BME100 s2014:T Group15 L5

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Contents

OUR TEAM

Name: Ariana L. Shults
Name: Ariana L. Shults
Name: Samantha J Hatley
Name: Samantha J Hatley
Name: Megan Mendieta
Name: Megan Mendieta
Name: Heston Scott Hamilton
Name: Heston Scott Hamilton
Name: Mohammed A. Tamim
Name: Mohammed A. Tamim
Name: Brenda Cardenas
Name: Brenda Cardenas


LAB 5 WRITE-UP

Background Information

SYBR Green Dye
SYBR Green Dye is a molecular dye that fluoresces very well with dsDNA and weakly with water or single stranded DNA. When it binds to the DNA (preferably double-stranded though single stranded will still work) this dye absorbs blue light and emits green light. It is used to quantify and visualize double stranded DNA. When SYBR Green Dye is used with water there is no fluorescence. The more dsDNA the more the SYBR Green Dye emits the light.


Single-Drop Fluorometer
An instrument that detects florescence in a sample size of a single drop of 160 μL. We used a smart phone fluorimeter in this experiment. The Single-Drop Fluorometer consists of an apparatus that hold a specific slide, one with a dot grid present, and a simple box that covers it. A phone is set up in a stand so it does not need a hand to hold it and let light in while the picture is being taken. In the area of the apparatus which holds the slide there is a LED light which shines thru a drop placed over the middle two wells on the special slide. This LED light is controlled by a switch on the side of the apparatus.


How the Fluorescence Technique Works
The fluorescence technique works by having the dsDNA give a visual color signal for when it is present and having the fluorimeter capture a picture of the fluorescence that was produced. The concentration of DNA can be measured through this technique.



Procedure

Smart Phone Camera Settings

  • Type of Smartphone: Galaxy S3
    • Flash: Inactivated
    • ISO setting: 800
    • White Balance: Auto
    • Exposure: Highest Setting
    • Saturation: Highest Setting
    • Contrast: Lowest Setting


Calibration

We Placed our smart phone on the cradle at a right angle from the slide. We then adjusted the height of the fluorimeter using the plastic trays so that our camera was able to take a picture of the sample drop sideways.

  • Distance between the smart phone cradle and drop =7.0cm


Solutions Used for Calibration

Initial Concentration of 2X Calf Thymus DNA solution (micrograms/mL) Volume of the 2X DNA solution (µL)Volume of the SYBR GREEN I Dye solution (µL) Final DNA concentration in SYBR Green I solution (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. Using gloves, find the "smooth" side of the glass slide.
  2. Turn on fluorimeter.
  3. Place a slide in the fluorimeter with the smooth side facing down.
  4. Set camera timer for 5 seconds. Calibrate the photo options and lay the smartphone on cradle with camera app on.
  5. Adjust height of fluorimeter to get a camera view of the slide nearly edge-on by placing on top of a stable, supporting lid.
  6. Place 80 uL drop of SYBR Green I solution on first 2 clear circles in middle of slide.
  7. Changing tips, place 80 uL drop of sample/calibration solution on top of the SYBR GREEN I drop.
  8. Adjust the slide so that the light illuminates the center of the drop and the drop focuses the light on the other side.
  9. Adjust distance between smartphone and fluorimeter to 7cm away (>4cm).
  10. Cover with light box but keep one flap up.
  11. Make sure drop is focused one more time.
  12. Depress the timer button on the camera to take the picture and lower the flap before picture is taken.
  13. Remove the 160 uL drop using same tip from slide and discard liquid, as well as micropipetter tip, in waste liquid container.
  14. Move the slide in the next position (center of next two circles). Once you have used all 5 possible measurement positions on the slide, switch slides.
  15. Repeat steps 1-14 until all 8 samples have been photographed accordingly.


Data Analysis

Representative Images of Samples

The following images show two samples in he fluorometer. The first pictures shows the negative control, the one with no DNA. The second pictures shows the positive control, the one with DNA.


Image J Values for All Samples


PCR Product TUBE LABEL Concentration Volume of the DILUTED PCR Product solution (µL) Volume of the SYBR GREEN I Dye solution (µL) INTDENS VALUES BASED ON 3 SEPARATE DROP MEASUREMENTS ' ' AVERAGE INTDENS VALUE Corrected PCR Concentration
1. 2.5 Calf Thymus2.2580807298707586841963247196497281.727.00
2. 0.5 Calf Thymus0.5080802282276215220130682492500908.76.00
3. 0.25 Calf Thymus0.2580801730534226285820321112008501.03.00
4. 0 Calf Thymus0.0080801464326144022416542331519594.30.00
5. + (DNA)1.7780804796701411439946935914534897.021.21
6. P11 (DNA)0.2180801310944126038416739441415090.72.49
7. P12 (DNA)0.5980801459086313843519422142179911.77.08
8. P13 (DNA)0.4780801793887184996621587871934213.35.61
9. - (DNA)0.2680801461537205286910751741529860.03.18
10. P21 (DNA)0.3980801915305146423819741331784558.74.71
11. P22 (DNA)0.1480801051004146447312965611270679.31.62
12. P23 (DNA)0.4680801927895232673815289471927860.05.57


Fitting a Straight Line

PCR Results Summary

Instructor's summary: You completed 8 PCR reactions in a previous lab. You used the SYBR Green I staining and imaging technique to measure the amount of amplified DNA in each PCR reaction. You used a standard curve (based on known concentrations of calf thymus DNA) to convert INTDEN values into DNA concentration. Your positive control and negative control samples should be used as threshold values for determining whether an unknown (patient) sample is truly positive or negative.


Your positive control PCR result was 21.21 μg/mL

Your negative control PCR result was 3.18 μg/mL


Write-in each patient ID and give both a qualitative (what the images looked like) and a quantitative description (μg/mL) of what you observed

Patient 90616 : The average corrected concentration of this patients DNA is 5.06 μg/mL. The following image shows an example of the patient's PCR sample in fluorometer.

Patient 91514 : The average corrected concentration of this patients DNA is 3.97 μg/mL. The following image shows an example of the patient's PCR sample in fluorometer.


Compare each patient's results to the positive control value and the negative control value. Draw a final conclusion for each patient (positive or negative) and explain why you made that conclusion.

Patient 90616 : This patient's results are less than the positive control, 16.15 μg/mL less, but they are higher than the negative control by 1.88 μg/mL. This patient is much closer to the negative control results therefore this patient has a negative test result.

Patient 91514 : This patient's results are less than the positive control by 17.24 μg/mL but higher than the negative control by 0.79 μg/mL. This patient is drastically closer to the negative control therefore this patient has a negative test result.




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