BME100 s2014:T Group4 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: Brian Kalen Name: Michael Spina Name: Daniel Munoz Name: Parker Davis Name: Rakan Aldrssary LAB 5 WRITE-UP Background Information SYBR Green Dye [Instructions: A short summary describing SYBR green dye] A photosenstive dye that reacts with certain DNA strands. The dye helps quantify how much DNA is present and therefore a sample with more DNA will appear more green. SYBR green stains the DNA strands in order to show how much DNA is in a sample when a beam of light is shot through the sample. SYBR green in high concentration is used in PCR similar to the lab performed. This helps us find out how much DNA is in a certain sample. When there is little to no DNA in the sample the dye will not stain as much and by consequence the sample will not shine with a green glow when light is shot through it. The SYBR green dye works best with double stranded DNA however, it has been shown to stain single stranded DNA and in some cases even RNA. Single-Drop Fluorimeter [Instructions: A description of the single-drop fluorimeter device. Add a PHOTO for bonus points] This single drop fluorimeter is a box that covers a black stand that can hold a bubble of solution. A slide is placed on the fluorimeter and the DNA sample is placed in drop form on the slide. The fluorimeter has a light switch on the side, and when the switch is on a beam of fluorescent light is shot across the device. When bubble of solution is placed on the slide the beam of light penetrates the solution and reflects certain contents of the solution. How the Fluorescence Technique Works [Instructions: In your own words] The DNA sample is placed on a slide and then shifted into the box so the sample is in darkness. Fluorescent light is then shot through the bubble in order to reflect how much DNA is present through how much green dye is displayed. Based on how much Green in this case is shown will show us how much DNA is present in the sample. The light pierces the bubble of solution, and the stained DNA strands are reflected as a green color due to the SYBR green dye. 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: Galaxy S 3 from Samsung Flash: None ISO setting: 800 White Balance: auto Exposure: +2.0 Saturation: auto Contrast: auto Calibration [Instructions: Describe how to set up your camera in front of the fluorimeter. Add a PHOTO of this set-up for bonus points.] The phone was placed in a holding tray so it could stand up on its own. Then the phone was set so that it had a timer and would take a picture 5 seconds after the camera was pushed. This gave us the time to close the box and allow the sample to be in complete darkness. This yielded the highest quality pictures for measurement. Distance between the smart phone cradle and drop = 7cm. [Instructions: See worksheet page 6.] Solutions Used for Calibration [Instructions: See worksheet page 6.] C+ ID: 31526 ID: 31526 ID: 31526 C+ P11 P12 P13 C- ID: 36055 ID: 36055 ID: 36055 C- P21 P22 P23 [Add more rows as needed] Placing Samples onto the Fluorimeter [Instructions: Step one, in your OWN words] Placed 80 microliters of SYBR Green in the two middle circles. [Instructions: Step two, in your own words] Placed 80 microliters of DNA solution ontop of the Green dye. [Instructions: Step three, in your own words] Then the light was turned on from the side of the fluorimeter. [Instructions: Step four, in your own words] The camera timers was started and the fluorimeter was pushed to the back of the dark box. [Instructions: Step five, in your own words] The back lid of the box was shut to ensure the sample was in complete darkness. [Instructions: Step six, in your own words] Wait five seconds for the camera timer to expire, and then take the sample out and save the picture for analysis. 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]