January2016/Experimental design

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Revision as of 09:06, 15 February 2016 by Anna Tong (talk | contribs) (→‎Protocol)
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We're basing these experiments on the Kim2015 paper.

These are the experiments we expect to run:

  • Ligate synthesized DNA into linearized plasmid
  • Transform plasmids into ecoli (DH5 alpha)
  • Stick extra DNA in TE buffer and freeze it
  • Grow up liquid culture and make glycerol stock
  • Do plasmid prep and put in freezer on TE buffer
  • Sequence plasmid
  • (optional: try to purify protein from e. coli and run gel)
  • Transform plasmid into yeast
  • Grow yeast on selective media and make glycerol stock
  • Grow yeast in bioreactor and induce expression of our protein
  • Run nickel column purification of extracellular media
  • If the above doesn't work, try to lyse cells and repeat purification
  • Run page gels of purifiction product

PLEASE HELP BY WRITING UP OR LINKING THE NECESSARY PROTOCOLS FOR THE ABOVE EXPERIMENTS

Create and prepare plasmid constructs

We need to ligate our synthesized DNA into the DNA 2.0 plasmid.

Supplies and reagents

  • DNA 2.0 plasmids pD1204
  • Our synthesized DNA from IDT: Both hCMP and full bovine
  • Electra Cloning Reagents Kit (already ordered from DNA 2.0)
  • ddH20 (at least 30 microliters)

Protocol

We're using the Electra System from DNA 2.0 which uses SapI sites. The protocol is here.

Experimental design

  1. Dissolve dry pD1204 plasmid DNA pellet in TE buffer
  2. Dissolve dry pJ1204-03C control plasmid DNA pellet in TE buffer

For each of the two IDT sequences:

  1. Dissolve dry DNA pellet from IDT in TE buffer
  2. Complete Electra Cloning Protocol using IDT sequence + pD1204 plasmid

Long term storage of unused DNA

Any remaining DNA from the previous step should be stored in case we want to re-do the experiment or try something else later.

Supplies and reagents

  • TE buffer (10 mM Tris-Cl, pH 7.5; 1 mM EDTA)
  • Our excess DNA from previous step
  • At least 9 cryotubes

Experimental design

Storing in TE buffer at -20C performs best - see Evaluation of DNA Plasmid Storage Conditions

Freeze/thaw cycles can damage the DNA, so best would be to store small single-use aliquots.

Transform plasmids into e. coli

Supplies and reagents

Approximate. What we actually use will depend on protocol. Anna is figuring out what the Insulin group did and will change this and link to their tried and tested protocol.

  • Our plasmid constructs: pD1204-hCMP, pD1204-BK (bovine kappa-casein) and control plasmid pD1204-03C
  • Competent E. coli (BioCurious has an excess that we can use)
  • Container full of crushed ice
  • 42 degrees C water bath
  • 37 degrees C shaking incubator
  • LB without amp
  • LB+amp plates
  • 1.5 mL eppendorf tubes (at least 15)

Protocol

Potential protocols to use:

Experimental design

Complete transformation protocol in duplicate or triplicate for each construct. In addition complete the protocol with no plasmid (negative control and with neither e. coli nor plasmid (contaminant check).

Grow up liquid culture

Once we have successful transformants we will need to pick colonies and grow them up in LB+amp.

Supplies and reagents

  • Our transformants
  • 37 C incubator with shaker
  • LB+amp
  • Tubes (size not important)

Experimental design

Pick successful transformants from each non-control LB+amp plate (assuming controls turned out as expected), dissolve in 37 C LB+amp tube and grow overnight in shaker in 37 C incubator.

Make glycerol stock

For long term -80 C storage we need to make glycerol stocks.

Supplies and reagents

  • LB+amp culture grown overnight with our transformants (from previous step)
  • Glycerol
  • dH20
  • Cryotubes

Protocols

Experimental design

For each of our transformants make at least three cryotubes containing a 50/50 mixture of autoclaved glycerol and the LB+amp with the transformants. Label it and shove it in our -40 C freezer (or -80 C if we have it operational).

Extract plasmid from liquid cultures

Supplies and reagents

  • LB+amp culture grown overnight with our transformants (from previous step)
  • BioMiga Plasmid MiniPrep kit 1
  • 10,000 RPM centrifuge

Protocols

Experimental design

We need to extract enough plasmid from each of our samples for the following three purposes:

  • Sequencing
  • Long term -20 C storage on TE buffer
  • Short term 4 C storage for upcoming experiments

Prep and send DNA in for sequencing

ToDo: Find a sequencing company that is cheap (and preferably local) and see how we need to prep our sample before sending it in.

Bioreactor growth

The plan is to grow our strain in a bioreactor. We'll need high aeration throughout the experiment.

The starting conditions for flask cultures used in the paper are:

  • 2% yeast extract (we'll need defined media with no uracil)
  • 2% glucose
  • 3% galactose

This is likely fine for our initial proof of concept. Figure 2b from the Kim2005 the paper is especially helpful in understanding the flask cultures growth.

Bioreactor measurements

Biomass

The cell concentration was measured by a spectrophotometer at 660 nm (Lambda 20, Perkin-Elmer, USA). -- Kim2015 paper

We have a working spectrophotometer that can handle 660 nm at both CCL and Biocurious :)

Glucose / Galactose concentration

Glucose, galactose, glycerol, and alcohols in the culture supernatant were analyzed at 50°C using a high-per-formance liquid chromatograph (1100 series, Agilent Technologies, USA) equipped with a Shodex-SH1011 packed column (/ 8 mm·300 mm, Showa Denko K.K., Japan) and a refractive index detector. -- Kim2015 paper

This equipment would cost around $15,000 so not within our price range.

We could get a GlucCell Glucose Monitoring System which is the same type of device used by diabetics but created especially for cell cultures. I wonder if there is a real difference or if it's just a marketing gimmick. If we buy one we should test it against a normal drug-store blood glucose meter. It can be bought for $360 and the test strips are just over $1 each and sold in packs of 50.

On its website the GlucCell is compared to the NOVA BioProfile Biochemical Analyzer so that's likely an industry standard analyzer. An older 200 series NOVA can be found on ebay for $400 in allegedly working condition and with a 6 month warranty, but it is unclear if it will need reagents/chemistry to function. I expect that it will since the product page for the newer 400 series lists the glucose test methodology as enzyme/amperometric. It is possible that it is using probes with fixated enzymes but I wonder what the lifetime on such probes would be. Also the manual is not available anywhere that I can find. Someone could contact the company and ask if they still sell reagents fro the 200 and which reagents/supplies we'd need. If it _doesn't_ need reagents then that would be a very useful piece of equipment!

Galactose would be cool to measure but it's not absolutely necessary. There are definitely galactose colorometric kits out there that will allow us to use our spectrophotometer to measure galactose.

High yield batch-fed culture

To get high concentrations Kim et al. used a batch-fed bioreactor and in the paper they detail the specifics of how they initialize it but the most important part is probably this:

During the production phase, the glucose concentration was maintained below 1 g/l and the galactose concentration at approximately 15 g/l. The temperature and pH were maintained at 30°C and 5.0 – 5.5, respectively, throughout the bioreactor operation. -- Kim2015

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