BME100 f2013:W900 Group1 L5

BME 100 Fall 2013	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
Group 1 Carter Hill Kaitlyn Allen Neema Jamali Crawford Pederson Riddhi Rohit LAB 5 WRITE-UP Background Information SYBR Green Dye SYBR Green Dye is a small dye that is actively fluorescent in the presence of dsDNA but does not fluoresce very well with a single strand of DNA or in water. It is used primarily as a nucleic acid stain. Single-Drop Fluorimeter A fluorimeter is a device that is used to measure and detect fluorescence 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: iPhone Flash: The flash was inactivated. ISO setting: ISO was set to 800. White Balance: White Balance was set to auto. Exposure: Exposure was set to highest setting. Saturation: Saturation was set to the highest setting. Contrast: Contrast was set to lowest setting. [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: iPhone Flash: The flash was inactivated. ISO setting: ISO was set to 800. White Balance: White Balance was set to auto. Exposure: Exposure was set to highest setting. Saturation: Saturation was set to the highest setting. Contrast: Contrast was set to lowest setting. Calibration 1. Use the switch for the Blue LED to turn on the excitation light. 2. Check the settings on the smartphone and turn on the camera of your smart phone if they can be adjusted. a. Turn the flash. b. Set ISO to 800 or higher if possible. c. Set white balance to auto. d. Set exposure to highest setting. e. Set saturation to the highest setting. f. Set contrast to lowest setting. 3. Place your smart phone on the cradle at a right angle from the slide and adjust the height of the fluorimeter using the plastic trays so that your camera takes a picture of the drop sideways. This is very helpful because it makes filtering the blue light easier using ImageJ. 4. Adjust the distance between the smartphone on its cradle and the first two rows of the slide so that it is as close as you can get without having a blurry image. You should be at least 4 cm away from the drop. 5. Using the ruler provided in the lab, record the distance between the smart phone cradle and drop. Make sure not to move the camera, or fluorimeter very often. The light collected will change slightly if there is a significant difference from one image to the next in these distances. [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 = 7.2 cm [Instructions: See worksheet page 6.] Solutions Used for Calibration [Instructions: See worksheet page 6.] Calf Thymus DNA solution concentration (microg/mL) Volume of the 2X DNA solution (μL) Volume of the SYBR GREEN I Dye solution (μL) Final DNA concentration in SYBR Green I 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 [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 Representative Images of Samples [Instructions: Show an IMAGE where you drew a circle around the droplet with the freehand tool for a sample with no DNA] [Instructions: Show an IMAGE where you drew a circle around the droplet with the freehand tool for a sample with DNA (positive signal)] Image J Values for All Samples [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.] TABLE GOES HERE Fitting a Straight Line [Instructions: Place an IMAGE of your Excel plot with a line of best fit here. See worksheet page 9]