IGEM:Caltech/2008/Ideas: Difference between revisions
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===Bioremediation (or not)=== | ===Bioremediation (or not)=== | ||
*So I guess I had failed to communicate my bigger picture about this idea. So removing materials is one thing that can happen, but the larger picture is getting a lot of independent bacteria (all in different states) together into one location such that information can be easily transmitted amongst the bacteria (through conjugation, etc). So say for instance that a particular bacteria has an important info that needs to be relayed to its neighbors. It can send a flag that will cause all the other bacteria is aggregate around it and pick up the signal. The neat thing about it would be that any bacteria can send a flag, so what we would get is a very dynamic network that has great potential. After the signal is sent, then all the bacteria can disperse and continue what they were doing before. So what we get is a bag of independent modules that can talk to each other (at least to its neighbors). I don't have an application for this, so maybe this idea is for the future. | |||
===Cholesterol Degradation=== | |||
*Could we make a strain of E. coli that circulates in the blood stream and feeds on cholesterol plaques as its food source? I know part of the 2007 UC Berkeley project, the bactoblood one, was to make E. coli not trigger sepsis when in the bloodstream. This chassis would be very useful for a project like this. | |||
**Similar idea, but use it for diabetes also and have E. coli feed off sugar. Maybe both? | |||
* | ===Bacterial Mouthwash=== | ||
*Disrupt biofilms | |||
*Minty smell | |||
*Taste good? | |||
===Gut microbiota=== | |||
*Food poisoning | |||
**[http://www.cbc.ca/health/story/2007/11/13/fecal-transplant.html Curing superbug infections] | |||
*Vitamins | |||
*Lactose intolerance | |||
==Older ideas== | |||
===Synthetic Biology Platform=== | ===Synthetic Biology Platform=== | ||
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*After reviewing UC Berkeley's BactoBlood in the 2007 iGEM Jamboree, Bacteriofood could be used to produce and carry vital nutrients that can maintain a healthy human. Most useful in third world countries where food is hard to come around. Bacteria being easy to grow and maintain, could be a simple way to feed the underfed. Just trying to throw out any idea that comes across. | *After reviewing UC Berkeley's BactoBlood in the 2007 iGEM Jamboree, Bacteriofood could be used to produce and carry vital nutrients that can maintain a healthy human. Most useful in third world countries where food is hard to come around. Bacteria being easy to grow and maintain, could be a simple way to feed the underfed. Just trying to throw out any idea that comes across. | ||
**Some thoughts - could we make bacteria more nutritious? I.e. you'd probably need an E. coli culture plus some list of vitamins/minerals/etc. Could we come up with that list of necessary extras and then engineer E. coli to remove a couple items from the list? | **Some thoughts - could we make bacteria more nutritious? I.e. you'd probably need an E. coli culture plus some list of vitamins/minerals/etc. Could we come up with that list of necessary extras and then engineer E. coli to remove a couple items from the list? | ||
===Endosymbiosis=== | ===Endosymbiosis=== | ||
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**Okay, looking into this a little more, transforming mitochondria is tough. It seems that you attach your DNA to a 'microprojectile,' physically shoot it into the cell, and hope that it lands in the mitochondria. It's a 'gene gun' - I'd heard of it for transforming plants, but apparently the same is true for mitochondria. Interesting, but a little unrealistic for a summer project. | **Okay, looking into this a little more, transforming mitochondria is tough. It seems that you attach your DNA to a 'microprojectile,' physically shoot it into the cell, and hope that it lands in the mitochondria. It's a 'gene gun' - I'd heard of it for transforming plants, but apparently the same is true for mitochondria. Interesting, but a little unrealistic for a summer project. | ||
**What about yeast parasites? | **What about yeast parasites? | ||
===Taking advantage of noise=== | |||
*From an engineering perspective, noise is usually a problem we need to overcome. But in biology, a uniform response simply means that your entire population gets wiped out simultaneously (think agricultural [http://en.wikipedia.org/wiki/Gros_Michel monocultures]). Biology often hedges its bets by producing a diversity of phenotypes, some fraction of which are favored in any given environment <cite>fluct1, fluct2</cite>. Can we do the same - continually producing a range of phenotypes and allowing the environment to select the ones best suited at that moment? | |||
**I've always liked the idea of directed evolution. Usually mutation occur at random throughout the genome, but a lot of the time it seems researchers only want a few genes to change. Instead of using the time consuming site directed or random mutagenesis, could we engineer a bacteria mutation a specif portion of its genome at an accelerated rate? I'm thinking something akin to the cre-lox in which the researcher could flank the stretch of DNA to be mutated by two DNA sequences, and then an enzyme or set of enzymes would catalyze the accelerated mutation of only that portion. The ter sites and Tus proteins are normally used to terminate E. coli genome replication by slowing down and kicking off the polymerase. Maybe a toned down ter-Tus system would be enough to screw up the polymerase as it passes through, but not totally derail it. | |||
***There are mutator strains that increase the genome-wide mutation rate. Ignoring implementation, I think it would be tricky (not impossible, but tricky) to find a niche for targeted in vivo mutation. Mutator strains are generally used when you don't know what your target is. If you know what your target is, the question is what the advantage is over error prone PCR. Best I can come up with is that you might want to hit multiple genomic locations simultaneously, such that error prone PCR would be really time consuming. But those situations seem relatively rare. | |||
*"In 2006, Collins's team described engineering mutations into the control region of a gene that confers antibiotic resistance to create two strains of the yeast Saccharomyces cerevisiae , one with noisier expression of the gene, one with something more steady. Faced with a lethal antibiotic, the noisier strain survived better5. This result supports the idea that noise is a form of 'bet hedging' for cells: a population is more likely to survive in a changing environment if its members are noisy because some are likely to be making the quantity of a protein best suited to that situation. “A system that is covering more possibilities has a greater chance of survival in unpredictable settings,” says Collins." [http://www.nature.com/news/2008/080507/full/453150a.html] | |||
===CO2 Bacteria=== | ===CO2 Bacteria=== | ||
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**You're talking about photosynthesis here - fixing CO2. It's an important problem, but one that industry is already working on (see [http://www.greencarcongress.com/2005/12/greenshift_lice.html this] for instance). | **You're talking about photosynthesis here - fixing CO2. It's an important problem, but one that industry is already working on (see [http://www.greencarcongress.com/2005/12/greenshift_lice.html this] for instance). | ||
**CO2 mineralization - can we precipitate it (limestone?). | **CO2 mineralization - can we precipitate it (limestone?). | ||
==Cool outputs== | ==Cool outputs== |
Revision as of 22:47, 8 May 2008
Big IdeasBioremediation (or not)
Cholesterol Degradation
Bacterial Mouthwash
Gut microbiota
Older ideasSynthetic Biology Platform
Ultrafast Color Changing Cells
Bacteriofood
Endosymbiosis
Taking advantage of noise
CO2 Bacteria
Cool outputsPimp my E. coli
Changing shape
Motility
Stickiness
Taste
Random thoughtsA more analog device
Others
Random Number Generator
Population Variability
E(motional) coli
System Order E. coli
References
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