Difference between revisions of "BME103:T930 Group 9"

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(Please finish by 11/7/2012)
==Initial Machine Testing==
==Initial Machine Testing==
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(Your group will add the results of your Fluorimeter measurements from Week 4 here)
<!--- Place two small Image J data images here. One showing the result of Water and the other showing the result of Calf Thymus DNA --->
<!--- Enter the values from your group's Data Analyzer table below. E6, F6, etc. are the excel cells from which you should copy your data. --->
{| {{table}}
|- style="background:#f0f0f0;"
| '''Sample''' || '''Integrated Density''' || '''DNA μg/mL''' || '''Conclusion'''
| PCR: Negative Control || E6 || F6 || G6
| PCR: Positive Control || E7 || F7 || G7
| PCR: Patient 1 ID #####, rep 1 || E8 || F8 || G8
| PCR: Patient 1 ID #####, rep 2 || E9 || F9 || G9
| PCR: Patient 1 ID #####, rep 3 || E10 || F10 || G10
| PCR: Patient 2 ID #####, rep 1 || E11 || F11 || G11
| PCR: Patient 2 ID #####, rep 2 || E12 || F12 || G12
| PCR: Patient 2 ID #####, rep 3 || E13 || F13 || G13
* '''Sample''' = <!--- explain what "sample" means --->
* '''Integrated Density''' = <!--- explain what "integrated density" means and how you did background subtraction to get this value --->
* '''DNA μg/mL''' = <!--- how you calculated this --->
* '''Conclusion''' = <!--- explain

Revision as of 14:17, 9 November 2012

Owwnotebook icon.png BME 103 Fall 2012 Home
Lab Write-Up 1
Lab Write-Up 2
Lab Write-Up 3
Course Logistics For Instructors
Wiki Editing Help
BME494 Asu logo.png


Name: Devraj Patel
Open PCR Machine Engineer and Research & Development Scientist
Name: Andrew Hensley
Experimental Protocol Planner
Name: Nathalie Vitale
Experimental Protocol Planner
Name: Ojeen Korkes
Research and Development Scientist
Name: Brandon Simmons
Open PCR Machine Engineer


Initial Machine Testing

The Original Design
This is an image of an Open PCR Machine. This machine regulates the temperature of the DNA smaples both heating and cooling samples to the preset temperature and times set up beforehand using the set up program. This heating and cooling seperates the DNA strands at high heat and then allows it to synthesize at low temperature.

Experimenting With the Connections

When we unplugged part 3, the LCD, from part 6, the Open PCR circuit Board, the LCD on the machine turned off and no information appeared on the LCD screen.

When we unplugged the white wire that connects part 6, the Open PCR circuit Board, to part 2, the heat sink, the machine no longer accurately regulates and controls the temperature and result in malfunction of heating the PCR tubes.

Test Run

On October 25 2012, we conducted our first test on our open PCR machine. We tested the machine to test the operation functionality. The initial test demonstrated the machine heat sink accuratly controlled and displayed the preprogrammed temperaute determined by the software on the computer. The overall successfullness of the machine was good, however it came with one difficulity, fluctuation of time to complete the preporgrammed cycles.


Polymerase Chain Reaction

Steps to Run PCR

  1. Connect the PCR machine to the computer.
  2. Open the 'OpenPCR' program on the computer.
  3. Label the tubes. This information should include the patient number (1 or 2) or control (+ or -), as well as the replication number (1, 2, or 3).
  4. Prepare the experiment by inserting the reactants into the PCR tubes. These tubes will consist of the patients DNA, along with the other provided mixing components*. After filling each tube, put it into the chamber at the top of the machine.
  5. Close and tighten the lid of the chamber.
  6. Customize the settings in the 'Thermal Cycler' program to include three stages: Stage 1 - one cycle that will heat the reactants up to 95 degrees Celcius for three minutes, Stage 2 - 35 cycles that will heat the reactancts to 95 degrees Celsius for 30 seconds, 57 degrees Celsius for 30 seconds, and 72 degrees Celsius for 30 seconds.
  7. Press start on the prgram to begin running the PCR.
  8. Collect and record data at the completion of the trial.

* Provided Mixing Components
a)TaqDNA polymerase (non-recombinant modified form)
d)reaction buffers (at optimal concentration for DNA template amplification)

Reagent Volume
Template DNA (20 ng) 0.2 μL
10 μM Forward Primer 1.0μL
10 μM Reverse Primer 1.0μL
GoTaq master mix 50μL
dH2O 47.8 μL
Total Volume 100.0 μL

The Patient Information

Patient Identification Number Gender Age
31542 Male 55
52125 Female 55

Flourimeter Measurements

Flourimeter Assembly Procedure

  1. Place a glass slide on the device.
  2. Using a pipette, add two drops of water to the slide.
  3. Turn on the blue LED light, and adjust the slide so that the light shines directly through the center of the water drop.
  4. Adjust the camera settings on a smartphone as follows:
    • Turn off the flash
    • Set exposure to the highest setting
    • Set saturation to the highest setting
    • Set contrast to the lowest setting
  5. Place the smartphone on the phone holder and position it in front the of fluorimeter device.
  6. Cover the entire setup with a black box in order to create as dark of an environment as possible.
  7. Take a picture with the smartphone. For best results, set the camera timer on the smartphone in order to be able to take a picture with the box completely closed.

How to Open Pictures Using Image J

  1. Using the smartphone, email the images to someone in the group with a computer.
  2. From the computer, open the email and download the images.
  3. Save the images to the computer.
  4. If the computer does not already have Image J installed, the program can be downloaded by going to http://rsb.info.nih.gov/ij/download.html
  5. In Image J, go to file, open, and then select the desired picture.

Research and Development

Specific Cancer Marker Detection - The Underlying Technology

In Week 3 of our PCR experiment, we studied the cancer marker in the PCR experiment was correlated to the breast and colorectal cancer. Based on conditional probabilities, we found that the frequency of this cancer found in Finland was 7.8%.

BONUS points: Use a program like Powerpoint, Word, Illustrator, Microsoft Paint, etc. to illustrate how primers bind to the cancer DNA template, and how Taq polymerases amplify the DNA. Screen-captures from the OpenPCR tutorial might be useful. Be sure to credit the source if you borrow images.

Summary: This is an image of how RNA primers bind to the cancer DNA template during the replication process. [1]
Source: [1]
Summary: This is an image of how Taq polymerases amplify the DNA. [2]
Source: [2]

For more information on the PCR DNA replication process, please visit this website: http://learn.genetics.utah.edu/content/labs/pcr/.


Sample Integrated Density DNA μg/mL Conclusion
PCR: Negative Control E6 F6 G6
PCR: Positive Control E7 F7 G7
PCR: Patient 1 ID #####, rep 1 E8 F8 G8
PCR: Patient 1 ID #####, rep 2 E9 F9 G9
PCR: Patient 1 ID #####, rep 3 E10 F10 G10
PCR: Patient 2 ID #####, rep 1 E11 F11 G11
PCR: Patient 2 ID #####, rep 2 E12 F12 G12
PCR: Patient 2 ID #####, rep 3 E13 F13 G13


  • Sample =
  • Integrated Density =
  • DNA μg/mL =
  • Conclusion =