BME103:W930 Group6

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(Protocols)
(Protocols)
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'''Fluorometer Setup'''<br>1. Remove fluorometer elements from container.<br> 2. Place 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 channel of the LED box.
'''Fluorometer Setup'''<br>1. Remove fluorometer elements from container.<br> 2. Place 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 channel of the LED box.

Revision as of 17:55, 13 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. (Written by Sairah F, Posted by William L).




Test Run

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




Protocols

Polymerase Chain Reaction

1. A Polymerase Chain Reaction(PCR) is used to amplify a single piece of DNA. The steps that lead up to the replication of a DNA sequence are denaturation, annealing, and extension which involve several different cycles ranging in terms of length of time and temperature. This results in the exponential replication of DNA.

2. The amplification of a patient’s DNA can be separated into three different steps.
a. The first cycle is described as denaturation of the DNA, which is a double strand, into two single strands. This is accomplished by separating the hydrogen bonds within the DNA.
b. Next is the annealing step which consists of the single strands of DNA being annealed to the primers. This step is done at a colder temperature than the denaturation and the DNA and primers are bonded by hydrogen bonds to form a double stranded nucleotide.
c. The final step is characterized by the raising of the temperature and the Taq DNA polymerase is used to replicate the DNA strands. Taq synthesizes new, double-stranded DNA molecules that are identical to the original double stranded target DNA region.

3. Components of the PCR Master Mix
• GoTaq Colorless Master Mix
• Upstream Primer
• Downstream Primer
• DNA Template
• Nuclease-Free Water

Reagent
Template DNA (20 ng)
10 µM Upstream Primer
10 µM Downstream Primer
GoTaq Master Mix
Nuclease-Free Water
Total Volume

Fluorometer Setup
1. Remove fluorometer elements from container.
2. Place 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 channel of the LED box.

Fluorometer Setup Part I
Fluorometer Setup Part I










4. Place Fluorometer Setup Part I onto lid from original container
5. While leaving the camera setup side of the container unsnapped, place container around Fluorometer Setup Part I.

Fluorometer Final Setup
Fluorometer Final Setup























Fluorometer Use
1. Remove container covering Fluorometer Final Setup.
2. Switch on blue LED.
3. Change camera settings by turning flash on, setting ISO to 800+, increasing exposure to maximum and disabling auto-focus.
4. Pipette two drops of water (volume of 130-160 microliters per drop) onto the slide in the channel of the LED box.
5. Focus LED light on the drops so that the middle of the drop is aligned with the line of light created by the LED.
6. Put the container covering back over the Fluorometer Final Setup.
6. Take 3 photos, making sure not to disturb the positioning and setup.
7. Remove the container covering while again taking care not to change the placement of the setup.
8. Remove slide and dispose of the used slide.
9. Place new slide into LED box, and do steps 4 through 6 again.
10. Note the type of smartphone used throughout the protocol, the distance from smartphone to the base of the LED box (in centimeters), and attach an image of each position of the drops.

Transferal of Fluorometer Data to ImageJ
1. Use a USB cable to connect the smartphone that was used to a computer with the ImageJ software.
2. Open the Start Menu and double click on My Computer or Computer.
3. Select Portable Devices where the smartphone should be listed and double-click the icon.
4. Locate the DCIM folder and open it, and continue to the sub-folder Camera.
5. Select each picture that needs to be transferred, then Copy and Paste them into the folder you choose to store them in.
6. Open ImageJ software from Start Menu or by double-clicking the ImageJ icon on the Desktop.
7. Once ImageJ software is open, click on File and select Open in the toolbar located in the top left of the computer screen.
8. Select Browse then select the image you want out of the folder where you stored your photos (in step 5)
9. Repeat steps 7 and 8 to continue process with different pictures.

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. (Written by Kim L, Posted by William L).

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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