Biosafety

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More information about biosafety

• Quick links of pubmed research :

1. [http://www.ncbi.nlm.nih.gov/pubmed?term=biosafety%20gmo Biosafety and GMO's]
2. [http://www.ncbi.nlm.nih.gov/pubmed?term=biosafety%20synthetic%20biology Biosafety in Synthetic Biology]
3. [http://www.ncbi.nlm.nih.gov/pubmed?term=issue%20synthetic%20biology 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.

-> [http://openwetware.org/wiki/How_safe_is_safe_enough:_towards_best_pratices_of_synthetic_biology 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 : [http://2009.igem.org/Team:Paris/Ethics_ethicalreport#top report]
• Report of Claire Mayer : [http://2012.igem.org/Team:Paris_Bettencourt/Human_Practice/Report 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 system

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.

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...

Name	Type	Description	Length
BBa_K1479017	Protein_Domain	just for test	100
BBa_K1479018	Protein_Domain	Just for test
BBa_K2086001	Coding	Serine Repeat Antigen (SerA)	1233
BBa_K914000	RNA	pLac-supD-T	241
BBa_K914009	Translational_Unit	P1003* Ser133->Amber Codon	967
BBa_K914011	Intermediate	supD-T - intermediate	178
BBa_K914012	Plasmid_Backbone	pSB1A2 with 1 amber mutation	2079
BBa_K914018	Translational_Unit	P1003** Kan resistant gene with 2 Amber Codon	967

Kill switch

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

More...

Name	Type	Description	Length
BBa_K1074011	Composite	PsdpRI+RBS+SDP	2207
BBa_K117000	Coding	Lysis gene (promotes lysis in colicin-producing bacteria strain)	144
BBa_K1172901	Coding	Alanine racemase from ''E. coli''	1080
BBa_K1172902	Device	alanine racemase (''alr'') under the control of the P''tac'' promoter	1134
BBa_K1172908	Device	Part 1 of the Biosafety-System Lac of Growth (pRha lacI alr)	2509
BBa_K1172909	Device	Biosafety-System araCtive (AraC)	3281
BBa_K1172911	Device	Biosafety-System Lac of Growth (lacI)	3600
BBa_K1172912	Device	Part 1 of the Biosystem TetOR alive (pRha TetR alr)	2042
BBa_K1184000	Coding	KillerRed	723
BBa_K1197007	Composite	IPTG dependent B.subtilis Kill Switch construct	2006
BBa_K1223001	Project	P.A.S.E. 1 cassette	2148
BBa_K1223002	Project	P.A.S.E. 2 cassette	1210
BBa_K1405008	Composite	A Kill Switch with "memory" time repressed by IPTG	2926
BBa_K1616005	Coding	Holin/endolysin reversed - RBS and double T7 terminator	1379
BBa_K1616013	Coding	ccdB reversed - RBS and double T7 terminator	575
BBa_K1639022	Composite	pCons-TetR-pTet-TevProtease Suicide Switch	1546
BBa_K1767001	Composite	P(Lac)IQ RBS Aiia RBS LuxR term term luxpR	1818
BBa_K1767002	Composite	P(Lac)IQ RBS Aiia RBS LuxR ter ter luxpR RBS tetR ter ter	2666
BBa_K1767003	Composite	P(Lac)IQ RBS Aiia RBS LuxR ter ter luxpR RBS tetR ter ter P(tetR) RBS mRFP1 ter ter	3597
BBa_K1767004	Composite	P(Lac)IQ RBS LuxR ter ter luxpR RBS tetR ter ter	1892
BBa_K1819008	Device	Promoter test circuit to analyze the kill switch efficiency	2725
BBa_K1820024	Generator	Phage inducible promoter 1997 +RBS+FspI + term	1160
BBa_K1820025	Generator	p2001-native RBS-Fsp1-B0015	1209
BBa_K1914000	Coding	E. coli Codon Optimised KillerOrange(EOKO)	717
BBa_K1914001	Device	pT7- E. coli optimised - KillerOrange (EOKO)	926
BBa_K1914003	Device	pT7- E. coli optimised - KillerRed (EOKR)	929
BBa_K1919100	Device	The device consist of temperature promotor and hokD coding gene.	1112
BBa_K2040122	Coding	KillerRed + NLS	744
BBa_K2086002	Composite	PyeaR - SerA	1499
BBa_K2150103	Coding	1204 toxin CDS	507
BBa_K2150104	Coding	6249 toxin CDS	319
BBa_K2232025	Composite	mazEF switch	1006
BBa_K2292002	Coding	Toxin-antitoxin mazEF	584
BBa_K2292006	Composite	MazEF kill switch	877
BBa_K2486026	Composite	pGadA-MazF kill switch	769
BBa_K2616002	Coding	Temperature Kill Switch	938
BBa_K2660006	Coding	N-Cas9	3459
BBa_K2660007	Coding	C-Cas9	648
BBa_K2757000	Composite	Art-175 fused with N-terminal DsbA 2-19 signal peptide and unidirectional pTet	1008
BBa_K2757001	Composite	Art-175 fused with N-terminal DsbA 2-19 signal peptide and bidirectional pTet	1065
BBa_K2817006	Composite	PcspA-RBS-mazF	535
BBa_K2896001	Coding	Thylakoid-bound SuperNova (for S. elongatus PCC 7942)	846
BBa_K2919000	DNA	ghoT toxin from E. coli K12	174
BBa_K302034	Translational_Unit	mazEF toxin-antitoxin cluster	607
BBa_K302035	Device	Sucrose-limitation induced kill switch	1006
BBa_K3036004	Composite	Cold triggered kill switch	649
BBa_K3036008	Coding	RelB with degradation-promoting tag RepA	1758
BBa_K3096052	RNA	CRISPR Array targeting the Plasmid DNA of the glucose dependent Exendin-4 expression system	147
BBa_K3096054	Composite	Cas3 Nuclease under the control of the AraC promoter pBAD	2803
BBa_K3096055	Composite	Type I CRISPR/Cas system surveillance complex Cascade ABCDE under the control of the AraC promoter	4487
BBa_K3190601	Composite	pGAL1-BI-I: BI-I CDS under inducible promoter	1181
BBa_K3215013	Composite	Tse2 Repressed by Arabinose Kill Switch	1950
BBa_K3215016	Composite	MazF repressed by IPTG Kill Switch	2886
BBa_K3237029	Composite	nucA	1754
BBa_K3273001	Coding	Serratia marcescens nucA nuclease	801
BBa_K3273008	Composite	Composite ADH2/TDH3 nucA	1849
BBa_K3273009	Composite	Composite HXT6 Bax	2039
BBa_K3273010	Composite	Composite MET 25 nucA	1113
BBa_K3317053	Coding	NucD	540
BBa_K3317059	Composite	NucE lysis construction	308
BBa_K3317060	Composite	NucD	572
BBa_K3317061	Composite	tetR repressed killswitch	1504
BBa_K3378002	Regulatory	Ferrous iron sensetive promoter fhuA1	55
BBa_K3512001	Coding	ccdB Toxin	306
BBa_K3588014	Composite	MazE-MazF Hypoxia induced kill switch	2211
BBa_K3634012	Composite	Glucose-Mediated Death Sensor	566
BBa_K3755043	RNA	Sok RNA	66
BBa_K3755045	Coding	Hok/Mok protein	217
BBa_K3755046	Composite	Double Regulated(trp+lac) Kill Switch	2352
BBa_K3848004	Composite	Lactate regulated kill switch	2837
BBa_K4133006	Coding	Repressor protein CtsR_Lp (Lactobacillus plantarum WCFS1) for Lactobacillus casei	468
BBa_K4133007	Regulatory	PclpC_Lp repressible promoter (Lactobacillus plantarum WCFS1)	59
BBa_K4133008	RBS	RBS_Lp (Lactobacillus plantarum WCFS1)	14
BBa_K4133009	Coding	Repressor protein CtsR_Lc (Lactococcus lactis) for Lactobacillus casei	456
BBa_K4133010	Regulatory	PclpC_Lc repressible promoter (Lactococcus lactis)	72
BBa_K4133011	RBS	RBS_Lc (Lactococcus lactis)	12
BBa_K4133012	Coding	LysKB317 (Endolysin) for Lactobacillus casei	894
BBa_K4202000	Coding	mazE(codon optimization for Bacillus subtilis)	249
BBa_K4202001	Coding	mazF(codon optimization for Bacillus subtilis)	421
BBa_K4202045	Generator	Sucrose regulated kill switch in Bacillus subtilis	1291
BBa_K4345020	Composite	5' UTR of hsp17 with ccdA fused to sfGFP	1197
BBa_K4345023	Composite	5' UTR of rpoH with ccdA fused to sfGFP	1395
BBa_K4345024	Composite	5' UTR of prfA with ccdA fused to sfGFP	1277
BBa_K515104	Composite	J23100 promoter - Antiholin	488
BBa_K515106	Composite	J23103 promoer - RBS B0034-RFP E1010 - Holin K112805 - endolysin K112806	1973
BBa_K5480009	Composite	Y38-DpnI-TrrnB	2353
BBa_K628006	Composite	Protegrin-1 Kill Switch	353
BBa_K879917	Plasmid_Backbone	LacO ori	2072
BBa_K879918	Plasmid_Backbone	TetO ori	2074

XNase

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

More...

Name	Type	Description	Length
BBa_K1172904	Coding	Rnase Ba (Barnase) from Bacillus amyloliquefaciens	339
BBa_K131000	Generator	ColE2 Operon	2640
BBa_K1479016	Promoter	-- No description --
BBa_K1479017	Protein_Domain	just for test	100
BBa_K150009	Generator	ColicinE1 Producer Controlled by 3OC6HSL Receiver Device	3180
BBa_K526001	Coding	ptrc*-Dpn	1552
BBa_K914001	Composite	pLac Colicin E2 Immunity protein	345
BBa_K914002	Intermediate	repressilator RBS Colicin E2 Immunity protein	282

All biosafety parts

Include previous parts plus other marked as biosafety only.

More...

Name	Type	Description	Length
BBa_K1074011	Composite	PsdpRI+RBS+SDP	2207
BBa_K117000	Coding	Lysis gene (promotes lysis in colicin-producing bacteria strain)	144
BBa_K1172901	Coding	Alanine racemase from ''E. coli''	1080
BBa_K1172902	Device	alanine racemase (''alr'') under the control of the P''tac'' promoter	1134
BBa_K1172904	Coding	Rnase Ba (Barnase) from Bacillus amyloliquefaciens	339
BBa_K1172905	Device	Part 1 of the Biosafety-System araCtive	2260
BBa_K1172908	Device	Part 1 of the Biosafety-System Lac of Growth (pRha lacI alr)	2509
BBa_K1172909	Device	Biosafety-System araCtive (AraC)	3281
BBa_K1172911	Device	Biosafety-System Lac of Growth (lacI)	3600
BBa_K1172912	Device	Part 1 of the Biosystem TetOR alive (pRha TetR alr)	2042
BBa_K1184000	Coding	KillerRed	723
BBa_K1197007	Composite	IPTG dependent B.subtilis Kill Switch construct	2006
BBa_K1223001	Project	P.A.S.E. 1 cassette	2148
BBa_K1223002	Project	P.A.S.E. 2 cassette	1210
BBa_K131000	Generator	ColE2 Operon	2640
BBa_K1363201	Composite	Anti-LPS factor(LALF) regulated by IPTG	2298
BBa_K1405008	Composite	A Kill Switch with "memory" time repressed by IPTG	2926
BBa_K1442006	Regulatory	Anti-theophylline Aptazyme	113
BBa_K1479005	Promoter	-- No description --	16
BBa_K1479007	RBS	Just for upload test	32
BBa_K1479008	Temporary	short short short	32
BBa_K1479009	Temporary	short short short	32
BBa_K1479011	Promoter	oh my god	11
BBa_K1479012	Temporary	short short short	32
BBa_K1479013	Temporary	short short short	32
BBa_K1479014	Temporary	Just for Test	36
BBa_K1479015	RBS	Just for test	16
BBa_K1479016	Promoter	-- No description --
BBa_K1479017	Protein_Domain	just for test	100
BBa_K1479018	Protein_Domain	Just for test
BBa_K150009	Generator	ColicinE1 Producer Controlled by 3OC6HSL Receiver Device	3180
BBa_K1554000	Regulatory	TA29 promoter	859
BBa_K1554004	Device	Yellow biosafety module for plants	3394
BBa_K1554005	Device	Blue biosafety module for plants	3364
BBa_K1616005	Coding	Holin/endolysin reversed - RBS and double T7 terminator	1379
BBa_K1616013	Coding	ccdB reversed - RBS and double T7 terminator	575
BBa_K1639022	Composite	pCons-TetR-pTet-TevProtease Suicide Switch	1546
BBa_K1720002	Regulatory	Hypoxia-induced promotor	707
BBa_K1767001	Composite	P(Lac)IQ RBS Aiia RBS LuxR term term luxpR	1818
BBa_K1767002	Composite	P(Lac)IQ RBS Aiia RBS LuxR ter ter luxpR RBS tetR ter ter	2666
BBa_K1767003	Composite	P(Lac)IQ RBS Aiia RBS LuxR ter ter luxpR RBS tetR ter ter P(tetR) RBS mRFP1 ter ter	3597
BBa_K1767004	Composite	P(Lac)IQ RBS LuxR ter ter luxpR RBS tetR ter ter	1892
BBa_K1774000	Project	CRISPR-Cas9 contaiment device repressed by arabinose and tryptophan	7191
BBa_K1819008	Device	Promoter test circuit to analyze the kill switch efficiency	2725
BBa_K1820024	Generator	Phage inducible promoter 1997 +RBS+FspI + term	1160
BBa_K1820025	Generator	p2001-native RBS-Fsp1-B0015	1209
BBa_K1914000	Coding	E. coli Codon Optimised KillerOrange(EOKO)	717
BBa_K1914001	Device	pT7- E. coli optimised - KillerOrange (EOKO)	926
BBa_K1914003	Device	pT7- E. coli optimised - KillerRed (EOKR)	929
BBa_K1919100	Device	The device consist of temperature promotor and hokD coding gene.	1112
BBa_K2040122	Coding	KillerRed + NLS	744
BBa_K2065003	Coding	CT52-Caspase9
BBa_K2086001	Coding	Serine Repeat Antigen (SerA)	1233
BBa_K2086002	Composite	PyeaR - SerA	1499
BBa_K2107001	Generator	Stationary Phase Promoter + Kil Protein	263
BBa_K2150102	Coding	136 toxin (yobR) CDS	744
BBa_K2150103	Coding	1204 toxin CDS	507
BBa_K2150104	Coding	6249 toxin CDS	319
BBa_K2150110	Device	LacI (constitutive) + Ptac + RiboJ + 1204 toxin	2040
BBa_K2152004	Other	Bacteriophage Phi X 174 lysis gene E with T7 and RBS	363
BBa_K2232025	Composite	mazEF switch	1006
BBa_K2292002	Coding	Toxin-antitoxin mazEF	584
BBa_K2292006	Composite	MazEF kill switch	877
BBa_K2365508	Composite	Bax induced part	1027
BBa_K2384009	Regulatory	TetR	847
BBa_K2384010	Regulatory	LacI	1427
BBa_K2384011	DNA	mf-Lon	2619
BBa_K2384014	Composite	Safeguard-toggle switch	5004
BBa_K2486026	Composite	pGadA-MazF kill switch	769
BBa_K2486027	Coding	MazF endoribonuclease	339
BBa_K2516003	Coding	Membrane-bound SuperNova (for C. reinhardtii)	969
BBa_K2616002	Coding	Temperature Kill Switch	938
BBa_K2660006	Coding	N-Cas9	3459
BBa_K2660007	Coding	C-Cas9	648
BBa_K2757000	Composite	Art-175 fused with N-terminal DsbA 2-19 signal peptide and unidirectional pTet	1008
BBa_K2757001	Composite	Art-175 fused with N-terminal DsbA 2-19 signal peptide and bidirectional pTet	1065
BBa_K2817006	Composite	PcspA-RBS-mazF	535
BBa_K2896001	Coding	Thylakoid-bound SuperNova (for S. elongatus PCC 7942)	846
BBa_K2919000	DNA	ghoT toxin from E. coli K12	174
BBa_K302034	Translational_Unit	mazEF toxin-antitoxin cluster	607
BBa_K302035	Device	Sucrose-limitation induced kill switch	1006
BBa_K3036004	Composite	Cold triggered kill switch	649
BBa_K3036008	Coding	RelB with degradation-promoting tag RepA	1758
BBa_K3096052	RNA	CRISPR Array targeting the Plasmid DNA of the glucose dependent Exendin-4 expression system	147
BBa_K3096054	Composite	Cas3 Nuclease under the control of the AraC promoter pBAD	2803
BBa_K3096055	Composite	Type I CRISPR/Cas system surveillance complex Cascade ABCDE under the control of the AraC promoter	4487
BBa_K3190601	Composite	pGAL1-BI-I: BI-I CDS under inducible promoter	1181
BBa_K3215013	Composite	Tse2 Repressed by Arabinose Kill Switch	1950
BBa_K3215016	Composite	MazF repressed by IPTG Kill Switch	2886
BBa_K3237029	Composite	nucA	1754
BBa_K3273001	Coding	Serratia marcescens nucA nuclease	801
BBa_K3273008	Composite	Composite ADH2/TDH3 nucA	1849
BBa_K3273009	Composite	Composite HXT6 Bax	2039
BBa_K3273010	Composite	Composite MET 25 nucA	1113
BBa_K3317053	Coding	NucD	540
BBa_K3317059	Composite	NucE lysis construction	308
BBa_K3317060	Composite	NucD	572
BBa_K3317061	Composite	tetR repressed killswitch	1504
BBa_K3378002	Regulatory	Ferrous iron sensetive promoter fhuA1	55
BBa_K3512001	Coding	ccdB Toxin	306
BBa_K3588014	Composite	MazE-MazF Hypoxia induced kill switch	2211
BBa_K3634012	Composite	Glucose-Mediated Death Sensor	566
BBa_K3634020	Coding	CviJI Endonuclease (+ ssrA deg. tag)	873
BBa_K3755043	RNA	Sok RNA	66
BBa_K3755045	Coding	Hok/Mok protein	217
BBa_K3755046	Composite	Double Regulated(trp+lac) Kill Switch	2352
BBa_K3848004	Composite	Lactate regulated kill switch	2837
BBa_K4133006	Coding	Repressor protein CtsR_Lp (Lactobacillus plantarum WCFS1) for Lactobacillus casei	468
BBa_K4133007	Regulatory	PclpC_Lp repressible promoter (Lactobacillus plantarum WCFS1)	59
BBa_K4133008	RBS	RBS_Lp (Lactobacillus plantarum WCFS1)	14
BBa_K4133009	Coding	Repressor protein CtsR_Lc (Lactococcus lactis) for Lactobacillus casei	456
BBa_K4133010	Regulatory	PclpC_Lc repressible promoter (Lactococcus lactis)	72
BBa_K4133011	RBS	RBS_Lc (Lactococcus lactis)	12
BBa_K4133012	Coding	LysKB317 (Endolysin) for Lactobacillus casei	894
BBa_K4139000	Coding	mcyH ABC Transporter for Microcystin Production	1617
BBa_K4139001	Composite	mcyH ABC Transporter for Microcystin Production (Composite)	1796
BBa_K4139002	Coding	mcyH crRNA for Lbu Cas13a (for E.coli)	57
BBa_K4139003	Composite	mcyH crRNA for Lbu Cas13a (Composite)	219
BBa_K4139004	Coding	mcyH crRNA for Lbu Cas13a (for Cyanobacteria)	57
BBa_K4139006	Coding	mcyH crRNA for Lwa Cas13a (for E.coli)	75
BBa_K4139007	Composite	mcyH crRNA for Lwa Cas13a (for E.coli, Composite)	237
BBa_K4139008	Coding	mcyH crRNA for Lwa Cas13a (for Cyanobacteria)	75
BBa_K4202000	Coding	mazE(codon optimization for Bacillus subtilis)	249
BBa_K4202001	Coding	mazF(codon optimization for Bacillus subtilis)	421
BBa_K4202045	Generator	Sucrose regulated kill switch in Bacillus subtilis	1291
BBa_K4345020	Composite	5' UTR of hsp17 with ccdA fused to sfGFP	1197
BBa_K4345023	Composite	5' UTR of rpoH with ccdA fused to sfGFP	1395
BBa_K4345024	Composite	5' UTR of prfA with ccdA fused to sfGFP	1277
BBa_K4706007	Coding	AtBAG6 induced S. cerevisae cell death	405
BBa_K4706013	Composite	Gal1 induced RFP A2 AtBAG6	2955
BBa_K4706015	Composite	SrpR repressable PHO5 phosphate dependent cell death	3532
BBa_K515104	Composite	J23100 promoter - Antiholin	488
BBa_K515106	Composite	J23103 promoer - RBS B0034-RFP E1010 - Holin K112805 - endolysin K112806	1973
BBa_K526001	Coding	ptrc*-Dpn	1552
BBa_K5480009	Composite	Y38-DpnI-TrrnB	2353
BBa_K628006	Composite	Protegrin-1 Kill Switch	353
BBa_K748007	Composite	Biofilm formation device. yddV gene with the IPTG inducible promoter.	1604
BBa_K772101	Composite	Self-Destruction Kit: Endolysin + Holin	839
BBa_K786031	Reporter	T7promoter-RSR-T7teminator	956
BBa_K843004	Device	T4 lysis device regulated by IPTG	2871
BBa_K879917	Plasmid_Backbone	LacO ori	2072
BBa_K879918	Plasmid_Backbone	TetO ori	2074
BBa_K914000	RNA	pLac-supD-T	241
BBa_K914001	Composite	pLac Colicin E2 Immunity protein	345
BBa_K914002	Intermediate	repressilator RBS Colicin E2 Immunity protein	282
BBa_K914009	Translational_Unit	P1003* Ser133->Amber Codon	967
BBa_K914011	Intermediate	supD-T - intermediate	178
BBa_K914012	Plasmid_Backbone	pSB1A2 with 1 amber mutation	2079
BBa_K914018	Translational_Unit	P1003** Kan resistant gene with 2 Amber Codon	967
BBa_K990005	Composite	LasR Device + T4 Lysis Device	2915

Physical Containment