Team:Stanford/Notebook/Brainstorming

Initial Brainstorming

Comments

For this week, please take your starred idea(s) and do as much research as possible over the next three days to determine

1. whether it is feasible,
2. if there are any parts in the parts library that could potentially be incorporated and
3. a basic blackbox diagram of "sensors", "reporters", "generators", etc. at the device level. Where you cannot easily build a nice diagram, state it clearly so we are aware of the difficulties you are facing.
4. Identify the basic project idea (i.e. trash eating bacteria, stress detecting cell, minicell production) and brainstorm a list of other applications for the basic project idea (i.e. a stress detecting cell can be used to monitor orthodontics and bone development).
5. Make a set of slides for this. You'll be pitching your ideas to a panel of graduate students this week and in coming weeks so please do a good job on this initial pitch.

Media:Brainstorming-Direction-Poll.pdf

Possible Projects

Vesicular Transport (*)

1. Previous Paris Team wanted to engineer superhighways across for communication: could pick up on this project?

2. Work on a project that deals with minicell production, targeting and packaging (possibly talk to Jerome Bonnet?)

3. Possibility of scaling up work done with single molecule transport (talk to Monica Ortiz in Endy's lab?)

• Christopher C Vanlang 04:07, 26 April 2010 (EDT):Some of our thoughts from last year

Long Distance Communication

1. Discussed the possibility of making vibrating cells

• Christopher C Vanlang 04:07, 26 April 2010 (EDT):Check out this [http://www.ncbi.nlm.nih.gov/pubmed/20080560 paper]

Brain-related projects: Increasing Neuron Efficiency, Myelin regeneration

1. Questions were raised concerning the feasibility of the application

• Perhaps these neurons would become more susceptible to noise?

• Could have adverse effects on other neuron functions

2. One possible application would be increasing the firing rate of muscles

Wound Treatment (*)

1. Try and establish a beneficial infection to avoid unwanted infections in the wound

• Could beneficial bacteria encourage scab formation or skin regrowth?
  • Whats the mechanism of scab formation? What factors are required? - Chris

2. Engineer classes of microbes that prevent the colonization of other microbes

• Needs to secrete something to kill/repress other bacteria, can't be harmful to host cells

3. Avoid detection by the immune system

• By what mechanisms do other beneficial E. coli prevent destruction by immune system?

• Would need a killswitch or some other mechanism to prevent immune resistance from spreading to unwanted bacteria

-Eliminate bacteria's ability to conjugate?

-Have two-step process to assemble cloaking device so that other cells couldn't replicate the device without both parts?

4. Bacteria need to be contained on the wound, cannot spread

• Link cell lysis response to absence of some substance found only in wound tissue?
  • What substances in wound tissue exist?

Pre-term labor indicator (*)

1. Unique idea and applicable to wide range of fields involving mechanical stress detection (bone regeneration, cell growth, etc.)

2. Downsides: Hard to determine the level of oxytocin - relation to pre-term labor.

3. Liked signal integration scheme in slides

4. First, we may need to determine baseline levels of oxytocin or progesterone - too complex?

Trash-eating bacteria (*)

1. Nice idea with related research being done on campus already: [http://www.stanford.edu/group/evpilot/ Craig Criddle's] lab in Y2E2

2. Expand the ideas so that the bacteria generate something that plants can use later.

• Christopher C Vanlang 04:07, 26 April 2010 (EDT):Look at our discussion from last year

Francisco says: Apparently, a lot of work has been done with different types of plastics and bacteria but there are many aspects we can improve.

Some interesting stories and their shortcomings/areas for improvement:

Styrofoam-eating strain of 'Pseudomonas putida' - styrofoam needs to be superheated to form the styrene oil the bacteria actually feeds on - that superheating produces toxic byproducts [http://www.scientificamerican.com/article.cfm?id=bacteria-turn-styrofoam-i]

Discovery of polystyrene-eating bacteria from mealworm beetles: [http://www.mnn.com/green-tech/research-innovations/blogs/high-school-girl-discovers-styrofoam-eating-bacterium]

'E. coli' that converts plant biomass to biodiesel [http://www.nature.com/nature/journal/v463/n7280/pdf/nature08721.pdf]

Desalination (*)

1. Huge problem, any traction is good

2. Light-powered water purification system is the best scenario

3. Downsides: difficult to pump water across a membrane

4. Possibly use reverse methods to pump everything else (but water) out?

5. Literature reports of bacteria that have water purification properties?

Oil spill clean-up (*)

1. Sequestering oil and easy collection of material is key to a project of this type

2. Possibly form a dialysis-bag like object that collect oil?

Clotting

1. Negative feedback system that shuts down the bacterial clotter

2. Bacteria stay on surface so we don't have to worry about immunogenicity issues

3. Value of creating bacteria if there are already in vitro and cheap ways to make clotting factors

Ratio Sensor Brainstorming (sRNA mechanism)

General Idea

One Idea to measure [B] / [A] (assume [A] ≠ 0)

• input A induces expression of GFP mRNA

• input B induces expression of GFP sRNA (sRNA that targets the GFP mRNA transcript)

• so for a given [A],
  • if [B] = 0, we should see glowing bacteria
  • if 0 < [B] < [A], we should see some glow
  • if [B] > [A], we should see no glow

Another Idea to measure [B] / [A] (assume [A] ≠ 0)

• input A induces expression of GFP mRNA and YFP sRNA

• input B induces expression of YFP mRNA and GFP sRNA

• so for a given [A],
  • if [B] = 0, we should see GREEN glowing bacteria
  • if 0 < [B] < [A], we should see some glow that is more GREEN than YELLOW.
  • if [B] > [A], we should see some glow that is more YELLOW than GREEN.

References

• here's a good reference: [http://www.springerlink.com/content/x6p4lqn1608267r1/fulltext.pdf Engineering RNA-based circuits]. It discusses different methods of regulation by RNA:
  • via base-pairing (small RNA)
  • shape-based (riboswitches)
  • catalytic (ribozymes)

• engineered riboregulators (possible mechanism for us) [http://www.nature.com/nbt/journal/v22/n7/pdf/nbt986.pdf Engineered riboregulators enable post-transcriptional control of gene expression]
  • Note: apparently does not work well in practice

• engineering those aforementioned sRNA's:
  • vague article [http://www.nature.com/nmeth/journal/v4/n12/full/nmeth1207-986b.html Engineers meet small RNA]
  • some specifics [http://www.ncbi.nlm.nih.gov/pmc/articles/PMC1994261/pdf/pbio.0050229.pdf Quantitative Characteristics of Gene Regulation by Small RNA]

Oil Spills & Blood Clotting Brainstorming

Discussed the possible strains of bacteria/metabolic pathways that could be made us of in an oil spill

3 Strains of naturally occurring bacteria: psuedomonas putida, alcanevorix, cycloelasticus,

Each can break down certain compoments, e.g. PAHs, Toluene, Xylene, Straight Chain alkanes

Certain problems are detailed below.

Split the problems into 4 solutions:

Distributions/Large Scale Production

Nitrogen Fixation/Phosphorus Supply

Why better than what has naturally evolved

Choke points in the metabolism

Some offshoots of the oil spill idea came into existence:

Using the straight chain splitting bacteria in place of cracking in a refinery (Alcanevorix)