BME103 s2013:T900 Group4 L3

BME 103 Spring 2013	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: Kinjal Ahir Role:Protocol Name: Student Role(s) Name: Student Role(s) Name: Student Role(s) Name: Amelia Lax Research and Design LAB 3 WRITE-UP Original System: PCR Results PCR Test Results Sample Name Ave. INTDEN* Calculated μg/mL Conclusion (pos/neg) Positive Control --- --- N/A Negative Control --- --- N/A Tube Label:___ Patient ID: ____ rep 1 --- --- --- Tube Label:___ Patient ID: ____ rep 2 --- --- --- Tube Label:___ Patient ID: ____ rep 3 --- --- --- Tube Label:___ Patient ID: ____ rep 1 --- --- --- Tube Label:___ Patient ID: ____ rep 2 --- --- --- Tube Label:___ Patient ID: ____ rep 3 --- --- --- * Ave. INTDEN = Average of ImageJ integrated density values from three Fluorimeter images Bayesian Statistics These following conditional statistics are based upon all of the DNA detection system results that were obtained in the PCR lab for 20 hypothetical patients who were diagnosed as either having cancer or not having cancer. Bayes Theorem equation: P(A|B) = P(B|A) * P(A) / P(B) Calculation 1: The probability that the sample actually has the cancer DNA sequence, given a positive diagnostic signal. A = [text description] = [frequency shown as a fraction] = [final numerical value] B = [text description] = [frequency shown as a fraction] = [final numerical value] P (B|A) = [text description] = [frequency shown as a fraction] = [final numerical value] P(A|B) = [answer] Calculation 3: The probability that the patient will develop cancer, given a cancer DNA sequence. A = [text description] = [frequency shown as a fraction] = [final numerical value] B = [text description] = [frequency shown as a fraction] = [final numerical value] P (B|A) = [text description] = [frequency shown as a fraction] = [final numerical value] P(A|B) = [answer] New System: Design Strategy We concluded that a good system Must Have: - Result easy to determine. - Simple OpenPCR Software: The OpenPCR Software shoulder be simple and easy to use and that would help lab experiments done faster, rather than the need to spend extra time to figure out how the software works. We concluded that we would Want a good system to have: - Low cost: OpenPCR $599 Fluorimeter $300. A low cost material would help since there is always a limited budge for the research experiment. This would allow us to buy more OpenPCR and fluorimeter and create more data results in the same amount of time. Phone camera should not be easily moveable when played in front of the fluorimeter. Phone camera adjustment can be time consuming and not setting it in the correct position/distance results data error. We concluded that a good system Must Not Have: - Troublesome USB Connectivity. USB connectivity should function well in order for OpenPCR machine to work. - Easy to mix drops during imaging. We concluded that a good system Should Avoid: - Avoid slow amplification. - Hard to adjust phone/ fluorimeter. The phone can be easily moved by accident, which requires readjustment between the phone and the fluorimeter. New System: Machine/ Device Engineering SYSTEM DESIGN We decided to have some addition of the fluorimeter to allow easy adjustment and positioning of the phone. The benefit of this addition is that it will help save time to try to readjust the phone in the correct position, and that photos can be taken better and more accurate, which give better and accurate data results. KEY FEATURES This new device will hold the camera phone in place. It will be able to connect temporarily to the fluorimeter, allowing the phone to be held in place. The device will also have an adjustable distance from the phone to the fluorimeter, as well as the height for more compability of other different phones, without trying to adding more heights to the phone or the fluorimeter. INSTRUCTIONS Step 1: Connect the base to the fluorimeter. Step 2: Set the camera phone into the base. Step 3: Set the height and distance. Step 4: Take Photo. New System: Protocols DESIGN We chose to add an extra device to the fluorimeter. However, protocols should remain the same. MATERIALS Supplied in the Kit Amount Smart phone 1 Reaction mix given more for more reactions Battery Software Supplied in the User Amount Filter water SYBR Green Primers DNA sample (negative and positive) PROTOCOLS PCR Protocol Step 1: Reaction mix Step 2: Add 2.5 μL of negative and positive DNA sample Step 3: Fluorometer gave the sample result DNA Measurement and Analysis Protocol Step 1: Set up the equipment Step 2: Put the smart phone and fluorometer in the dark box Step 3: Major the distance between the fluorometer and phone. Step 4: Run the samples Step 5: Take a picture of the experiment Step 6: Repeat this trial with different samples Step 7: Use Image J and make a circle around the drop. New System: Research and Development BACKGROUND DESIGN Primers for PCR Our primers address the following design needs Design specification 1 - explanation of how an aspect of the primers addresses any of the specifications in the "New System: Design Strategy" section Design specification 2 - explanation of how an aspect of the primers addresses any of the specifications in the "New System: Design Strategy" section Etc. New System: Software [THIS SECTION IS OPTIONAL. If your team has creative ideas for new software, and new software is a key component included in your new protocols, R&D, or machine design, you may describe it here. You will not receive bonus points, but a solid effort may raise your overall page layout points. If you decide not to propose new software, please delete this entire section, including the ==New System: Software== header.]