BME103:W930 Group3: Difference between revisions
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'''The Original Design'''<br> | '''The Original Design'''<br> | ||
[[Image:Openpcr.png]]<br> | [[Image:Openpcr.png]]<br> | ||
The Open PCR machine is designed to perform polymerase chain reactions which replicate DNA segments. Enzymes and nucleic acid are added to a sample of DNA. Then, primers are used to select a specific genetic sequences. Due to the thermal cycling that is done by the Open PCR machine the segment of DNA that is selected by the primers is exponentially replicated. Essentially the goal of the Open PCR machine is signal amplification. The signal that is being amplified is the selected DNA segment. This is very useful, because a genetic marker for a disease can be selected and then amplified so that doctors will know whether or not the patient has that specific sequence. This particular Open PCR machine is a relatively cheap and easy to use machine for completing this process. | The Open PCR machine is designed to perform polymerase chain reactions which replicate DNA segments. Enzymes and nucleic acid are added to a sample of DNA. Then, primers are used to select a specific genetic sequences. Due to the thermal cycling that is done by the Open PCR machine the segment of DNA that is selected by the primers is exponentially replicated. Essentially the goal of the Open PCR machine is signal amplification. The signal that is being amplified is the selected DNA segment. This is very useful, because a genetic marker for a disease can be selected and then amplified so that doctors will know whether or not the patient has that specific sequence. This particular Open PCR machine is a relatively cheap and easy to use machine for completing this process.<br> | ||
'''Experimenting With the Connections'''<br> | '''Experimenting With the Connections'''<br> | ||
Revision as of 00:33, 7 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 TeamLAB 1 WRITE-UP(Please finish by 11/7/2012) Initial Machine TestingThe Original Design If the Arduino UNO board is disconnected fron the LCD screen, then then LCD screen will not be able to display information; this includes information such as the current cycle of the PCR and the current tempereture. If the Arduino UNO board is disconnected from the 16-tube PCR block, then the LCD wouldn't be able to display any temperatures, this is because temperatures in the 16-tube block are not being monitored.
The experiences of first testing the Open PCR machine, on October 24th, 1012, were of mixed results. As for the set up of the Open PCR, things went fairly well. Connecting the Open PCR to a computer was not a problem and neither was finding a suitable location to let the machine run. However, the first computer we connected the Open PCR to had problems running the Open PCR software. The experiment design part of the software would not allow for editing of the number of cycle, resting temperature, time length of the cycles and all other variables of the experiment. The software might have been corrupted or the computer may not have been running correctly; whatever the case, the Open PCR had to be moved to another computer in order to solve this problem. The use of the second computer allowed for editing of the experimental variables and the initiation of the experiment. However, further problems arose once the experiment was in progress. From the beginning of the experiment the Open PCR machine being used took a considerable amount of time on the cooling part of the cycle, much longer than the other groups running the experiment. If the machine does not cool down correctly and to the right temperature, then the PCR cannot move onto the next cycle. And eventually, due to this problem, the Open PCR machine became stuck on the cooling part of cycle 5 of 30 and would not move forward in the experiment. After trouble shooting from TA's and the professor the problem could not be reverse and additional amplified DNA samples will have to be created for group 3.
ProtocolsPolymerase Chain Reaction Polymerase Chain Reaction is a biochemical technology that is used in molecular biology to amplify single/multiple copies of a piece DNA, generating thousands to millions of copies of a targeted DNA sequence. To do so, PCR relies on thermal cycling, which consists of repeated cycles of heating and cooling the samples in order to melt the DNA and have the enzymes replicate the targeted strand if found. Primers, which are short DNA fragments, have complementary sequences to the target strand of DNA, in addition to a DNA polymerase, which allows selective and repeated amplification of the target strand. As the cycles progress, the DNA is used as a template for exponential amplification (or creation of copies). How to Amplify a DNA Sample with PCR
Components of GoTaq® Colorless Master Mix
Fluorimeter Assembly ProcedureResearch and DevelopmentSpecific Cancer Marker Detection - The Underlying Technology
Bayes Rule: Predicting the possibility of cancer.
Bayes Theorem: (.008)/(.008+0.095)=7.8% (BONUS points: Use a program like Powerpoint, Word, Illustrator, Microsoft Paint, etc. to illustrate how primers bind to the cancer DNA template, and how Taq polymerases amplify the DNA. Screen-captures from the OpenPCR tutorial might be useful. Be sure to credit the source if you borrow images.)
Results(Your group will add the results of your Fluorimeter measurements from Week 4 here)
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