BME103:T130 Group 6 l2

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Owwnotebook icon.png BME 103 Fall 2012 Home
Lab Write-Up 1
Lab Write-Up 2
Lab Write-Up 3
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Name: Jocelynn Christensen
Role: R & D Scientist
Name: Ryan Uchimura
Role: Experimental Protocol Planner/Coolest person ever
Name: Sam Zimmerman
Role: OpenPCR Machine Engineer)
Name: Adam Helland
Name: Dakota Styck


PCR Machine Improvements

Design Goals:
Expand Sample Size; which will increase efficiency
Add Tabs to the Bottom of the Lid; this will make it so that the user knows when the lid is on completely without crushing the samples.

Thermal Cycler Engineering

Our re-design is based upon the Open PCR system originally designed by Josh Perfetto and Tito Jankowski.

System Design

Key Features



Supplied in the Kit

PCR Flourimeter
gloves/labcoat - 1 flourimeter - 1
PCR machine - 1 Box - 1
Pipets - 8 Smartphone holder - 1
PCR reaction mix - 8 tubes, 50 μL each
PCR holding tray - 1

Supplied by User

PCR Flourimeter
Computer - 1 Smartphone/Camera - 1
DNA - 8 samples Image J Software - 1

PCR Protocol

DNA Measurement Protocol
1. Take the file box and place it upside down (after it's been emptied) so that there is now an area that will restrict as much light as possible from coming through in the pictures.
2. Place the hydrophobic slide in the center of the fluorimeter and align it so that the row of dots is directly in the middle of the blue lazer.
3. Using a pipet, place two droplets of water gently on the middle hole of the slide.
4. Next use the pipet to add two droplets of the PCR solution for the first sample with the two water droplets. This must be done cautiously so that the droplets will stay in the center and adhere to each other properly.
5. Turn on the light source on and place the fluorimeter as far back as possible inside the upside down box.
6. Turn the camera on a smart phone and adjust the settings accordingly. Inactivate the flash, set iso to 800 (or higher if possible), set white balance to auto, exposure to the highest setting, saturation to highest setting and contrast to the lowest setting.
7. Place a smartphone camera into the cradle and then move the cradle in front of the fluorimeter at the perfect distance for good resolution (may take some adjusting).
8. Take a picture of the mixture on the fluorimeter (best done if camera is on a timer so that you can fully close the box and avoid excess light exposure.
9. Repeat steps 2-8 for each sample.

1. Download the Image J software
2. Open Image J
3. To chose your pictures click 'file' and 'open' then select the image you wish to analyze
3. Once your image is opened highlight and click on "analyze", "set measurements", and check the boxes "area" "integrated density" and "mean gray value" in order to just analyze the pieces for this lab.
4. After this you have to highlight and click "image", "color", then click "split channels"
5. This splits the image you have into three new images. For this assignment just keep the image "green" and disregard the others.
6. Then analyze the droplet in the picture to get the info for integrated density, mean gray value, and area.
7. Repeat steps for one picture of each sample.
8. Save your data in an excel page for easy access at another time

Research and Development

Background on Disease Markers

Primer Design