BME100 s2015:Group7 9amL5

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Lab Write-Up 1 | Lab Write-Up 2 | Lab Write-Up 3
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Contents

OUR TEAM

Name: Brandon Hansen
Name: Brandon Hansen
Name: Harris Tran
Name: Harris Tran
Name: Luke Shaffer
Name: Luke Shaffer
Name: Jaid Coronel
Name: Jaid Coronel


LAB 5 WRITE-UP

Procedure

Smart Phone Camera Settings

  • Type of Smartphone: Android
    • Flash: None
    • ISO setting: 800
    • White Balance: Auto
    • Exposure:Low
    • Saturation:Low
    • Contrast:Low


Calibration

  • Distance between the smart phone cradle and drop = 21cm

The cellular device used in the data collecting process requires modifications to the setup. Since the Android device for this collection process does not properly fit the cradle provided, the group balances the Android phone on its bottom and--with the help of a brace--prop up against the elevated fluorimeter. With this setup, it eliminates the issue of stability, is allows easier adjustment if desired , and is easier to deconstruct upon clean-up.


Solutions Used for Calibration

Final DNA concentration in SYBR Green I solution (The Means Of Each Sample Taken)

0.0 μg/mL (Water Solution Blank) 0.5 μg/mL (Calf Thymus DNA) 1.0 μg/mL (Calf Thymus DNA) 2.0 μg/mL (Calf Thymus DNA) 5.0 μg/mL (Calf Thymus DNA)



Placing Samples onto the Fluorimeter

  1. Step one: Locate and gather all equipment.
  2. Step two: Put on gloves, insert glass (smooth side down) onto fluorimeter
  3. Step three: Calibrate fluorimeter by placing 80μL of SYBR Green I on the first two holes, after adding a new tip, add 80μL of sample onto previous drop
  4. Step four: turn fluorimeter on and adjust slide to align the light beam with the liquid
  5. Step five: Take picture with smartphone. Record distance from phone to liquid
  6. Step six: Turn off fluorimeter, remove slide and clean off liquid
  7. Step seven: Repeat procedures 2-6; substitute 80μL of sample with the subsequent 5 samples
  8. Step eight: Mix unknown PCR from previous week with the red solution provided
  9. Step nine: Proceed through procedures with 80μL SYBR Green I with 5 new mixtures


Data Analysis

Representative Images of Negative and Positive Samples

Solution with low DNA concentration Solution with high DNA concentration

Image J Values for All Calibrator Samples

The values of each sample collected through ImageJ


Calibration curve

Charting the values of each sample presented in the chart above


PCR Results Summary

  • Our positive control PCR result was (on average, if not close to) 0.5 μg/mL
  • Our negative control PCR result was (on average, if not close to) 0.0 μg/mL

Observed results

  • Patient #1 : For each sample collect from this patients, the PCR result shows a notable amount of SYBR Green I indicator-coloring present in the solution. Comparing to the results of the calibrations droplets obtained and cataloged (above), it can be concluded this patient possess a significant level of green that suppresses the positive threshold for the disease. Meaning, this patient have contracted the disease and should be quarantined (for safety measures).
  • Patient #2 : For each sample collect from this patients, the PCR result shows a notable amount of SYBR Green I indicator-coloring present in the solution. However, the amount of the indicator-coloring are significantly less than Patient #1. Comparing to the results of the calibrations droplets obtained and cataloged (above), it can be concluded this patient does not possess a significant level of green that suppresses the positive threshold for the disease; instead, almost meeting the absolute negative threshold. Meaning, this patient does not carries the disease, is clean, and is able to roam around without any worries of infecting others.

Conclusions

SEE ABOVE




SNP Information & Primer Design

Background: About the Disease SNP SNP is the most common genetic variation. In fact, on average most SNP have little or no negative effect for the human population. Instead SNP is used as a tool for discovery. Importantly, SNP is used by scientists to mark and find the associated diseases. There is much still to discover about SNP. The more we learn, the more beneficial SNP seems to become.

Primer Design and Testing

Using the method of specific primer design can help identify certain portion of A DNA sample after its PCR cycle. Specific primer can be cataloged into databases, with appropriate characteristics associated to a specific sequences. In this case, a reliable online database assists in matching the disease-associated allele found within a series of nucleotides (rs268). From here, the PCR cycle results in the multiplication of this desire portion; assisting in furthering the research of the DNA strand. And since SNP marks the varies degree of differential within a DNA strand, it serves to assist in the crucial discovery of other important differences.

The result of the genome search through the available databse (left showing a match, right showing no result)


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