BME100 s2015:Group14 12pmL5

From OpenWetWare
Jump to: navigation, search
Owwnotebook icon.png BME 100 Spring 2015 Home
People
Lab Write-Up 1 | Lab Write-Up 2 | Lab Write-Up 3
Lab Write-Up 4 | Lab Write-Up 5 | Lab Write-Up 6
Course Logistics For Instructors
Photos
Wiki Editing Help
BME494 Asu logo.png


OUR TEAM

Name: Nathan Francois
Name: Lexi Bounds
Name: Dakota Graham
Name: Thor Kissman
Name: Justin Mieth


LAB 5 WRITE-UP

Note to the grader - the info in this lab report was completed after the time deadline. No one in the group was aware that the lab report was due on April 7th at midnight. We have done our best to complete the report as soon as possible despite being late.

Procedure

Smart Phone Camera Settings

  • Type of Smartphone: iPhone 5s
    • Flash: Off
    • ISO setting: Default
    • White Balance: Auto
    • Exposure: Default
    • Saturation: Default
    • Contrast: Default


Calibration
Using the cradle provided, place the phone to be used onto the cradle. Make sure the camera is turned on. Then, position the camera at a distance where the camera is at the same height as the center of the drop. Doing so will provide the most accurate results.

  • Distance between the smart phone cradle and drop = 5.0 cm


Solutions Used for Calibration (Note: Only the Final DNA Concentration column values were used)

Initial Concentration of 2X Calf Thymus DNA (µg/mL) Volume of 2X DNA solution (µL) Volume of SYBR GREEN I Dye Solution (µL) Final DNA Concentration (µg/mL)
5 80 80 2.5
2 80 80 1
1 80 80 0.5
0.5 80 80 0.25
0.25 80 80 0.125
0 80 80 0


Placing Samples onto the Fluorimeter

  1. Wearing a pair of gloves, identify which side of the slide is “smooth”.
  2. Turn on the fluorimeter.
  3. Place the fluorimeter on the table.
  4. Place the slide in the fluorimeter with the smooth side down.
  5. Place the smartphone on the cradle.
  6. Adjust the height of the fluorimeter or camera so that the camera can take a side-shot of the center of the drop.
  7. Record the distance between the cradle and the fluorimeter light.
  8. Using the micropipette, place an 80 µl drop of the SYBR GREEN I in the middle of the first two rows of the slide between two of the small hydrophilic dots.
  9. Using a new micropipette tip, place an 80 µl drop of the first concentration of calf thymus DNA on top of the SYBR solution.
  10. Move the slide so that the blue LED light is focused by the drop. It should hit the middle of the black fiber optic fitting on the other side of the drop.
  11. Cover the fluorimeter as best as possible with the light box.
  12. Take 3 independent images of the drop with the camera.
  13. Remove the light box without moving the smartphone. (If the phone was moved, rearrange so that the distance matches the recorded distance)
  14. Using the micropipette, remove the 160 µl drop from the slide. Dispose of the micropipette tip used.
  15. Move the slide into the next clean hydrophilic dot position.
  16. Repeat steps 8-15 for the remaining concentrations of calf thymus DNA.
  17. Dispose of all materials responsibly and in their correct locations when done.


Data Analysis

Representative Images of Negative and Positive Samples

Positive Signal on ImageJ
Negative Signal on ImageJ



Image J Values for All Calibrator Samples (Values given in RAWINTDEN Drop - Background)

Final Concentration of DNA solution (ug/mL) Image 1 Image 2 Image 3 Mean St. Dev.
2.5 16684465 16066772 14173580 15641605.67 1308323.61
1 8078091 6669219 4855423 6534244.33 1615568.28
0.5 20016429 19470750 21676492 20387890.33 1148830.75
0.25 4444616 5071592 4658391 4724866.33 318730.22
0.125 3673678 4208643 4653738 4178686.33 490716.26
0 330973 228782 323620 294458.33 56996.07


Calibration curve
Calibration curve.jpg


PCR Results Summary

  • Our positive control PCR result was 2.09 μg/mL
  • Our negative control PCR result was -8.50 μg/mL

Observed results

  • Patient 80565 : The drops turned bright green in color. The calculated concentration had a mean of 14.76 μg/mL for the three different primer mixes together.
  • Patient 87710 : The drops did not show any significant change. The calculated concentration had a mean of -5.11 μg/mL for the three different primer mixes together.

Conclusions

  • Patient 80565 : This patient had a greater concentration measured than the positive control. Therefore, the patient is positive.
  • Patient 87710 : This patient had a greater concentration measured than the negative control, but the value was still negative and much more so than the positive control. Therefore, this patient is negative.




SNP Information & Primer Design

Background: About the Disease SNP The disease SNP under observation in this study is termed rs268, and it is a pathogenic SNP found on one of the alleles coding for lipoprotein lipase (LPL). It is found in humans at the 8:19956018 chromosome location, and the SNP involves a switch from an adenine nucleotide to a guanine nucleotide. The effect of this polymorphism on LPL is that it can disrupt the decomposition of lipoproteins. It can also lead to issues with protein binding and receptor binding. The possible results of these effects are diseases such as metabolic syndrome, coronary heart disease, and coronary artery disease.

Primer Design and Testing After primers were designed for non-disease DNA, as well as SNP-carrying DNA, the primers were tested with the UCSC In-Silico Pro website. For the non-disease carrying forward and reverse primers, the result of the simulation was a 220 base pair DNA sequence matching a sequence from the non-disease LPL gene. For the disease carrying forward and reverse primers, no match was found even though the strand created from the non-disease primers differed by only one base pair. This shows that the disease primer designed is effective in only binding to the disease-carrying DNA, and not to non-carrying DNA. This makes it useful for testing for the presence of the SNP in patients.

Non-Disease Primer Results
Disease Primer Results