BME103:T930 Group 9 l2

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 TEAM Devraj Patel Open PCR Machine Engineer Brandon Simmons Open PCR Machine Engineer Andrew Hensley Experimental Protocol Planner Nathalie Vitale Experimental Protocol Planner Ojeen Korkes Research and Development Scientist LAB 2 WRITE-UP Thermal Cycler Engineering Our re-design is based upon the Open PCR system originally designed by Josh Perfetto and Tito Jankowski. System Design Open PCR Gen 2 Key Features We introduced two new designs to create a machine that would allow to the PCR machine to be more portable and reduce the need for external equipment besides the machine itself. One of the features is a better performing LCD screen with attached four analog buttons on the bottom of screen that allow for the programer to program the machine and eliminate the need of a computer to program. Since the programmer will now be able to change the program on the machine itself the internal PCR Board will have to be modified to allow the programe to be stored and set in the PCR Board. With these small design changes will elimnate the reliance on other technologies to operate the machine and increase mobilitly. Instructions To add these design changes first the previous LCD screen would need to be removed and the cut out the space for the screen larger with screen template to allow for the bigger screen with attached buttons. Attach new screen to the previous cable attaching the previous LCD screen. Take out the PCR board and install the modified PCR board using previous mounting spots, allowing for the program to be set and stored in the internal memory of the new PCR board. Reassemble machine and test for operating efficiency. Protocols Materials PCR Protocol DNA Measurement Protocol Research and Development Background on Disease Markers 1) Emphysema is a lung disease; it causes damage to the small air sacs, alveoli, and small airways in your lungs. This damage obstructs airflow when a patient with Emphysema exhales. “Most emphysema cases are caused by smoking, but about 3 percent of cases are caused by an inherited deficiency in a protein that normally protects the alveoli.” This protein is alpha-1 antitrypsin[1]. Moreover, Emphysema is characterized by loss of elasticity due to the action of alpha-1 antitrypsin deficiency. The marker that is being used is rs709932[2].This SNP is associated with Emphysema due to AAT deficiency. The sequence associated with Emphysema due to AAT deficiency is C(A)T , while a normal sequence is C(G)T, which is located on the 14 chromosome. The gene alteration leads to a mutated human protein. It goes from R[Arg] to H[His]. Emphysema due to AAT deficiency rs709932 Missense CGT→CAT R[Arg]→H[His] Chromosome 14 2) Hemophilia A is an inherited disease that is considered to be a rare blood disorder. It is the most common type of hemophilia. Patients with Hemophilia A suffer longer bleeding and thus, it can damage their tissues and organs. “It is also known as factor VIII deficiency or classic hemophilia.” Sometimes this disease may lead to death. Patients don’t clot normally because a protein needed to form blood clot is missing or reduced. “Approximately one in 5,000 males born in the United States has hemophilia." [3]. The marker that is being used is rs137852466 [4]. This SNP is associated with Hemophilia A. The sequence associated with Hemophilia A is C(G)C , while a normal sequence is C(A)C, which is located on the X chromosome.The gene alteration leads to a mutated human protein. It goes from R[Arg] to H[His]. Hemophilia A rs137852466 Missense CGC→CAC R[Arg]→H[His] Chromosome X Primer Design 1.) Forward primer:5" 3" Reverse primer: 5" GAACTCCTCC[C]TACCCTCAA 3" 2.) Forward primer:5" 3" Reverse primer:5" GCACTCTTC[C]CATGGAGTTG 3" Illustration