BME100 s2015:Group1 12pmL5: Difference between revisions
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{| style="wikitable" width="700px" | {| style="wikitable" width="700px" | ||
|- valign="top" | |- valign="top" | ||
| [[Image: | | [[Image:AndreNguyen.jpg|100px|thumb|Name: Andre Nguyen]] | ||
| [[Image: | | [[Image:jpacker.jpg|100px|thumb|Name: Jake Packer]] | ||
| [[Image:KaylenaConklin.jpg|100px|thumb|Name: Kaylena Conklin]] | | [[Image:KaylenaConklin.jpg|100px|thumb|Name: Kaylena Conklin]] | ||
| [[Image: | | [[Image:jhernandez.jpg|100px|thumb|Name: Jorge Hernandez]] | ||
| [[Image:BME103student.jpg|100px|thumb|Name: student]] | | [[Image:BME103student.jpg|100px|thumb|Name: student]] | ||
| [[Image:BME103student.jpg|100px|thumb|Name: student]] | | [[Image:BME103student.jpg|100px|thumb|Name: student]] | ||
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'''Calibration'''<br> | '''Calibration'''<br> | ||
<!-- INSTRUCTIONS: In the space below, briefly describe how to set up your camera in front of the fluorimeter. Add a PHOTO of this set-up for bonus points. --> | <!-- INSTRUCTIONS: In the space below, briefly describe how to set up your camera in front of the fluorimeter. Add a PHOTO of this set-up for bonus points. --> | ||
For this lab, the phone that was used was placed in a horizontal fashion. The camera was on the right side facing the drop of fluid. In an attempt to keep the phone perpendicular to the table, tape was applied to the phone and then attached to the cradle. Earphones were attached to the phone for the purpose of | For this lab, the phone that was used was placed in a horizontal fashion. The camera was on the right side facing the drop of fluid. In an attempt to keep the phone perpendicular to the table, tape was applied to the phone and then attached to the cradle. Earphones were attached to the phone for the purpose of timing the pictures being taken. This was especially helpful since we did not have to continue to close and open the black box to pressure the capture button on the smartphone. It also mitigated any movement of the smartphone from its original position. | ||
<!-- INSTRUCTIONS: Type the distance between your phone cradle and the drop after the equal sign. --> | <!-- INSTRUCTIONS: Type the distance between your phone cradle and the drop after the equal sign. --> | ||
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'''Solutions Used for Calibration''' | '''Solutions Used for Calibration''' | ||
[[Image:Lab5CalibrationRawData.jpg]] | |||
'''Placing Samples onto the Fluorimeter''' | |||
# Set the micropipette to 80 microliters | |||
# Collect the CYBER green in the micropipette | |||
# The light from the Fluorimeter should be shining on the first two rows of dots | |||
# Place the CYBER green in between the two dots so that the light beam goes straight through the center of the bubble of fluid | |||
# Eject tip from micropipette and put a new one on | |||
# While still on the 80 microliter setting, collect the pcr product that has been mixed with the buffer solution | |||
# Place the PCR solution inside of the CYBER green that is already on the slide | |||
# Close the box and take pictures | |||
'''Web Page Results''' | |||
[[Image:screen shot 1.jpg]] | |||
[[Image:screen shot 2.jpg]] | |||
[[Image:screen shot 3.jpg]] | |||
<br> | <br> | ||
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'''Representative Images of Negative and Positive Samples''' | '''Representative Images of Negative and Positive Samples''' | ||
<!-- INSTRUCTIONS: (1) Show ONE image where you drew a circle around the droplet with the freehand tool for any sample with *no* DNA. (2) Show ONE image where you drew a circle around the droplet with the freehand tool for a sample *with* DNA (positive signal). -If you include more than two images, you will not receive any additional credit. --> | <!-- INSTRUCTIONS: (1) Show ONE image where you drew a circle around the droplet with the freehand tool for any sample with *no* DNA. (2) Show ONE image where you drew a circle around the droplet with the freehand tool for a sample *with* DNA (positive signal). -If you include more than two images, you will not receive any additional credit. --> | ||
'''Negative''' | |||
[[Image:Lab5NegativeOval.jpg]] | |||
'''Positive''' | |||
[[Image:Lab5PositiveOval.jpg]] | |||
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<!-- INSTRUCTIONS: Show a table for the ImageJ calf thymus DNA data. '''To save time on typing a new Wiki table from scratch''', use THIS TOOL to auto-generate a Wiki table: http://excel2wiki.net/wikipedia.php. 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. --> | <!-- INSTRUCTIONS: Show a table for the ImageJ calf thymus DNA data. '''To save time on typing a new Wiki table from scratch''', use THIS TOOL to auto-generate a Wiki table: http://excel2wiki.net/wikipedia.php. 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. --> | ||
[[Image:Lab5PatientRawData.jpg]] | |||
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<!-- INSTRUCTIONS: Place an image of your Excel plot with a line of best fit here. --> | <!-- INSTRUCTIONS: Place an image of your Excel plot with a line of best fit here. --> | ||
[[Image:Lab5CalibrationCurve.jpg]] | |||
'''PCR Results Summary''' | '''PCR Results Summary''' | ||
<!-- INSTRUCTIONS: You completed 8 PCR reactions and used the SYBR Green I staining and imaging technique to measure the amount of amplified DNA in each PCR reaction. You used a standard curve (based on known concentrations of calf thymus DNA) to convert INTDEN values into DNA concentration. Your positive control and negative control samples should be used as '''threshold''' values for determining whether an unknown (patient) sample is truly positive or negative. Replace the underscore with your claculated initial concentration values.--> | <!-- INSTRUCTIONS: You completed 8 PCR reactions and used the SYBR Green I staining and imaging technique to measure the amount of amplified DNA in each PCR reaction. You used a standard curve (based on known concentrations of calf thymus DNA) to convert INTDEN values into DNA concentration. Your positive control and negative control samples should be used as '''threshold''' values for determining whether an unknown (patient) sample is truly positive or negative. Replace the underscore with your claculated initial concentration values.--> | ||
* Our positive control PCR result was | * Our positive control PCR result was 2.5 μg/mL | ||
* Our negative control PCR result was | * Our negative control PCR result was 0 μg/mL | ||
<u>Observed results</u> | <u>Observed results</u> | ||
<!-- INSTRUCTIONS: Replace the underscore with each patient ID. After the colon, write both a qualitative (what the images looked like) and a quantitative description (μg/mL) of what you observed --> | <!-- INSTRUCTIONS: Replace the underscore with each patient ID. After the colon, write both a qualitative (what the images looked like) and a quantitative description (μg/mL) of what you observed --> | ||
* Patient | * Patient 96837 : The droplet did not have a green shade that correlated with the positive control. | ||
* Patient | * Patient 39617 : The droplet glowed green. This was a similar shade to that of the positive control. | ||
<u>Conclusions</u> | <u>Conclusions</u> | ||
<!-- INSTRUCTIONS: Compare each patient's results to the positive control value and the negative control value. Draw a final conclusion for each patient (positive or negative) and explain why you made that conclusion. --> | <!-- INSTRUCTIONS: Compare each patient's results to the positive control value and the negative control value. Draw a final conclusion for each patient (positive or negative) and explain why you made that conclusion. --> | ||
* Patient | * Patient 96837 : Negative. This patient's sample did not contain enough mutated DNA for the SYBR Green I to react and therefore it was concluded that the sample was negative. | ||
* Patient | * Patient 39617 : Inconclusive. This sample did not fully correlate with either the positive or negative control and therefore, it was determined to be inconclusive. | ||
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'''Background: About the Disease SNP''' | '''Background: About the Disease SNP''' | ||
<!-- INSTRUCTIONS: This content is from PCR Lab D. Write a summary, at least five sentences long, about the disease SNP in your own words. --> | <!-- INSTRUCTIONS: This content is from PCR Lab D. Write a summary, at least five sentences long, about the disease SNP in your own words. --> | ||
Disease SNP's is a mutation in the DNA that causes a higher risk factor for certain diseases. The acronym SNP stands for single nucleotide polymorphism, and refers to the body's tendency and ability to change a single base pair, morphing an entire section of the genome. The specific SNP that was tested in this lab was a SNP for for cardiovascular disease. A normal sequence in the 8:19956018 region looks like AATCTGGGCTATGAGATCAA. However, in this particular mutation, AATCTGGGCTATGAGATCAA changes to AGTCTGGGCTATGAGATCAA. As a result, the organism with this new, morphed sequence is at risk of cardiovascular disease, specifically (in our case) coronary heart disease. | |||
'''Primer Design and Testing''' | '''Primer Design and Testing''' | ||
<!-- INSTRUCTIONS: Write a short summary of the results of your primer test. Underneath your summary, include a screen capture of the results web page. You may crop the image so that it only includes the relevant information. --> | <!-- INSTRUCTIONS: Write a short summary of the results of your primer test. Underneath your summary, include a screen capture of the results web page. You may crop the image so that it only includes the relevant information. --> | ||
The primer test showed that there was a mutation that occurred in the patients DNA sequence. | |||
Latest revision as of 00:22, 8 April 2015
BME 100 Spring 2015 | 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
LAB 5 WRITE-UPProcedureSmart Phone Camera Settings
Data AnalysisRepresentative Images of Negative and Positive Samples
PCR Results Summary
Observed results
Conclusions
SNP Information & Primer DesignBackground: About the Disease SNP Disease SNP's is a mutation in the DNA that causes a higher risk factor for certain diseases. The acronym SNP stands for single nucleotide polymorphism, and refers to the body's tendency and ability to change a single base pair, morphing an entire section of the genome. The specific SNP that was tested in this lab was a SNP for for cardiovascular disease. A normal sequence in the 8:19956018 region looks like AATCTGGGCTATGAGATCAA. However, in this particular mutation, AATCTGGGCTATGAGATCAA changes to AGTCTGGGCTATGAGATCAA. As a result, the organism with this new, morphed sequence is at risk of cardiovascular disease, specifically (in our case) coronary heart disease. Primer Design and Testing The primer test showed that there was a mutation that occurred in the patients DNA sequence.
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