Biosafety

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More information about biosafety

  • Quick links of pubmed research :
  1. Biosafety and GMO's
  2. Biosafety in Synthetic Biology
  3. Issues of Synthetic Biology

We encourage you to do this kind of research as part of your bibliography for whatever project you are working on.

  • Here is the link to an openwetware page that should be improved by the community. This report exists to improve biosafety practices in synthetic biology, raise good questions, and encourage collaboration in exploring the issue.

-> How safe is Safe Enough?

  • Link to the biosafety recommendation page of iGEM:

Safety page

It includes book, papers and other useful references.

Recommendation from Human Practice Teams

  • Report of Sara Aguiton : report
  • Report of Claire Mayer : report

Conclusion of these reports :

  • daily and local efforts : An ethical reflection on practices, discourses and social interactions.
  • A responsible position regarding what scientific paradigms, through concepts, perceptions and values, are emerging with this field.
  • The need to raise awareness of synthetic biology in the population so people can decide in the most enlightened way possible if they want of this new technology and its applications.
  • The need of a discussion between society’s different decision makers to set goals and a definition of what they would consider benefits and acceptable risks.
  • Zero risk is impossible to achieve as no containment system can be 100% safe (bacteria can always escape).
  • There is a lack of quantitative data evaluating the probability of failure of any synthetic biology engineered system, in particular containment systems.
  • There is a lack of quantitative data evaluating the risk of HGT assuming containment systems failed.
  • The compiling of the wiki screen shows that no containment systems created in iGEM is robust: they lack the above quantification and are mostly one mutation away from failure. We call for major effort of the iGEM community to quantify available containment systems and search for new solutions.
  • The need for an INDEPENDENT cohort of scientists to test experimentally any application of synthetic biology that requires release into the environment.

Proposals to improve this page (Feel free to add ideas)

  1. Add a biosafety grade, that could quantify the degree of robustness. For instance, in semantic containment with amber mutation, we score the robustness with the number of amber mutations.

Example of biosafety systems

Here are reported biosafety systems that teams created. The risk and hazards of these systems are assessed through fault tree analysis, a top-down approach used in engineering field.

Team Fault Tree Analysis Guesstimation
Paris Bettencourt 2012
FTA PB12.png
Notation Failure component Failure mode Consequence Probability
P1 physical containment leakage DNA/cell escape experiment, estimation : 4.10-6
P2 DNA uptake DNA transferred into natural strain HGT transconjugant to donor ratio in HGT is typically < 10-5 [4], assume this is the rate per generation
P3 semantic containment genetic failure HGT With 3 amber mutations, probability to recover at least 50% of efficiency : 10-18
P4 population suicide no surrounding cells with enough toxin no death not estimated : consider it as 1 meanwhile
P5 toxin production genetic failure no DNA degradation (w/o antitoxin), no death (with antitoxin) estimation : 10-6
P6 mutant fitness beneficial mutation out-competition of the mutant not determined, considered as 1.
P7 delay system genetic failure no antitoxin degradation estimation : 10-6
P8 restriction enzyme genetic failure no antitoxin degradation estimation : 10-6
P9 restriction site genetic failure no antitoxin degradation 10-9

Semantic Containment

Here are parts that would add a semantic containment to genes, or parts that would allow the cell to read semantic containments gene.


More...
NameTypeDescriptionLength
BBa_K1479017Protein_Domainjust for test100
BBa_K1479018Protein_DomainJust for test 
BBa_K2086001CodingSerine Repeat Antigen (SerA)1233
BBa_K914000RNApLac-supD-T241
BBa_K914009Translational_UnitP1003* Ser133->Amber Codon967
BBa_K914011IntermediatesupD-T - intermediate178
BBa_K914012Plasmid_BackbonepSB1A2 with 1 amber mutation2079
BBa_K914018Translational_UnitP1003** Kan resistant gene with 2 Amber Codon967


Kill switch

Here are parts that could trigger cell death through disruption at the level of the protein and the cell.


More...
NameTypeDescriptionLength
BBa_K1074011CompositePsdpRI+RBS+SDP2207
BBa_K117000CodingLysis gene (promotes lysis in colicin-producing bacteria strain)144
BBa_K1172901CodingAlanine racemase from ''E. coli''1080
BBa_K1172902Devicealanine racemase (''alr'') under the control of the P''tac'' promoter1134
BBa_K1172908DevicePart 1 of the Biosafety-System Lac of Growth (pRha lacI alr)2509
BBa_K1172909DeviceBiosafety-System araCtive (AraC)3281
BBa_K1172911DeviceBiosafety-System Lac of Growth (lacI)3600
BBa_K1172912DevicePart 1 of the Biosystem TetOR alive (pRha TetR alr)2042
BBa_K1184000CodingKillerRed723
BBa_K1197007CompositeIPTG dependent B.subtilis Kill Switch construct2006
BBa_K1223001ProjectP.A.S.E. 1 cassette2148
BBa_K1223002ProjectP.A.S.E. 2 cassette1210
BBa_K1405008CompositeA Kill Switch with "memory" time repressed by IPTG2926
BBa_K1616005CodingHolin/endolysin reversed - RBS and double T7 terminator1379
BBa_K1616013CodingccdB reversed - RBS and double T7 terminator575
BBa_K1639022CompositepCons-TetR-pTet-TevProtease Suicide Switch1546
BBa_K1767001CompositeP(Lac)IQ RBS Aiia RBS LuxR term term luxpR1818
BBa_K1767002CompositeP(Lac)IQ RBS Aiia RBS LuxR ter ter luxpR RBS tetR ter ter2666
BBa_K1767003CompositeP(Lac)IQ RBS Aiia RBS LuxR ter ter luxpR RBS tetR ter ter P(tetR) RBS mRFP1 ter ter 3597
BBa_K1767004CompositeP(Lac)IQ RBS LuxR ter ter luxpR RBS tetR ter ter1892
BBa_K1819008DevicePromoter test circuit to analyze the kill switch efficiency2725
BBa_K1820024GeneratorPhage inducible promoter 1997 +RBS+FspI + term1160
BBa_K1820025Generatorp2001-native RBS-Fsp1-B00151209
BBa_K1914000CodingE. coli Codon Optimised KillerOrange(EOKO)717
BBa_K1914001DevicepT7- E. coli optimised - KillerOrange (EOKO)926
BBa_K1914003DevicepT7- E. coli optimised - KillerRed (EOKR)929
BBa_K1919100DeviceThe device consist of temperature promotor and hokD coding gene.1112
BBa_K2040122CodingKillerRed + NLS744
BBa_K2086002CompositePyeaR - SerA1499
BBa_K2150103Coding1204 toxin CDS507
BBa_K2150104Coding6249 toxin CDS319
BBa_K2232025CompositemazEF switch1006
BBa_K2292002CodingToxin-antitoxin mazEF584
BBa_K2292006CompositeMazEF kill switch 877
BBa_K2486026CompositepGadA-MazF kill switch 769
BBa_K2616002CodingTemperature Kill Switch938
BBa_K2660006CodingN-Cas93459
BBa_K2660007CodingC-Cas9648
BBa_K2757000CompositeArt-175 fused with N-terminal DsbA 2-19 signal peptide and unidirectional pTet1008
BBa_K2757001CompositeArt-175 fused with N-terminal DsbA 2-19 signal peptide and bidirectional pTet1065
BBa_K2817006CompositePcspA-RBS-mazF535
BBa_K2896001CodingThylakoid-bound SuperNova (for S. elongatus PCC 7942)846
BBa_K2919000DNAghoT toxin from E. coli K12174
BBa_K302034Translational_UnitmazEF toxin-antitoxin cluster607
BBa_K302035DeviceSucrose-limitation induced kill switch1006
BBa_K3036004CompositeCold triggered kill switch649
BBa_K3036008CodingRelB with degradation-promoting tag RepA1758
BBa_K3096052RNACRISPR Array targeting the Plasmid DNA of the glucose dependent Exendin-4 expression system147
BBa_K3096054CompositeCas3 Nuclease under the control of the AraC promoter pBAD2803
BBa_K3096055CompositeType I CRISPR/Cas system surveillance complex Cascade ABCDE under the control of the AraC promoter4487
BBa_K3190601CompositepGAL1-BI-I: BI-I CDS under inducible promoter1181
BBa_K3215013CompositeTse2 Repressed by Arabinose Kill Switch1950
BBa_K3215016CompositeMazF repressed by IPTG Kill Switch2886
BBa_K3237029CompositenucA1754
BBa_K3273001CodingSerratia marcescens nucA nuclease801
BBa_K3273008CompositeComposite ADH2/TDH3 nucA1849
BBa_K3273009CompositeComposite HXT6 Bax2039
BBa_K3273010CompositeComposite MET 25 nucA1113
BBa_K3317053CodingNucD540
BBa_K3317059CompositeNucE lysis construction308
BBa_K3317060CompositeNucD572
BBa_K3317061CompositetetR repressed killswitch1504
BBa_K3378002RegulatoryFerrous iron sensetive promoter fhuA155
BBa_K3512001CodingccdB Toxin306
BBa_K3588014CompositeMazE-MazF Hypoxia induced kill switch 2211
BBa_K3634012CompositeGlucose-Mediated Death Sensor566
BBa_K515104CompositeJ23100 promoter - Antiholin488
BBa_K515106CompositeJ23103 promoer - RBS B0034-RFP E1010 - Holin K112805 - endolysin K1128061973
BBa_K628006CompositeProtegrin-1 Kill Switch353
BBa_K879917Plasmid_BackboneLacO ori2072
BBa_K879918Plasmid_BackboneTetO ori2074


XNase

Here are parts that could trigger cell death through disruption at the level of the DNA or RNA.


More...
NameTypeDescriptionLength
BBa_K1172904CodingRnase Ba (Barnase) from Bacillus amyloliquefaciens339
BBa_K131000GeneratorColE2 Operon2640
BBa_K1479016Promoter -- No description --  
BBa_K1479017Protein_Domainjust for test100
BBa_K150009GeneratorColicinE1 Producer Controlled by 3OC6HSL Receiver Device3180
BBa_K526001Codingptrc*-Dpn1552
BBa_K914001CompositepLac Colicin E2 Immunity protein345
BBa_K914002Intermediaterepressilator RBS Colicin E2 Immunity protein282


All biosafety parts

Include previous parts plus other marked as biosafety only.


More...
NameTypeDescriptionLength
BBa_K1074011CompositePsdpRI+RBS+SDP2207
BBa_K117000CodingLysis gene (promotes lysis in colicin-producing bacteria strain)144
BBa_K1172901CodingAlanine racemase from ''E. coli''1080
BBa_K1172902Devicealanine racemase (''alr'') under the control of the P''tac'' promoter1134
BBa_K1172904CodingRnase Ba (Barnase) from Bacillus amyloliquefaciens339
BBa_K1172905DevicePart 1 of the Biosafety-System araCtive2260
BBa_K1172908DevicePart 1 of the Biosafety-System Lac of Growth (pRha lacI alr)2509
BBa_K1172909DeviceBiosafety-System araCtive (AraC)3281
BBa_K1172911DeviceBiosafety-System Lac of Growth (lacI)3600
BBa_K1172912DevicePart 1 of the Biosystem TetOR alive (pRha TetR alr)2042
BBa_K1184000CodingKillerRed723
BBa_K1197007CompositeIPTG dependent B.subtilis Kill Switch construct2006
BBa_K1223001ProjectP.A.S.E. 1 cassette2148
BBa_K1223002ProjectP.A.S.E. 2 cassette1210
BBa_K131000GeneratorColE2 Operon2640
BBa_K1363201Composite Anti-LPS factor(LALF) regulated by IPTG2298
BBa_K1405008CompositeA Kill Switch with "memory" time repressed by IPTG2926
BBa_K1442006RegulatoryAnti-theophylline Aptazyme 113
BBa_K1479005Promoter -- No description -- 16
BBa_K1479007RBSJust for upload test32
BBa_K1479008Temporaryshort short short32
BBa_K1479009Temporaryshort short short32
BBa_K1479011Promoteroh my god11
BBa_K1479012Temporaryshort short short32
BBa_K1479013Temporaryshort short short32
BBa_K1479014TemporaryJust for Test36
BBa_K1479015RBSJust for test16
BBa_K1479016Promoter -- No description --  
BBa_K1479017Protein_Domainjust for test100
BBa_K1479018Protein_DomainJust for test 
BBa_K150009GeneratorColicinE1 Producer Controlled by 3OC6HSL Receiver Device3180
BBa_K1554000RegulatoryTA29 promoter859
BBa_K1554004DeviceYellow biosafety module for plants3394
BBa_K1554005DeviceBlue biosafety module for plants3364
BBa_K1616005CodingHolin/endolysin reversed - RBS and double T7 terminator1379
BBa_K1616013CodingccdB reversed - RBS and double T7 terminator575
BBa_K1639022CompositepCons-TetR-pTet-TevProtease Suicide Switch1546
BBa_K1720002RegulatoryHypoxia-induced promotor707
BBa_K1767001CompositeP(Lac)IQ RBS Aiia RBS LuxR term term luxpR1818
BBa_K1767002CompositeP(Lac)IQ RBS Aiia RBS LuxR ter ter luxpR RBS tetR ter ter2666
BBa_K1767003CompositeP(Lac)IQ RBS Aiia RBS LuxR ter ter luxpR RBS tetR ter ter P(tetR) RBS mRFP1 ter ter 3597
BBa_K1767004CompositeP(Lac)IQ RBS LuxR ter ter luxpR RBS tetR ter ter1892
BBa_K1774000ProjectCRISPR-Cas9 contaiment device repressed by arabinose and tryptophan7191
BBa_K1819008DevicePromoter test circuit to analyze the kill switch efficiency2725
BBa_K1820024GeneratorPhage inducible promoter 1997 +RBS+FspI + term1160
BBa_K1820025Generatorp2001-native RBS-Fsp1-B00151209
BBa_K1914000CodingE. coli Codon Optimised KillerOrange(EOKO)717
BBa_K1914001DevicepT7- E. coli optimised - KillerOrange (EOKO)926
BBa_K1914003DevicepT7- E. coli optimised - KillerRed (EOKR)929
BBa_K1919100DeviceThe device consist of temperature promotor and hokD coding gene.1112
BBa_K2040122CodingKillerRed + NLS744
BBa_K2065003CodingCT52-Caspase9 
BBa_K2086001CodingSerine Repeat Antigen (SerA)1233
BBa_K2086002CompositePyeaR - SerA1499
BBa_K2107001GeneratorStationary Phase Promoter + Kil Protein263
BBa_K2150102Coding136 toxin (yobR) CDS744
BBa_K2150103Coding1204 toxin CDS507
BBa_K2150104Coding6249 toxin CDS319
BBa_K2150110DeviceLacI (constitutive) + Ptac + RiboJ + 1204 toxin2040
BBa_K2152004OtherBacteriophage Phi X 174 lysis gene E with T7 and RBS363
BBa_K2232025CompositemazEF switch1006
BBa_K2292002CodingToxin-antitoxin mazEF584
BBa_K2292006CompositeMazEF kill switch 877
BBa_K2365508CompositeBax induced part1027
BBa_K2384009RegulatoryTetR847
BBa_K2384010RegulatoryLacI1427
BBa_K2384011DNAmf-Lon2619
BBa_K2384014CompositeSafeguard-toggle switch5004
BBa_K2486026CompositepGadA-MazF kill switch 769
BBa_K2486027CodingMazF endoribonuclease339
BBa_K2516003CodingMembrane-bound SuperNova (for C. reinhardtii)969
BBa_K2616002CodingTemperature Kill Switch938
BBa_K2660006CodingN-Cas93459
BBa_K2660007CodingC-Cas9648
BBa_K2757000CompositeArt-175 fused with N-terminal DsbA 2-19 signal peptide and unidirectional pTet1008
BBa_K2757001CompositeArt-175 fused with N-terminal DsbA 2-19 signal peptide and bidirectional pTet1065
BBa_K2817006CompositePcspA-RBS-mazF535
BBa_K2896001CodingThylakoid-bound SuperNova (for S. elongatus PCC 7942)846
BBa_K2919000DNAghoT toxin from E. coli K12174
BBa_K302034Translational_UnitmazEF toxin-antitoxin cluster607
BBa_K302035DeviceSucrose-limitation induced kill switch1006
BBa_K3036004CompositeCold triggered kill switch649
BBa_K3036008CodingRelB with degradation-promoting tag RepA1758
BBa_K3096052RNACRISPR Array targeting the Plasmid DNA of the glucose dependent Exendin-4 expression system147
BBa_K3096054CompositeCas3 Nuclease under the control of the AraC promoter pBAD2803
BBa_K3096055CompositeType I CRISPR/Cas system surveillance complex Cascade ABCDE under the control of the AraC promoter4487
BBa_K3190601CompositepGAL1-BI-I: BI-I CDS under inducible promoter1181
BBa_K3215013CompositeTse2 Repressed by Arabinose Kill Switch1950
BBa_K3215016CompositeMazF repressed by IPTG Kill Switch2886
BBa_K3237029CompositenucA1754
BBa_K3273001CodingSerratia marcescens nucA nuclease801
BBa_K3273008CompositeComposite ADH2/TDH3 nucA1849
BBa_K3273009CompositeComposite HXT6 Bax2039
BBa_K3273010CompositeComposite MET 25 nucA1113
BBa_K3317053CodingNucD540
BBa_K3317059CompositeNucE lysis construction308
BBa_K3317060CompositeNucD572
BBa_K3317061CompositetetR repressed killswitch1504
BBa_K3378002RegulatoryFerrous iron sensetive promoter fhuA155
BBa_K3512001CodingccdB Toxin306
BBa_K3588014CompositeMazE-MazF Hypoxia induced kill switch 2211
BBa_K3634012CompositeGlucose-Mediated Death Sensor566
BBa_K3634020CodingCviJI Endonuclease (+ ssrA deg. tag)873
BBa_K515104CompositeJ23100 promoter - Antiholin488
BBa_K515106CompositeJ23103 promoer - RBS B0034-RFP E1010 - Holin K112805 - endolysin K1128061973
BBa_K526001Codingptrc*-Dpn1552
BBa_K628006CompositeProtegrin-1 Kill Switch353
BBa_K748007CompositeBiofilm formation device. yddV gene with the IPTG inducible promoter.1604
BBa_K772101CompositeSelf-Destruction Kit: Endolysin + Holin839
BBa_K786031ReporterT7promoter-RSR-T7teminator956
BBa_K843004DeviceT4 lysis device regulated by IPTG2871
BBa_K879917Plasmid_BackboneLacO ori2072
BBa_K879918Plasmid_BackboneTetO ori2074
BBa_K914000RNApLac-supD-T241
BBa_K914001CompositepLac Colicin E2 Immunity protein345
BBa_K914002Intermediaterepressilator RBS Colicin E2 Immunity protein282
BBa_K914009Translational_UnitP1003* Ser133->Amber Codon967
BBa_K914011IntermediatesupD-T - intermediate178
BBa_K914012Plasmid_BackbonepSB1A2 with 1 amber mutation2079
BBa_K914018Translational_UnitP1003** Kan resistant gene with 2 Amber Codon967
BBa_K990005CompositeLasR Device + T4 Lysis Device2915


Physical Containment


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