BME103:T130 Group 12 l2
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Lab Write-Up 1
Lab Write-Up 2
Lab Write-Up 3
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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.
Below is the top part of the general body of the PCR machine. It will be altered so buttons can be placed next to the LED screen.
Design changes on the top body part will include changing the layout so that it may fit input buttons that will be connected and programmed internally later. These buttons will allow an individual to set up cycling details and will remove the need of an external computer to run the device.
1. Remove the knob on the lid 2. Once the knob is removed, the bolt will be able to be removed. 3. Lower the bottom heating plate to the desired height 4. Lower the higher heating plate so the difference in space between the two plates was similar as before
For the top body part
1. Attach the part as you would normally 2. Connect the input buttons to the circuit board.
DNA Measurement Protocol
1. With a permanent marker, number your transfer pipettes at the bulbs so that you only use if for one sample. With the permanent marker number your Eppendorf tubes at the top.
2. Transfer each sample seperatly (using one pipette per sample) into an Eppendorf tube containing 400 mL of buffer. Label this tube with the number of your sample. Get your entire sample into this Eppendorf tube. You can use this sample number transfer pipette to place only this sample drop onto the fluorescent measuring device.
3. Take the specially labeled Eppendorf tube containing Sybr Green I using the specifically labeled pipette only place two drops on the first two centered drops as seen on the video.
4. Now take your diluted sample and place two drops on top of the Syber Green I solution drops.
5. Align the light going through the drop, as seen in the video.
6. After setting up the Flourimeter and the samples set a Smartphone’s photo settings to the ones listed. Inactivate the flash Set ISO To 800 (or higher if possible) Set White Balance to Auto Set Exposure to Highest Setting Set Saturation to the Highest Setting Set Contrast to Lowest Setting
7. Place the Flourimeter in the light box.
8. Let the smart-phone operator take as many pictures using the light box as he/she wants. Their goal is to take pictures clear enough so ImageJ can take data from the images.
9. Once they have taken enough photos of that sample give the Flourimeter back to the sample preparer to prepare the next sample.
10. Now either rerun the sample again or discard that sample and it’s pipette. Keep the Sybr Green I labeled pipette.
11. Repeat this procedure for all the samples. You can run 5 samples per glass slide.
12. As the last sample run the water from the scintillation vial as a blank using the same procedure as with the other samples.
Research and Development
Background on Disease Markers
HIV is a virus that causes A.I.D.S. (acquired immunodeficiency syndrome). HIV affects the immune system by attacking specific cells that help the immune system work. These include the T Cells that help the white blood cells fend off bacteria, disease, and viruses. A SNP related HIV is rs1024611 and it affects Chromosome 17. http://www.ncbi.nlm.nih.gov/projects/SNP/snp_ref.cgi?rs=1024611
The primer that can be used to detect HIV is ATA and its reverse TAT. A diseased allele will only give results because of the way the PCR works and how the primers will attach. If the sample has the disease then the primer will attach to the DNA and as the PCR goes through its cycles there will be a multitude of the same DNA strand with the SNP rs1024611. If the sample does not have the disease allele then there will be no interaction with the DNA and the primer, therefore there will be no change from the original and the end results.