Difference between revisions of "BME103:T930 Group 9 l2"

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(Thermal Cycler Engineering)
(Research and Development)
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Chromosome 14<br>
Chromosome 14<br>

Revision as of 11:32, 28 November 2012

Owwnotebook icon.png 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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Devraj Patel
Open PCR Machine Engineer
Brandon Simmons
Open PCR Machine Engineer
Andrew Hensley
Experimental Protocol Planner
Nathalie Vitale
Experimental Protocol Planner
Ojeen Korkes
Research and Development Scientist


Thermal Cycler Engineering

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

System Design
Open PCR Gen 2
BRANDON'S lab 2.png

Key Features
We introduced two new designs to create a machine that would allow to the PCR machine to be more portable and reduce the need for external equipment besides the machine itself.

The first of the two features is a better performing LCD screen with attached four analog buttons on the bottom of screen that allow for the programmer to program the machine and eliminate the need of a computer to program. The four analog buttons will include: Increase, Decrease, Temp/Time, Start/Stop/Restart. These buttons will allow the programmer to prepare a PCR experiment sequence without the use of external equipment, such as a computer equipped with PCR software. These buttons will be placed directly below the LCD screen, so that they can be easily accessible and usable.

The second of the two features includes a new internal PCR Board, which is configured with the new LCD screen. Since the programmer will now be able to change the program on the machine itself, the internal PCR Board will have to be modified to allow the program to be stored and set in the PCR Board. The changes that need to be taken with this equipment are to wire the buttons from the LCD screen to the PCR Board, so that the inputs by the user can be recognized by the system and the PCR board will also need a new program implemented into the system that can understand the user inputs as well. With these small design changes, we will eliminate the reliance on other technologies to operate the machine and increase its overall mobility.

To add these design changes, first, the previous LCD screen would need to be removed and new space must be cut out for the larger screen with attached buttons, underneath the LCD screen space that is already there. Second, the wiring for the new screen must be taken care of for the user's inputs to be read. So, we must attach the new screen to the previous cable attaching the previous LCD screen and create wiring that connects the four buttons to the new PCR board. Thirdly, we must take out the PCR board and install the modified PCR board using previous mounting spots, allowing for the program to be set and stored in the internal memory of the new PCR board. Remembering to install the new wiring with both the new LCD screen and the analog buttons, we can reassemble machine and test for operating efficiency.



PCR Protocol

DNA Measurement Protocol

Research and Development

Background on Disease Markers

1) Emphysema is a lung disease; it causes damage to the small air sacs, alveoli, and small airways in your lungs. This damage obstructs airflow when a patient with Emphysema exhales. “Most emphysema cases are caused by smoking, but about 3 percent of cases are caused by an inherited deficiency in a protein that normally protects the alveoli.” This protein is alpha-1 antitrypsin[1]. Moreover, Emphysema is characterized by loss of elasticity due to the action of alpha-1 antitrypsin deficiency.

The marker that is being used is rs709932[2].This SNP is associated with Emphysema due to AAT deficiency. The sequence associated with Emphysema due to AAT deficiency is C(A)T , while a normal sequence is C(G)T, which is located on the 14 chromosome. The gene alteration leads to a mutated human protein. It goes from R[Arg] to H[His].

Emphysema due to AAT deficiency
Missense CGT→CAT
Chromosome 14

2) Hemophilia A is an inherited disease that is considered to be a rare blood disorder. It is the most common type of hemophilia. Patients with Hemophilia A suffer longer bleeding and thus, it can damage their tissues and organs. “It is also known as factor VIII deficiency or classic hemophilia.” Sometimes this disease may lead to death. Patients don’t clot normally because a protein needed to form blood clot is missing or reduced. “Approximately one in 5,000 males born in the United States has hemophilia." [3].

The marker that is being used is rs137852466 [4]. This SNP is associated with Hemophilia A. The sequence associated with Hemophilia A is C(G)C , while a normal sequence is C(A)C, which is located on the X chromosome.The gene alteration leads to a mutated human protein. It goes from R[Arg] to H[His].

Hemophilia A
Missense CGC→CAC
Chromosome X

Primer Design

1.) Forward primer:5" TTGGCCTCTTCGGTGTCCCC 3" ( at position 75849051 )
Reverse primer: 5" GAACTCCTCC[C]TACCCTCAA 3"

2.) Forward primer:5" TGCTGGTTTTAGCACTGACA 3" (at position 5009175)
Reverse primer:5" GCACTCTTC[C]CATGGAGTTG 3"


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