BME103:T130 Group 17

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Owwnotebook icon.png BME 103 Fall 2012 Home
Lab Write-Up 1
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Lab Write-Up 3
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Name: Jorge Jimenez
Research Development Specialist
Name: Ricardo Robles
Research Development Specialist
Name: Jennifer Begin
Experimental Protocol Planner
Name: Finola Roy
Experimental Protocol Planner)
Name: Kevin Zenner
Open PCR Machine Engineer


Initial Machine Testing

The Original Design
(Add image of the full OpenPCR machine here, from the Week 3 exercise. Write a paragraph description for visitors who have no idea what this is)
Image of the Open PCR

Experimenting With the Connections

When the PCB board of the LCD screen was disconnected from the PCB circuit board the display output was turned off.

When the white wire connecting the 16 tube PCR block to the PCB circuit board ability to regulate the temperature of the PCR was lost.

Test Run

After finishing the diagnostic analysis, the PCR was tested by setting thermal cycler program to three stages. Stage one was one cycle of 95 °C for 3 minutes, the second stage was 35 cycles, 95 °C for 30 seconds, 50 °C for 30 seconds, 72 °C for 30 seconds, stage three was one cycle of 72 °C for 3 minutes. The test run lasted for about an hour and thirty minutes and confirmed that the temperature readings on the LED of the PCR machine and the computer matched.


Polymerase Chain Reaction

(Add your work from Week 3, Part 1 here)

Flourimeter Measurements

(Add your work from Week 3, Part 2 here)

Research and Development

Specific Cancer Marker Detection - The Underlying Technology

The r17879961 sequence will produce a cancer mutation at Chromosomes 22 of the gene sequence. The normal sequence has a T ( thymine) nucleotide at chromosome 22 while the mutation sequence has an associated C (cytosine) nucleotide. The Open PCR machine is able to determine whether or not the r17879961 sample has cancer by replicating the desired mutation exponentially. Positive and negative strands are inserted into the PCR with a certain primer. The primer in the reaction is designed to attach to the C nucleotide that signifies cancer mutation. One strand has the primer, while the other strand does not. Open PCR will replicate the strand with the certain primer, causing an exponential growth. The negative strand will grow in a linear fashion. The PCR process goes through 30 cycles to complete this. After the PCR process, fluorescent dye is added to the solutions. The fluorescent dye will cause the DNA with double strands to glow. Since the PCR has grown the double stranded positive DNA exponentially the fluorescent dye glows brighter. Therefore the cancer DNA is in the sample with the glow.

First Step Second Step Third Step Fourth Step Fifth Step Sixth Step Seventh Step Eighth Step


(Your group will add the results of your Fluorimeter measurements from Week 4 here)