BME103:W930 Group6

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(Add your work from Week 3, Part 1 here)<br>
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Fluorimeter Setup<br>1. Remove Fluorimeter elements from container.<br> 2. Place camera or smartphone into the black stand, creating the camera setup.<br>3. Position camera setup parallel to the LED box so that the camera is shooting along the chanel of the LED box.
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Fluorometer Setup<br>1. Remove Fluorometer elements from container.<br> 2. Place camera or smartphone into the black stand, creating the camera setup.<br>3. Position camera setup parallel to the LED box so that the camera is shooting along the chanel of the LED box.
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[[Image:IMAG0367.jpg|200px|thumb|left|Flourometer Setup Part I]]
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'''Fluorimeter Measurements'''<br>
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'''Fluorometer Measurements'''<br>
==Research and Development==
==Research and Development==

Revision as of 13:59, 12 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

WilliamResearch and Development
William
Research and Development
Name: KimResearch and Development
Name: Kim
Research and Development
Name: AntonioExperimental Protocol Planner
Name: Antonio
Experimental Protocol Planner
Name: JasonExperimental Protocol Planner
Name: Jason
Experimental Protocol Planner
Name: MalcolmExperimental Protocol Planner
Name: Malcolm
Experimental Protocol Planner
Name: JoshMachine Engineer
Name: Josh
Machine Engineer
Name: SairahMachine Engineer
Name: Sairah
Machine Engineer

LAB 1 WRITE-UP

Initial Machine Testing

SolidWorks mock up of Open PCR machine
SolidWorks mock up of Open PCR machine

The Original Design

(Write a paragraph description for visitors who have no idea what this is)





Experimenting With the Connections

When we unplugged the LCD screen (part 3) from the Open PCR circuit board (part 6), the screen went blank the machine had no visual output.

When we unplugged the white wire that connects to the OpenPCR circuit board (part 6) the heating block (part 2, unlabeled), the machine lost temperature output and the arduino could not monitor the heat of the block and had no accurate control over the temperature.




Test Run

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




Protocols

Polymerase Chain Reaction

(Add your work from Week 3, Part 1 here)

Fluorometer Setup
1. Remove Fluorometer elements from container.
2. Place camera or smartphone into the black stand, creating the camera setup.
3. Position camera setup parallel to the LED box so that the camera is shooting along the chanel of the LED box.

Flourometer Setup Part I
Flourometer Setup Part I




Fluorometer Measurements

Research and Development

Specific Cancer Marker Detection - The Underlying Technology

A single nucleotide polymorphism is a variation in a single DNA nucleotide. The four DNA nucleotides are represented using the letters A, T, C and G. These variations occur normally throughout DNA and represent the most common form of genetic variation among people. They occur at a rate of 1 per every 100 to 300 bases along the 3-billion-base human genome. SNPs are point mutations that have been evolutionarily successful enough to recur in a significant proportion of the population of a species. In other words, SNPs are evolutionarily stable, meaning they do not change much from generation to generation. This allows SNPs to be considered highly conserved within the population and therefore serve as ideal biological markers for genetic research. In order for a sequence variation to be classified as a SNP it must occur in at least 1% of the population. Millions of SNPs have been identified in the human genome and cataloged in accessible databases.

SNPs can occur with a gene, which is the coding region of DNA, or in a non-coding region. Because only about 3-5% of DNA actually codes for the production of proteins, most SNPs are found within non-coding regions. Since SNPs can be located near a gene associated with a certain disease, or occasionally within that gene, researchers have been able to pinpoint various diseases on the genome map. SNPs found within a gene, or somewhere in the regulatory region of a gene, are of particular interest because they are more likely to alter the biological function of the gene and therefore, the function of the protein.

It is important to remember that SNPs do not cause or identify a disease state directly, but allow for the possible diagnosis or assists in determining the likelihood that someone will develop a particular illness. They also have the ability to help predict an individual’s response to certain drugs, environmental factors, chemicals, toxins, etc. In fact, since SNPs occur most frequently in the non-coding regions of DNA, they do not produce physical changes in people and have no effect on health or development.

Polymerase Chain Reaction and SNPs

A polymerase chain reaction experiment uses a set of nucleotide primers to amplify a specific section of DNA. Specifically, this diagnostic is testing for the presence of the cancer-linked rs17879961 SNP mutation. Since this SNP creates a new DNA sequence, primers can be made to only bind to the mutated DNA sequence. As a result, the PCR test can be run with a unique primer that will only bind if the target DNA shows rs17879961 mutation, allowing the test to identify the presence or absence this cancer-linked SNP. In rs17879961, there is an anomalous A-T pair that creates a new and unique DNA sequence specific to this cancer-linked mutation. Thus, only a specific primer will bind to the targeted sequence and, as a result, the PCR will only react if the specific mutation is present.

(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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