Team:Edinburgh/Wiki Watch

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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 Control of cell density with a killer gene.
ZJU-China Using different oxygen levels in biofilms to control different expression patterns.
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 Something with Nuclear Hormone Receptors: ligand activated transcription factors.
DTU-Denmark Using sRNA for post-transcriptional regulation.
DTU-Denmark-2 A new assembly method using uracil-excision based cloning.
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 (Software) GUI for designing synthetic systems.
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.
HU-Micro
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 (Software) "BioGuide".
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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