BME103 s2013:T900 Group8 L2

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 Error creating thumbnail: Unable to save thumbnail to destination Name: Anthony Zingale Role: Experimental Protocol Planner Error creating thumbnail: Unable to save thumbnail to destination Name: Josh Snyder Role: Machine Tester Error creating thumbnail: Unable to save thumbnail to destination Name: Adam Pak Role: Experimental Protocol Planner Error creating thumbnail: Unable to save thumbnail to destination Name: Sunhine Silvas Role: Machine Tester Error creating thumbnail: Unable to save thumbnail to destination Name: Renee Tran Role:Research and Development Scientist LAB 2 WRITE-UP Background Information SYBR Green Dye 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 Error creating thumbnail: Unable to save thumbnail to destination 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 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 Data Analysis Representative 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] 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 Excel plot with a line of best fit 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.