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| [http://openwetware.org/wiki/IGEM:Harvard/2007/Brainstorming/423to59 Brainstorming, 4/23 to 5/9]<br> | | [http://openwetware.org/wiki/IGEM:Harvard/2007/Brainstorming/423to59 Brainstorming, 4/23 to 5/9]<br> |
| [http://openwetware.org/wiki/IGEM:Harvard/2007/Brainstorming/miscpre59 Misc Brainstorming, pre-5/9]<br> | | [http://openwetware.org/wiki/IGEM:Harvard/2007/Brainstorming/miscpre59 Misc Brainstorming, pre-5/9]<br> |
| | [http://openwetware.org/wiki/IGEM:Harvard/2007/Brainstorming/405 Brainstorming from Second Meeting, 4/05]<br> |
| [http://openwetware.org/wiki/IGEM:Harvard/2007/Brainstorming/319 Brainstorming from First Meeting, 3/19] | | [http://openwetware.org/wiki/IGEM:Harvard/2007/Brainstorming/319 Brainstorming from First Meeting, 3/19] |
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| I hope you'll consider presenting more on this on Monday. Even if not, the thought is intriguing. I understand the hesitation to use antibiotics (presumably, resistance?), but my presentation on adaptamers tomorrow might have lightly-related ideas - since the potential uses of adaptamers are quite broad, we could potentially target drugs or bacteria-killing substrates to the cells. As you said, the legal and practical implications would probably cause me to discard the idea, but at least it's tangentially related.
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| Stephanie
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| --------------
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| I wanted to put forth an idea -- vitamin production & microbial therapy.
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| The idea comes from the fact that vit B producing microbes inhabit the ruminant gut so these animals almost never have B-deficiency.
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| But for humans, without a proper diet, we end up getting diseases like Beriberi.
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| *the other thing is the bioavailability of these vitamins whether we ingest them as food or as pills -- 'microbial therapy' could solve this by coupling these production loops in our engineered bacteria
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| One way to put an end to this could be synthesizing bacteria that can inhabit the human stomach and produce vitamins of all kinds.
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| ...that's the idea
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| Response (Stephanie):
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| I really like this idea. I wonder what potential limitations there are, etc. Did you find any interesting readings on this?
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| Response (Alex):
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| The great convenience of this is that E. Coli is not only a well-understood model organism, but also one of the most abundant gut flora. If we can actually introduce genes for vitamin synthesis, this is actually feasible. The only problem is that the genes which would do our vitamin synthesis would leach energy from the bacteria and make them less competitive than the native E. coli. Hence the native bacteria would eventually crowd out the modified ones.h
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| ==Project Ideas 3/19/07==
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| '''Brainstorming with Sammy, Alex, Shaunak, Stephanie, Mingming, Perry, and George.'''
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| ''TFs and Advisors in attendance Nick, Mike, Harris, Tamara, George Church, Jagesh Shah, William Shih, and Alain Viel.''
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| Biological Based Fuel Cells
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| Bacterial that Respond to (by fluorescence) or Degrade Plaque
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| Viruses as a Transfer Mechanism
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| Engineering ''E. coli'' to Resist Mutations
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| <br> --The intention is prevention of evolution that would ruin biological parts; however, we recognize that directed evolution is a useful tool in 'discovering' potentially useful parts and mutations.
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| http://www.seas.harvard.edu/projects/weitzlab/Jeremy%20web%20page.htm
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| Cellulose to EtOH in Algae or other system
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| ""~~Some Papers on this Subject (added by SAV, feel free to add more)11:22, 2 April 2007 (EDT)""
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| <br>
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| Lynd, Zyl, et al. "Consolidated bioprocessing of cellulosic biomass: an update" Current Opinion in Biotechnology 2005, 16:577-583
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| ---This paper gives a pretty good overview of research into consolidated bioprocessing of cellulose into ethanol, and some of the main problems as well. If we're interested in looking at fuels, this is definitely a good paper to look at.
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| Jeffries, Thomas. "Engineering yeasts for xylose metabolism" Current opinion in biotechnology 2006, 17:320-326.
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| ---This paper looks at turning xylose into ethanol via yeasts, and recent results in this field of research. If we think we might not want to use bacteria, this is a good overview.
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| Sticklen, Mariam. "Plant genetic engineering to improve biomass characteristics for biofuels." Current Opinion in Biotechnology 2006, 17:315-319
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| --Looks at problems from biomass cellulose, such as lignin, and current research into ways to treat it. Also looks at other ways to engineer plants. I think less relevant for us, but still interesting as a way for getting a feel of some of the issues surrounding biomass cellulose
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| Fatty Acid Production and Degradation for Energy
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| Molecular Motors
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| Sequestration of Toxic Compounds by Bacteria (arsenic)
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| Bacterial Surface Expression
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| Vascular Tissues
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| Artificial Vascularization in Bacterial Biofilms
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| Bacterial Biosensors (Detection in the Environment) (Water Samples)
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| ==Project Ideas from Second Meeting (04/05/07)==
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| Additional notes added by Stephanie; please contact her with questions.
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| * Selection mechanisms for key/lock riboregulators (see 2006 Berkeley Project)
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| - Though sequence complementary is necessary, which allows little variation in that region, the rest of the RNA might differ
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| <br> - The RNA acts as a "key" to release the lock; only when both are present, allows for expression
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| <br> - This can allow for creation of networks, if the expression "unlocked" is for another key
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| <br> - Monitored by Red Fluorescent Protein, experimentally
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| <br> - Advantage = fast response
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| <br> - Can be used for either activation or inhibition
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| <br> - Suggestion: look into the Duke group: human encryption<br>
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| * Biofuel & light sensitive proton pump ([[Background_Reading|see background reading #3]]) (Pseudomonas Putida for exportation of short chain alkanes)
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| * Powering medical devices
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| - Bacteria that can extract energy from sugars in blood and convert these to electricity
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| <br> - Question posed: how often do the devices need energy? A: Depends on specific devices
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| <br> - Related idea: implantable devices that release, or even synthesize, drugs
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| * Artificial cells
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| * Use of psuedomonas putida? (bacterial strain)
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| - High tolerance to many saturated alkanes (can we get it to form octane?)
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| <br> - Issue: export vs. metabolism
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| * Quorum sensing and biofilms
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| * Mirror image proteins
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| * Nonribosomal synthesis of proteins
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| * Radon sensor (practical considerations of working with Radon)
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| <br> Short discussion of project logistics: rather than attempting to tackle multiple projects at once (as we will tend to be overambitious!), perhaps we can propose a sequence of experiments that we would like to attempt over the summer. We should treat these as 'checkpoints' and finish one before proceeding to the next.
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