Brainstorm Area

Interesting Links

• iGEM Idea Exchange
• TK: Wanted Parts
• iGEM:Projects categorized
• Synthetic_Biology:Vectors/Wishlist

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

1. Salt water purification (Sriram) (Orr)
2. Buoyant Bacteria (Saeed) (Orr)
3. Impulse Signal (Daniel) (Sriram)
4. Melatonin Compensation (Saeed) (Tim)
5. Microrganism Muscle (Daniel) (Tim)
6. 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.
  
  

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
  
  

MicroOrganism muscle

• make a group of cells contract
  
  

Enzyme Modulation

• express different enzymes in different period of time and measure flux
  
• metabolic control analysis
  
  

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
  
  

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:
  

1. 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)
   
2. 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)
   
3. 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
  
  

Xylitol production

• already attempted, see [1]
  
  

New Antibiotic Cassettes

• Biobricks exist for Ampicillin, Kanamycin, Chloramphenicol, and Tetracycline.
  
• New biobricks needed (see TK:Wishlist), integrate into larger project?
  
• Cationic peptides, Rhodostreptomycins [2]
  
  

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
  
  

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
  
  

Water Soluble Vitamin Production

• produce Vitamins B and C.
  
  

Stop Quorum Signalling -> Quenching AHL

• aiiA enzyme [3] already has a biobrick Part:BBa_C0060 but it is not secreted.
  
• halogenated furanones [4] [5] 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. [6], 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.