"
Team:TUDelft/Brainstorm
From 2009.igem.org
(Difference between revisions)
(→Buoyant Bacteria) |
|||
| Line 46: | Line 46: | ||
===Water Soluble Vitamin Production=== | ===Water Soluble Vitamin Production=== | ||
| - | + | * produce Vitamins B and C.<br/> | |
| - | * produce Vitamins B and C. | + | |
| - | + | ||
| - | + | ||
===Stop Quorum Signalling -> Quenching AHL=== | ===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.<br/> | |
| - | * 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.<br/> |
| - | + | * [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].<br/> | |
| - | * 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=== | ===Biological Isotope Separation=== | ||
| - | + | * is it even possible?<br/> | |
| - | * 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.<br/> |
| - | + | * possible applications: remove radioactive isotopes from body (cancer treatments), separate heavy water from ocean water, remove carbon 14 and potassium 40 from body/food.<br/> | |
| - | * 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. | + | * 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.<br/> |
| - | + | ||
| - | * 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=== | ===Saltwater Purification=== | ||
| - | + | * + heavy metal extraction<br/> | |
| - | * + heavy metal extraction | + | * diatoms<br/> |
| - | + | * Dead Sea organisms<br/> | |
| - | * diatoms | + | * 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<br/> |
| - | + | ||
| - | * 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=== | ===Xylitol production=== | ||
| - | + | * already attempted, see [http://openwetware.org/images/0/03/6-bolaji.pdf]<br/> | |
| - | * already attempted, see [http://openwetware.org/images/0/03/6-bolaji.pdf] | + | |
| - | + | ||
| - | + | ||
===Melatonin Compensation=== | ===Melatonin Compensation=== | ||
| - | + | * compensate the reduction in melatonin levels caused by the invention of electrical lights<br/> | |
| - | * 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]<br/> |
| - | + | * would need to implement melatonin detection, synthesis, and a clock<br/> | |
| - | * 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=== | ===New Antibiotic Cassettes=== | ||
| - | + | * Biobricks exist for Ampicillin, Kanamycin, Chloramphenicol, and Tetracycline.<br/> | |
| - | * Biobricks exist for Ampicillin, Kanamycin, Chloramphenicol, and Tetracycline. | + | * New biobricks needed (see TK:Wishlist), integrate into larger project?<br/> |
| - | + | * Cationic peptides, Rhodostreptomycins [http://mit.edu/biology/sinskey/www/Kurosawa2008.pdf]<br/> | |
| - | * 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=== | ===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.<br/> | |
| - | * 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<br/> |
| - | + | ||
| - | * 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=== | ===Close proximity phage expression=== | ||
| - | + | * once a cell is close enough to a target, produce phages and explode<br/> | |
| - | * once a cell is close enough to a target, produce phages and explode | + | |
| - | + | ||
| - | + | ||
===Anti-Venom System=== | ===Anti-Venom System=== | ||
| - | + | * inject bacteria after being bitten<br/> | |
| - | * inject bacteria after being bitten | + | * sense which venom and produce proper anti-venom<br/> |
| - | + | ||
| - | * sense which venom and produce proper anti-venom | + | |
| - | + | ||
| - | + | ||
===Birth Control Yoghurt=== | ===Birth Control Yoghurt=== | ||
| - | + | * attacks sperm<br/> | |
| - | * attacks sperm | + | * animal use<br/> |
| - | + | ||
| - | * animal use | + | |
| - | + | ||
| - | + | ||
===Buoyant Bacteria=== | ===Buoyant Bacteria=== | ||
| - | |||
* for metal extraction from old mines or ocean<br/> | * for metal extraction from old mines or ocean<br/> | ||
* 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]<br/> | * 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]<br/> | ||
Revision as of 19:17, 14 May 2009
Brainstorm Area
Interesting Links
Interesting Papers (provided by Domenico)
- Design and Construction of a Double Inversion Recombination Switch for Heritable Sequential Genetic Memory
- A tunable synthetic mammalian oscillator
- Programming gene expression with combinatorial promoters
- Photoreceptor Proteins, “Star Actors of Modern Times”: A Review of the Functional Dynamics in the Structure of Representative Members of Six Different Photoreceptor Families
- Environment-specific combinatorial cis-regulation in synthetic promoters
- Implementing Arithmetic and Other Analytic Operations By Transcriptional Regulation
- Engineering BioBrick vectors from BioBrick parts
- Model-guided design of ligand-regulated RNAi for programmable control of gene expression
- 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 [1] already has a biobrick Part:BBa_C0060 but it is not secreted.
- halogenated furanones [2] [3] decrease binding activity of LuxR.
- Bonnie Bassler's research, inhibit quorum signaling with molecules structurally similar to AHL. Her recent TED Talk.
Biological Isotope Separation
- is it even possible?
- according to this book in section 2.6.5. [4], 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 [5]
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 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 [6]
Paper Based Microfluidics with bacteria
- Improve the processing outlined in 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 gas vesicles
- Might be used in mining (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:
- 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?
- 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 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
