, drugs and chemicals, which is managed properly could enhance the lives of many people worldwide.'</em></p>
 +
<p></p>
 +
<p></p>
 +
<p><strong>Also we consulted Prof. Bobik, Thomas A, who is also an expert in BMC.[http://www.biomedexperts.com/Profile.bme/130876/Thomas_A_Bobik].</strong></P>
 +
<p>Here is his reply.</P>
 +
<p><em>In my opinion there is no chance that engineering a microcompartment into E. coli will create a superbug. Such microcompartments are already produced by certain species of E. coli and they are not superbugs. Moreover, most genetic changes made the lab reduce the fitness of the organism in nature. The microcompartment is not associated with any major virulence factors or toxins. Martin Warren’s group in Kent UK has made a Citrobacter MCP in E. coli. Comprehensive lab procedures to prevent the escape of engineered organisms, potentially harmful or not, should be used.</em></P>
 +
<p><strong>Thanks to them ,our primary concerns are lifted.Thank you very much for your help and kindness!O(∩_∩)O~</strong></p>
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==Key Questions==
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==answering key questions==
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<p>For iGEM 2010 teams are asked to detail how they approached any issues of biological safety associated with their projects. Specifically, teams should consider the following questions: </p>
<p>For iGEM 2010 teams are asked to detail how they approached any issues of biological safety associated with their projects. Specifically, teams should consider the following questions: </p>
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<p>No. Our strains ,promoters and linked genes(amd, GFP, etc.) are conisdered to cause no harm to the environment.Also we make sure that the residual bacteria are killed every time our experiments were over.</p>
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<p></p>
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<p></p>
     <li><strong> Do any of the new BioBrick parts (or devices) that you made this year raise any safety issues? If yes,
     <li><strong> Do any of the new BioBrick parts (or devices) that you made this year raise any safety issues? If yes,
       </strong>
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<p>No.As have been shown in the part of  [[Team:USTC/Project/safe|Consulting with Experts]] </p>
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<p></p>
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<p></p>
     <li><strong>Is there a local biosafety group, committee, or review board at your institution? </strong>
     <li><strong>Is there a local biosafety group, committee, or review board at your institution? </strong>
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    <li><strong>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></li>
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<p></p>
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<p></p>
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<p>No.But there are some good trends towards it.More and more people come to realize that bio-safety issues should be carefully considered. Besides more measures such as risk estimation etc.are taken to ensure more safer biological research. For more information[[Team:USTC/Project/safe|Safety Issues in China]]</p>
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Latest revision as of 22:56, 27 October 2010

An Integrated Platform Based on Bacterial Microcompartment for de novo Proteinaceous Artificial Organelles

Overview

Thanks to the study of synthetic biology ,more efficient ways to produce medical treatments, to solve pollution problems.etc. have been available.But it may also lead to synthesis or redesign of harmful pathogens (e.g., smallpox) by malicious actors.So it is necessary that we make sure we conduct experiment with a non-infectious host organism and estimate the potential risks before and when doing the experiment.Besides,strictly following some standards on synthetic biology concerning the safety is also required.

Experimental Safety

  • Just like any other practical activities in school science, all microbiology investigations require the user to adopt good laboratory practice. The preliminary experiment training made sure that every one of us get familiar with the whole system of basic microbiology investigations and get adroit skills especially for those in related majors.
  • Several regulations has been set to guarantee personal protection.

Poison.jpg

    • Food or drink should not be stored or consumed in a laboratory or prep room that is used for microbiology.
    • No-one should lick labels, apply cosmetics, chew gum, suck pens or pencils or smoke in a laboratory or prep room.
    • Facilities should be provided within the laboratory or prep room for hands to be washed with soap after handling microbial cultures and whenever leaving the lab.
    • Paper towels or some other hygienic method should be used for drying hands. If contamination of the hands is suspected, then they should be washed immediately with soap and water.
    • Cuts or abrasions should be protected by the use of waterproof dressings or by wearing disposable gloves.
    • Safety glasses should be worn in some certain circumstances,eg. when using a UV lamp.
  • Work Safety in our lab is categorized into two levels as follows:
    • Level 1: organisms we work with have little known risk and are observed in the closed containers in which they are grown. Microbes (K12) we growing is tested as non-risk and harmless, furthermore, by culturing closed containers which are taped before examination and remain unopened unless the cultures inside have been killed by the autoclave sterilizer. We made every effort to exclude any possibility of unsafety.
    • Level 2: biological reagents we use are considered on environmental and human safety. We choose GelRed instead of EB as our nuleic acid stains.

Safety Issues in China

On the June 24, 2010， a symposium was held in Suzhou by CAST new ideas new doctrine Academic Salon, discussing biological safety issues in China.

The issues includes

***how to limit the abuse of synthetic biology technology and prevent bio-hacking, biological terrorists, in order to protect public safety.

***What the influence of synthetic life may be on the ecosystem

how to control the polution manipulated genes may do to the environment

etc. For more information>>[http://www.biols.cas.cn/xwdt/zhxw/201007/t20100701_2890628.html]

Security

We held a discussion on this open-security delima and generated some suggestions for this issue.

  • Precaution
    • A declaration is extremely necessary: The declaration should include not only the authorship but also the committement not to misuse the project.Obviously, a general declaration for all the iGEM projects is needed.
    • The registration information for OpenWetWare should be audited under a strict standard: Although an extensvie group of users means a large influence, the armory of synthetic biology world without any fence would be a threat to our society since none can guarantee all the prospective users are research-oriented.
  • Sanction: Given the unpredictability and severity of crimes in biology field, the levels of punishment are hard to define. However, any possible damage should have a punishment level in the scope of legal regulations.

Consulting with Experts

In case we may neglect some potential risks of the Bacterial Microcompartment (BMC) encoded by pdu operon from Salmonella enterica,we also wrote a letter consulting the safety issues of BMC to Prof. Martin Warren (one of the writers of Synthesis of Empty Bacterial Microcompartments, Directed Organelle Protein Incorporation, and Evidence of Filament-Associated Organelle Movement [http://www.sciencedirect.com/science?_ob=ArticleURL&_udi=B6WSR-4YX6M74-H&_user=1555926&_coverDate=04%2F23%2F2010&_rdoc=1&_fmt=high&_orig=search&_origin=search&_sort=d&_docanchor=&view=c&_searchStrId=1507901721&_rerunOrigin=scholar.google&_acct=C000053683&_version=1&_urlVersion=0&_userid=1555926&md5=7792f360749d8fdb12d3e537c5df4ce5&searchtype=a]

Below are the qustions and his answers.

1) Some people think the E.coli we are engineering could evolve into some superbug with the help of the BMC.What do you think the chances of that may be? What measure do you think we should take to prevent that?

'You are probably doing the engineering in an E. coli laboratory strain - which is quite safe and unlikely to survive if released. Moreover, there is no evidence that the BMC confers any great advantage - E. coli has already lost the pdu operon so it cannot be that important.'

2) Beside doing the experiment,we have already organized a campus-wide talk to extend awareness on synthetic biology as well as to instill a scientific and responsible attitude towards it.To what extent do you think that can help eliminate people's panic over our work? Have you ever done something similar?

'The important thing is not to be arrogant with science - take on people's concerns and answer each question they raise. Synthetic biology is an amalgamation of genetic and metabolic engineering. As such, Nature has been doing this for 3.5 billion years. We still have a lot to learn and we do have to be careful. Nonetheless, synthetic biology offers genuine hope for the enhanced production of biofuels, vitamins, drugs and chemicals, which is managed properly could enhance the lives of many people worldwide.'

Also we consulted Prof. Bobik, Thomas A, who is also an expert in BMC.[http://www.biomedexperts.com/Profile.bme/130876/Thomas_A_Bobik].

Here is his reply.

In my opinion there is no chance that engineering a microcompartment into E. coli will create a superbug. Such microcompartments are already produced by certain species of E. coli and they are not superbugs. Moreover, most genetic changes made the lab reduce the fitness of the organism in nature. The microcompartment is not associated with any major virulence factors or toxins. Martin Warren’s group in Kent UK has made a Citrobacter MCP in E. coli. Comprehensive lab procedures to prevent the escape of engineered organisms, potentially harmful or not, should be used.

Thanks to them ,our primary concerns are lifted.Thank you very much for your help and kindness!O(∩_∩)O~

Key Questions

For iGEM 2010 teams are asked to detail how they approached any issues of biological safety associated with their projects. Specifically, teams should consider the following questions:

  1. Would any of your project ideas raise safety issues in terms of:
    • researcher safety,
    • public safety, or
    • environmental safety?

    2. No. Our strains ,promoters and linked genes(amd, GFP, etc.) are conisdered to cause no harm to the environment.Also we make sure that the residual bacteria are killed every time our experiments were over.

  2. Do any of the new BioBrick parts (or devices) that you made this year raise any safety issues? If yes,
    • did you document these issues in the Registry?
    • how did you manage to handle the safety issue?
    • How could other teams learn from your experience?

    3. No.As have been shown in the part of [[Team:USTC/Project/safe|Consulting with Experts]]

  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?

    4. No.But there are some good trends towards it.More and more people come to realize that bio-safety issues should be carefully considered. Besides more measures such as risk estimation etc.are taken to ensure more safer biological research. For more information[[Team:USTC/Project/safe|Safety Issues in China]]

 

Retrieved from "http://2010.igem.org/Team:USTC/Project/safe"