User:Christine Doan/Notebook/Synthetic Biology/2014/02/25

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RAISE

  • Max: colleague Colin Forward
    • Research associate from IST
    • PhD student in evolutionary computing
  • Meeting up with him end of this week
  • Bioremediation

Optical tweezers

  • Ryan
  • Works by surface tension
  • Di-electrophoresis: keep a droplet floating in solution back and forth
    • Droplet in oil
    • Thin film above the light has more of a charge
    • Voltage wets the surface
    • Grounds the potential
    • Can be used to read pH
  • Need Android and Arduino programmers
  • Coat the ITO (indium tin oxide)[1] film with TIOPC, an optical-electric dye
    • Not transparent, but the ITO side would be
    • Could coat it with Teflon or something
    • Don't need the sputtering - just spin-coat it
  • Daniel: can't you just get a sheet of glass for like $5?
  • Ryan: but we need it to be as close to the light source as possible. We can just get it done for us online for $40. Running electricity generates heat, needs a cooling mechanism, lowest resistance
  • Max: what common lab protocol can this be used for?
    • Transfection
    • Purified plasmid, bacteria
    • Concentrations
    • Reduce reagent volumes
  • Daniel: can't you use like a nano-electro-wetting needle to insert the genetic material? Then you would know for sure that it's in there
    • You can do that, definitely
  • Max: what is the speed in unit per time?
  • Daniel: before, you have to set up all the vials and devices beforehand and get it all ready
  • Christine: what about transitioning between how we do it now to how we're going to be doing it, like bacteria in microcentrifuge tubes and plating afterward?
    • That's the beauty of ports and microfluidic chips, reagent pools
  • No plan of selling or patenting these things
  • Server farm, stacks of screens the size of laptops
  • Daniel: could probably finish all the "-omics" with that
  • Auto-calibration with different light intensities, camera picks up droplet movement
  • Area where it transfers from one kind of electro-wetting to another kind which is completely transparent
    • DLP setup, optical tweezers, use a cell phone to move things around
  • Move single particles, trap single cells, manipulate single molecules
  • Layer of oil with water droplets going through
    • How are the droplets form from a giant mass of liquid?
      • PDMS has microchannels like a lab-on-a-chip
      • Connecting hundreds of different reagents
      • Micropumps
      • Micromolecular biology lab in a box
  • Max: feedback and monitoring?
    • A/C electricity runs between two different planes
    • Frequency manipulates particles

Bioremediation

  • Collect dead biomass, burn it in a low-oxygen environment,
  • Biochar or charcoal
    • Porous
    • Helps plants transfer carbon
  • Gene-series knock-outs at the microfluidic level
  • Computing / programming
  • Daniel: the problem now is the probability of knocking out part of gene is small, mRNA transcribed, move the droplet, don't worry about degradation, no plasmids, no antibiotic resistance, to isolate the part of the enzyme of a bacteria that sequesters a mal-chemical like arsenic
  • engineer an organism that does exactly that, to sequester different heavy metals, like previous iGEM projects
    • Run river water over biosensors that would change colors for each metal
    • Concentration thresholds to cause formation of endospores and dies
  • Max: what problem do college students cause that we can tie in with bioremdiation?
    • Jesse: Bug that eats cigarette butts
      • Nicotine-less tobacco plant to transfect
      • Cellulose acetate [2]
    • Symbiotic organism with the plant?
  • Who are we marketing to?
    • Parks and rec
    • Universities
    • Social enterprise lab with grants for bioremediation ($250 Phase 0 grants)
      • Flagship
      • Don't need to propose a solution for problems specifically?
    • Water sample analysis?
      • Show how we can fix that in a short amount of time
    • Organism in the Amazon that breaks down polystyrene
    • Daniel: Break down oil or other chemical compound? How to find out what substrates to test?
    • Ryan: phages or WBCs to make immunoglobulins for ELISAs and things like that, high-throughput to test compound binding
    • Daniel: synthetic evolution: similar motifs, find things in nature and imitate
      • Christine: Torrey Pines tea-bag chemistry
      • Combinatorial biology [3]
  • Water at different pHs
  • Find another solution / buffer that isn't too crazy of a concentration
  • Max: does something like this exist already? If so, what makes what we're trying to do different?
    • Something is patented, but rare
    • DMD (digital mirror) chip to move things around instead of the cell-phone glass, etching in one step, microchannel system made at the same time as the drops moving around
  • What is the light source?
    • Can absorb at 720 or 860 nm
    • Build a laser? No, use a cell phone light, LCD display
    • Resolution? 520dpi right now
    • 57 microns is in metric
  • Shaina: we'd still have to find or make a program for it
    • Idea: make a game
    • Flash and Android are easy to program
    • Make money through ads while people play games to calibrate our microfluidic chip for us
    • crowd-sourced
  • Daniel: incorporate our GFP bacteria, use EEGs so users can move them with their brains, have them bump into each other, if we want to go to another exhibition as a club

FamiLAB GFP class

  • Google Doc for formal application of class
  • Pipettes
  • Split costs among all of us as evenly as possible
  • Brooks said <$2000 is easy to recover with 6+ willing participants already
  • Carthal Garvey's DIY kit is only offered as a perk in exchange for donations on kickstarter, NOT an actual product to be ordered and shipped ASAP

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