BME103:T130 Group 11

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: Timothy Peterson R and D Name: Sharon Gooi Role: Experimental Protocol Planner Name: student Role(s) Name: student Role(s) Name: student Role(s) Name: student Role(s) LAB 1 WRITE-UP Initial Machine Testing The Original Design The PCR machine heats up the DNA so that enzymes can "unzip" the two strands of DNA. This process happens in cycles so that the DNA will seperate and duplicate a multitude of times. A certain amount of primer is used to duplicate the DNA specific to the amount of original DNA. By amplifying the amount of DNA, a proper diagnosis of a certain gene can be made. Experimenting With the Connections When we unplugged the LCD screen from the circuit board, the machine's screen shut off. When we unplugged the white wire that connects the circuit board to tube PCR block, the machine stopped reading the temperature. Test Run We first tested the PCR machine on the 18th of October, 2012. The LCD screen readings matched the reading on the computer PCR program, and the machine worked well and efficiently. 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 During Week 2, there were eight samples that PCR was run on. These samples consisted of a positive control, a negative control, three samples from Patient 1 and three samples from Patient 2. Patient 1 ID #: 11640 Gender: Female Age: 54 years old Patient 2 ID #: 29292 Gender: Male Age: 63 years old Flourimeter Measurements Tubes Description Eppendorf Tube Label Pipette Label Positive Control + + Negative Control - - Patient 1 Sample 1 1a 1a Patient 1 Sample 2 1b 1b Patient 1 Sample 3 1c 1c Patient 2 Sample 1 2a 2a Patient 2 Sample 2 2b 2b Patient 2 Sample 3 2c 2c DNA Measurement Operator: Smartphone Image Number 2 Drops SYBRGr 2 Drops Comments (insert data here) (insert data here) (Insert data here) (insert data here) (insert data here) (insert data here) (Insert data here) (insert data here) (insert data here) (insert data here) (Insert data here) (insert data here) (insert data here) (insert data here) (Insert data here) (insert data here) (insert data here) (insert data here) (Insert data here) (insert data here) (insert data here) (insert data here) (Insert data here) (insert data here) (insert data here) (insert data here) (Insert data here) (insert data here) (insert data here) (insert data here) (Insert data here) (insert data here) (insert data here) (insert data here) (Insert data here) (insert data here) (insert data here) (insert data here) (Insert data here) (insert data here) ImageJ Software Processor Sample or Background ID Area and x, y, w, h, info Mean Pixel Value INTDEN RAWINTDEN INTDEN (IF DIFFERENT) (insert data here) (insert data here) (Insert data here) (insert data here) (insert data here) (insert data here) (insert data here) (Insert data here) (insert data here) (insert data here) (insert data here) (insert data here) (Insert data here) (insert data here) (insert data here) (insert data here) (insert data here) (Insert data here) (insert data here) (insert data here) (insert data here) (insert data here) (Insert data here) (insert data here) (insert data here) (insert data here) (insert data here) (Insert data here) (insert data here) (insert data here) (insert data here) (insert data here) (Insert data here) (insert data here) (insert data here) (insert data here) (insert data here) (Insert data here) (insert data here) (insert data here) (insert data here) (insert data here) (Insert data here) (insert data here) (insert data here) (insert data here) (insert data here) (Insert data here) (insert data here) (insert data here) (insert data here) (insert data here) (Insert data here) (insert data here) (insert data here) (insert data here) (insert data here) (Insert data here) (insert data here) (insert data here) (insert data here) (insert data here) (Insert data here) (insert data here) (insert data here) (insert data here) (insert data here) (Insert data here) (insert data here) (insert data here) (insert data here) (insert data here) (Insert data here) (insert data here) (insert data here) (insert data here) (insert data here) (Insert data here) (insert data here) (insert data here) Data Analyzer Description INTDEN with background subtracted DNA Concentration, micrograms/ml WATER BLANK 0 DNA CALF THYMUS, 2 microg/ml 2 (Insert) (insert) (Insert) (Insert) (insert) (Insert) (Insert) (insert) (Insert) (Insert) (insert) (Insert) (Insert) (insert) (Insert) (Insert) (insert) (Insert) (Insert) (insert) (Insert) Research and Development Specific Cancer Marker Detection - The Underlying Technology PCR helps to detected certain types of genes. In this case it is used to find out a specific type of cancer. In the process of detecting the cancer, primers are made to compliment a DNA strand that has the cancer gene in it. If a subject has the cancer in their DNA, the primers will bind to strand, whereas a subject without the cancer would not have a primer attach to their DNA strand. The r1787996 SNP is linked to the cancer sequence. The codon ATC is the sequence for cancer where the ATT means there is no cancer. In PCR, the ATC cancer sequence is detected because the primers will only attach to the DNA strands that have the ATC sequence. The ATT, non-cancer, strands will not bind with the primers. Only the combined primer DNA strand will be detected thus alerting 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 (Your group will add the results of your Fluorimeter measurements from Week 4 here)