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Team:UIUC-Illinois/Meeting Minutes
From 2010.igem.org
UNDER CONSTRUCTION
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4/25/10
Need to define project!!
Oil:
Benzo[a]pyrene—one bacteria can degrade it if they have a second source of energy.
Emulsification—increase surface area for oil degredation. Lots of current focus in this area.
Also trying to develop fertilizers for bioremediation of oil—contain nitrogen and phosphate, emulsifiers to help the bacteria degrade oil.
Usually quorum dependent secretion of emulsifiers
Keywords: oil bioremediation, oil bioaugmentation,Aromatics, aliphatic hydrocarbon chains.
Most bacteria can only degrade a select few, not a variety of compounds. Aromatic rings are carcinogenic.
Metals:
One of the problems with metals is that it’s difficult to clone out the necessary components—lots of things needed to make it work. Sulfur iron clusters in many of the proteins, many enzymes going into making the actual cluster which is the catalytic core of the enzyme. Metals usually as terminal electron acceptor—involved in electron transport chain, use lots of cytochromes which are different in all organisms. You’d need to get all the cytochromes too to make the pathway work.
One pathway, reduces selenium, uses a few enzymes, only three to construct the reductase. Pathway completely mapped out.
A lot of secretion, biominerilization occurs outside the cell. Some organisms can do this inside the cell—requires less enzymes, but hard to amass them into large quantities. But could sonicate cells to release the metals.
Quantum Dots: related to semi-conductors. Nanocrystals of different metals, conductive properties based on the molecular arrangement of the crystals. Used for nano-technology. Grouping electrons to use for “quantum computing”.
E.coli can reduce gold.
Other stuff:
Send in some grants, submitting project proposal sometime this week. We’re going to stay with the decoder but find some application if possible.
Meeting Wednesday night, 20 min, officially have a project. 9:30, RSO.
4/23/10
Summer meetings, bootcamp overview (already covered in previous team meeting)
Metals: May not be as easy of just transplanting the pathway—secrete cytochromes to grab the metal, shuttling system. Check pathways, could be difficult.
Maybe looking at oil—oil had different compositions, increase efficiency to degrade only what’s in the specific spill. Oil classified by sulfur and viscosity—find something that’s Sulfur sensitive.
Documentary possibly—I think I may have missed some info on this?
Biosafety: which strains (DH5a), safety precautions, emergency contacts (mckinley). Basically listing what you’re working with. finish hopefully before we get into bootcamp week.
Competition: nov. 5th-7th MIT, planning on 2 advisors coming as of now, Courtney, Dr. Rao.
IGB access: 9-5 can get in no problem, no need for prox card. Has to be someone here if we’re here at night, we can’t be alone in the lab. Not likely that’d we’d get afterhours access. Weekend, keep it within normal hours, 12-6ish.
Oil has bigger implications—industries looking for ways to take care of oil. Look into aromatics, alkanes, alkenes, paraffin, olefin, biodegradation.
Get the decoder to work!
Build each detector separately, put into one system at the end.
4/21/10
Biomineralization metal sensing, instead of a promoter, precipitate the metal. Short pathways. Pathways that detoxify. 4-5 enzymes per metal pathway. Sensing stuff in registry. Inputs are soluble metals.
Nanofabrication.
How could it help people: precipitated form is non-toxic, while soluble is toxic.
Input: soluble metal, pick out clump of dirt on the quad, has soluble metal.
Really marketable, direct application, no human testing.
There’s metal everywhere, don’t need a lot to do this.
Decoder: if gold, pathway to precipitate gold. If silver inputs, precipitate both. Etc.
meeting with advisors friday, 12:00 third floor, north side conference room IGB.
4/16/10
Project proposals:
1. Matt, Steve, Bob:
Bacterial Thermo-regulator:
Get bacteria to maintain homeostasis in fluctuating external temperature
Introduce genes coding for temperature sensitive genes or RNA to act as promoters to start a process to release a large amount of heat.
Applications: for high temp. microbes, applications to thermophiles in industrial applications, central heating, anywhere heat is used.
Problems: enzyme stability—reduction of Nitrous oxide. Does it diffuse into cells? How do we get it into cells? Metabolic rate?
cspA mRNA changes conf. at low temp. (temperature sensitive RNA). Responds to cold shock. Cis regulator. Changes secondary structure depending on the temp. of the environment. Check Kyoto project—wanted bacteria to raise temp. of mars so life could be maintained.
N2O reduction—released 82.05 kJ/mol, only need one enzyme (nitrous oxide reductase).
Feasibility: strength of the promoter would have to coincide well with metabolic rate, trial and error to find right balance.
Cooling: to maintain homeostasis, would need to find way to cool the bacteria. Maybe reverse the process we’d be using to generate heat. Require another set of genes, promoter. Heat sensitive lambda promoter in registry. Exocytosis to cool the cell, similar to how mammals maintain homeostasis, sweating.
Insulator—capsule?
Comments: e.coli has advanced heat shock system. Many proteins to stabilize, involves mRNA. Cold just slowing down rate of reactions. Hard to get bacterial density up in a solution to generate enough heat. Possible spin to try to evolve a thermophilic version of e.coli, then sequence genomes. But there wouldn’t really be a biobrick.
Insulator/capsule under temperature dependent promoter is feasible.
Evolution at specific temperatures.
2. Amanda, Meagan:
Multiple contaminant whole cell biosensor in e.coli
Builds off bacterial decoder from last year
Water contamination techniques. Detection techniques today are not always reliable.
whole cell biosensor: sensing component (usually resistance gene) reporter gene.
biosensors have been done in the past but only single input and single output. Ours would take multiple inputs to give an output based on the input.
arsenic, lead.
ars operon—resistance gene, pump to pump out arsenic. Couple it to a reporter gene
pbrr—protein that binds selectively to lead ions. Clones into e.coli before so feasible.
theoretically simple, practical application of last year’s project.
problems: need to make it more sensitive than it is in nature for the ars operon. Not entirely sure what the products of the ars operon are. Don’t know much about lead sensing component. Need appropriate inputs, research what compounds are in water, what’s feasible to detect.
past projects: the traffic light project—altered promoter such that it’s stronger or weaker than wild type. Possible way to sense different levels of contaminants. We could alter ars promoter in similar way.
increasing sensitivity.
Comments: not exactly a true application of last year’s decoder, maybe have it detect something beneficial vs something dangerous like ars. Or make a degrader instead for endocrine disrupters or estrogen. Pathogen contamination, parasites.
Didn’t get anything for synthetic RNA project b/c I was presenting
Post-presentation comments:
Synthetic RNA—easy to manipulate but not necessarily an effective regulator. No real definite application. Continuing the decoder: we’d have to find a direct application, something that needs to be decoded. Or maybe even just get it to work since we have the parts. New inputs/outputs. Degrade contaminants.
We chose the decoder!
Think of what we can add to it, what we can decode, degradation of estrogen and endocrine disrupters. Still gonna use small RNA, 2 to 4 decoder
4/11/10
Meeting with advisors to present project proposals Friday 5:00-6:30. Possibly a professional picture 4:45 for the brochure.
Francis went over project proposal research. See the googledoc for comments.
Top three projects to present: Thermoregulator
Arsenic/lead detector
Engineering Posttranscriptional regulation in prokaryotes
Additional research throughout the week on these projects.
What's Going on this week:
Thursday: Undergraduate Research Symposium 1:30-2:45 Pine Lounge in the Union
Friday: Meeting with Advisors 12:00-1:00, Igb fellows symposium 3:30-4:45, Professional Picture 4:45, Project Meeting 5:00-6:30.
see the google calendar for more info
4/10/10
General:
Spark—Old article and contacts, but still reachable
MCB Open House—Next week
Undergraduate Research Symposium—Next week
Lab:
Moved into 3500 IGB
We’ll just buy glassware—we can get what we need as we need it
Project Overviews with advisors
Meeting next Friday—Team picture at 4:45, meeting 5-6:30
Grants
Company Contact List—adding non-profit organizations
3/19/10
Meeting with advisors
One advisor said something about iGEM for regional advisors meeting for proposal. Courtney had meeting with ihotel for planning—rooms, dates. We may have to host dinner, possibly at IGB. We have to come up with a portion of the funds. Needs list of team member’s school affiliation. Tentative schedule: First night cocktail party, dinner. Conference at iHotel. We pretty much just pay for food. First day box lunch, possible dinner. Sunday, offer breakfast, people leave. Estimating 100 people attending. Maybe poster session highlighting IGB work, vendor show (vendors pay to participate, location source of funding for iGEM!).
Maybe the union as an option, visitors can walk around campus. Hampton out by Beckman.
We were given 500 dollars to come up with cooperate brochure. Who we are, description of research, donation possibilities.
We may need new space if our current space gets taken. Possible use of training lab. If we go with training lab, we’ll have to find equipment list. Ie: pipette sets, power supply, thermocycler, tabletop centrifuge, hot plate, glassware, gel boxes. Maybe borrow stuff from senior design lab from bioengineering.
Put together list of supplies that we need donated. We can ask around to see what we can get donated.
Lab training sessions early may or late june with prof. Rao. Courtney may be able to do some lab training in a couple weeks as well.
Advisor Availability this summer: Daycare on campus closes for 2 weeks in summer, so Courtney won’t be here then. Prof. Rao: june will be on and off Prof. Jin: Second and third week of june out of town. Prof. Manaster has to look stuff up, she’ll get back to us. prof. Rao wants some of our smelly e. coli. Credit Hours possibility—possibly getting fall credit for summer work so tuition isn’t an issue. Probably 4 hours of credit.
