BME103 s2013:T900 Group2 L2

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| [[Image:BME103student.jpg|100px|thumb|Name: William Scott]]
| [[Image:BME103student.jpg|100px|thumb|Name: William Scott]]
| [[Image:BME103student.jpg|100px|thumb|Name: Joe Sansone <br> Protocol Specialist]]
| [[Image:BME103student.jpg|100px|thumb|Name: Joe Sansone <br> Protocol Specialist]]
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| [[Image:BME103student.jpg|100px|thumb|Name: student]]
 
| [[Image:Photo(3).jpg‎|100px|thumb|Name: Shang Ruan <br> Open PCR Machine Engineer]]
| [[Image:Photo(3).jpg‎|100px|thumb|Name: Shang Ruan <br> Open PCR Machine Engineer]]
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Revision as of 03:40, 2 April 2013

BME 103 Spring 2013 Home
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Lab Write-Up 1
Lab Write-Up 2
Lab Write-Up 3
Course Logistics For Instructors
Photos
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Image:BME494_Asu_logo.png


Contents

OUR TEAM

Name: Andy Son
Name: Andy Son
Mitch Riggs  Open PCR Machine Engineer/ Team Leader
Mitch Riggs
Open PCR Machine Engineer/ Team Leader
Name: William Scott
Name: William Scott
Name: Joe Sansone  Protocol Specialist
Name: Joe Sansone
Protocol Specialist
Name: Shang Ruan  Open PCR Machine Engineer
Name: Shang Ruan
Open PCR Machine Engineer


LAB 2 WRITE-UP

Background Information

SYBR Green Dye
SYBR Green dye is a dye used as an indicator in molecular biology. It emits green light when bound to double helix DNA and illuminated with blue light. Source: http://en.wikipedia.org/wiki/SYBR_Green_I


Single-Drop Fluorimeter
[A description of the single-drop fluorimeter device. Image of Device from http://openwetware.org/wiki/BME103 2012-11-01_11.53.50.jpg]


How the Fluorescence Technique Works
[In your own words, a summary of the information from page 9 of the worksheet]



Procedure

Smart Phone Camera Settings

  • The smartphone used for the camera was the Android Google Nexus 4. An app named Camera Self-Timer was installed to create a window in which the camera can shoot a picture in which the fluorimeter could then be covered in darkness for the most accurate results.
    • Flash: No flash was used
    • ISO setting: Unknown (could not be altered)
    • White Balance: White balance was set on auto
    • Exposure: Exposure was set on auto
    • Saturation: Saturation was set on high
    • Contrast: Contrast was set on low


Calibration

The camera was placed on a cradle that was in approximately equal height of the fluorimeter. If the cradle and camera needed to be taller in order to be of equal height to the fluorimeter, the cradle was then placed on a stacked glass case until the camera was parallel. The distance from the cradle to the fluorimeter was about 7 cm. After creating a solution for calibration the camera was then set on a self-timer of 10 seconds and then the fluorimeter was encased in a box and covered for complete darkness for the most accurate results. After the beep indicating that the picture was taken the cycle was then complete and the process was then repeated for each solution. Image of setup as shown from http://openwetware.org/wiki/BME103 BME103_Group9_FluorimeterSetup.jpg

  • Distance between the smart phone cradle and drop = 7cm


Solutions Used for Calibration

Calf Thymus DNA Solution (microg/mL) Volume 2X DNA Solution (uL) Volume SYBR GREEN I Solution (uL) Fina DNA concentration in PicoGreen Assay (ng/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 blank


Placing Samples onto the Fluorimeter

  • Step 1: A micro pipette was obtained and 80uL of the SYBR GREEN I was dispensed in the center of the first two rows of the slide. Once done 80uL of the desired solution (calf thymus at various concentrations or just water) was added to the mixture on the slide.
  • Step two: After the desired mixture was placed onto the slide it was then positioned so that the droplet was centered with the small opening on the apparatus where the blue LED light originates from.
  • Step three: After collecting the qualitative data with picture captures, the sample was removed from the slide and discarded appropriately. Then the above steps were repeated for all concentrations of DNA making sure not cross contaminate the mixtures by using different slide rows for each trial.
  • Step four: Once all experimental trials were done the work station was cleaned by discarding the slides in the appropriate sharps container as well as dispensing the DNA solutions appropriately. The data was compiled and tabulated for further analysis.


Data Analysis

Representative Images of Samples

[Water Droplet (control/blank) Water_droplet_blank.jpg]

[High Concentrated DNA Solution Drop with SYBR Dye High_concentration_DNA_drop.jpg]


Image J Values for All Samples

DNA final concentration (ng/mL) Ave. Mean Ave. IntDen
2.5 109.55 4920177
1 98.36 4687729
0.5 58.41 2081008
0.25 49.45 1679326
0.125 47.1 1396192
0 35.93 1195111


Fitting a Straight Line
[ Integrated Density of DNA Droplets with SYBR Dye Line_of_best_fit.jpg]




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