Team:UC-Santa Cruz/Safety

From 2013.igem.org

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<b>**Safety forms were approved by David Lloyd and Julie McNamara. <br><br>
<b>**Safety forms were approved by David Lloyd and Julie McNamara. <br><br>
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<b> 1) Please describe the chassis organism(s) you will be using for this project. If you will be using more than one chassis organism, provide information on each of them:</b>
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1) Please describe the chassis organism(s) you will be using for this project. If you will be using more than one chassis organism, provide information on each of them:</b>
<p>
<p>
<ul>
<ul>
<li> Species: E. coli <br>
<li> Species: E. coli <br>
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<li> Strain: TG1 and Epi300 <br>
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<li> Strain: K12 derived Life Technologies TOP10 strain <br>
<li> Risk Group: 1 <br>
<li> Risk Group: 1 <br>
<li> Risk Group Source Link: http://www.absa.org/riskgroups/bacteriasearch.php?genus=Escherichia&species=coli <br>
<li> Risk Group Source Link: http://www.absa.org/riskgroups/bacteriasearch.php?genus=Escherichia&species=coli <br>
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<br>
<br>
<ul>
<ul>
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<li> Species: Caulobacter crescentus <br>
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<li> Strain: CB15 and CB15N <br>
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<li> Risk Group: 1 <br>
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<li> Risk Group Source Link: http://www.baua.de/en/Topics-from-A-to-Z/Biological-Agents/TRBA/pdf/TRBA-466.pdf?__blob=publicationFile&v=3 <br>
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<li> Disease risk to humans? If so, which disease?: Ubiquitous presence in environmental water supplies including human drinking water and swimming pools. Single case reported of Caulobacter acting as a pathogen in a human.<br>
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</ul>
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</p>
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<br><br>
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<b> 2) Highest Risk Group Listed: 1 <br>
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See pg 52 of Caulobacter PDF document above for risk group for Caulobacter crescentus. </b>
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<br><br>
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<b> 3) List and describe all new or modified coding regions you will be using in your project. (If you use parts from the 2013 iGEM Distribution without modifying them, you do not need to list those parts.)</b>
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 +
<p>
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<ul>
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<li> Part name: BBa_K559000 <br>
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<li> Where did you get the physical DNA for this part (which lab, synthesis company, etc): Provided by IGEM <br>
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<li> What species does this part originally come from?: Halobacterium <br>
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<li> What is the Risk Group of the species?: 1 <br>
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<li> What is the function of this part, in its parent species?: Rhodopsin pump for establishing a H ion gradient across the cell membrane. <br>
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</ul>
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 +
<ul>
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<li> Part name: DivJ <br>
 +
<li> Where did you get the physical DNA for this part (which lab, synthesis company, etc): Cloned from Caulobacter cerscentus genomic DNA. <br>
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<li> What species does this part originally come from?: Caulobacter crescentus <br>
 +
<li> What is the Risk Group of the species?: 1 <br>
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<li> What is the function of this part, in its parent species?: Protein tag for targeting a protein to one pole of Caulobacter crescentus. <br>
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</ul>
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 +
<ul>
 +
<li> Part name: TipF <br>
 +
<li> Where did you get the physical DNA for this part (which lab, synthesis company, etc): Cloned from Caulobacter cerscentus genomic DNA. <br>
 +
<li> What species does this part originally come from?: Caulobacter crescentus <br>
 +
<li> What is the Risk Group of the species?: 1 <br>
 +
<li> What is the function of this part, in its parent species?: Protein tag for targeting a protein to one pole of Caulobacter crescentus. <br>
 +
</ul>
 +
 +
<ul>
 +
<li> Part name: StpX <br>
 +
<li> Where did you get the physical DNA for this part (which lab, synthesis company, etc): Cloned from Caulobacter cerscentus genomic DNA. <br>
 +
<li> What species does this part originally come from?: Caulobacter crescentus <br>
 +
<li> What is the Risk Group of the species?: 1 <br>
 +
<li> What is the function of this part, in its parent species?: Protein tag for targeting a protein to one pole of Caulobacter crescentus. <br>
 +
</ul>
 +
 +
<ul>
 +
<li> Part name: PflI <br>
 +
<li> Where did you get the physical DNA for this part (which lab, synthesis company, etc): Cloned from Caulobacter cerscentus genomic DNA. <br>
 +
<li> What species does this part originally come from?: Caulobacter crescentus <br>
 +
<li> What is the Risk Group of the species?: 1 <br>
 +
<li> What is the function of this part, in its parent species?: Protein tag for targeting a protein to one pole of Caulobacter crescentus. <br>
 +
</ul>
 +
 +
<ul>
 +
<li> Part name: KR2 Na Pumping Rhodopsin <br>
 +
<li> Where did you get the physical DNA for this part (which lab, synthesis company, etc): Synthesized, using G blocks from IDT <br>
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<li> What species does this part originally come from?: Marine Flavobacterium Krokinobacter eikastus <br>
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<li> What is the Risk Group of the species?: Unlisted, likely 1 based on wide environmental distribution and lack of pathogenicity for marine flavobacterium <br>
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<li> What is the function of this part, in its parent species?: Function is speculated as being for establishing a Na gradient across the cell membrane to drive specific nutrient cotransporters. <br>
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</ul>
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 +
</p>
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<b> 4) Do the biological materials used in your lab work pose any of the following risks? Please describe.</b>
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<li> a. Risks to the safety and health of team members or others working in the lab?
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<br> No known health risks posed by the materials used. Preventive measures such as PPE (Personal Protective Equipment) are in place to avoid any unforeseen risks and good laboratory practice are in place. <br>
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 +
<li> b. Risks to the safety and health of the general public, if released by design or by accident?
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<br> No known health risks posed by the materials used. Caulobacter is non-infectious and widely distributed in fresh waters including drinking water and swimming pools. E coli K12 is not pathogenic. Preventive measures such as sterilization of materials prior to disposal are in place to avoid any unforeseen risks. <br>
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 +
<li> c. Risks to the environment, if released by design or by accident?
 +
<br>No known environmental risks posed by the materials used. All materials utilized have been studied extensively and are considered safe by all competent agencies. Preventive measures such as sterilization of materials prior to disposal are in place to avoid any unforeseen risks.
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 +
<li>d. Risks to security through malicious misuse by individuals, groups, or countries?
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<br> No known security risks posed by the materials used. All materials utilized have been studied extensively and are considered safe by all competent agencies. Preventive measures such as sterilization of materials prior to disposal are in place to avoid any unforeseen risks. <br>
 +
<p>
 +
<b> 5) . If your project moved from a small-scale lab study to become widely used as a commercial/industrial product, what new risks might arise? (Consider the different categories of risks that are listed in parts a-d of the previous question.) Also, what risks might arise if the knowledge you generate or the methods you develop became widely available?</b> </p>
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<br>Project is in its early phase, with significant changes in design to come. The current materials are not to the level of functional biomachine for wide distribution.
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<b> 6)  Does your project include any design features to address safety risks? </b>
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<br>No<br>
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<b> 7) What safety training have you received (or plan to receive in the future)? Provide a brief description, and a link to your institution’s safety training requirements, if available.
 +
<br>Every person working in the laboratory has passed a campus wide laboratory safety test, completed after receiving an on-line laboratory safety class. This is part of the University of California Chemical Hygiene Plan. Please see http://learningcenter.ucsc.edu/Introduction_to_Laboratory_Safety <br>
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8) Under what biosafety provisions will/do you work?</b>
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<br>a. Link to institutional biosafety guidelines- http:/ehs.ucsc.edu/programs/research-safety/biosafety/index.html
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<br>b.  Does your institution have an Institutional Biosafety Committee, or and equilivalent group? If yes, have you discussed your project with them?
 +
<br>Yes the University has an Institutional Biosafety Committee. We have worked with our campus Environmental Health and Safety Group to ensure we are compliant with safety regulations. Our project has not raised sufficient biosafety issues to provoke discussions with the Biosafety Committee.
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<br>c. Does your country have national biosafety regulations or guidelines? Please provide a link to these regulations or guidelines if possible- See OSHA USA regulations for laboratory safety requirements- http://www.osha.gov/SLTC/laboratories/
 +
<br>d. What is the WHO Biosafety level rating of our laboratory- Biosafety level 1

Latest revision as of 05:05, 27 September 2013

**Safety forms were approved by David Lloyd and Julie McNamara.

1) Please describe the chassis organism(s) you will be using for this project. If you will be using more than one chassis organism, provide information on each of them:

  • Species: E. coli
  • Strain: K12 derived Life Technologies TOP10 strain
  • Risk Group: 1
  • Risk Group Source Link: http://www.absa.org/riskgroups/bacteriasearch.php?genus=Escherichia&species=coli
  • Disease risk to humans? If so, which disease?: "E. coli K-12 is not considered a human or animal pathogen nor is it toxicogenic. Any concerns for E. coli K-12 in terms of health considerations are mitigated by its poor ability to colonize the colon and establish infections (http://epa.gov/oppt/biotech/pubs/fra/fra004.htm).


  • Species: Caulobacter crescentus
  • Strain: CB15 and CB15N
  • Risk Group: 1
  • Risk Group Source Link: http://www.baua.de/en/Topics-from-A-to-Z/Biological-Agents/TRBA/pdf/TRBA-466.pdf?__blob=publicationFile&v=3
  • Disease risk to humans? If so, which disease?: Ubiquitous presence in environmental water supplies including human drinking water and swimming pools. Single case reported of Caulobacter acting as a pathogen in a human.



2) Highest Risk Group Listed: 1
See pg 52 of Caulobacter PDF document above for risk group for Caulobacter crescentus.



3) List and describe all new or modified coding regions you will be using in your project. (If you use parts from the 2013 iGEM Distribution without modifying them, you do not need to list those parts.)

  • Part name: BBa_K559000
  • Where did you get the physical DNA for this part (which lab, synthesis company, etc): Provided by IGEM
  • What species does this part originally come from?: Halobacterium
  • What is the Risk Group of the species?: 1
  • What is the function of this part, in its parent species?: Rhodopsin pump for establishing a H ion gradient across the cell membrane.
  • Part name: DivJ
  • Where did you get the physical DNA for this part (which lab, synthesis company, etc): Cloned from Caulobacter cerscentus genomic DNA.
  • What species does this part originally come from?: Caulobacter crescentus
  • What is the Risk Group of the species?: 1
  • What is the function of this part, in its parent species?: Protein tag for targeting a protein to one pole of Caulobacter crescentus.
  • Part name: TipF
  • Where did you get the physical DNA for this part (which lab, synthesis company, etc): Cloned from Caulobacter cerscentus genomic DNA.
  • What species does this part originally come from?: Caulobacter crescentus
  • What is the Risk Group of the species?: 1
  • What is the function of this part, in its parent species?: Protein tag for targeting a protein to one pole of Caulobacter crescentus.
  • Part name: StpX
  • Where did you get the physical DNA for this part (which lab, synthesis company, etc): Cloned from Caulobacter cerscentus genomic DNA.
  • What species does this part originally come from?: Caulobacter crescentus
  • What is the Risk Group of the species?: 1
  • What is the function of this part, in its parent species?: Protein tag for targeting a protein to one pole of Caulobacter crescentus.
  • Part name: PflI
  • Where did you get the physical DNA for this part (which lab, synthesis company, etc): Cloned from Caulobacter cerscentus genomic DNA.
  • What species does this part originally come from?: Caulobacter crescentus
  • What is the Risk Group of the species?: 1
  • What is the function of this part, in its parent species?: Protein tag for targeting a protein to one pole of Caulobacter crescentus.
  • Part name: KR2 Na Pumping Rhodopsin
  • Where did you get the physical DNA for this part (which lab, synthesis company, etc): Synthesized, using G blocks from IDT
  • What species does this part originally come from?: Marine Flavobacterium Krokinobacter eikastus
  • What is the Risk Group of the species?: Unlisted, likely 1 based on wide environmental distribution and lack of pathogenicity for marine flavobacterium
  • What is the function of this part, in its parent species?: Function is speculated as being for establishing a Na gradient across the cell membrane to drive specific nutrient cotransporters.


4) Do the biological materials used in your lab work pose any of the following risks? Please describe.

  • a. Risks to the safety and health of team members or others working in the lab?
    No known health risks posed by the materials used. Preventive measures such as PPE (Personal Protective Equipment) are in place to avoid any unforeseen risks and good laboratory practice are in place.
  • b. Risks to the safety and health of the general public, if released by design or by accident?
    No known health risks posed by the materials used. Caulobacter is non-infectious and widely distributed in fresh waters including drinking water and swimming pools. E coli K12 is not pathogenic. Preventive measures such as sterilization of materials prior to disposal are in place to avoid any unforeseen risks.
  • c. Risks to the environment, if released by design or by accident?
    No known environmental risks posed by the materials used. All materials utilized have been studied extensively and are considered safe by all competent agencies. Preventive measures such as sterilization of materials prior to disposal are in place to avoid any unforeseen risks.
  • d. Risks to security through malicious misuse by individuals, groups, or countries?
    No known security risks posed by the materials used. All materials utilized have been studied extensively and are considered safe by all competent agencies. Preventive measures such as sterilization of materials prior to disposal are in place to avoid any unforeseen risks.

    5) . If your project moved from a small-scale lab study to become widely used as a commercial/industrial product, what new risks might arise? (Consider the different categories of risks that are listed in parts a-d of the previous question.) Also, what risks might arise if the knowledge you generate or the methods you develop became widely available?


    Project is in its early phase, with significant changes in design to come. The current materials are not to the level of functional biomachine for wide distribution.

    6) Does your project include any design features to address safety risks?
    No
    7) What safety training have you received (or plan to receive in the future)? Provide a brief description, and a link to your institution’s safety training requirements, if available.
    Every person working in the laboratory has passed a campus wide laboratory safety test, completed after receiving an on-line laboratory safety class. This is part of the University of California Chemical Hygiene Plan. Please see http://learningcenter.ucsc.edu/Introduction_to_Laboratory_Safety
    8) Under what biosafety provisions will/do you work?
    a. Link to institutional biosafety guidelines- http:/ehs.ucsc.edu/programs/research-safety/biosafety/index.html
    b. Does your institution have an Institutional Biosafety Committee, or and equilivalent group? If yes, have you discussed your project with them?
    Yes the University has an Institutional Biosafety Committee. We have worked with our campus Environmental Health and Safety Group to ensure we are compliant with safety regulations. Our project has not raised sufficient biosafety issues to provoke discussions with the Biosafety Committee.
    c. Does your country have national biosafety regulations or guidelines? Please provide a link to these regulations or guidelines if possible- See OSHA USA regulations for laboratory safety requirements- http://www.osha.gov/SLTC/laboratories/
    d. What is the WHO Biosafety level rating of our laboratory- Biosafety level 1

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