BME103:T130 Group 5

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! scope="col" |100.0μL
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{| border="1" cellpadding="4"
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!width = "90" colspan = "4"|Sample Description (8 samples)
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|Positive control: cancer DNA template
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|Patient 1: 68754, F, 57y
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|Patient 1: 68754, F, 57y
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|Patient 1: 68754, F, 57y
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|-
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|Negative control: no DNA template
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|Patient 2: 66913, M, 66y
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|Patient 2: 66913, M, 66y
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|Patient 2: 66913, M, 66y
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|}<br><br>
'''Flourimeter Measurements'''<br>
'''Flourimeter Measurements'''<br>

Revision as of 18:53, 1 November 2012

BME 103 Fall 2012 Home
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Lab Write-Up 1
Lab Write-Up 2
Lab Write-Up 3
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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 1 WRITE-UP

Initial Machine Testing

PCR Machine

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)


Experimenting With the Connections

When we unplugged (part 3) from (part 6), the machine ... (did what? fill in your answer)

When we unplugged the white wire that connects (part 6) to (part 2), the machine ... (did what? fill in your answer)


Test Run

(Write the date you first tested Open PCR and your experience(s) with the machine)




Protocols

Polymerase Chain Reaction

Polymerase Chain Reaction (PCR) is a process that uses DNA polymerase to synthesize a large number of copies of a target DNA sequence. PCR is dependent on short DNA fragments called primers. After the DNA has been denatured by heating and then cooled to a temperature suitable for the primers to bind to their complementary sequences, the primers bind to areas adjacent to each side of the targeted DNA sequence. Once the primers are in place, the polymerase extends them into large complimentary strands. The DNA is then denatured once again, then cooled, the primers bind to the complimentary sequence and then the polymerase extends them. Repeating this process results in an exponential amplification of the target DNA sequence.

Amplifying a patient's DNA sample using PCR can be done as follows:

  1. Collect biological samples from patients or target group.
  2. Combine samples with reagents primers to the sample. These primers will enable the DNA to "unzip" and duplicate the target region using the extra base pairs mixed into the solution.
  3. Place the DNA sample and reagents into a PCR machine, and program the machine to carry out the desired sequences.
  4. Allow the machine to cycle. Once complete, collect the amplified DNA and test.



In our experiment, a PCR master mix from Promega containing bacterially derived Taq DNA polymerase, dNTPs, MgCl2 and reaction buffers was used.


Reagent Volume
Template DNA (20 ng) 0.2μL
10μM forward primer 1.0μL
10μM reverse primer 1.0μL
GoTaq master mix 50μL
dH2O 47.8μL
Total Volume 100.0μL



Sample Description (8 samples)
Positive control: cancer DNA template Patient 1: 68754, F, 57y Patient 1: 68754, F, 57y Patient 1: 68754, F, 57y
Negative control: no DNA template Patient 2: 66913, M, 66y Patient 2: 66913, M, 66y Patient 2: 66913, M, 66y


Flourimeter Measurements

(Add your work from Week 3, Part 2 here)




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

(Your group will add the results of your Fluorimeter measurements from Week 4 here)


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