Brainstorm Area

Interesting Links

• [http://openwetware.org/wiki/IGEM:Idea_exchange iGEM Idea Exchange]
• [http://openwetware.org/wiki/Tk:wanted_parts TK: Wanted Parts]
• [http://openwetware.org/wiki/IGEM:Projects_categorized iGEM:Projects categorized]
• [http://openwetware.org/wiki/Synthetic_Biology:Vectors/Wishlist Synthetic_Biology:Vectors/Wishlist]

Interesting Papers (provided by Domenico)

• [http://www.plosone.org/article/info:doi/10.1371/journal.pone.0002815 Design and Construction of a Double Inversion Recombination Switch for Heritable Sequential Genetic Memory]
• [http://www.nature.com/nature/journal/v457/n7227/full/nature07616.html A tunable synthetic mammalian oscillator]
• [http://www.nature.com/msb/journal/v3/n1/full/msb4100187.html Programming gene expression with combinatorial promoters]
• [http://pubs.acs.org/doi/abs/10.1021/ar020219d Photoreceptor Proteins, “Star Actors of Modern Times”: A Review of the Functional Dynamics in the Structure of Representative Members of Six Different Photoreceptor Families]
• [http://www.nature.com/msb/journal/v5/n1/full/msb20091.html Environment-specific combinatorial cis-regulation in synthetic promoters]
• [http://www.ploscompbiol.org/article/info:doi%2F10.1371%2Fjournal.pcbi.1000064 Implementing Arithmetic and Other Analytic Operations By Transcriptional Regulation]
• [http://www.jbioleng.org/content/2/1/5 Engineering BioBrick vectors from BioBrick parts]
• [http://authors.library.caltech.edu/13255/ Model-guided design of ligand-regulated RNAi for programmable control of gene expression]
• [http://www.nature.com/nbt/journal/vaop/ncurrent/abs/nbt.1536.html Diversity-based, model-guided construction of synthetic gene networks with predicted functions]

Brainstorm Ideas

Impulse Signal

• one suggestion (by Federico C.) from the idea exchange was to create a self-destructing plasmid, which would express once and than destroy itself with a restriction endonuclease in its code.

Water Soluble Vitamin Production

• produce Vitamins B and C.

Stop Quorum Signalling -> Quenching AHL

• aiiA enzyme [http://www.msk.or.kr/jsp/view_old_journalD.jsp?paperSeq=2133] already has a biobrick [http://partsregistry.org/Part:BBa_C0060 Part:BBa_C0060] but it is not secreted.

• halogenated furanones [http://mic.sgmjournals.org/cgi/content/full/151/11/3589?view=long&pmid=16272381] [http://mic.sgmjournals.org/cgi/content/full/148/4/1119?view=long&pmid=11932456] decrease binding activity of LuxR.

• [http://www.molbio.princeton.edu/index.php?option=content&task=view&id=27 Bonnie Bassler]'s research, inhibit quorum signaling with molecules structurally similar to AHL. Her recent [http://www.ted.com/index.php/talks/bonnie_bassler_on_how_bacteria_communicate.html TED Talk].

Biological Isotope Separation

• is it even possible?

• according to this [http://jol.liljenzin.se/BOOK.HTM book] in section 2.6.5. [http://jol.liljenzin.se/KAPITEL/CH02NY3.PDF], both chlorella algae and E.coli have isotope enrichment properties (hydrogen, deuterium). no references given.

• possible applications: remove radioactive isotopes from body (cancer treatments), separate heavy water from ocean water, remove carbon 14 and potassium 40 from body/food.

• another paper is Bioseparation of Lithium Isotopes by Using Microorganisms, Sakaguchi, Takashi | Tomita, Osamu, Resource and Environmental Biotechnology [Resour. Environ. Biotechnol.]. Vol. 3, no. 2-3, pp. 173-182. 2000. havent found a copy online.

Saltwater Purification

• + heavy metal extraction

• diatoms

• Dead Sea organisms

• [http://www3.interscience.wiley.com/journal/117915599/abstract?CRETRY=1&SRETRY=0; Lyotropic liquid crystals] - Lyotropic liquid crystal (LLC) structures can be used as selective membranes to seperate between certain chemicals (e.g. removing salt molecules from water molecules). If it is possible, we could design a bacteria that would have the LLC as a membrane, culture this bacteria and put it in saltwater, so that it removes the salt from the water, and then remove the bacteria altogether. Question is, can LLC be used as a bacterial membrane?

Xylitol production

• already attempted, see [http://openwetware.org/images/0/03/6-bolaji.pdf]

Melatonin Compensation

• compensate the reduction in melatonin levels caused by the invention of electrical lights

• has been linked to lots of medical problems, see review paper [http://www.psy.ohio-state.edu/nelson/documents/JPinealRes2007.pdf The dark side of light at night: physiological, epidemiological, and ecological consequences]

• would need to implement melatonin detection, synthesis, and a clock

New Antibiotic Cassettes

• Biobricks exist for Ampicillin, Kanamycin, Chloramphenicol, and Tetracycline.

• New biobricks needed (see TK:Wishlist), integrate into larger project?

• Cationic peptides, Rhodostreptomycins [http://mit.edu/biology/sinskey/www/Kurosawa2008.pdf]

Paper Based Microfluidics with bacteria

• Improve the processing outlined in [http://www.rsc.org/delivery/_ArticleLinking/ArticleLinking.cfm?JournalCode=LC&Year=2008&ManuscriptID=b811135a&Iss=12 FLASH: A rapid method for prototyping paper-based microfluidic devices], see papers from Whitesides group at Harvard.

• use light sensor and output hydrophobic/hydrophilic chemicals that can coat the cellulose in the paper placed on an agar plate

Close proximity phage expression

• once a cell is close enough to a target, produce phages and explode

Anti-Venom System

• inject bacteria after being bitten

• sense which venom and produce proper anti-venom

Birth Control Yoghurt

• attacks sperm

• animal use

Buoyant Bacteria

• for metal extraction from old mines or ocean

Excrement Degradation Bacteria

• dog excrements degrades quickly

• can be used in as excrement degrader instead of waste tank in portable toilets or [http://en.wikipedia.org/wiki/Deodorize deodorizing] excrements in chemical toilets

Additional Processing of Excretion for Energy

• Zero Growth -> convert everything to product

Targeted Delivery

• use THC for medical benefits without any psychoactive effects

microRNA and P53

• inhibit miRNA to increase activity of tumor-suppressor gene p53

• needs targeted delivery system

Synchronization -> Flashing Colony

• synchronized flashing

• covalent modification

Sensor Reporter Spatially Displaced

Kalman Filter

• integrate into larger project

Stopping a Cytokine storm

• something which could break the feedback loop in a cytokine storm

MicroOrganism muscle

• make a group of cells contract

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