BME103:T130 Group 3 l2

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BME 103 Fall 2012 Home
Lab Write-Up 1
Lab Write-Up 2
Lab Write-Up 3
Course Logistics For Instructors
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Name: Serena KaplanResearch and Development
Name: Serena Kaplan
Research and Development
Name: Gabe McInnisOpen PCR Machine Engineer
Name: Gabe McInnis
Open PCR Machine Engineer
Name: Blake EichlerExperimental Protocol Planner
Name: Blake Eichler
Experimental Protocol Planner
Name: Sierra MorrisExperimental Protocol Planner
Name: Sierra Morris
Experimental Protocol Planner
Name: Zazu MoloiOpen PCR Machine Engineer
Name: Zazu Moloi
Open PCR Machine Engineer
Name: Katelin VaughnResearch and Development
Name: Katelin Vaughn
Research and Development


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




PCR Protocol

1.) The DNA samples were heated to ninety-five degrees Celsius (95°C) for one (1) minute to unzip the two single strands.
2.) They were then cooled to fifty-seven degrees Celsius (57°C) for ten (10) seconds and the primers were attached to their matching sequences.
3.) They were then heated back to seventy-two degrees Celsius (72°C) for ten (10) seconds and polymerase extended the DNA strands by attaching the correct free nucleotides in order on the single strands.

GoTaq Mix Components For 100μl reaction volume:
2X GoTaq Colorless Master Mix
10 μM upstream primer
10 μM downstream primer
DNA template
Nuclease-Free Water to

Reagent Volume
Template DNA (20 ng)0.1μL
10μM forward primer0.5μL
10μM reverse primer0.5μL
GoTaq master mix25.0μL
Total Volume50.0μL

DNA Measurement Protocol

Fluorimeter Setup
1.) The lid was first taken off the the box and one of its sides was unbuttoned in order to create a flap.
2.) The box was the flipped upside down in order to create a dark environment for the camera.
3.) A hydrophobic slide was then inserted into the flourimeter.
4.) Finally, the camera phone was placed in the stand.

Fluorimeter Measurements
1.) Label transfer pipettes and tubes
2.) Transfer each sample separately into tube containing 400μl of buffer
3.) Take the specifically labeled tube containing SYBR GREEN 1 and place 2 drops on the first 2 centered drops
4.) Place 2 drops of diluted sample on top of the SYBR GREEN 1 drop
5.) Align light through drop
6.) Take pictures using light box
7.) Repeat for each sample.
8.) Run water as BLANK using same procedure

ImageJ Instructions
1.) Open ImageJ
2.) Click ANALYZE tool bar and select SET MEASUREMENTS
4.) Upload image to ImageJ
5.) Select IMAGE then COLOR and then SPLIT CHANNELS
6.) Only use green channel
7.) Use OVAL tool and select the entire drop of liquid
8.) Go to ANALYZE and then MEASURE
9.) Drag circle to the background of the image
10.) Record results
11.) Repeat if necessary

Research and Development

Background on Disease Markers

Primer Design


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