BME103:T130 Group 7 l2: Difference between revisions
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| [[Image:EmilyBMElab.jpg|100px|thumb|Name: Emily Thompson<br>Research & Development Scientist<br>]] | | [[Image:EmilyBMElab.jpg|100px|thumb|Name: [http://openwetware.org/wiki/User:Emily_Thompson Emily Thompson]<br>Research & Development Scientist<br>]] | ||
| [[Image:vivwiki.jpg|100px|thumb|Name: Vivian Benjes<br>Experimental Protocol Planner/ Research & Development<br>]] | | [[Image:vivwiki.jpg|100px|thumb|Name: [http://openwetware.org/wiki/User:Vivian_Rose_Benjes Vivian Benjes]<br>Experimental Protocol Planner/ Research & Development<br>]] | ||
| [[Image:francesfbook.jpg|100px|thumb|Name: Frances Marrett<br>Experimental Protocol Planner/ Editor<br>]] | | [[Image:francesfbook.jpg|100px|thumb|Name: Frances Marrett<br>Experimental Protocol Planner/ Editor<br>]] | ||
| [[Image:ChrisBMElab.jpg|100px|thumb|Name: [http://openwetware.org/wiki/User:Christopher_M._Glass Chris Glass]<br>Open PCR Machine Engineer/ Experimental Protocol Planner<br>]] | | [[Image:ChrisBMElab.jpg|100px|thumb|Name: [http://openwetware.org/wiki/User:Christopher_M._Glass Chris Glass]<br>Open PCR Machine Engineer/ Experimental Protocol Planner<br>]] | ||
| [[Image:RyanBMElab.jpg|100px|thumb|Name: | | [[Image:RyanBMElab.jpg|100px|thumb|Name: [http://openwetware.org/wiki/User:Ryan_T._Frantz Ryan Frantz]<br>Open PCR Machine Engineer<br>]] | ||
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==Thermal Cycler Engineering== | ==Thermal Cycler Engineering== | ||
Our re-design is based upon the [http://openpcr.org Open PCR] system originally designed by Josh Perfetto and Tito Jankowski.<br> | Our [http://www.youtube.com/watch?v=MJY70uV4qbI&feature=youtu.be re-design] is based upon the [http://openpcr.org Open PCR] system originally designed by Josh Perfetto and Tito Jankowski.<br> | ||
Latest revision as of 12:20, 5 December 2012
BME 103 Fall 2012 | Home People Lab Write-Up 1 Lab Write-Up 2 Lab Write-Up 3 Course Logistics For Instructors Photos Wiki Editing Help | |||||
OUR TEAMLAB 2 WRITE-UPThermal Cycler EngineeringOur re-design is based upon the Open PCR system originally designed by Josh Perfetto and Tito Jankowski.
ProtocolsMaterials
Thermal Cycler for PCR reaction Supplied by User Sterile gloves PCR Protocol Polymerase Chain Reaction
DNA Measurement Protocol
To analyze the DNA samples after they've been amplified, a fluorimeter can be used. The Fluorimeter aparatus consists of a hydrophobic Teflon surface on a glass slide. There is an array of 3x10 glass wells on the surface to anchor drops in position for photographing. First, two drops of the cybergreen solution should be placed with a sterile pipet. Then two drops of amplified sample DNA should be added to the cybergreen solution with another sterile pipet. It is important to place the DNA on top of the cybergreen in order to achieve the best results and to avoid contamination of the DNA samples. The drops should then be photographed in the provided dark box with the door shut to eliminate excess background light. The slide was then moved back by two columns for the next sample. This procedure can be replicated for each of the samples. A smartphone with adjustable settings can be used to take a photo of the samples. To achieve the best results the following settings should be used. - Exposure to highest setting Picture Analysis: The pictures of each sample should be analyzed using the "image j" software. This software is open source and can be obtained free of charge. The pictures, taken with the settings listed above, can be uploaded to the "image j" software then the images can be separated into their composite colors, red, blue, and green. The green portion of the images can then analyzed using the analyze option in the software and its "INTDEN" can be recorded. Interpreting results: The cybergreen solution allows the amount of DNA in a sample to be determined by its "INTDEN". The cybergreen glowed green in the presence of DNA and while this glow is not visable to the naked eye, the smart phone in conjunction with "image j" is able to quantify the luminosity in terms of the "INTDEN". The brighter samples contain more DNA and have higher "INTDEN" value. This indicates that the sample reacted with the primers better. By providing positive and negative controls in the experiment the various samples can be compared and their reaction to the PCR primer can be determined. Research and DevelopmentBackground on Disease Markers
Primer Design Normal bp sequence: bp sequence with Alzheimer's associated SNP:
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