Team:NYMU-Taipei/Safety

From 2013.igem.org

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==The chassis organisms we used for this project==
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==Introduction==
 
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Our ''Bee. coli'' expresses some antimicrobial peptides such as defensin and abaecin to fight against ''Nosema cerenae''. There is probability that ''Bee. coli'' contaminates the natural environment and cause death to other species. Therefore, light-induced lysis system was created to ensure our ''Bee. coli'' only lives inside of the bee.
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{| class="wikitable"
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|-
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!  !! Species  !! Strain no/name !! Risk Group !!  Disease risk to humans? If so, which disease
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|-
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| 1 || ''E. coli'' K 12 || DH5 alpha  || [http://www.absa.org/riskgroups/bacteriasearch.php?genus=&species=coli 1] || Yes. May cause irritation to skin, eyes, and respiratory tract, may affect kidneys. However, 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.
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|-
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| 2 || ''E. coli'' K 12 || MG1655 || [http://www.absa.org/riskgroups/bacteriasearch.php?genus=&species=coli 1] || Same as above
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|-
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|}
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==Background==
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==List and description of all new or modified coding regions we used==
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===Blue Light Sensing Device===
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{| class="wikitable"
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|-
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!  !! Part number  !! Where did us get the physical DNA for this part !! What species does this part originally come from? !! What is the Risk Group of the species? !! What is the function of this part, in its parent species?
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|-
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| 1 || BBa_K1104100 || Bioresource Collection and Research Center || Escherichia coli K-12 substr. MG1655 || 1 || An enzyme involved in the cleavage of mannose
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|-
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| 2 || BBa_K1104200 || Bioresource Collection and Research Center || Escherichia coli K-12 substr. MG1655 || 1 || DNA-binding transcriptional dual regulator
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|-
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| 3 || BBa_K1104300 || National Ilan University || Apis mellifera || 1 || antimicrobial peptide
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| 4 || BBa_K1104301 || National Ilan University || Apis mellifera || 1 || antimicrobial peptide
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|-
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| 5 || BBa_K1104400 || National Taipei University of Technology || Zymomonas mobilis || 1 || alcohol dehydrogenase
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|-
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| 6 || BBa_K1104401 || National Taipei University of Technology || Zymomonas mobilis || 1 || pyruvate decarboxylase
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|-
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|}
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We chose to use [http://parts.igem.org/Part:BBa_K592016|K592016] as our light sensing device. K592016 consists two parts: YF1 and FixJ. YF1 IS a blue-light sensor protein. It works in conjunction with its response regulator, FixJ. When exposed to blue-light, they can activate K592006, the blue-light sensing promoter.
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==Do the biological materials used in our lab work pose any of the following risks?==
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===Lysis Device===
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'''Risks to the safety and health of team members or others working in the lab?'''
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The lysis device is composed of promoter K592006, the blue-light sensing promoter, and the lysis protein K896999, which is a lethal 91 amino acid membrane protein that induces lysis in ''E. coli''.
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==Circuit design and Experimental Method==
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All the biological materials used in our lab are safe to the workers in the lab. Every species we worked with belongs to BL1.
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===Circuit Device===
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'''Risks to the safety and health of the general public, if released by design or by accident?'''
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K592016 is cloned after constitutive promoter J23102, so the proteins YF1 and FixJ were continuing produced. When exposed to blue light, the inactive YF1 and FixJ will be change to their active form and induce the downstream gene of promoter K592006. In our circuit, the lysis protein K896999 will be produced and kill our Bee. coli which escaped from the midgut of a bee.
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Every species we worked with belongs to BL1. They do no harm to human.
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[[File:NYMU_Self destruction device.png|thumb|800px|center|Circuit Device]]
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'''Risks to the environment, if released by design or by accident?'''
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Every species we worked with belongs to BL1. They do no harm to the environment. In addition, we have designed a lysis system to ensure our genetic modified E. coli will not survive in the natural environment.
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'''Risks to security through malicious misuse by individuals, groups, or countries?'''
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All the biological materials used in our lab are safe, and all the products of the coding sequences are innocuous to human, so the risk of malicious misuse is low.
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==If our project moved from a small-scale lab study to become widely used as a commercial/industrial product, what new risks might arise?==
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If our design works and is introduced into a commercial/industrial product, it means the bees will be immune to certain pathogens. This might exert pressure on the survival of these pathogens. Also, pathogen-resistant bees would threaten the survival of natural bees.
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 +
==Does our project include any design features to address safety risks?==
 +
Light-inducible lysis system is created to ensure our Bee. coil only lives inside of the bee. In addition, we have decided upon encapsulation as being the method to send our Bee. coli into the bee. Since the capsule will only dissolve in a bee’s gut, our Bee. coli will not wantonly spread.
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==What safety training have we received?==
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We received safety training by our instructors according to the Occupational Safety and Health Act of our country. [http://ces.web.ym.edu.tw/front/bin/ptlist.phtml?Category=18 Our institution’s safety training requirements]
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==Under what biosafety provisions we work?==
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'''Please provide a link to our institution biosafety guidelines.'''
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[http://ces-e.web.ym.edu.tw/front/bin/home.phtml http://ces-e.web.ym.edu.tw/front/bin/home.phtml] &
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[http://ces.web.ym.edu.tw/front/bin/home.phtml http://ces.web.ym.edu.tw/front/bin/home.phtml]
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'''Does our institution have an Institutional Biosafety Committee, or an equivalent group?'''
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Yes, there is an institution in our school called NYMU Center of Environmental Protection and Safety and Health. We had discussed with them and modified the design of the bacteria biosafety lysis system.
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'''Does our country have national biosafety regulations or guidelines?'''
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Yes, our country has national biosafety regulations and [http://www.nsc.gov.tw/bio/public/Attachment/691415403671.doc guidelines].
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'''According to the WHO Biosafety Manual, what is the BioSafety Level rating of our lab?'''
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The BioSafety Level rating of our lab is category 1.
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'''What is the Risk Group of our chassis organisms?'''
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The Risk Group of our chassis organisms, E. coli (K12) strain DH5α and strain MG1655, is the Risk Group 1. They match with our lab's BSL rating.
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==Faculty Advisor Name==
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===Chuan-Hsiung Chang===
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===Experimental Method===
 
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First, we substitute lysis protein K896999 with green fluorescent protein E0040. By this way, we can test the efficiency of the circuit.
 
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[[File:NYMU_Testing Circuit.png|thumb|800px|center|Testing Circuit]]
 
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Next, by comparing the number of colonies of the plate that is exposed to light and the plate that is blocked from light after 16 hours of in incubator, we can characterize the function of our device.
 
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[[File:NYMU_Light is block by aluminum foil.png|thumb|500px|center|Right: Light is block by aluminum foil.<br>Left: Plate is exposed to light.]]
 
{{:Team:NYMU-Taipei/Footer}}
{{:Team:NYMU-Taipei/Footer}}

Latest revision as of 20:27, 27 September 2013

National Yang Ming University


Contents

The chassis organisms we used for this project

Species Strain no/name Risk Group Disease risk to humans? If so, which disease
1 E. coli K 12 DH5 alpha [http://www.absa.org/riskgroups/bacteriasearch.php?genus=&species=coli 1] Yes. May cause irritation to skin, eyes, and respiratory tract, may affect kidneys. However, 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.
2 E. coli K 12 MG1655 [http://www.absa.org/riskgroups/bacteriasearch.php?genus=&species=coli 1] Same as above

List and description of all new or modified coding regions we used

Part number Where did us get the physical DNA for this part What species does this part originally come from? What is the Risk Group of the species? What is the function of this part, in its parent species?
1 BBa_K1104100 Bioresource Collection and Research Center Escherichia coli K-12 substr. MG1655 1 An enzyme involved in the cleavage of mannose
2 BBa_K1104200 Bioresource Collection and Research Center Escherichia coli K-12 substr. MG1655 1 DNA-binding transcriptional dual regulator
3 BBa_K1104300 National Ilan University Apis mellifera 1 antimicrobial peptide
4 BBa_K1104301 National Ilan University Apis mellifera 1 antimicrobial peptide
5 BBa_K1104400 National Taipei University of Technology Zymomonas mobilis 1 alcohol dehydrogenase
6 BBa_K1104401 National Taipei University of Technology Zymomonas mobilis 1 pyruvate decarboxylase

Do the biological materials used in our lab work pose any of the following risks?

Risks to the safety and health of team members or others working in the lab?

All the biological materials used in our lab are safe to the workers in the lab. Every species we worked with belongs to BL1.

Risks to the safety and health of the general public, if released by design or by accident?

Every species we worked with belongs to BL1. They do no harm to human.

Risks to the environment, if released by design or by accident?

Every species we worked with belongs to BL1. They do no harm to the environment. In addition, we have designed a lysis system to ensure our genetic modified E. coli will not survive in the natural environment.

Risks to security through malicious misuse by individuals, groups, or countries?

All the biological materials used in our lab are safe, and all the products of the coding sequences are innocuous to human, so the risk of malicious misuse is low.

If our project moved from a small-scale lab study to become widely used as a commercial/industrial product, what new risks might arise?

If our design works and is introduced into a commercial/industrial product, it means the bees will be immune to certain pathogens. This might exert pressure on the survival of these pathogens. Also, pathogen-resistant bees would threaten the survival of natural bees.

Does our project include any design features to address safety risks?

Light-inducible lysis system is created to ensure our Bee. coil only lives inside of the bee. In addition, we have decided upon encapsulation as being the method to send our Bee. coli into the bee. Since the capsule will only dissolve in a bee’s gut, our Bee. coli will not wantonly spread.

What safety training have we received?

We received safety training by our instructors according to the Occupational Safety and Health Act of our country. [http://ces.web.ym.edu.tw/front/bin/ptlist.phtml?Category=18 Our institution’s safety training requirements]

Under what biosafety provisions we work?

Please provide a link to our institution biosafety guidelines.

[http://ces-e.web.ym.edu.tw/front/bin/home.phtml http://ces-e.web.ym.edu.tw/front/bin/home.phtml] & [http://ces.web.ym.edu.tw/front/bin/home.phtml http://ces.web.ym.edu.tw/front/bin/home.phtml]

Does our institution have an Institutional Biosafety Committee, or an equivalent group?

Yes, there is an institution in our school called NYMU Center of Environmental Protection and Safety and Health. We had discussed with them and modified the design of the bacteria biosafety lysis system.

Does our country have national biosafety regulations or guidelines?

Yes, our country has national biosafety regulations and [http://www.nsc.gov.tw/bio/public/Attachment/691415403671.doc guidelines].

According to the WHO Biosafety Manual, what is the BioSafety Level rating of our lab?

The BioSafety Level rating of our lab is category 1.

What is the Risk Group of our chassis organisms?

The Risk Group of our chassis organisms, E. coli (K12) strain DH5α and strain MG1655, is the Risk Group 1. They match with our lab's BSL rating.

Faculty Advisor Name

Chuan-Hsiung Chang

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