Difference between revisions of "Research document covering May-June"

Latest revision as of 18:53, 13 June 2012

Research

Entries are in order by date

5/17/2012

We generated and rated a list from tekla labs ([[1]]). We plan to research the following items and have assigned items to people (H=Holmes M=Mazul)

Things we are very interested in: Temp controlled: 37C chamber for a microscope, with or without CO2 capabilities (M)

Incubator temperature control (H,M) Water bath (We didn’t assign anyone to this) Block heaters with controlled temperature (for eppendorf tubes) Others Orbital shaker table (M) Vortexer mixer (M)

Things we are interested Electroporator Centrifuge/Microcentrifuge (H) Isolation table (eliminates vibrations, essentially is a suspension system for delicate instruments) Fume Hood or Tissue Culture Hood (H) Sonicator bath Gel Electroporation box Simple function generator (electrical equipment) (M)

These items will be left later: cell culture microscope (ambitious, but we get a lot of demand for “how to” documents that cover microscope repair) Bifocal dissecting microscope

Goal By May 31st we want to have a definite focus and our ideas chosen.

5/17/2012 to 6/3/2012

Research

• 37C chamber for a microscope, with or without CO2 capabilities (M)
  • [[2]]
• An attempt to make a DIY incubator documented online
  • [the associated person behind it]

• Incubator temperature control (H,M)

[[3]]

• • This is the software we want. It is an ardiniou controlled device (requires fridge + $100 worth of parts). Its original purpose is to control temperatures for “Homebrewing” alcohols
• Water bath (We didn’t assign anyone to this)
• Block heaters with controlled temperature (for eppendorf tubes)
• Orbital shaker table (M)

[[4]]

• • A DIY shaker, the design is ($140) and 2 years old.
    • It appears to be for small scale plates (the ones we used in Essy’s lab to grow cells)
    • It produces no heat which is important in incubators that can’t cool
    • We can scale up the device for 500mL-4L flasks (common for bacteria)
• Vortexer mixer (M)
• Centrifuge/Microcentrifuge (H) (In the lab I work in we do something called a cytospin for single cell suspension which are frequently used in pathology labs. I’m not sure if it’s something you might be interested in but it works the same way as a centrifuge. It spins - Andrew)
  • There appears to be an attachment that converts a Dremel to a centrifuge ($50)
  • [[5]]
  • [[6]]
  • A hand driven centrifuge ($80 dollars)
    • [[7]]
• A PopSci Writer mentions in an article that cheap centrifuges on Ebay are approx ($100)

[[8]] Also, safety is a major concern due to the rotor- if there are imperfections in it, a dangerous accident can occur Fume Hood or Tissue Culture Hood (H) Simple function generator (electrical equipment) (M)

Articles or Devices of Interest openpcr.org This is an opensource, build it yourself kit for a thermocycler that connects to a PC. Cost is $600. This is the direction we want- sell a kit for a common lab equipment. http://www.nature.com/news/2010/101006/full/467650a.html an article about DIY biotech in Nature Journal http://diybio.org/ The DIY bio website, a place to check on news of the “scene” http://sciencenewstop.blogspot.com/2012/01/diybio-re-suggestions-for-viral.html http://sciencenewstop.blogspot.com/2012/05/re-diybio-help-required-in-sourcing.html https://groups.google.com/forum/#!topic/diybio/mcZ7bHsaCqg Interesting idea- way to incorporate microscope in incuabtor http://www.popsci.com/diy/article/2011-10/video-smart-petri-dish-images-cells-using-smartphone-camera-and-legos Very good idea! Combines cell phone, CCD chips to reduce time in cell culture Idea- research ways to save time in the lab, combine common electronics (cell phone, cameras, etc) to update basic lab equipment https://groups.google.com/forum/?fromgroups#!forum/diybio forum for DIYBIo https://groups.google.com/forum/?fromgroups#!topic/diybio/hwY7KRcnvY0 http://openwetware.org/wiki/DIYbio/FAQ/Equipment This is a good source to see what equipment labs use and what other people have done in DIY

6/03/2012

Choosing Devices to Concentrate On

Andrew and Scott researched devices and chose 1-2 to focus their efforts on. Scott- 37C Incubator with temperature control and CO2 regulation Primary Focus- Mammalian cells Secondary Focus- Bacteria and algae Requires: insulated box, heating elements, controller, algorithm for temp +C02 control, electricity Target Group: DIY interested in mammalian cells, brain cells, tissue in place with dependable power source Andrew - Electroporator Requires an electric current Appropriate voltage, amperage

Goals By June 10th present a 5-minute talk to everyone detailing: Mandatory: Materials Component List Costs Target User Problems to address If Possible: Multiple design possibilities

Also, discuss our progress on Wednesday (10am Texas time). Update each other regularly throughout the week also.

What to Research Further Electroporator Technical Threshold V,A needed to different cell types Specific circuit components Incubator Technical Marketing What problem will our device address? DIY, HS teachers, college labs specific problems Funding

Research On Goals From 6/03/2012 Electroporator Technical Threshold V,A needed to different cell types Specific circuit components Pulse generators http://pages.towson.edu/jsaunder/Saunders%20Publications/46.Pulse%20Generators%20for%20Electrofusion%20and%20Electroporation.pdf Older article referencing older dseigns of electroporators and pulse gens for them http://www.bio-rad.com/webroot/web/pdf/lsr/literature/4006174B.pdf good source with theory of capacitance and discharge device does 1 sample at a time Incubator Technical Marketing What problem will our device address? DIY, HS teachers, college labs specific problems

Funding

http://www.kickstarter.com/projects/930368578/openpcr-open-source-biotech-on-your-desktop?ref=live

6/06/2012

Meeting updates Andrew-Read Article “A simple and effective electroporation apparatus” Materials list Stainless steel sheets Capacitor (will check specifics, need to do calculations. possibly 12 microfarads) Resistor (possibly 2000 ohms) Target specimens Bacteria and/or Fungi (Volume range: 20 to 200 microliter) Goal this week Dimensions of BioRad Cuvette (0.1cm to 0.4cm gaps) Complete calculations Rough design of electroporator Possible exterior materials: good insulators some dry wood I guess. Can we automate the device? (this paper was written in 1990 it is pulse driven) Microfluidics, chambers, can we 3d print a chamber? Multiple specimens? Meeting Notes and Things to Research Meeting at UNC Library (Sergio, Scott) Discussed vortexer, function generator, temp controlled +C02 incubator Tossed the function generator since old ones are cheap and QC is a problem Vortexer is a go Idea- build an off-center attachment for an electric toothbrush motor Target toward MS, HS, developing nation labs Battery operated? Things to research: Vortexer Oscillating movement of motorized shaft Whatforces do current vortexers (dyi+pro) produce? Uniform front end that is usable for eppendorfs, tubes? Temperature controlled incubator cost effectiveness of components (heat source, insulation) possibilities- foam, insulation from houses, ceramic tiles, concrete, sand materials- aluminum, metal size- bacteria culture- 2x2x4ft (shaking table inside) mammalian- 8 cubic ft (2x2x2) (nonshaking)

Meeting at Durham Hackerspace (Splatspace) We met 3-4 people who are interested in collaborating with us. Drew, Peter, James, Marco There is Scrapexchange, which sells lab equipment (and junk) per pound. we can find devices and parts there There are 2 focuses here: one is to build DIY, research quality devices. The other is to buy/build devices for use at the hackerspace and perform genetic engineering/biotech experiments like glow-in-the-dark beer (yeast that express GFP) Meetings Tuesday 7pm and Sunday 6-9 pm.

Research on goals from June 5-6th

Temperature controlled incubator http://www.labdepotinc.com/c-441-co2-incubator.php Manufacturer of incubators. They note particular key components of incubator: HEPA Filtration easy to sterilize insides “contamination control, decontamination and precise temperature and CO2 control for years of constant performance through constant thinking.” http://www.nuaire.com/co2-incubators/ Manufacturers of incubators key characteristics: contamination control, minimal culture desiccation, and consistent culturing.

6/10/2012

Scrap Exchange Visit When is a good time for everyone to visit Scrap Exchange? Alternatively, we can hit it multiple days in case they get new lab equipment Tuesday June 12- I will be free to visit before the Splat meeting

6/12/2012

Meeting (Foo, Holmes Skype 11am est) and Research

Discussed ongoing vortexer, incubator research

• Speyer Paper
  • Discharge used was 1300 volt
• Biorad electroporator
  • 4 dollars per cuvette
  • $2000 for a new Biorad
• Ebay- cheapest electroporator is 800$
• Cell Porator
  • http://www.labrepco.com/pdfs/CellPorator.pdf
• Example electroporator protocol
  • http://depts.washington.edu/bakerpg/protocols/electroporation.html
  • http://userpages.umbc.edu/~jwolf/m7.htm
• Target cost goal?
  • Openpcr=$600
  • Used electroporators $800
  • We want to save people at least $500 dollars, so our manufacture price is $200-300
    • Ideally $200-300
    • $500 is minimum goal

Design issues-

• minimizing area between electrodes
  • Biorad-0.1 mm gap

Research questions

• Cuvette vs open sample design?
• Cheap source of cuvettes
• Design for a wide range of cuvettes?
• More DIY and current devices
• Insides of an electroporator
  • NAND gate

6/12/2012

Scrapexchange visit. They have a science aisle and many other aisles of various scrap (some electrical). I observed in the science aisle: pipette tip boxes, various sterilized pipette (disposable), bottles, and syringes; nalgene bottles (for storing reagents), tubes, and glass bottles/tubes. Also, they had a bunch of sterilized electroporator tubes!

• Gene Pulser Cuvetter (E. coli)
  • 0.1 cm gap
• BTX electroporation, “cuvettes plus”