Team:INSA Toulouse/contenu/safety/iGEM safety

From 2013.igem.org

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<td style="border-right:1px solid #e5e6e6;">DH5-alpha</td>
<td style="border-right:1px solid #e5e6e6;">DH5-alpha</td>
<td style="border-right:1px solid #e5e6e6;">1</td>
<td style="border-right:1px solid #e5e6e6;">1</td>
-
<td style="border-right:1px solid #e5e6e6;"><a href="www.absa.org/riskgroups/bacteriasearch.php?genus=&species=coli" target="_blank">Link</a></td>
+
<td style="border-right:1px solid #e5e6e6;"><a href="http://www.absa.org/riskgroups/bacteriasearch.php?genus=&species=coli" target="_blank">Link</a></td>
<td>Yes. May cause irritation to skin, eyes, and respiratory tract, may affect kidneys.</td>
<td>Yes. May cause irritation to skin, eyes, and respiratory tract, may affect kidneys.</td>
</tr>
</tr>
<tr >
<tr >
-
<td style="border-right:1px solid #e5e6e6; border-top:1px solid #e5e6e6;"><i>E.coli</i> (K12)</td>
+
<td style="border-right:1px solid #e5e6e6; border-top:1px solid #e5e6e6;"><i>E. coli</i> (K12)</td>
<td style="border-right:1px solid #e5e6e6;border-top:1px solid #e5e6e6;">DH5-1</td>
<td style="border-right:1px solid #e5e6e6;border-top:1px solid #e5e6e6;">DH5-1</td>
<td style="border-right:1px solid #e5e6e6;border-top:1px solid #e5e6e6;">1</td>
<td style="border-right:1px solid #e5e6e6;border-top:1px solid #e5e6e6;">1</td>
-
<td style="border-right:1px solid #e5e6e6;border-top:1px solid #e5e6e6;"><a href="www.absa.org/riskgroups/bacteriasearch.php?genus=&species=coli">Link</a></td>
+
<td style="border-right:1px solid #e5e6e6;border-top:1px solid #e5e6e6;"><a href="http://www.absa.org/riskgroups/bacteriasearch.php?genus=&species=coli" target="_blank">Link</a></td>
<td style="border-top:1px solid #e5e6e6;">Yes. May cause irritation to skin, eyes, and respiratory tract, may affect kidneys.</td>
<td style="border-top:1px solid #e5e6e6;">Yes. May cause irritation to skin, eyes, and respiratory tract, may affect kidneys.</td>
</tr>
</tr>
<tr >
<tr >
-
<td style="border-right:1px solid #e5e6e6;border-top:1px solid #e5e6e6;"><i>E.coli</i> (K12)</td>
+
<td style="border-right:1px solid #e5e6e6;border-top:1px solid #e5e6e6;"><i>E. coli</i> (K12)</td>
<td style="border-right:1px solid #e5e6e6;border-top:1px solid #e5e6e6;">MG1655</td>
<td style="border-right:1px solid #e5e6e6;border-top:1px solid #e5e6e6;">MG1655</td>
<td style="border-right:1px solid #e5e6e6;border-top:1px solid #e5e6e6;">1</td>
<td style="border-right:1px solid #e5e6e6;border-top:1px solid #e5e6e6;">1</td>
-
<td style="border-right:1px solid #e5e6e6;border-top:1px solid #e5e6e6;"><a href="www.absa.org/riskgroups/bacteriasearch.php?genus=&species=coli">Link</a></td>
+
<td style="border-right:1px solid #e5e6e6;border-top:1px solid #e5e6e6;"><a href="http://www.absa.org/riskgroups/bacteriasearch.php?genus=&species=coli" target="_blank">Link</a></td>
<td style="border-top:1px solid #e5e6e6;">Yes. May cause irritation to skin, eyes, and respiratory tract, may affect kidneys.</td>
<td style="border-top:1px solid #e5e6e6;">Yes. May cause irritation to skin, eyes, and respiratory tract, may affect kidneys.</td>
</tr>
</tr>
<tr >
<tr >
-
<td style="border-right:1px solid #e5e6e6;border-top:1px solid #e5e6e6;"><i>E.coli</i> (K12)</td>
+
<td style="border-right:1px solid #e5e6e6;border-top:1px solid #e5e6e6;"><i>E. coli</i> (K12)</td>
<td style="border-right:1px solid #e5e6e6;border-top:1px solid #e5e6e6;">BL21-DE3</td>
<td style="border-right:1px solid #e5e6e6;border-top:1px solid #e5e6e6;">BL21-DE3</td>
<td style="border-right:1px solid #e5e6e6;border-top:1px solid #e5e6e6;">1</td>
<td style="border-right:1px solid #e5e6e6;border-top:1px solid #e5e6e6;">1</td>
-
<td style="border-right:1px solid #e5e6e6;border-top:1px solid #e5e6e6;"><a href="www.absa.org/riskgroups/bacteriasearch.php?genus=&species=coli">Link</a></td>
+
<td style="border-right:1px solid #e5e6e6;border-top:1px solid #e5e6e6;"><a href="http://www.absa.org/riskgroups/bacteriasearch.php?genus=&species=coli" target="_blank">Link</a></td>
 +
<td style="border-top:1px solid #e5e6e6;">Yes. May cause irritation to skin, eyes, and respiratory tract, may affect kidneys.</td>
 +
</tr>
 +
<tr >
 +
<td style="border-right:1px solid #e5e6e6;border-top:1px solid #e5e6e6;"><i>E. coli</i> (K12)</td>
 +
<td style="border-right:1px solid #e5e6e6;border-top:1px solid #e5e6e6;">XL1-Blue</td>
 +
<td style="border-right:1px solid #e5e6e6;border-top:1px solid #e5e6e6;">1</td>
 +
<td style="border-right:1px solid #e5e6e6;border-top:1px solid #e5e6e6;"><a href="http://www.absa.org/riskgroups/bacteriasearch.php?genus=&species=coli" target="_blank">Link</a></td>
<td style="border-top:1px solid #e5e6e6;">Yes. May cause irritation to skin, eyes, and respiratory tract, may affect kidneys.</td>
<td style="border-top:1px solid #e5e6e6;">Yes. May cause irritation to skin, eyes, and respiratory tract, may affect kidneys.</td>
</tr>
</tr>
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<td style="border-right:1px solid #e5e6e6; border-top:1px solid #e5e6e6;">CV026</td>
<td style="border-right:1px solid #e5e6e6; border-top:1px solid #e5e6e6;">CV026</td>
<td style="border-right:1px solid #e5e6e6; border-top:1px solid #e5e6e6;">2</td>
<td style="border-right:1px solid #e5e6e6; border-top:1px solid #e5e6e6;">2</td>
-
<td style="border-right:1px solid #e5e6e6; border-top:1px solid #e5e6e6;"> <a href="http://www.absa.org/riskgroups/bacteriasearch.php?genus=Chromobacterium">Link</a></td>
+
<td style="border-right:1px solid #e5e6e6; border-top:1px solid #e5e6e6;"> <a href="http://www.absa.org/riskgroups/bacteriasearch.php?genus=Chromobacterium" target="_blank">Link</a></td>
<td style="border-top:1px solid #e5e6e6;">Yes. Pathogen for humans and vertebrates, but normally no transmission between the two host groups. It rarely infects humans, but when it does it causes skin lesions, sepsis, and liver abscesses that may be fatal.</td>
<td style="border-top:1px solid #e5e6e6;">Yes. Pathogen for humans and vertebrates, but normally no transmission between the two host groups. It rarely infects humans, but when it does it causes skin lesions, sepsis, and liver abscesses that may be fatal.</td>
</tr>
</tr>
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<tr>
<tr>
<td style="border-right:1px solid #e5e6e6;font-size:12px;">BBa_K1132000</td>
<td style="border-right:1px solid #e5e6e6;font-size:12px;">BBa_K1132000</td>
-
<td style="border-right:1px solid #e5e6e6;">Pol T7</td>
+
<td style="border-right:1px solid #e5e6e6;">T7 Polymerase</td>
<td style="border-right:1px solid #e5e6e6;">PCR extraction from genomic DNA of <i>E. coli</i> K12 BL21-DE3</td>
<td style="border-right:1px solid #e5e6e6;">PCR extraction from genomic DNA of <i>E. coli</i> K12 BL21-DE3</td>
<td style="border-right:1px solid #e5e6e6;">Bacteriophage T7</td>
<td style="border-right:1px solid #e5e6e6;">Bacteriophage T7</td>
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<td style="border-right:1px solid #e5e6e6;border-top:1px solid #e5e6e6;">Tp901 sites<br>
<td style="border-right:1px solid #e5e6e6;border-top:1px solid #e5e6e6;">Tp901 sites<br>
Bxb1 sites<br>
Bxb1 sites<br>
-
P7<br>
+
pT7<br>
BBa_B0015<br>
BBa_B0015<br>
Bba_J61048</td>
Bba_J61048</td>
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<td style="border-right:1px solid #e5e6e6;border-top:1px solid #e5e6e6;">Bacteriophage TP901<br>
<td style="border-right:1px solid #e5e6e6;border-top:1px solid #e5e6e6;">Bacteriophage TP901<br>
Bacteriophage BXB1<br>
Bacteriophage BXB1<br>
-
Artificial sequence <a href="http://www.ncbi.nlm.nih.gov/pubmed/23539178">(Bonnet et al. 2013)</a><br>
+
Artificial sequence <a href="http://www.ncbi.nlm.nih.gov/pubmed/23539178" target="_blank">(Bonnet et al. 2013)</a><br>
Double terminator<br>
Double terminator<br>
T1 terminator</td>
T1 terminator</td>
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<td style="border-right:1px solid #e5e6e6;border-top:1px solid #e5e6e6;">Tp901 sites<br>
<td style="border-right:1px solid #e5e6e6;border-top:1px solid #e5e6e6;">Tp901 sites<br>
Bxb1 sites<br>
Bxb1 sites<br>
-
P7<br>
+
pT7<br>
BBa_B0015</td>
BBa_B0015</td>
<td style="border-right:1px solid #e5e6e6;border-top:1px solid #e5e6e6;">Gene synthesis (GeneCust)</td>
<td style="border-right:1px solid #e5e6e6;border-top:1px solid #e5e6e6;">Gene synthesis (GeneCust)</td>
<td style="border-right:1px solid #e5e6e6;border-top:1px solid #e5e6e6;">Bacteriophage TP901<br>
<td style="border-right:1px solid #e5e6e6;border-top:1px solid #e5e6e6;">Bacteriophage TP901<br>
Bacteriophage BXB1<br>
Bacteriophage BXB1<br>
-
Artificial sequence <a href="http://www.ncbi.nlm.nih.gov/pubmed/23539178">(Bonnet et al. 2013)</a><br>
+
Artificial sequence <a href="http://www.ncbi.nlm.nih.gov/pubmed/23539178" target="_blank">(Bonnet et al. 2013)</a><br>
Double terminator</td>
Double terminator</td>
<td style="border-right:1px solid #e5e6e6;border-top:1px solid #e5e6e6;">1</td>
<td style="border-right:1px solid #e5e6e6;border-top:1px solid #e5e6e6;">1</td>
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BBa_I712074</td>
BBa_I712074</td>
<td style="border-right:1px solid #e5e6e6;border-top:1px solid #e5e6e6;">Gene synthesis (GeneCust)</td>
<td style="border-right:1px solid #e5e6e6;border-top:1px solid #e5e6e6;">Gene synthesis (GeneCust)</td>
-
<td style="border-right:1px solid #e5e6e6;border-top:1px solid #e5e6e6;">E. coi (K12) FimE<br>
+
<td style="border-right:1px solid #e5e6e6;border-top:1px solid #e5e6e6;">E. coli (K12) FimE<br>
Bacteriophage PhiC31<br>
Bacteriophage PhiC31<br>
T7 Promoter</td>
T7 Promoter</td>
Line 202: Line 209:
BBa_I712074</td>
BBa_I712074</td>
<td style="border-right:1px solid #e5e6e6;border-top:1px solid #e5e6e6;">Gene synthesis (GeneCust)</td>
<td style="border-right:1px solid #e5e6e6;border-top:1px solid #e5e6e6;">Gene synthesis (GeneCust)</td>
-
<td style="border-right:1px solid #e5e6e6;border-top:1px solid #e5e6e6;">E. coi (K12) FimE<br>
+
<td style="border-right:1px solid #e5e6e6;border-top:1px solid #e5e6e6;">E. coli (K12) FimE<br>
Bacteriophage PhiC31<br>
Bacteriophage PhiC31<br>
T7 Promoter</td>
T7 Promoter</td>
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   <h3 class="title3">Risks</h3>
   <h3 class="title3">Risks</h3>
-
   <p class="texte">The two chassis strains (<i>E.coli, C. violaceum</i>) are potential pathogenes for humans. For <i>E. coli</i>, the risks are minimal, but good laboratory practises were applied to avoid possible contaminations. For <i>C. violaceum</i>, all experiments involving this strain will be performed in a P2 facility and under the supervision of a member of the permanent staff who is the manager of the P2 facility.<br>
+
   <p class="texte">The two chassis strains (<i>E. coli, C. violaceum</i>) are potential pathogenes for humans. For <i>E. coli</i>, the risks are minimal, but good laboratory practises were applied to avoid possible contaminations. For <i>C. violaceum</i>, all experiments involving this strain will be performed in a P2 facility and under the supervision of a member of the permanent staff who is the manager of the P2 facility.<br>
There is no environmental risks.
There is no environmental risks.
-
<br>
+
<br><br>
-
<i>C. violaceum</i> is used only for parts characterisation and is not part of the original project. For the project itself, only the <i>E.coli</i> K12 is used and the potential risks of converting the project into a commercial product are already assessed for industrial purposes.<br>
+
<i>C. violaceum</i> is used only for parts characterisation and is not part of the original project. For the project itself, only the <i>E. coli</i> K12 is used and the potential risks of converting the project into a commercial product are already assessed for industrial purposes.<br>
-
In the potential case where some parts should be used for other purposes than research, precautions shoud be taken to assess the safety of these microorganisms. No parts will be introduced into <i>C. violaceum</i>, avoiding possible antibiotic resistance of the strain.<br>
+
In the potential case where some parts should be used for other purposes than research, precautions shoud be taken to assess the safety of these microorganisms. No parts will be introduced into <i>C. violaceum</i>, avoiding possible antibiotic resistance of the strain.<br><br>
All students receive a 2 hours safety course provided by the biosafety commitee executive. All of them were required to take a test at the end, and all of them passed.<br>
All students receive a 2 hours safety course provided by the biosafety commitee executive. All of them were required to take a test at the end, and all of them passed.<br>
-
There is an institutional biosafety commitee. The project was approved by several teachers of the institute.<br>
+
There is an institutional biosafety commitee. The project was approved by several teachers of the institute.<br><br>
The Biosafety level of our lab is 2. The institute has a P2 room fully equiped for manipulating level 2 risk group organisms.<br>
The Biosafety level of our lab is 2. The institute has a P2 room fully equiped for manipulating level 2 risk group organisms.<br>
The chassis organism risk group is 1. However, we also use a level 2 test chassis that is only manipulated in the P2 facility.</p>
The chassis organism risk group is 1. However, we also use a level 2 test chassis that is only manipulated in the P2 facility.</p>

Latest revision as of 20:22, 4 October 2013

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iGEM Safety

Safety forms were approved on September 29, 2013 by the iGEM Safety Committee.

Chassis Organism

Species Strain n°/name Risk Group Risk group source link Disease risk to humans? If so, which disease?
E.coli (K12) DH5-alpha 1 Link Yes. May cause irritation to skin, eyes, and respiratory tract, may affect kidneys.
E. coli (K12) DH5-1 1 Link Yes. May cause irritation to skin, eyes, and respiratory tract, may affect kidneys.
E. coli (K12) MG1655 1 Link Yes. May cause irritation to skin, eyes, and respiratory tract, may affect kidneys.
E. coli (K12) BL21-DE3 1 Link Yes. May cause irritation to skin, eyes, and respiratory tract, may affect kidneys.
E. coli (K12) XL1-Blue 1 Link Yes. May cause irritation to skin, eyes, and respiratory tract, may affect kidneys.
Chromobacterium violaceum CV026 2 Link Yes. Pathogen for humans and vertebrates, but normally no transmission between the two host groups. It rarely infects humans, but when it does it causes skin lesions, sepsis, and liver abscesses that may be fatal.

New and/or Modified Coding Regions

Part number Description Where did we 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?
BBa_K1132000 T7 Polymerase PCR extraction from genomic DNA of E. coli K12 BL21-DE3 Bacteriophage T7 1 RNA Polymerase
BBa_K1132001 Tp901 sites
Bxb1 sites
pT7
BBa_B0015
Bba_J61048
Gene synthesis (GeneCust) Bacteriophage TP901
Bacteriophage BXB1
Artificial sequence (Bonnet et al. 2013)
Double terminator
T1 terminator
1 Recombinase site
Recombinase site
Promoter region
Transcription terminator
Transcription terminator
BBa_K1132002 Tp901 sites
Bxb1 sites
pT7
BBa_B0015
Gene synthesis (GeneCust) Bacteriophage TP901
Bacteriophage BXB1
Artificial sequence (Bonnet et al. 2013)
Double terminator
1 Recombinase site
Recombinase site
Promoter region
Transcription terminator
BBa_K1132003 FimE sites
PhiC31 sites
BBa_I712074
Gene synthesis (GeneCust) E. coli (K12) FimE
Bacteriophage PhiC31
T7 Promoter
1 Recombinase site
Recombinase site
Promoter region
BBa_K1132004 FimE sites
PhiC31 sites
BBa_I712074
Gene synthesis (GeneCust) E. coli (K12) FimE
Bacteriophage PhiC31
T7 Promoter
1 Recombinase site
Recombinase site
Promoter region
BBa_K1132005 BBa_R0040
riboregulator R0.1
BBa_B0015
BBa_R0065
riboregulator R0.2
Gene synthesis (GeneCust) TetR promoter
Artificial sequence
Double terminator
Promoter (lambda cI and luxR regulated)
Artificial sequence
1 Promoter region
RNA sequence for regulation
Transcription terminator
Promoter region
RNA sequence for regulation
BBa_K1132006 BBa_R0040
riboregulator R1.1
BBa_B0015
BBa_R0065
riboregulator R1.2
Gene synthesis (GeneCust) TetR promoter
Artificial sequence
Double terminator
Promoter (lambda cI and luxR regulated)
Artificial sequence
1 Promoter region
RNA sequence for regulation
Transcription terminator
Promoter region
RNA sequence for regulation
BBa_K1132007 BBa_R0040
riboregulator R2.1
BBa_B0015
BBa_K592006
riboregulator R2.2
Gene synthesis (GeneCust) TetR promoter
Artificial sequence
Double terminator
FixK2 promoter
Artificial sequence
1 Promoter region
RNA sequence for regulation
Transcription terminator
Promoter region
RNA sequence for regulation
BBa_K1132008 BBa_R0040
riboregulator R4.1
BBa_B0015
BBa_R0082
riboregulator R4.2
Gene synthesis (GeneCust) TetR promoter
Artificial sequence
Double terminator
OmpR-controlled promoter
Artificial sequence
1 Promoter region
RNA sequence for regulation
Transcription terminator
Promoter region
RNA sequence for regulation
BBa_K1132009 PhiC31 integrase From the plasmid A24 from Suiti Laboratory (MIT) bacteriophage phiC31 1 Recombinase
BBa_K1132010 Tp901 integrase From the parts KC529324 from Jerome Bonnet bacteriophage Tp901 1 Recombinase

Risks

The two chassis strains (E. coli, C. violaceum) are potential pathogenes for humans. For E. coli, the risks are minimal, but good laboratory practises were applied to avoid possible contaminations. For C. violaceum, all experiments involving this strain will be performed in a P2 facility and under the supervision of a member of the permanent staff who is the manager of the P2 facility.
There is no environmental risks.

C. violaceum is used only for parts characterisation and is not part of the original project. For the project itself, only the E. coli K12 is used and the potential risks of converting the project into a commercial product are already assessed for industrial purposes.
In the potential case where some parts should be used for other purposes than research, precautions shoud be taken to assess the safety of these microorganisms. No parts will be introduced into C. violaceum, avoiding possible antibiotic resistance of the strain.

All students receive a 2 hours safety course provided by the biosafety commitee executive. All of them were required to take a test at the end, and all of them passed.
There is an institutional biosafety commitee. The project was approved by several teachers of the institute.

The Biosafety level of our lab is 2. The institute has a P2 room fully equiped for manipulating level 2 risk group organisms.
The chassis organism risk group is 1. However, we also use a level 2 test chassis that is only manipulated in the P2 facility.