BME103 s2013:T900 Group8 L2

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Lab Write-Up 1
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Lab Write-Up 3
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Contents

OUR TEAM

Name: Anthony ZingaleRole: Experimental Protocol Planner
Name: Anthony Zingale
Role: Experimental Protocol Planner
Name: Josh SnyderRole: Machine Tester
Name: Josh Snyder
Role: Machine Tester
Name: Adam PakRole: Experimental Protocol Planner
Name: Adam Pak
Role: Experimental Protocol Planner
Name: Sunhine SilvasRole: Machine Tester
Name: Sunhine Silvas
Role: Machine Tester
Name: Renee TranRole:Research and Development Scientist
Name: Renee Tran
Role:Research and Development Scientist


LAB 2 WRITE-UP

Background Information

SYBR Green Dye

molecluar diagram of SYBR Green I
molecluar diagram of SYBR Green I

SYBR Green I is a dye that is used as a nucleic acid stain in several fields such as biochemistry, and molecualr biology. SYBR Green I can be diluted and a small amount of it can go a long way. This dye was useful in this experiment because, when the drop of DNA is put on the glass slide there is a blue ray of light that is turned on, which then passes through the drop. The way that this compund, SYBR Green, works is by absorbing the blue light and emitting green light. When we taking a picture of the drop under dark conditions the green emmited light can be visible. This compound is part of the cyanine synthetic dye family, this words comes from the word "cyan" which is blue-green. That this why green light is emitted.

Single-Drop Fluorimeter
[Add a PHOTO for bonus points] The Single-Drop Fluorimeter is a box shaped device that shines a specific light spectrum to activate the florescent dye in the sample.The light is turned on by a switch on the side of the devices. The sample is placed on specially made glass slide that is perforated and hydro-phobic, the slide can then be placed into the Fluorimeter.


How the Fluorescence Technique Works
[In your own words, a summary of the information from page 9 of the worksheet]
This method is used to examine and analyze the protiens, nucleic acids, ligands, and other interactions in order to study the protine orientations and actions. The different components in this technique, by micropipeting SYBR Green I and DNA onto a special glass plate and shining a blue light through it are the begining steps to analyzing the DNA stands in the drop.


Procedure


Smart Phone Camera Tech Specs

Phone : iphone 4
Tech specs "
5-megapixel iSight camera

Video recording, HD (720p) up to 30 frames per second with audio

VGA-quality photos and video at up to 30 frames per second with the front camera

Tap to focus video or still images

LED flash

Photo and video geotagging
"

Source of Tech specs http://www.apple.com/iphone/iphone-4/specs.html

Smart Phone Camera Settings

Settings : Settings used in lab Observations
Flash: Turned off N/A
ISO setting: ISO setting 80-1000 No control over ISO settings
White Balance: Auto White balance No control over white balance
Exposure: Auto exposure No control over exposure
Saturation: Very high No control over saturation
Contrast: Very high No control over contrast
Source: http://www.imaging-resource.com/PRODS/IPHONE4/IPHONE4A.HTM This source was used to find out what were the defult settings of iphone 4


  • No additional phones or cameras used


Calibration

Diagram of the set up
Diagram of the set up

Distance and angles between the smart phone and =

  • cradle = 3.62cm
  • table = 5.67cm
  • angle from camera to drop = approx 90°


Solutions Used for Calibration

Solution Concetration of SYBR green
1 None (Water)
2 0.25 micrograms per ml
3 0.05 micrograms per ml
4 1.0 micrograms per ml
5 2.0 micrograms per ml
6 5.0 micrograms per ml


Placing Samples onto the Fluorimeter Procedures

  • Aquire following materials :
Materials :
Set of read SYBR green(5 samples)
Water
pipette
Superhydrophobic surface
cradle
Smart phone
Box
plastic base
small box to set up the phone
  1. Calibrate phone
  2. Carefully palce one drop of sample onto Superhydrophobic surface
  3. Place Superhydrophobic surface onto cradle
  4. Place the big box over cradle to create a dark room
  5. Set up smart phone using plastic base
  6. Take a picture
  7. Repeat steps 2-6 for all 6 samples
  8. Measure distances of phone to table and to cradle
  9. Analyze pictures and write down the observations



Data Analysis

Representative Images of Samples

A drawn circle using the freehand tool for a sample with no DNA'Image:Water1.png'
Image:Water2.png

A drawn circle using the freehand tool for a sample with DNA (positive signal) Image:Positive1.png
Image:Positive_2.png‎


Image J Values for All Samples [See worksheet page 5]

Area Mean IntDen RawIntDen xy (adj. den.)
17602 0.198 3481 3481 01.81E+03
17602 0.095 1674 1674
36076 5.046 182030 182030 0.251.82E+05
36076 0.006 226 226
22608 27.577 623453 623453 0.56.32E+05
22608 0.033 748 748
29288 79.88 2339514 2339514 12.34E+06
29288 0.016 464 464
40452 113.098 4575047 4575047 24.57E+06
40452 0.007 292 292
40734 110.281 4492170 44921705 4.49E+06
40734 0.151 6144 6144



Fitting a Straight Line
Excel plot with a line of best fit Image:Stuufff!!!.png

In order for a linear pattern effect the last set of data is not included. If included, a curve would have been created due to human error during experimentation.


Conclusion
The objectives of the lab were met. The fluorimeter technique was mastered and calibrated. The formula to determine the magnitude of the light from a given concentration was found to be y = 4.0 x 10^6 (x) - 272558[2.7 x 10^6]. This can be used to find the concentration of DNA in an unknown sample by measuring the magnitude of light coming off the drop using the freehand tool mentioned above.



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