BME103:T930 Group 15 l2: Difference between revisions
(4 intermediate revisions by 2 users not shown) | |||
Line 33: | Line 33: | ||
'''Key Features'''<br> | '''Key Features'''<br> | ||
With the changes incorporated with the re-design of the Open PCR machine, the main design changes were to the LCD display screen, front side wall, and the motherboard. The changes would involve moving the location of the LCD display screen to the front side wall as well as adding buttons to the the wall that allow the Open PCR machine to be programmed instead of inputting the desired parameters into a computer with a USB cable. | With the changes incorporated with the re-design of the Open PCR machine, the main design changes were to the LCD display screen, front side wall, and to the motherboard. The changes would involve moving the location of the LCD display screen to the front side wall as well as adding buttons to the the wall that allow the Open PCR machine to be programmed instead of inputting the desired parameters into a computer with a USB cable. In order for the program to be on the machine itself, the motherboard would have to be re-programmed so that a computer connected to the Open PCR machine with a USB would no longer be needed to run the machine. | ||
'''Instructions'''<br> | '''Instructions'''<br> | ||
Line 117: | Line 117: | ||
<!--- A description of the diseases and their associated SNP's (include the database reference number and web link) ---> | <!--- A description of the diseases and their associated SNP's (include the database reference number and web link) ---> | ||
<br>Rs33927012 is a cancer mutation in the DNA sequence that produces breast thyroid cancer. The mutation if found on the gene SDHB(6390), and the mutation is a change from a T to a C (TCT → CCT), in the sequence 5’-GAAGGATGAATCTCAGGAGG-3’. This cancer is most associated with Cowden-like syndrome. With this mutation symptoms are increased manganese superoxide dismutase function, and increased reactive oxygen species. This disease was found within two women with a wide age range, 29 and 54. What both patients had in common was that they had thyroid cancer, and both had a family history of breast cancer and papillary thyroid carcinoma. | |||
http://omim.org/entry/185470#0015<br> | |||
Line 124: | Line 127: | ||
<!--- Include the sequences of your forward and reverse primers. Explain why a disease allele will give a PCR product and the non-disease allele will not. ---> | <!--- Include the sequences of your forward and reverse primers. Explain why a disease allele will give a PCR product and the non-disease allele will not. ---> | ||
<br>Reverse Primer: | |||
5’-CCACACTCCTGGCAATCATCT-3’ | |||
Forward Primer: | |||
5’-GAAGGATGAACCTCAGGAGG-3’ (cancer primer) | |||
A diseased allele will give the PCR a product because the primer that is given is specific for the disease. The primer will attach itself to the single stranded DNE at a sequence that matches the primer. If there is a replication as a product of a real time PCR run, then the DNA is positive for the cancer mutation and disease. If no replication takes place then the DNA is negative for the cancer mutation and disease.<br> | |||
Line 131: | Line 141: | ||
<!--- Include an illustration that shows how your system's primers allow specific amplification of the disease-related SNP ---> | <!--- Include an illustration that shows how your system's primers allow specific amplification of the disease-related SNP ---> | ||
[[image:BME_103_Lab_2.jpg|600px]] | |||
<!-- ##### DO NOT edit below this line unless you know what you are doing. ##### --> | <!-- ##### DO NOT edit below this line unless you know what you are doing. ##### --> | ||
|} | |} | ||
L |
Latest revision as of 08:25, 29 November 2012
BME 103 Fall 2012 | Home People Lab Write-Up 1 Lab Write-Up 2 Lab Write-Up 3 Course Logistics For Instructors Photos Wiki Editing Help | ||||||||||||||||||||||||||||||||
OUR TEAMLAB 2 WRITE-UPThermal Cycler EngineeringOur re-design is based upon the Open PCR system originally designed by Josh Perfetto and Tito Jankowski.
Key Features With the changes incorporated with the re-design of the Open PCR machine, the main design changes were to the LCD display screen, front side wall, and to the motherboard. The changes would involve moving the location of the LCD display screen to the front side wall as well as adding buttons to the the wall that allow the Open PCR machine to be programmed instead of inputting the desired parameters into a computer with a USB cable. In order for the program to be on the machine itself, the motherboard would have to be re-programmed so that a computer connected to the Open PCR machine with a USB would no longer be needed to run the machine. Instructions The instructions on how to build the machine would be relatively the same as the before except for a few small changes. The front side wall would have to have a few more instructions to incorporate the LCD screen on it as well as the buttons used to program the machine. Besides that, the instructions to build the Open PCR machine would be the same as before.
ProtocolsMaterials Cover to go over PCR machine || 1
PCR Protocol
Research and DevelopmentBackground on Disease Markers
http://omim.org/entry/185470#0015
Primer Design
Forward Primer: 5’-GAAGGATGAACCTCAGGAGG-3’ (cancer primer) A diseased allele will give the PCR a product because the primer that is given is specific for the disease. The primer will attach itself to the single stranded DNE at a sequence that matches the primer. If there is a replication as a product of a real time PCR run, then the DNA is positive for the cancer mutation and disease. If no replication takes place then the DNA is negative for the cancer mutation and disease.
Illustration |
L