BME103:T930 Group 2: Difference between revisions
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==Results== | ==Results== | ||
[[Image:BME103_Group2_CALFTHYMUS.jpg|150px|Calf Thymus Trial]] | [[Image:BME103_Group2_CALFTHYMUS.jpg|150px|Calf Thymus Trial]] | ||
Positive Control | |||
[[Image:BME103_Group2_WATER.jpg|150px|Water Trial]] <br><br> | [[Image:BME103_Group2_WATER.jpg|150px|Water Trial]] <br><br> | ||
[[Image:BME103_Group2_SAMPLE_1-1.jpg|150px|Patient ID 15308 Sample 1]] | [[Image:BME103_Group2_SAMPLE_1-1.jpg|150px|Patient ID 15308 Sample 1]] | ||
[[Image:BME103_Group2_SAMPLE_1-2.jpg|150px|Patient ID 15308 Sample 2]] | [[Image:BME103_Group2_SAMPLE_1-2.jpg|150px|Patient ID 15308 Sample 2]] | ||
[[Image:BME103_Group2_SAMPLE_1-3.jpg|150px|Patient ID 15308 Sample 3]] <br><br> | [[Image:BME103_Group2_SAMPLE_1-3.jpg|150px|Patient ID 15308 Sample 3]] <br><br> | ||
[[Image:BME103_Group2_SAMPLE_2-1.jpg|150px|Patient ID 36372 Sample 1]] | [[Image:BME103_Group2_SAMPLE_2-1.jpg|150px|Patient ID 36372 Sample 1]] [[Image:BME103_Group2_SAMPLE_2-2.jpg|150px|Patient ID 36372 Sample 2]] | ||
[[Image:BME103_Group2_SAMPLE_2-2.jpg|150px|Patient ID 36372 Sample 2]] | |||
[[Image:BME103_Group2_SAMPLE_2-3.jpg|150px|Patient ID 36372 Sample 3]] | [[Image:BME103_Group2_SAMPLE_2-3.jpg|150px|Patient ID 36372 Sample 3]] | ||
Revision as of 11:41, 15 November 2012
BME 103 Fall 2012 | Home People Lab Write-Up 1 Lab Write-Up 2 Lab Write-Up 3 Course Logistics For Instructors Photos Wiki Editing Help | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
OUR AWESOME TEAMLAB 1 WRITE-UPInitial Machine Testing
Unplugging the LED interface cable from the processing chip caused the display of the machine to turn off. The blank screen meant that the machine stopped sending data to display. Unplugging anything from the circuit board causes it not to work because no electricity can be sent.
Test Run Our initial testing of the PCR machine went quite well. We used the Open PCR software to program our custom cycle quite easily. Once the PCR was connected to the computer via USB we continued to run the trial. During the run we made sure that the temperature displayed on the LED display match the temperature on the computer program. The temperatures matched the entire duration of the experiment. The test run carried out flawlessly, just a bit slowly.
ProtocolsPolymerase Chain Reaction
Stage one: 1 cycle, 95°C for 3 minutes Stage two: 35 cycles, 95°C for 30 seconds, 57°C for 30 seconds, 72°C for 30 seconds Stage three: 72°C for 3 minutes Final hold: 4°C
Patient 1
Patient 2
Flourimeter Assembly Instructions: 1. Gather materials (PCR Machine, tools optional)
Research and DevelopmentSpecific Cancer Marker Detection - The Underlying Technology The r17879961 DNA was sequenced to determine the chain of nucleotides that it is composed of. A section of this DNA shows a change in the allele sequence; one which might indicate cancer. In the sequence, a change from "ATT" to "ACT" is the specific indication marker for cancer. The artificial primer that is introduced to the DNA chain is meant to be a complimentary strand that matches up with the "ACT" and surrounding nucleotide sequence ("TGA"). When the primer attaches successfully, it allows the Taq polymerase to finish attaching nucleotides to the sequence. The number of strands will be doubled in this case, and by using the PCR replication machine, the sample will be heated and cooled in specific intervals. These intervals are meant to manipulate the DNA and do things such as separate a strand, cool it down so it is able to bind, as well as stretch it out. This process will, ultimately, result in exponential DNA replication. If the primer does not attach successfully, then this means the person does not have a cancer-indicating sequence, and it will, therefore, not replicate the DNA exponentially. If the DNA replicates exponentially, then the fluorescent dye will show, and this would indicate a cancerous genome.
The illustration below shows the PCR process when the primer attaches to the DNA and the Taq polymerase and is able to complete the DNA chain, in coordination with the PCR machine temperature cycles. It is shown that throughout the process, the DNA replicates at an exponential rate.
These matched up with the section of the DNA in the 22nd chromosome if the sequence did indicate cancer. The cancer sequence would be complimentary to the primer, it is: "TACACTGCA". This would yield a positive result A non-cancerous sequence is shown below ("TACATTGCA"), which would not attach to the primer and would yield a negative result. When the primer attaches to the cancerous sequence, it works, and the replication process can begin: When the primer tries to attach to a non-cancerous sequence, it fails, because the "T" and "G" do NOT connect, and therefore the replication process is not exponential:
Results
Given the results of all the DNA testing and evaluation we conclude that Patient 1 (ID 15308) contains the cancerous gene tested for, and that Patient 2 (ID 36372) did not.
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