BME100 s2014:T Group14 L5

BME 100 Spring 2014	Home People Lab Write-Up 1 | Lab Write-Up 2 | Lab Write-Up 3 Lab Write-Up 4 | Lab Write-Up 5 | Lab Write-Up 6 Course Logistics For Instructors Photos Wiki Editing Help
OUR TEAM Name: Caitlin R. Byrne Name: Megan McGuire Name: Wade Savage Name: Theo Hall LAB 5 WRITE-UP Background Information SYBR Green Dye SYBR Green I is a dye that is used as a nucleic acid stain in molecular biology. The dye binds to DNA and results in a DNA and dye complex that reflects blue light and emits a green light that binds to double stranded DNA. This can be used in some methods of a quantitative polymerase chain reaction. This dye can also work on RNA, because RNA also is made up of nucleic acids. The dye will bind to the RNA and work in the exact way it would when bound to the DNA. SYBR Green I is declared safe to work with and does not have waste disposal issues. However is has the cabable of binding to DNA with a high affinity. This means that safety gloves must be worn at all times to prent the SYBR Green dye from getting on the skin. Single-Drop Fluorimeter [Instructions: A description of the single-drop fluorimeter device. Add a PHOTO for bonus points] How the Fluorescence Technique Works [Instructions: In your own words] Procedure Smart Phone Camera Settings [Instructions: The type of smart phone you used and how you adjusted the camera settings, if applicable (see worksheet page 4).] Type of Smartphone: Flash: ISO setting: White Balance: Exposure: Saturation: Contrast: [Instructions: If you used an additional phone, describe the other type of smart phone you used and how you adjusted the camera settings, if applicable. If not, delete this part] Type of Smartphone: Flash: ISO setting: White Balance: Exposure: Saturation: Contrast: Calibration [Instructions: Describe how to set up your camera in front of the fluorimeter. Add a PHOTO of this set-up for bonus points.] Distance between the smart phone cradle and drop = [Instructions: See worksheet page 6.] Solutions Used for Calibration [Instructions: See worksheet page 6.] row 1 cell 1 row 1 cell 2 row 1 cell 3 row 1 cell 4 row 2 cell 1 row 2 cell 2 row 2 cell 3 row 2 cell 4 row 3 cell 1 row 3 cell 2 row 3 cell 3 row 3 cell 4 [Add more rows as needed] Placing Samples onto the Fluorimeter [Instructions: Step one, in your OWN words] [Instructions: Step two, in your own words] [Instructions: Step three, in your own words] [Instructions: Step etc., in your own words] Data Analysis Basic Set Up of the Flourimeter Procedure After setting up the stand on which we place the slide (rough side up), we made sure that the cell phone that would be taking the pictures was level with the slide. Because SYBR Green 1 dye is light sensitive, it is best to conduct the experiment by taking photos in a dark environment. Our "dark room" in a sense is provided by a black file folder box. This helps block out light when the picture is taken. Keeping in mind that we were working with a light sensitive material, we kept SYBR Green underneath tin foil as to not hinder the experiment. (Personal Photo) Representative Images of Samples Positive DNA Test The SYBR Green 1 dye causes the diseased DNA to glow when exposed to the blue light. (Personal Photo) Negative DNA Test In the absense of diseased DNA SYBR Green 1 does not make the drop glow green, and it's a fairly obvious difference in color. (Personal Photo) Image J Values for All Samples PCR Product Table PCR Product Tube Label dDNA ndDNA 1a 1b 1c 2a 2b 2c Volume of Dilute PCR Product Solution 80 80 80 80 80 80 80 80 Volume of SYBR Green 1 in Solution 80 80 80 80 80 80 80 80 Intdens based on 3 Separate Drop Measurements 2949516 295136 414970 240148 382969 269159 837877 305779 ' 2648136 164943 297687 238968 434590 278027 795755 287146 ' 2942463 228896 525723 247055 427061 292295 8838335 335964 Average Intdens Value 2846705 229658.3 412793.3 242057 414873.3 279827 3490656 309629.7 PCR Product Table Calculations PCR Product Tube Label dDNA ndDNA 1a 1b 1c 2a 2b 2c Average IntDens Value 2846705 229658.3 412793.3 242057 414873.3 279827 3490656 309629.7 PCR Product Concentration 3.096757 -0.08891 0.134016 -0.07382 0.136548 -0.02784 3.880622 0.008438 Corrected PCR Product Concentration 37.16109 -1.06691 1.608195 -0.8858 1.638578 -0.33409 46.56747 0.101252 Just to note, we seem to have a mismeasurement on 1a measurement 2 we believe it's human error, or just taken down wrong [Instructions: See worksheet page 8. To save time on typing a new Wiki table from scratch, use THIS TOOL to auto-generate a Wiki table: Excel-to-Wiki Converter. Copy the headers and values from the Excel spreadsheet you made, paste them into the form field, click submit, copy the Wiki code that the tool generated, and replace TABLE GOES HERE (below) with your auto-generated code.] Fitting a Straight Line