BME103 s2013:T900 Group8 L2: Difference between revisions
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{| style="wikitable" width="700px" | {| style="wikitable" width="700px" | ||
|- valign="top" | |- valign="top" | ||
| [[Image:BME103student.jpg|100px|thumb|Name: | | [[Image:BME103student.jpg|100px|thumb|Name: Anthony Zingale<br>Role: Experimental Protocol Planner]] | ||
| [[Image: | | [[Image:Chemistry_catHe group 8.jpg|100px|thumb|Name: Josh Snyder<br>Role: Machine Tester]] | ||
| [[Image: | | [[Image:BME103 Group8 PAK.jpg.jpg|thumb|Name: Adam Pak<br>Role: Experimental Protocol Planner]] | ||
| [[Image:BME103student.jpg|100px|thumb|Name: Sunhine Silvas<br>Role: Machine Tester]] | |||
| [[Image:BME103student.jpg|100px|thumb|Name: | | [[Image:^_^.png |100px|thumb|Name: Renee Tran<br>Role:Research and Development Scientist]] | ||
| [[Image: | |||
|} | |} | ||
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'''SYBR Green Dye'''<br> | '''SYBR Green Dye'''<br><br> | ||
[[Image:200px-SYBR_Green_I.png|200px|thumb|frame|right|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'''<br> | '''Single-Drop Fluorimeter'''<br> | ||
''[ | ''[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. <br> | ||
'''How the Fluorescence Technique Works'''<br> | '''How the Fluorescence Technique Works'''<br> | ||
''[In your own words, a summary of the information from page 9 of the worksheet]'' | ''[In your own words, a summary of the information from page 9 of the worksheet]''<br> | ||
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. | |||
<br> | <br> | ||
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==Procedure== | ==Procedure== | ||
<br> | |||
'''Smart Phone Camera Tech Specs'''<br> | |||
{| {{table}} width=700 | |||
|- | |||
| Phone : || iphone 4 | |||
|- | |||
| Tech specs || "<br>5-megapixel iSight camera<br> | |||
Video recording, HD (720p) up to 30 frames per second with audio<br> | |||
VGA-quality photos and video at up to 30 frames per second with the front camera<br> | |||
Tap to focus video or still images<br> | |||
LED flash<br> | |||
Photo and video geotagging<br>"<br> | |||
|- | |||
| Source of Tech specs || http://www.apple.com/iphone/iphone-4/specs.html | |||
|} | |||
'''Smart Phone Camera Settings'''<br> | '''Smart Phone Camera Settings'''<br> | ||
{| {{table}} width=700 | {| {{table}} width=700 | ||
|-style="background:#f0f0f0;" | |||
| 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'''<br> | '''Calibration'''<br> | ||
[[Image:BME_group8_lab_2_write_up.png|400px|thumb|Diagram of the set up]]<br> | |||
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''' | |||
{| {{table}} width=700 | |||
|-style="background:#f0f0f0;" | |||
| 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 | |||
|} | |||
''' | |||
{| {{table}} | |||
'''Placing Samples onto the Fluorimeter Procedures''' | |||
* Aquire following materials : | |||
{| {{table}} | |||
|-style="background:#f0f0f0;" | |||
| 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 | ||
|} | |} | ||
# Calibrate phone | |||
# Carefully palce one drop of sample onto Superhydrophobic surface | |||
# Place Superhydrophobic surface onto cradle | |||
# Place the big box over cradle to create a dark room | |||
# Set up smart phone using plastic base | |||
# Take a picture | |||
# Repeat steps 2-6 for all 6 samples | |||
# Measure distances of phone to table and to cradle | |||
# Analyze pictures and write down the observations | |||
<br> | <br> | ||
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'''Representative Images of Samples''' | '''Representative Images of Samples''' | ||
'' | ''A drawn circle using the freehand tool for a sample with no DNA'[[Image:Water1.png]]'<br>[[Image:Water2.png]]<br><br> | ||
'' | ''A drawn circle using the freehand tool for a sample '''with''' DNA (positive signal)'' | ||
[[Image:Positive1.png]]<br>[[Image:Positive_2.png]]<br> | |||
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{| {{table}} width=700 | {| {{table}} width=700 | ||
|- | |- | ||
| | | Area || Mean || IntDen || RawIntDen ||x||y (adj. den.) | ||
|- | |||
|17602|| 0.198|| 3481|| 3481 ||0||1.81E+03 | |||
|- | |||
|17602 || 0.095|| 1674 || 1674 || || | |||
|- | |||
|36076 || 5.046 || 182030 ||182030 || 0.25||1.82E+05 | |||
|- | |||
|36076 || 0.006 || 226 || 226|| || | |||
|- | |||
|22608 || 27.577 || 623453 || 623453 || 0.5||6.32E+05 | |||
|- | |||
|22608 || 0.033 || 748 || 748 || || | |||
|- | |||
|29288 || 79.88 || 2339514 || 2339514 || 1||2.34E+06 | |||
|- | |||
|29288|| 0.016|| 464 || 464 |||| | |||
|- | |||
|40452 || 113.098 || 4575047 || 4575047 || 2||4.57E+06 | |||
|- | |||
|40452 || 0.007 || 292 || 292|| || | |||
|- | |- | ||
| | |40734 || 110.281 || 4492170 || 4492170||5 ||4.49E+06 | ||
|- | |- | ||
| | |40734 || 0.151 || 6144 || 6144 || || | ||
|} | |} | ||
'''Fitting a Straight Line'''<br> | '''Fitting a Straight Line'''<br> | ||
'' | ''Excel plot with a line of best fit | ||
[[Image:Stuufff!!!.png]]<br> | |||
''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.''<br> | |||
<br> | |||
<br> | |||
'''Conclusion'''<br> | |||
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. | |||
<br> | <br> | ||
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Latest revision as of 09:40, 2 April 2013
BME 103 Spring 2013 | Home People Lab Write-Up 1 Lab Write-Up 2 Lab Write-Up 3 Course Logistics For Instructors Photos Wiki Editing Help | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
OUR TEAM
LAB 2 WRITE-UPBackground InformationSYBR Green Dye 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
Procedure
Smart Phone Camera Settings
Calibration Distance and angles between the smart phone and =
Placing Samples onto the Fluorimeter Procedures
Data AnalysisRepresentative Images of Samples A drawn circle using the freehand tool for a sample with no DNA'' A drawn circle using the freehand tool for a sample with DNA (positive signal)
Image J Values for All Samples [See worksheet page 5]
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.
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