Team:Edinburgh/Wiki Watch

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Revision as of 23:03, 2 September 2011

Wiki Watch

I carried out my orders until arrested. I had no sense that I was
spying, and I ask that this be taken into account in deciding my verdict.

— Witold Pilecki

In order to help collaboration between teams, as well as for our own enlightenment, we put together the following list of projects. This page is now linked from the Community page, and we hope others have found it useful.

Also, you might check [http://igemwatch.net/ Dr Tom Ellis's blog] for descriptions of some projects.

Americas
Team	Notes
Alberta	Converting biomass to biodiesel using [http://en.wikipedia.org/wiki/Neurospora_crassa Neurospora crassa].
Arizona State	Countering antibiotic resistance with [http://en.wikipedia.org/wiki/CRISPR CRISPR].
Baltimore	Creation of a [http://en.wikipedia.org/wiki/Taq_polymerase Taq polymerase] BioBrick.
Bard-Annandale	Logical construct involving quorum sensing and Lux genes.
Berkeley	Stress-repressed promoter in front of stress-producing (toxic) product to regulate its level.
British Columbia	Production of [http://en.wikipedia.org/wiki/Monoterpene monoterpenes] in yeast, to investigate their anti-fungal properties.
Brown-Stanford	Mars! [http://en.wikipedia.org/wiki/Sporosarcina_pasteurii S. pasteurii] to make calcium carbonate; biosensor; cyanobacteria/E. coli symbiosis.
BU Wellesley Software	(Software) Involves plasmid design, recombinases, and tuberculosis?
BYU Provo	AND gate: OxyR (input: H2O2) + [http://en.wikipedia.org/wiki/Riboswitch riboswitch] (input: high temperature). Output via [http://en.wikipedia.org/wiki/Cre-Lox_recombination Cre-Lox].
Calgary	Biosensor for [http://en.wikipedia.org/wiki/Naphthenic_acid naphthenic acids].
Caltech	Bioremediation of organic pollutants, especially [http://en.wikipedia.org/wiki/Endocrine_disruptor endocrine disruptors].
Colombia	E. coli that recognise fungal pathogens by their [http://en.wikipedia.org/wiki/Chitin chitin], and destroy it or induce plant defenses.
Columbia-Cooper	Using metal-binding peptides to form [http://en.wikipedia.org/wiki/Quantum_dot quantum dots].
Cornell	E. coli that will lyse themselves upon receiving some specific light wavelength.
Duke	Something to do with "increasing the robustness of bacterial gene networks".
Gaston Day School	Nitrate detector with output as Red Fluorescent Protein.
GeorgiaState	BioBricks from [http://en.wikipedia.org/wiki/Pichia_pastoris Pichia pastoris] promoters. Characterise with GFP.
GeorgiaTech	Countering antibiotic resistance with [http://en.wikipedia.org/wiki/CRISPR CRISPR].
Grinnell	Secretion of [http://en.wikipedia/org/wiki/biofilm biofilm]-degrading compounds from [http://en.wikipedia.org/wiki/Caulobacter_crescentus Caulobacter crescentus].
Harvard	Improved targetting of gene therapy using [http://en.wikipedia.org/wiki/Zinc_finger zinc finger] DNA binding proteins.
Hunter-NYC	Removal of metal ions from contaminated water, using lipase secretion tag.
ITESM Mexico	[http://en.wikipedia.org/wiki/Arabinose Arabinose] biosensor with (concentration dependent) output using GFP or CFP.
IvyTech-South Bend	Arsenic biosensor with output via smell. May use E. coli or S. cerevisiae.
Johns Hopkins	Production of vitamins and minerals in S. cerevisiae.
Lethbridge	Bioremediation e.g. of heavy metals.
McGill	Control of mammalian cells using light.
Michigan	Bind DNA-binding protein to E. coli membrane; attach to surfaces that have oligonucleotides.
Minnesota	Light-induced silicatein fused to ompA or Ice Nucleation Protein for 3D printing.
Missouri Miners	Alteration of [http://ecoliwiki.net/colipedia/index.php/ompR ompR] system to activate at different glucose concentrations.
MIT	Mammalian [http://en.wikipedia.org/wiki/Juxtacrine_signalling juxtacrine signalling] and [http://en.wikipedia.org/wiki/G_protein-coupled_receptor G protein-coupled receptors].
Nevada	Sugar production from cyanobacteria, to feed E. coli that make biofuel.
Northwestern	Detection of [http://en.wikipedia.org/wiki/Pseudomonas_aeruginosa Pseudomonas aeruginosa] by using its quorum sensing system.
NYC Software	(Software) Genome analysis focusing on radiation tolerance.
NYC Wetware	Making E. coli radiotolerant by using genes from [http://en.wikipedia.org/wiki/Deinococcus_radiodurans Deinococcus radiodurans].
Panama	Synthesis of rhamnolipids.
Penn	Cell-cell communication via light.
Penn State	Radiation detector using Phage Lambda lytic switch system.
Purdue	Bistable toggle switch using [http://en.wikipedia.org/wiki/Phytochrome phytochromes].
Queens Canada	Using [http://en.wikipedia.org/wiki/C._elegans the worm] for sensing pollutants by swimming to them.
Rutgers	Bacteria responding to lasers; addition of numbers in bacteria; BioBrick validation.
Tec-Monterrey	Production of high fructose syrup using membrane-bound fusion proteins.
Toronto	Incorporating a magnetosome system into E. coli?
TorontoMaRSDiscovery
UANL Mty-Mexico	Logic gates taking light signals as inputs.
UCSF	Production of biofilms with S. cerevisiae, by cell display of adhesive proteins.
UC Davis	Mutagenesis on promoters and repressors to produce new behaviours.
UIUC-Illinois	Different plasmids in a cell; choose which is active by making one go to high copy number.
UNAM-Genomics Mexico	Hydrogen production in [http://en.wikipedia.org/wiki/Rhizobium_etli Rhizobium etli] in [http://en.wikipedia.org/wiki/Phaseolus_vulgaris Phaseolus vulgaris].
UNAM-ITESM Mexico City	Rubber-degrading bacteria.
UNICAMP-EMSE Brazil	Detect mammal's stress by [http://en.wikipedia.org/wiki/Catecholamine catecholamines] and [http://en.wikipedia.org/wiki/Nitric_oxide nitric oxide]; regulate it with [http://en.wikipedia.org/wiki/Cytokine cytokines].
uOttawa	Improving S. cerevisiae for use with BioBricks.
USC	Countering antibiotic resistance with [http://en.wikipedia.org/wiki/CRISPR CRISPR].
Utah State	Production of valuable compounds using the cyanobacterium [http://en.wikipedia.org/wiki/Synechocystis Synechocystis].
UTP-Panama	Various.
UT Dallas	Repair of human tissue using bacteria.
VCU	Various projects involving the cyanobacterium [http://en.wikipedia.org/wiki/Synechococcus Synechococcus elongatus].
Virginia	Using S. cerevisiae to produce factors which heal human wounds.
Virginia Tech	Fluorescent proteins that fold and degrade quickly, to be used as reporters.
Washington	Alkanes in E. coli; luciferase in yeast; [http://en.wikipedia.org/wiki/Gluten gluten]-cleaving enzyme; [http://en.wikipedia.org/wiki/Magnetosome magnetosomes] in E. coli.
WashU	[http://en.wikipedia.org/wiki/Carotene B-Carotene] and [http://en.wikipedia.org/wiki/Ionone B-Ionone] production in S. cerevisiae.
Waterloo	Creation of ribozymes that will excise out of an RNA transcript.
West Point	Detect Vibrio cholerae by letting it lyse E. coli, releasing β-galactosidase.
Wisconsin-Madison	Biosensors to detect biofuels?
Yale	Production of antifreeze using E. coli and a gene from the Rhagium inquisitor beetle.
Asia
Team	Notes
ArtScienceBangalore
CBNU-Korea	Synthesising a minimal chromosome; somehow involving [http://en.wikipedia.org/wiki/Vibrio_cholerae V. cholerae].
CTGU-Yichang
Fudan-Shanghai	Nitrate detection; switching between different colour production; something else.
HIT-Harbin	Yoghurt bacteria that stop producing acid once the yoghurt is acidic enough.
HKU-Hong Kong	Silencing specific genes with a modified histone-like nucleoid structuring protein.
HKUST-Hong Kong	Degrading [http://en.wikipedia.org/wiki/Indole indole] using toluene-4-monooxygenase, to boost antibiotic susceptibility.
HokkaidoU Japan	Type III secretion system to inject stuff into eukaryotic cells.
Hong Kong-CUHK	Light-driven ion pump to produce electricity.
HSU
HUST-China	Modification of gut-colonising bacteria to degrade alcohol and prevent people being drunk.
IIT Madras	Modular biosensors.
KAIST-Korea	Artistic E. coli, expressing fluorescence in response to quorum sensing molecules.
KAIT Japan
KIT-Kyoto	Using quorum sensing to turn on and off GFP expression for aesthetic purposes.
Korea U Seoul	Production of [http://en.wikipedia.org/wiki/Alkane alkanes] from glucose.
Kyoto	Attracting insects with light, trapping them with gum, and digesting them.
Macquarie Australia	"Bacterial light switch" involving [http://en.wikipedia.org/wiki/Phytochrome bacteriaphytochrome] and [http://en.wikipedia.org/wiki/Heme_oxygenase heme oxygenase].
Nanjing
NCTU Formosa	Temperature controlled expression; testing with [http://en.wikipedia.org/wiki/Carotenoid carotenoid], violacein, and [http://en.wikipedia.org/wiki/Butanol butanol] synthesis.
NYMU-Taipei	Something involving magnetosomes to transduce a signal; also DNA for information storage.
Osaka	Radiation dosimeter using DNA repair systems to detect radiation.
OUC-China	Promotion and inhibition of bacterial strains by each other.
Peking R	Something involving [http://en.wikipedia.org/wiki/Riboswitch riboswitches] and synthetic ribosome binding sites.
Peking S	Something with cell-cell communication.
Rajasthan
SJTU-BioX-Shanghai	Translational control.
SYSU-China	Bacteria that move towards ionising radiation and absorb radioisotopes.
Tianjin	Adjusting the yeast TOR (Target Of Rapamycin) protein to aid survival in [http://en.wikipedia.org/wiki/Lignocellulose lignocellulose].
Tokyo-NoKoGen	Bacteria that absorb radioactive [http://en.wikipedia.org/wiki/Caesium caesium].
Tokyo Metropolitan	Killer E. coli that swim to some "target" and kill it.
Tokyo Tech	Rock/Paper/Scissors bacteria; urea production; [http://en.wikipedia.org/wiki/Isoprene isoprene] for cloud seeding.
Tsinghua	Something involving movement of proteins.
Tsinghua-A	Oscillation between red and green fluorescence, using quorum sensing.
TzuChiU Formosa	Conversion of CO to CO2 using [http://en.wikipedia.org/wiki/Carbon_monoxide_dehydrogenase carbon monoxide dehydrogenase] in [http://en.wikipedia.org/wiki/Rhodospirillum_rubrum Rhodospirillum rubrum].
UNIST Korea	An organism which will kill itself upon escape from the lab.
UQ-Australia	24-hour bacterial oscillator.
UST-Beijing	Bile acid sensor involving [http://en.wikipedia.org/wiki/Liver_X_receptor_beta LXR-Β].
USTC-China	"Self-organized bacteria"; project involves [http://en.wikipedia.org/wiki/Riboswitch riboswitches].
USTC-Software	(Software) Visual tool for analysing dynamics of biological systems.
UT-Tokyo	Bacteria that respond to stress by creating a signal, which other bacteria swim towards.
VIT Vellore	Enteric bacteria producing drugs or other compounds for the body.
Waseda-Japan	Responding to different colours of light, detected by CcaS and CcaR.
WHU-China	Bacterial communication with light; also colour photography using E. coli.
XMU-China	Something involving GFP.
ZJU-China	Something involving using biofilms.
Europe
Team	Notes
Amsterdam	Make E. coli psychrophilic (cold loving).
BCCS-Bristol
Bielefeld-Germany	Cell-free biosensor for bisphenol A.
Bilkent UNAM Turkey	Production of protein from algae e.g. [http://en.wikipedia.org/wiki/Chlamydomonas_reinhardtii Chlamydomonas reinhardtii].
Cambridge	Bacterial expression of [http://en.wikipedia.org/wiki/Reflectin reflectins] from Loligo squid.
CongoDRC-Bel Campus	Vaccine for [http://en.wikipedia.org/wiki/Mycobacterium_ulcerans Mycobacterium ulcerans].
Copenhagen	Removal of pharmaceutical products from water with [http://en.wikipedia.org/wiki/Cytochrome_P450 cytochrome P450].
Debrecen Hungary
DTU-Denmark	Using sRNA for post-transcriptional regulation.
Dundee	Creation of [http://en.wikipedia.org/wiki/Bacterial_microcompartment bacterial microcompartments].
Edinburgh	Display of cellulases on M13 (via pVIII) or on cell surface (via Ice Nucleation Protein).
ENSPS-Strasbourg
EPF-Lausanne	Creation of new [http://en.wikipedia.org/wiki/Transcription_factor transcription factors].
ETH Zurich	Biological smoke detector by detection of [http://en.wikipedia.org/wiki/Acetaldehyde acetaldehyde].
Fatih Turkey	Using [http://en.wikipedia.org/wiki/B._subtilis B. subtilis] to detect E. coli?
Freiburg	A cheaper system for protein purification.
Glasgow	Light-controlled expression of bacteria inside biofilms.
Grenoble	Determination of metal concentration by growing reporter bacteria on an IPTG gradient.
Groningen	Remember that an input has occurred; use a biological [http://en.wikipedia.org/wiki/AND_gate AND gate] to count occurrences.
Imperial College London	Something involving [http://en.wikipedia.org/wiki/Auxin auxin], and dealing with soil erosion.
KULeuven	Creation and prevention of ice with Ice Nucleation Protein and Anti Freeze Protein.
LMU-Munich	Metal biosensors with a focus on quantification.
Lyon-INSA-ENS	Biofilter for radioactive waste.
METU-Ankara	Methane biosensor and methane conversion into methanol.
METU-BIN Ankara	(Software) Web based tool for construct planning.
METU Turkey SoftLab
Nairobi	Engineering a fungus to kill insects.
NTNU Trondheim	Detection of bacterial stress; based on the E. coli "[http://en.wikipedia.org/wiki/Stringent_response stringent response]" which produces ppGpp.
Paris Bettencourt	Passing signals e.g. RNA from cell to cell via nanotubes.
Potsdam Bioware	Directed evolution of cyclic peptides for therapeutics. Use phage display, error-prone PCR.
Sevilla	Biological circuits using multiple different genotypes at once.
Strathclyde Glasgow
St Andrews	Production of anti-microbial peptides in E. coli to kill bacteria.
TU-Delft	Expressing mussel glue protein in E. coli to attach to stuff, with inducible detachment.
TU Munich	3D printing by immobilising E. coli in a gel; turn on genes iff 2 different colour lasers hit.
UCL London	Using [http://en.wikipedia.org/wiki/DNA_gyrase gyrase] to increase supercoiling of plasmids.
UEA-JIC Norwich	Glow-in-the-dark bacteria, protists, and moss.
ULB-Brussels	Tools for inserting or deleting genes in the main E. coli chromosome.
UNIPV-Pavia	Regulating a quorum sensing molecule by negative feedback.
UNITS Trieste	Synthetic biome where bacteria and eukaryotic cells depend on each other to survive.
UPO-Sevilla	Biological memory with bistable toggle switches.
Uppsala-Sweden	Light-induced gene expression.
UTP-Poland
Valencia	Production of antimicrobial peptides to clean up drinking water.
Wageningen UR	Oscillating, synchronised gene expression in E. coli, and communication along fungal [http://en.wikipedia.org/wiki/Hypha hyphae].
Warsaw	Cell-free cloning using [http://www.neb.com/nebecomm/products/productM0269.asp phi29 DNA polymerase]; also insertion of stuff into main genome.
WITS-CSIR SA	E. coli that search for a ligand then, upon finding it, return to a point of origin and report.

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