Team:TUDelft/Brainstorm

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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]

Top 6 Ideas

Salt water purification (Sriram) (Orr)
Buoyant Bacteria (Saeed) (Orr)
Impuls Signal (Daniel) (Sriram)
Melatonin Compensation (Saeed) (Tim)
Microrganism Muscle (Daniel) (Tim)
Enzyme Modulation (Daniel) (Sriram)

The names behind the ideas indicates who is going to search background information on the subject and inspect the feasibility and application for the ideas.

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

After some research, we found that this project might not be as feasible as we imagined. Searching for the keywords 'desalination' and 'bacteria' resulted in articles about the biofilm created by bacteria to deteriorate the proper function of reverse osmosis (RO) 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
Gvp genes of B. megaterium can be expressed functionally in Escherichia coli, rendering it buoyant by its [http://www.sciencedirect.com/science?_ob=ArticleURL&_udi=B6TD0-4GHBP6F-1&_user=10&_rdoc=1&_fmt=&_orig=search&_sort=d&view=c&_acct=C000050221&_version=1&_urlVersion=0&_userid=10&md5=c7578acb7860d2a68c667623b672f5d1 gas vesicles]
Might be used in mining ([http://en.wikipedia.org/wiki/In-situ_leach in-situ leach], otherwise known as solution mining, is a technique where acid is pumped into a mine, separating the ore from the soil by dissolving the ore and the ore being pumped to the surface)
Several issues that need to be accounted for:

[http://www3.interscience.wiley.com/cgi-bin/fulltext/121493777/HTMLSTART Anaerobiosis inhibits gas vesicle formation in halophilic archea] – gas vesicles that allow buoyancy for bacteria require oxygen to exist. This is a major problem with mines (blackdamp – oxygen replaced by other gases)
Density of target ore – In-situ leach is often used for uranium, and can be used for copper and gold as well, all dense metals, and for buoyancy to occur, the bacteria need to have a sufficient density to allow the ore to float (copper least dense with 8.9 g/cm3, gold most dense with 19.3 g/cm3)
Amount of energy put into bacterial buoyancy – is using bacteria for the buoyancy really more efficient (energy-wise and time-wise) then normal pumping of the ore to the surface?

[http://www3.interscience.wiley.com/journal/117860406/abstract Biosorption] – the 3 strains S. acidiscabies W-12, M. luteus W-20 and Bacillus sp. W-28 were found to be the most tolerating of high acidity levels and heavy metal environment. Those tolerant strains were also found to be able to absorb up to 80% aluminium and copper, and 60% uranium from mining sites

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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@@ Line 137: / Line 137: @@
 #[http://www3.interscience.wiley.com/cgi-bin/fulltext/121493777/HTMLSTART Anaerobiosis inhibits gas vesicle formation in halophilic archea] – gas vesicles that allow buoyancy for bacteria require oxygen to exist. This is a major problem with mines (blackdamp – oxygen replaced by other gases)<br/>
 #Density of target ore – In-situ leach is often used for uranium, and can be used for copper and gold as well, all dense metals, and for buoyancy to occur, the bacteria need to have a sufficient density to allow the ore to float (copper least dense with 8.9 g/cm3, gold most dense with 19.3 g/cm3)<br/>
-#Amount of energy put into bacterial buoyancy – is using bacteria for the buoyancy really more efficient (energy-wise and time-wise) then normal pumping of the ore to the surface?<br/><br/>
+#Amount of energy put into bacterial buoyancy – is using bacteria for the buoyancy really more efficient (energy-wise and time-wise) then normal pumping of the ore to the surface?<br/>
 * [http://www3.interscience.wiley.com/journal/117860406/abstract Biosorption] – the 3 strains S. acidiscabies W-12, M. luteus W-20 and Bacillus sp. W-28 were found to be the most tolerating of high acidity levels and heavy metal environment. Those tolerant strains were also found to be able to absorb up to 80% aluminium and copper, and 60% uranium from mining sites