How much does cancer research cost? Part II

gel-webThis follows on from my earlier (rather unimaginatively titled How much does cancer research cost Part I !). I am working through a typical day in a cell biology research lab working out how much it costs to do a days work.

So far we’ve made it to 10:30am and spent about £60. It gets more expensive as the day goes on

11am

If you want to study genes you would carry out a PCR.  If you want to study proteins you would probably start with an SDS-PAGE gel.  SDS-PAGE stands for

S – Sodium

D-Dodecyl

S- Sulphate

SDS (has the chemical formula C12H25SO4Na) You can see a picture of it’s chemical structure  on Answers.com It is used at low concentrations in soaps, bubble baths, toothpaste and shaving foam, it’s the bit of soap that makes it bubble (or lather). The sodium (or “Na” part) is the same chemical element that is found in table salt.

P – Poly

A – Acrylamide

G – Gel

E – Electrophoresis

Poly means many, so a polyacrylamide gel has many subunits of acrylamide joined together (-CH2CHCONH2-), acrylamide can damage your nerves so you wear gloves, a lab coat and safety glasses when you handle it.  There is no point in killing your nerve cells unnecessarily. Polyacrylamide doesn’t damage nerves, but even when your gels have set, it’s best to use gloves in case there is still some unpolymerised acrylamide. Usually polyacrylamide gels have to be disposed of in a separate bin and don’t go into normal lab waste.

Polyacrylamide gels look like a very thin layer of clear jelly, the small ones (“mini-gels”) are usually about the size and thickness of a credit card. The word electrophoresis means separating things using electricity. So you connect up your gel to a power supply unit (plugged into a normal electrical socket) and let it “run” for 1-2 hours (if it’s a mini-gel, bigger gels can run overnight)

SDS-PAGE gels need a lot of different chemicals, most of which you can buy from the chemical company Sigma.  You can read about these chemicals in detail on the wikipedia entry on SDS-PAGE. I’ll just outline the costs. Many of the individual chemicals are quite cheap, they last for months, if not years, so the actual cost of the ingredients of a “lab” made mini gel is about £2-£4

Tris £30 for 100g
Glycine £30 for 500g
SDS £40 for 100g
APS £13 for 25g
TEMED £12 for 25 ml

SDS is a very fine powder, so you need to wear a mask when you weigh it out to stop yourself coughing. Once it’s dissolved in water it won’t make you choke.  TEMED stinks, so you usually use that in a fume hood.  It takes about half an hour to mix all the ingredients and get the gel set up.

You can watch a YouTube video from GeneEd, that explains the theory behind electrophoresis.

This short video (30 seconds) by be115 shows the actual gel equipment you would use in a lab.  The equipment shown is made by a company called BioRAd. The actual equipment costs £300 to £400 but will last 5 years or more if looked after carefully.

1 pm

Hopefully you’ve got your proteins quantified when your gel is setting. If you manage to get your gel on at lunch time then you can eat while it is “running”.

3 pm

As long as there have been no disasters (e.g. your buffer hasn’t leaked), you should be able to take your gel out of the equipment (“the tank”) and put it on to “western blot”.

Western blotting transfers the proteins from your credit card sized bit of gel onto a shiny, brittle bit of paper called a “membrane”.  Membranes are a lot tougher and easier to handle than gels, which is why scientists use them.

The equipment to carry out a mini blot costs about £300-£400, but like the gel equipment should last 5 years or longer (I’ve worked in some labs where the tanks and blotters are more than 15 years old).  The most expensive bit of blotting is the membrane.  It costs £160 for 10 sheets (each sheet is 20cm by 20cm), which is enough to last a month or two. You can buy PVDF from the company GE Healthcare. You also need Tris and Glycine to make the buffer (the same stuff mentioned earlier for the electrophoresis gels)

5 pm

It takes about half an hour to dismantle a mini gel and set up a blot.  The actual blotting can be done in an hour or left overnight.  It depends how late you want to work.  A lot of people like to get the blotting done and get their western into primary antibody overnight, but I think I’ll leave it blotting overnight and we’ll start adding up the cost of the really expensive stuff (the antibodies) tomorrow.

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