BME103:T130 Group 5 l2

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Contents

OUR TEAM

Name: Wade PatrickMachine Engineer
Name: Wade Patrick
Machine Engineer
Name: Liann KleinMachine Engineer
Name: Liann Klein
Machine Engineer
Name: Haylee PoncyProtocol Planner
Name: Haylee Poncy
Protocol Planner
Name: Kyle LabbanProtocol Planner
Name: Kyle Labban
Protocol Planner
Name: Alexandria LamR&D Scientist
Name: Alexandria Lam
R&D Scientist

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.


System Design


Key Features


Instructions





Protocols

Materials

Supplied in the Kit Amount
PCR Machine 1
Extra screws 5
CD containing programming application 1
Operations instruction manual 1
10 ft Extension cord 1


Supplied by the User Amount
Standard sized test tubes 16
DNA Primer Amounts vary per experiment
DNA Samples Amounts vary per experiment
Computer 1
Pipettes 16
Sybr Green Amounts vary per experiment
Refrigerator 1
Power source N/A

PCR Protocol

Create a step-by-step procedure for setting up and running PCR reactions. Your instructions should include everything from adding reagents to the tubes, to programming the PCR machine and running the reaction.


DNA Measurement Protocol 1. Collect samples generated from "PCR Protocol". 2. Using separate pipettes for each individual sample, transfer the 150μL into the larger test tubes containing the proper solution. 3. Using the fluorimeter equiptment, add two drops of each sample, followed by two drops of SYBR green. 4. Close the system down, preventing any light from entering the system, and record a photo to visually measure the presence of a positive or negative result. 5. Using a different pipette, clear the sample from the glass tray, move the tray forward, and repeat with the next sample. 6. Continue until all samples have been measured and photographed.

Research and Development

Bayesian statistics

A=Alzheimer's B=Positive test Result

P(A / B) = P(B / A)P(A) / P(B)

Background on Disease Markers

An SNP related to Alzheimer's disease is rs1466662 (http://www.ncbi.nlm.nih.gov/projects/SNP/snp_ref.cgi?rs=1466662). It is located on chromosome four, the intron region of NM_001142552.1 and arises from a missense mutation replacing an A with a T. It is the most significant SNP outside of the SNP linked to APOE.


Primer Design


The backwards primer is TAT TTT TAG AAG CGA TAA AA. The forwards primer is GCC TCT TTG CCC TCT GTT TT. An allele not containing the disease will not have the sequence that allows the primers to bind. If the primers cannot bind, then that means Taq polymerase does not know where to bind. If Taq polymerase does not bind, then the sequence does not get replicated.


Illustration



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