BME103:T130 Group 10

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(OUR TEAM)
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| [[Image:BME103student.jpg|100px|thumb|Name: Jeffery Ramirez<br>Protocol Planner]]
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| [[Image:BME103student.jpg|100px|thumb|Name: Jeffery Ramirez<br>Role: Protocol Planner]]
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| [[Image:BME103student.jpg|100px|thumb|Name: Tyler Tamasauckas <br>R&D Specialist]]
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| [[Image:BME103student.jpg|100px|thumb|Name: Tyler Tamasauckas <br>Role: R&D Specialist]]
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| [[Image:BME103student.jpg|100px|thumb|Name: Alexander Baldwin <br>Open PCR Machine Engineer]]
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| [[Image:BME103student.jpg|100px|thumb|Name: Alexander Baldwin <br>Role: Open PCR Machine Engineer]]
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| [[Image:BME103student.jpg|100px|thumb|Name: Frances Lakers<br>R&D Specialist; Data Analyzer]]
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| [[Image:BME103student.jpg|100px|thumb|Name: Frances Lakers<br>Role: R&D Specialist; Data Analyzer]]
| [[Image:BME103student.jpg|100px|thumb|Name: student<br>Role(s)]]
| [[Image:BME103student.jpg|100px|thumb|Name: student<br>Role(s)]]
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Revision as of 20:52, 14 November 2012

BME 103 Fall 2012 Home
People
Lab Write-Up 1
Lab Write-Up 2
Lab Write-Up 3
Course Logistics For Instructors
Photos
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Contents

OUR TEAM

Name: Jeffery RamirezRole: Protocol Planner
Name: Jeffery Ramirez
Role: Protocol Planner
Name: Tyler Tamasauckas Role: R&D Specialist
Name: Tyler Tamasauckas
Role: R&D Specialist
Name: Alexander Baldwin Role: Open PCR Machine Engineer
Name: Alexander Baldwin
Role: Open PCR Machine Engineer
Name: Frances LakersRole: R&D Specialist; Data Analyzer
Name: Frances Lakers
Role: R&D Specialist; Data Analyzer
Name: studentRole(s)
Name: student
Role(s)

LAB 1 WRITE-UP

Initial Machine Testing

The Original Design
(Add image of the full OpenPCR machine here, from the Week 3 exercise. Write a paragraph description for visitors who have no idea what this is)
The OpenPCR machine is designed to isolate and replicate certain sequences of DNA through heating and cooling the samples. There are several parts to it, most of which can only be seen if one of the outside walls is taken out. The samples of DNA are placed in small tubes and are then placed in the heating area, where they are repeatedly heated and cooled during several cycles to achieve the desired result. The time for a cycle is usually a few minutes, and there are usually several cycles in a run, so it may last over an hour.

Experimenting With the Connections

When the circuit board (part 6) was unplugged from the display (part 3), the display turned off and no longer registered any signal. The display was no longer functional, but turned on again once the wire between the two parts was reconnected.

When the circuit board was unplugged from the heating element, the heating element was no longer able to control its temperature. Although it still had power, it was not being controlled by the circuit board.


Test Run

The first test run completed on the OpenPCR machine was on October 25, 2012. The test was successful, and was completed in roughly the time expected, give or take a few minutes. Once the settings were put to the correct levels, the set up was quite simple. The samples were placed inside the heating unit, then the test run started. It took over an hour, but was completed successfully with no malfunctioning pieces of equipment.




Protocols

Polymerase Chain Reaction

1.)HOW PCR WORKS

The Polymerase Chain Reaction machine, PCRm for short, works by cycling DNA through different temperatures to amplify the desired strand so the sample can be compared with other DNA. First, the DNA is denatured by heating the samples to such temperature that the hydrogen bonds holding the double-stranded molecule together are broken. The sample is then cooled, which allows a primer to bind to the target DNA. In the third step, the sample is heated back up so an enzyme can replicate the DNA. In the final step, a fluorescent dye binds to the new double-stranded DNA. This process is repeated many times, amplifying the target strand to an analyzable quantity.

2.)STEPS TO AMPLIFY DNA

The actual steps for PCR are quite simple.

Step 1. The PCRm lid is heated to 100°C and the sample tubes are heated to 95°C. This temperature is held constant for 3 minutes.

Step 2. The PCRm is then set to run 30 consecutive temperature cycles. Each cycle consists of heating to 95°C for 30 seconds, cooling to 57°C for 30 seconds, and finally, heating to 72°C for 30 seconds.

Step 3. After the series of cycles is completed, the PCRm temperature is then held at 72°C for 3 minutes.

Step 4. The PCRm is then kept constant at 4°C

3.)COMPONENTS OF PCR MIX

4.)TABLE OF REAGENTS AND VOLUMES USED

5.)SAMPLE DESCRIPTIONS


Fluorimeter Measurements


1.)PHOTO OF SETUP

2.)STEPS TO ASSEMBLE THE FLUORIMETER

To assemble the Fluorimeter, there are a few easy steps that need to be followed. The first step is to unbutton the front flaps and open the lid. Take out the interior contents which include the slide that the liquid is put on and the cell phone stand. Once this is done, close the lid so that only the front is open. Place your liquid on the slide, turn on the light and place it inside the box. Then put a cell phone with a camera in the cell phone stand. Align the camera with the drop of liquid on the slide. After this step, the Fluorimeter is set up. Refer to the image above for a photo representation of the set up.

3.)USING IMAGE J




Research and Development

Specific Cancer Marker Detection - The Underlying Technology

(Add a write-up of the information discussed in Week 3's class)

(BONUS points: Use a program like Powerpoint, Word, Illustrator, Microsoft Paint, etc. to illustrate how primers bind to the cancer DNA template, and how Taq polymerases amplify the DNA. Screen-captures from the OpenPCR tutorial might be useful. Be sure to credit the source if you borrow images.)




Results

Sample Integrated Density DNA μg/mL Conclusion
PCR: Negative Control E6 F6 G6
PCR: Positive Control E7 F7 G7
PCR: Patient 1 ID #####, rep 1 E8 F8 G8
PCR: Patient 1 ID #####, rep 2 E9 F9 G9
PCR: Patient 1 ID #####, rep 3 E10 F10 G10
PCR: Patient 2 ID #####, rep 1 E11 F11 G11
PCR: Patient 2 ID #####, rep 2 E12 F12 G12
PCR: Patient 2 ID #####, rep 3 E13 F13 G13


KEY

  • Sample =
  • Integrated Density =
  • DNA μg/mL =
  • Conclusion =


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