BME103 s2013:T900 Group4

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BME 103 Spring 2013 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: student: Kinjal Ahir Role(Experimental protocol planner)
Name: student: Kinjal Ahir Role(Experimental protocol planner)
Name: Zach Young, Role:Initial Machine Testing
Name: Zach Young, Role:Initial Machine Testing
Name: Amelia LaxResearch and Development
Name: Amelia Lax
Research and Development
Name: studentRole(s)
Name: student
Role(s)
Name: studentRole(s)
Name: student
Role(s)
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 9 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

Thermal Cycler Program

DNA Sample, 50 μL each: patient ID's from the UnderGrad Teaching Assistant(UGTA).

Positive control Patient 1 Patient 1 Patient1
cancer DNA template ID: 85158 ID: 85158 ID: 85158
Replicate 1 Replicate 2 Replicate 3
Tube label: A+ Tube label: B1 Tube label: C1 Tube label: D1
Negative Control: no Patient 2 Patient 2 Patient 2
DNA template ID: 17818 ID: 17818 ID: 17818
Replicate 1 Replicate 2 Replicate 3
Tube label: A- Tube label: B2 Tube label: C2 Tube label: D2

DNA Sample Set-up Procedure

  1. Step 1: Student were Provided with 8 tubes of 50 μL PCR reaction mix, 8 tubes of 50 μL diluted template + primers, and disposable transfer pipettes.
  2. Step 2: Protocol planner labeled the test tube that is provided above.
  3. Step 3: 50μL of each DNA sample Mix in to test tube.
  4. Step 4: Protocol planner set up the DNA and ran the PCR reactions.


PCR Reaction Mix

  • In the PCR reaction mix there is Mix contains Taq DNA polymerase, MgCl2, dNTP's, forward primer, reverse primer.

DNA/ primer mix

  • In the DNA/ primer mix there is patient's DNA.






Research and Development

Basic DNA components:

DNA Template
DNA Polymerase
DNA Primers
Nucleotides

Procedure:
First, the components are combined and heated. Once the reaction is heated to a temperature of 95 degrees Celsius, the hydrogen bonds between the DNA strands break and create two separate DNA sequences. After that, leave it to cool down to a temperature of around 55 degrees Celsius. This allow the DNA polymerase is going the bind the DNA sequence with the DNA Primer with hydrogen bonding. Once, the DNA polymerase is bound, it is going to take some of the free nucleotides from the surrounding area and complete the DNA strand. The result is a two separate DNA sequences, with two DNA strand identical to the first one. Repeatedly doing the steps multiple times and the result will give a total of 4 double DNA strands, and so on...

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.)





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