BME100 s2014:W Group9 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 Mohammed Mousa, Maryam Ibrahim, Quintin Woods, Kayla Cummins, Kyndal Sorenson LAB 5 WRITE-UP Background Information SYBR Green 1 Dye SYBR Green 1 Dye is used as a nucleic acid stain and has numerous uses in the biology world. It is a small molecular dye that illuminates effectively while in the presence of double-stranded DNA, but does not illuminate as well when mixed with water or single-stranded DNA. The green dye can be placed in a sample with possible DNA and will glow a bright green if DNA is present. This is the most common use of the dye and helps qualitatively analyze if DNA is present in a substance. The dye can also be placed inside a PCR mixture and this allows the dye to bind to the single-stranded DNA. It can still be used with both, and additionally RNA. Single-Drop Fluorimeter The Single-Drop Fluorimeter is a small and black plastic box with two notches where the multi-welled slide can fit in. It has a switch located on the right hand side that allows for the blue LED light to be turned on or off. The slide of the fluorometer is aligned so that the blue LED shines through a drop placed over two middle wells. The slide has holes along it to allow for a sample to be placed in them. Placing the drops must be carefully done to ensure no overflow. (This image was borrowed from another group because we did not take a picture of our set-up.) How the Fluorescence Technique Works The fluorometer has a slide with small holes where drops of sample DNA were placed. The slide layer is made of Teflon, giving the slide texture to allow the sample drop to maintain its "drop" shape. The reason this is necessary is because the light from the fluorometer can go directly through the drop to increase the intensity of the DNA glow. It also allows for the SYBR Green to move to the surface, which allows for the glow to be seen on the top of the drop. All of this makes it easier to observe and analyze whether the sample has a green glow, and whether there was DNA present in the sample. 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 4s Flash: Off ISO setting: NA White Balance: NA Exposure: NA Saturation: NA Contrast: NA Calibration For the calibration, the phone was placed into the cradle and the self-timer was readied. The flourimeter was 6 cm away from where the drop was going to be placed and the slide was placed into the holder. A sample of DNA was placed onto the slide using the micropipette. The black box was placed over the cradle and flourimeter and the picture was taken. This process was repeated for every DNA sample. ' Distance between the smart phone cradle and drop = 6 cm [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 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]