Difference between revisions of "Spring 11:QRT-PCR"

Revision as of 20:04, 4 April 2011

Looking for weekly reports?

Or LabView QRT-PCR version info?

To-Do

Last updated 15:14, 4 April 2011 (EDT)

TONIGHT:

• Learn LabView

LATER:

• get used to version 2.712.
• convert RTD code in 2.712 to Thermistor code
• make sure code can cycle temperature well.
• test heat transfer equation with sample vs block thermistor (practice for doing it with heated lid)
• construct heated lid
  • design electronics
    • measure real resistance of length of resistance wire
    • will I need to isolate the circuit, since it's drawing so much current (1-3 A)?
  • design physical setup
• get heat transfer equation b/w sample, block with heated lid

• find out: can thermistor actually stick in sample? or should it just be near the lid?

Weekly goals

as of 15:03, 4 April 2011 (EDT)

• 3/25: Optics finished. Code started.
• 4/1: Heated lid finished.
• 4/8: No really, heated lid finished. Updated heat transfer function. Kinda know LabView.
• 4/15: Successful PCR.
• 4/22: Optics are ready for QRT-PCR!
• 4/29: Successful QRT-PCR from the side.
• 5/6: QRT-PCR from the top. Now which one was better?

Research notes

• Heated Lid
• Fiber Optic

Useful Links

• | Resistance wire temperature table
• | Calculations with resistance wire

Progress Notes

4/4/11

Posted 15:00, 4 April 2011 (EDT)

I now know the reason for the background signal. The fiber optic cable is auto-fluorescing. BOO. It works okay for now (there is a small, but extant difference between H20 and SYBR+dsDNA), but in order to do any serious testing, I'll need to change the design. Or get a new fiber optic

It might, in fact, be time to get rid of the fiber optic all together. But I will also look around for fiber optics that really, really do not fluoresce.

4/1/11

Posted 15:50, 1 April 2011 (EDT)

Officially ordered 29-gauge wire.

The optics *do* detect a difference between water and SYBR dsDNA, but it's a fairly small difference. I think this small difference is due to the HUGE amount of background signal at the carrier frequency. Why is this happening? My current hypothesis is that the dichroic mirror is directly reflecting some light from the blue LED into the photodiode... but with the filters in place, this shouldn't be happening!

Question: how good are the filters we're using? Could they still be letting some other light through? (maybe we need another blue filter in front of the blue LED).

Steven went over with me some of the different existing versions of the LabView code. I will be working with versions 2.700 and later. Not all of them work. I will take notes on this; take a look at QRT-PCR:LabView-versions.

3/28/11

Turns out my calculations were all messed up before! With corrected calculations, and the data from [www.heatersplus.com], I decided on 29-gauge resistance wire for our heated lid.

3/22/11

Getting the temperature calculation right earned me a level-up... meaning I got to graduate to the Current Version of the Code. Got a brief intro to it. It's pretty complicated.

3/20/11

Based on model system (blue LED + ND filter), I don't think gain is high enough. Increased gain of transimpedance amp from 2.5e4 to 2.5e5. Well, it didn't help that much. So it's back the way it was. In any case, we get a significant signal (~0.25 units amplitude) with the model system. Huzzah!

After much wrestling with simple math, the temperature sensing is largely working! yay

3/18/11

Optical setup appears to be working.

3/16/11

Added dichroic mirror.

Question: how can I verify the optical setup? it seems to respond to driving signal, not fluorescence.

TODO: put away 25mm lens