BME103:T930 Group 6 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 Name: Nicholas Sterkowitz Open PCR machine engineer Name: Dominic Ilardi Open PCR machine engineer Name: Alexandra Nazareno Experimental Protocol Planner Name: Amanda Sweig Experimental Protocol Planner Name: Taylor Deegan Research and Development(s) 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 To begin with we will change the frame from a wooden construction to recycled aluminum. This will maintain the light-weight portability of the machine, but will greatly reduce the fire hazard of heating a wooden box to the required temperatures. We will also add an additional row and column to the heating block to increase the product output without too much change to the overall size or cost of the machine. Key Features Instructions Protocols Materials Supplied in PCR Kit Amount PCR Machine 1 Fluorometer Box 1 Calf Thymus 0.5 mL SYBR Green (diluted) 1.5 mL Camera Stand 1 Glass Plates 2 Calibration DNA 0.5 mL GoTaq Polymerase and Buffer Solution 10 mL Small Test Tubes 25 Large Test Tubes 25 Supplied by User Amount Smartphone Camera 1 Laptop 1 ImageJ Download 1 Power Supply 1 DNA Sample At least 3 samples PCR Protocol 1. Using a micro-pipette, transfer 1.0-1.5 mL of desired DNA sample into at least three test tubes. 2. reagent solution 3. place tubes into holder in PCR machine 4. program cycles on OpenPCR 5. Run reaction DNA Measurement Protocol Research and Development Background on Disease Markers The SNP chosen for the lab is linked with Alzheimer's disease. Alzheimer's disease is the most common form of dementia. It has no cure and worsens as it progresses. Dementia is a loss of brain function and Alzheime's disease affects memory, thinking, and behavior.The associated SNP's for an increase in risk of Alzheimer's disease is rs1050283, which is located on the 12 chromosome.Information avaliable from the NCBI website: http://www.ncbi.nlm.nih.gov/snp?term=rs1050283 Primer Design The sequence that is connected with an increase risk of Alzheimer's disease is GGCTGGGCOCGGACATGGAGGACGTG[C/T]GCGGCCGCCTGGTGCAGTACCGCGG. The increase risk comes from the base change C to a T. The reverse primer would be GGAGGACGTG[T]GCGGCCGCCT and the forward primer would be CCTCCTGCAG[A]CGCCGGCGGA. A diseased allele will produce a PCR product because the gene associated with an increase risk that is trying to be tested for will have a T base in place of the normal C base. If the gene has this change in bases then the primers will be able to attach to the strands of DNA because the primers are designed to only attach to that specific sequence. Illustration