BME100 f2017:Group15 W1030 L5

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Lab Write-Up 1 | Lab Write-Up 2 | Lab Write-Up 3
Lab Write-Up 4 | Lab Write-Up 5 | Lab Write-Up 6
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OUR TEAM

Name: Nathan Moorman
Name: Cole ALvarez
Name: Lauren Seliger
Name: Kasandra Sanchez
Name: Kylie Mercer


LAB 5 WRITE-UP

PCR Reaction Report

The pre-lab reading and quiz was very helpful in preparing our group members for this lab. The practice activities were vital in helping us learn how to use the pipette during the PCR experiment. Only one of our group members worked with the micropipettor while the rest were able to learn through observation. It was very helpful for our group to see examples and instructions before going into the lab.

The first and second stop on the pipettor were easy to understand. The first stop was used to draw up the liquid from the initial test tube. The second stop is then used to release that liquid from the pipettor. By pressing the second stop, a greater volume is released from the pipettor than was entered which allows for all of the liquid to come out. As the lab group went through the steps, we took our time to make sure all the liquid was drawn in and expelled at proper volume to make sure the results would be precise every time. We were also very careful about ejecting the tip from the pipette every time as to not contaminate any of the other substances.

At the end of the reaction, it was fairly clear that each tube did not contain the exact amount of substance every time. We could visually see that some tubes were filled slightly more than other tubes. This probably means that after the PCR reaction mix ran through the thermocycler, there was less than 100 microliters of the reactant. This may have been caused by not being careful enough when drawing the proper amount of liquid during the first lab. These smalls errors could possibly lead to inconsistencies in our data. All of the liquid from each PCR mix tube was extracted completely. We made sure to do this even though not every tube had exactly the same amount of liquid inside.

We did not have to change our labeling scheme. Our labels from the first part of this lab continued to work well.

Fluorimeter Procedure

Imaging set-up
The fluorimeter was turned on and the slide was positioned so that the fluorescent light beams directly on the center of the circles. The camera was then placed exactly 10 centimeters away from the fluorimeter on the phone mount. Then, the phone was set to take 3 photos in 5 second intervals on a timer. The cover of the fluorimeter was then closed and the phone was enclosed in darkness. This allows for the photos to be taken 3 times without the overhead lighting interfering.

Placing Samples onto the Fluorimeter

  1. Place the fluorimeter on the table and turn it on
  2. Place the slide face down in the fluorimeter
  3. Place Iphone 6 on the mount with timer set to take photo
  4. Adjust the fluorimeter until the image looks clear
  5. Use a ruler to measure how far away the Iphone mount is from the fluorimeter. This ensures that it is the exact same distance for all of the photos.
  6. Using the micropipette, take 80 uL of the SYBR Green solution and place it on the center of the 2nd row of circles on the slide
  7. Place 80 uL of the Calf Thymus Liquid on top of the SYBR Green drop
  8. Adjust the slide so the light is centered on the drop
  9. Press the timer button on the smartphone and close the flaps of the box so the slide and phone are completely enclosed
  10. Repeat the step above three times to ensure that you have three images of the drop
  11. Remove the 160 uL drop from the slide and eject the tip from the micropipette and grab a new one
  12. Repeat steps 1-11 for each volume of the Calf Thymus Liquid. When finished, follow these steps again for the PCR reaction mix


Data Collection and Analysis

Images of High, Low, and Zero Calf Thymus DNA

HighConcentration1.PNG High Concentration - 5 μg/mL DNA sample

LowConcentration3.PNG Low Concentration - 0.5 μg/mL DNA sample

NoConcentration1.PNG No Concentration - 0.0 μg/mL DNA sample


Calibration curves
DotPlot1!.PNG
DotPlot2!.PNG
Images of Our PCR Negative and Positive Controls
Positive:
PositiveControl2.PNG
Negative:
NegativeControl1.PNG
Calibration Mean Values
Initial Concentration of 2X Calf Thymus DNA solution (micrograms/mL) Final DNA Concentration in SYBR Green I Solution (µg/mL) Sample Number RAWINTDEN DROP-BACKGROUND image 1 RAWINTDEN DROP-BACKGROUND image 2 RAWINTDEN DROP-BACKGROUND image 3 MEAN Standard Deviation
5 2.5 C-1 2911339 3014552 2911064 2945652 59669.59742
2 1 C-2 5105538 525290 5348565 2128131 2788987.409
1 0.5 C-3 4688113 4641966 4828659 4719579 97242.82319
0.5 0.25 C-4 3849388 2635361 3842893 3442547 69905.4136
0.25 0.125 C-5 14632474 9968090 14446978 13015847 2641064.324
0 0 C-6 947832 1211383 1205599 1121605 150519.3291
PCR Results: Summary
  • Our positive control PCR result was 6893300.143 μg/mL
  • Our negative control PCR result was 763713.6713 μg/mL
Observed results
  • Patient 76014 (positive control) : no green pigment appeared even though the volume fluctuated from 0μg/mL to 2μg/mL.
  • Patient 66716 (negative control): no green pigment appeared even though the volume fluctuated from 0μg/mL to 2μg/mL
Conclusions
  • Patient 76014 (positive control) : Positive; The DNA sequence was very similar to the samples used for this patient.
  • Patient 66716 (negative control): Positive; The DNA sequence was very similar to the samples used for this patient.
PCR Results: PCR Concentrations Solved
PCR Product TUBE LABEL MEAN (of RAWINTDEN DROP-BACKGROUND PCR Product Concentration (µg/mL) Total Dilution Initial PCR Product Concentration (µg/mL)
Positive 13296015.33 57444.1 12 6893300.143
Negative 1900250.333 19000250.333 12 763713.6713
Patient 1-1 13257838.67 572730.4644 12 6872765.573
Patient 1-2 6306439.5 261143.9355 12 3133727.226
Patient 1-3 2325703.667 82713.14334 12 992557.72
Patient 2-1 2154924.333 75058.20387 12 900698.4464
Patient 2-2 2817688 104765.6376 12 1257187.652
Patient 2-3 2253407.333 79472.56353 12 953670.7624