BME103:T930 Group 16

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'''Specific Cancer Marker Detection - The Underlying Technology'''<br>
'''Specific Cancer Marker Detection - The Underlying Technology'''<br>
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A Polymerase chain reaction is a machine that amplifies a single or a few strands of DNA to generate millions of copies of that DNA sequence. Using this technology scientist can determine whether a patient has a positive or negative result towards cancer. A method of getting this data is called the PCR detection method, a method that relies on thermal cycling, switching back and forth to melt DNA and then connect primers. This is a method that can be used to detect whether a patient has positive result for cancer, because a sample of DNA can be taken and whether that connects to the primers and creates a chain reaction, scientist can determine whether this DNA is positive or negative towards cancer. An example of proving this method can be seen using the r17879961 SNP, a cancer-associated sequence, using the PCR detection method we can prove that r17879961 SNP is actually associated with cancer. Because it carries with the Polymerase chain reaction, and to further prove the patient has a positive result for cancer, we use fluorescent dye and if the DNA glows in the solution, then the results are positive for cancer. <br>
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A Polymerase chain reaction is a machine that amplifies a single or a few strands of DNA to generate millions of copies of that DNA sequence. Using this technology scientist can determine whether a patient has a positive or negative result towards cancer. A method of getting this data is called the PCR detection method, a method that relies on thermal cycling, switching back and forth to melt DNA and then connect primers. This is a method that can be used to detect whether a patient has positive result for cancer, because a sample of DNA can be taken and whether that connects to the primers and creates a chain reaction, scientist can determine whether this DNA is positive or negative towards cancer. An example of proving this method can be seen using the r17879961 SNP, a cancer-associated sequence, using the PCR detection method we can prove that r17879961 SNP is actually associated with cancer. Because it carries with the Polymerase chain reaction, and to further prove the patient has a positive result for cancer, we use fluorescent dye and if the DNA glows in the solution, then the results are positive for cancer.
(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.)
(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.)

Revision as of 23:14, 8 November 2012

BME 103 Fall 2012 Home
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Lab Write-Up 1
Lab Write-Up 2
Lab Write-Up 3
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Contents

Group 16

Name: Omar Moreno Salinas, and Rachel JuettenOpen PCR, ImageJ Software Processor, Data Compiler, and Analyzers
Name: Omar Moreno Salinas, and Rachel Juetten
Open PCR, ImageJ Software Processor, Data Compiler, and Analyzers
Name: Maggie McClure, and Swetha SwanminathanProtocol Persons: Sample Prep & Application
Name: Maggie McClure, and Swetha Swanminathan
Protocol Persons: Sample Prep & Application
Name: Marianna SinghDNA Measurement Operator
Name: Marianna Singh
DNA Measurement Operator
Name: Muawiya Ali Al-KhalidiR&D Scientest
Name: Muawiya Ali Al-Khalidi
R&D Scientest

LAB 1 WRITE-UP

Initial Machine Testing

The Original Design
Image:group 16.png


Experimenting With the Connections

When the heat sink is unplugged from the circuit board, the LCD screen turned off. When we unplugged the white wire that connected the circuit board to the heating block the temperature reading on the LCD screen dropped drastically.

Test Run

We first tested open PCR on October 18, 2012. We learned how to take accurate temperatures using the open PCR machine. Using open PCR we were able to make a polymerase chain reaction. In order for this to occur, open PCR had to send the DNA through different sets of temperatures to heat it up to separate the strands and expose the bases, then cool it down for the primers to bind to the sequences, and also heat it back up to attain an extension of the copy of the new DNA. Which was conducted in an hour and thirty minutes.




Protocols

Polymerase Chain Reaction

Reagent Volume
Template DNA (20ng) 0.2 μL
10 μM forward primer 1.0 μL
10 μM reverse primer 1.0 μL
GoTaq master mix 50.0 μL
dH2O 47.8 μL
Total Volume 100.0 μL

Here is the patient information:


92136 M 54 Years


62276 F 61 Years

Flourimeter Measurements

Image:FlouimeterMeasurements.jpg




Research and Development

Specific Cancer Marker Detection - The Underlying Technology

A Polymerase chain reaction is a machine that amplifies a single or a few strands of DNA to generate millions of copies of that DNA sequence. Using this technology scientist can determine whether a patient has a positive or negative result towards cancer. A method of getting this data is called the PCR detection method, a method that relies on thermal cycling, switching back and forth to melt DNA and then connect primers. This is a method that can be used to detect whether a patient has positive result for cancer, because a sample of DNA can be taken and whether that connects to the primers and creates a chain reaction, scientist can determine whether this DNA is positive or negative towards cancer. An example of proving this method can be seen using the r17879961 SNP, a cancer-associated sequence, using the PCR detection method we can prove that r17879961 SNP is actually associated with cancer. Because it carries with the Polymerase chain reaction, and to further prove the patient has a positive result for cancer, we use fluorescent dye and if the DNA glows in the solution, then the results are positive for cancer.

(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.)




Results

Sample ID area mean IntDen RawIntDen IntDen Differences IR2 129768 66.2 8591662 8591662 2.564 83328 13.667 1138855 1138855 positive control 94508 52.71 4981557 4981557 1.34 48708 22.306 1086499 1086499 DNA calfthymus 147200 85.108 12538430 12538430 3.214 116232 27.49 3195234 3195234 1R1 119480 120.987 14455570 14455570 3.286 81792 59.967 4904821 4904921 1R3 127409 103.704 13212871 13212871 4.087 85796 15.553 1334411 1334411 negative control 112816 87.582 9880697 9880697 2.833 75504 21.81 1646771 1646771 2R1 216728 57.551 12472923 12472923 3.642 109452 17.229 1885786 1885786 2R2 236664 93.344 22091168 22091168 6.45 9698 34.469 3342359 3342359 2R3 12112 94.768 11477553 11477553 2.951 73244 39.572 2898384 2898384 water 103144 88.078 9084688 9084688 133788 43.453 5813460 5813460
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