Team:Paris Bettencourt/Human Practice/WikiScreen

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iGEM Paris Bettencourt 2012

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Wiki Screen

Team	Year	Project Name	Project Summary	Biosafety Idea	Efficiency
St. Andrews	2011	Kill switch engage!	Kill switch	Kill switch. "Our kill switch is designed by inserting an antimicrobial peptide (AMP) gene into E.Coli" Read More	Used the LIVE/DEAD Baclight Bacterial Viability kit, but don't have any quantitative results in terms of number or proportion of cell death. "The relationship between the concentration of arabinose and the amount and rate of cell death seems linear in nature."
Imperial College	2011	Auxin	Engineer bacteria to accelerate plant root development	Toxin/antitoxin. Consits of the insertion of the Holin + Endolysine and Anti Holin genes. Holin is a protein that forms pores in cell membranes Anti-holin binds to holin, inhibiting it's action. Once pores are formed by holin, lysozyme can access the periplasmic space and degrade the cell wall, causing cell lysis. Read More	Anti-holin was expressed in cells, but no experiments for this system have been made. "It seems very likely that our GM E. coli have been able to survive in soil and retain their plasmid for six weeks despite competition and selective pressure against the plasmid."
Bristol	2010	AgrEcoi	Bacteria that detects and signals the presence of nitrates	Encapsulation in a gel. We encapsulated our bacteria in beeds made out of a non toxic gel. Read More	Due to the beads, "bacteria are kept separate from the environment, reducing public safety fears." No quantification provided.
Colombia	2011	Defense aid for coffee plantations against fungi ("Detect and alert" system)	Detect chitin,and alert the plant by stimulating an early hypersensitive response against infection.	A few ideas but no design: Amplification mostly from start to stop codon to avoid hidden pathogenicity + blast of sequences to confirm Cloning in vectors without a mobilizable origin or TRA region. Growth curve of the strain to confirm low dissemination. Develop a strategy to monitory the presence of the modified bacteria in the crops fields based on color markers (no design made). Read More	No results
British Columbia	2011	iSynthase	Optimize production of terpenes in Saccharomyces cerevisiae yeast (to help trees fight invading beetles and fungi)	A few ideas (no design): Contain a tracking system to detect their presence e.g. a non-coding DNA code akin to a fingerprint Contain a suicide system to enable effective elimination of the organism when so desired What experts say	No results
Peking	2010	Heavy metal decontamination kit	Heavy metal bioreporter and bioabsorbent engineering	A few superficial ideas: Make the plasmid toxic for any bacteria it may transfer to. Plasmid can’t be replicated in another bacteria Read More	No results
Brown-Stanford	2011	REGObricks PowerCell	Projects which could be useful for a space travelling: REGObricks brings the principle of In-Situ Resource Utilization to bear on the problem of constructing, maintaining and expanding shelter for human inhabitants on the desolate Martian landscape. By producing macromolecules essential to bacterial growth, PowerCell will form a metabolic foundation for the biological systems which will eventually enable a settlement on Mars.	Not about biosafety, but: The team used GelRed, a DNA dye produced by Biotium Inc, as a non-toxic alternative to ethidium bromide (EtBr). Let's use it too! They do not believe that their BioBrick parts will have any negative effect on the environment. But they could be interested by our project! Read More	Not applicable
KULeuven	2011	E.D. FROSTI	CONTROLLING ICE FORMATION. Bacterium E.D. Frosti induces ice crystallization, using the ice-nucleating protein (INP), or inhibits ice crystal formation, using the anti-freeze protein (AFP), depending on the given stimulus. These proteins will be extracellularly anchored at E.D. Frosti’s cell membrane.	Suicide mechanism: DNA nuclease. (ideas) Destruction of the DNA > bacteria dies, but keeps its shape so it can still do its job (functional protein are at the surface of the membrane). The suicide mechanism activity is mediated by an “AND”-gate system: the cell death mechanism is only activated when one of the two stimuli is given, AND a sudden decrease in temperature (a cold-shock) occurs Read More	No constructions, no results.
LMU-Munich	2011	Metal Sensor	Biosensor to detect metals in waste water	One idea (no design): Every potentially pathogenic or hazardous biobrick should be cloned in a special backbone containing the sequences of the present backbones AND an inducible killing gene cassette. This killing cassette is induced by a normaly absent reagent that could easily be added in case of contamination Read More	No results.
Lyon-INSA-ENS	2011	Cobalt Buster	Decontamination of radioactive cobalt in water by a biofilm	Biofilm & Adherence = confinement bacterias easy purification of water Read More	No quantitative results.
METU-Ankara	2011	MethanE.COLIc	Sensing methane gas and converting it into methanol	Kill switch = Toxin temperature induced Holin + Endolysine Induced when T°>42°C Read More	No quantitative results.
Caltech	2011	Bioremediation of Endocrine Disruptors Using Genetically Modified Escherichia Coli	Endocrine-disrupting chemicals (EDCs) are chemicals that interact with the endocrine system by binding to hormone receptors, causing problems in sexual development and reproduction of organisms	Biosafety ideas: Water filtration system for containment of microbes (filters all microbes, does not retain free DNA). Use the ccdB gene (BBa_P1016 and BBa_P1010)on a plasmid in conjunction with an E. coli strain such as DB3.1 (BBa_V1005). The plasmid will code for the “death gene” which will kill any cell that does not code for immunity in its genome. If a native microorganism would uptake this man-made plasmid, it would die, preventing the propagation of the recombinant DNA in the environment (Featured Parts: Cell Death). Another similar “suicide” containment system uses streptavidin (BBa_J36841) (Kaplan, Mello et al. 1999; Urgun-Demirtas, Stark et al. 2006). This protein binds very tightly to biotin, a required co-enzyme for many metabolic pathways. This makes biotin unavailable and causes cell death. Kaplan et al. reported cell counts were reduced 99.9% in eight hours after their system was activated by absence of pollutant to degrade. Read More	No results
Berkeley	2010	[1]	Choa Choa's Delivery Service	Clotho Framework: Clotho implements the current biosafety standards as outlined by the NIH and the CDC. Whenever a new part is instantiated, Clotho BLAST's its sequence against a databank of known virulence factors and pathogens and returns the RG number of the highest match. This framework ensures that every part in Clotho has a RG value associated with it. In addition, when composite parts are made by joining basic parts, the composite part is also assigned a BSL number. Finally, all strains in Clotho have a risk group. Read More	Not applicable.
WITS-CSIR_SA	2011	Biotweet	Engineer bacteria to allow them to transport packets of chemicals, and then form a network.	Promoter responsive to synthetic chemicals not present in nature. Read More	Not applicable.
ULB-Brussels	2011	One-step gene insertion or deletion system	An easy way to allowing the insertion and/or deletion of genes in the E. coli chromosome in a minimal number of steps	FLP recombination to remove resistance gene, eg. FRT - Cm - FRT will remove the Cm resistance gene Read More	"All 32 candidates that contained pINDEL grew on LB but none of them grew on LB Cm plates indicating that all of them have lost the antibiotic resistance cassette, sgowing the the DEL function of pINDEL functions properly."
Johns Hopkins	2011	VitaYeast	They want to make bread with yeast producing Vitamin	their yeast strain lacks functional pathways for seven essential aa. Read More
Kyoto	2009	p1 : Gene Switch Depending on Duplication	How to express a gene after a certain lifespan. The use Linear DNA, in which a repressor will be degraded after few cell division.	"they want to control exact cell’s life time (or death time) depending on the number of cell division times. They get rid of the exonucelase problem by inserting multiple protein binding site that will be degraded when division occurs, but not with exonucleases. The repressor gene is degraded after a certain time." Read More
UNICAMP-EMSE_Brazil	2011	stress wars	Coli based production of anti-stress compounds in the organism to improve the quality of life	"no design but two suggestions : One suggestion in the biosafety of the researcher is to include in the iGEM parts kit the bacterial less endotoxicchassi (developed by Berkeley UC 2007), to avoid serious septic problems in the case of an accident that leads to an intense contact with the bacteria (eye or bloodstream contact, inhalation or ingestion). Another suggestion for population and environment safety is to (somehow) include in all biobricks an operating unit that detects if the bacteria is not in a culture media (detects some molecule produced through the metabolism of a specific media constituent) and express lysozyme to kill it if it's released in the environment (idea inspired by Team UNICAMP-Brazil 2009)." Read More
Illinois-Tools	2009	Interactive Metabolic Pathway Tools (IMP Tools)	Open source, web based program that involves model-guided cellular engineering where new metabolic functions can be added to existing microorganisms. It takes a user-defined input compound, output compound, and weighting scheme and determines the ideal pathway from the starting to the ending compound	By limiting ATP produced we lessen the chances of a cell growing vigorously and being a potential danger to the environment. The actual means to prevent this is by creating a script that will analyze ATP consumption and production. With this information, you are able to adjust the ATP metabolism in whatever way you want. You will be able to keep the production low enough so cell processes can still occur and allow the cell to grow to an extent but not high enough that it can potentially grow out of control Read More
Harvard	2009	Optical communication	Our team has constructed a system that allows for interspecies, bacteria-to-yeast optical communication	A bacterial blackboard using a yeast two hybrid system and luciferase proteins. The blackboard can only be activated with a certain frequency of light, and must be erased with a different frequency of light. Read More
Michigan	2009	The Toluene Terminator	The Toluene Terminator is a Pseudomonas putida device that aims to: identify the toxic compound toluene in an environmental setting (e.g. a spill into soil from an underground petrol tank), move to and uptake it, metabolize it, destroy itself when all of the toluene has been metabolized.	A kill switch that operates through the Enterobacteria phage T4 Lysis Device (lysozyme, holin, and antiholin) created by the Berkley 2008 team. We proposed two mechanisms for cell lysis: arabinose inducible suicide mechanism suicide mechanism with tunable repression. See the designs
Queens Canada 2011	2011	Nemoremediation	Engineering C.elegans for advanced bioremediation	Kill switch. MRT-2 mutant Kill Switch This is an indirect kill switch. The teams plans to use a mutant strain of bacteria which has losts its molecules for immortality. It can reproduce for only a couple generation and will then become sterile, leading to the extinction of this bacteria population. RNAi Kill Switch RNAi knockout is a method of gene regulation where double stranded RNA (dsRNA) is introduced to the worm, binding to gene products such as specific RNAs (mRNA), thereby decreasing or eradicating RNA activity by recycling said products. Only a few dsRNA molecules per cell are required to produce effective interference. Read More	MRT-2 mutant Kill Switch "Given that the germ-line of the mrt-2 mutant has a limited number of generations in which it can reproduce, our created strain is timed for eventual extinction of a span between 2 months and 1 year, with the average being 6.25 months". However, no experiment is provided, and so we do not know how they obtained these numbers, but we could assume they come from the literature. RNAi Kill Switch No results
Unist Korea	2011	CHOp-Coli-LATE	Safety device that is off when bateria senses the that it is in its native environment (the fermentor) but that activates and leads to bacterial suicide when the bacteria escapes the fermentor (it senses that it is in a non native environment).	Self killing device that will activate if the bacteria's environment changes and lyse the bacteria's DNA. Turns on in the presence of: low temperature, light, change of osmolality. Read More	The team managed to have the sensor part work (the bacteria can efficiently sense a change in light, temperature and osmolality. However they did not manage to get the lysis module to work. Therefore this system was never completed, so there are no results available in terms of its efficency to prevent bacterial escape from the fermentor.
Tokyo NoKoGen	2011	EcoLion	E. coli collecting heavy metal ions	Collecting E.coli with phototaxis or aggregation Kill switch: Holin/Endolysin system (for the reamining bacteria that were excaped collecting) Read More	Collection E.coli: The team did not get conclusive results for phototaxis. The team showed that bacteria with the aggregation module aggregaated more then the control, although they were not able to control this aggregation: their iPTG inducible promoter gave results expected if it was a constitutively active one, suggesting leakage. Kill switch: Within 2 hours after addition of IPTG, the OD660 went down by 80%, indicating that the lysis genes were successfully induced by IPTG. However, we should wonder if 80% is good enough...

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   <p style="text-align:right;"> [https://2011.igem.org/Team:Tokyo-NoKoGen/photocontrol Read More] </p>
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-*'''''Collection E.coli''''' The team did not get conclusive results for phototaxis.  The team showed that bacteria with the aggregation module aggregaated more then the control, although they were not able to control this aggregation: their iPTG inducible promoter gave results expected if it was a constitutively active one, suggesting leakage.
+*'''''Collection E.coli:''''' The team did not get conclusive results for phototaxis.  The team showed that bacteria with the aggregation module aggregaated more then the control, although they were not able to control this aggregation: their iPTG inducible promoter gave results expected if it was a constitutively active one, suggesting leakage.
 *'''''Kill switch:''''' Within 2 hours after addition of IPTG, the OD660 went down by 80%, indicating that the lysis genes were successfully induced by IPTG. However, we should wonder if 80% is good enough...
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