BME103:T930 Group 6 l2

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Contents

OUR TEAM

Name: Nicholas SterkowitzOpen PCR machine engineer
Name: Nicholas Sterkowitz
Open PCR machine engineer
Name: Dominic IlardiOpen PCR machine engineer
Name: Dominic Ilardi
Open PCR machine engineer
Name: Alexandra NazarenoExperimental Protocol Planner
Name: Alexandra Nazareno
Experimental Protocol Planner
Name: Amanda SweigExperimental Protocol Planner
Name: Amanda Sweig
Experimental Protocol Planner
Name: Taylor DeeganResearch and Development(s)
Name: Taylor Deegan
Research and Development(s)

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 PCR Kit Amount
PCR Machine 1
Fluorometer Box 1
Calf Thymus 0.5 mL
SYBR Green (diluted) 1.5 mL
Camera Stand 1
Glass Plates 2
Calibration DNA 0.5 mL
GoTaq Polymerase and Buffer Solution 10 mL
Small Test Tubes 25
Large Test Tubes 25


Supplied by User Amount
Smartphone Camera 1
Laptop 1
ImageJ Download 1
Power Supply 1
DNA Sample At least 3 samples


PCR Protocol

1. Using a micro-pipette, transfer 1.0-1.5 mL of desired DNA sample into at least three test tubes.

2. reagent solution

3. place tubes into holder in PCR machine

4. program cycles on OpenPCR

5. Run reaction


DNA Measurement Protocol

Research and Development

Background on Disease Markers


The SNP chosen for the lab is linked with Alzheimer's disease. Alzheimer's disease is the most common form of dementia. It has no cure and worsens as it progresses. Dementia is a loss of brain function and Alzheime's disease affects memory, thinking, and behavior.The associated SNP's for an increase in risk of Alzheimer's disease is rs1050283, which is located on the 12 chromosome.Information avaliable from the NCBI website: http://www.ncbi.nlm.nih.gov/snp?term=rs1050283


Primer Design


The sequence that is connected with an increase risk of Alzheimer's disease is GGCTGGGCOCGGACATGGAGGACGTG[C/T]GCGGCCGCCTGGTGCAGTACCGCGG. The increase risk comes from the base change C to a T. The reverse primer would be GGAGGACGTG[T]GCGGCCGCCT and the forward primer would be CCTCCTGCAG[A]CGCCGGCGGA. A diseased allele will produce a PCR product because the gene associated with an increase risk that is trying to be tested for will have a T base in place of the normal C base. If the gene has this change in bases then the primers will be able to attach to the strands of DNA because the primers are designed to only attach to that specific sequence.


Illustration


Primer.jpg

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