BME103 s2013:T900 Group2 L3: Difference between revisions
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| [[Image:BME103student.jpg|100px|thumb|Name: William Scott<br>Role(R&D Scientist)]] | | [[Image:BME103student.jpg|100px|thumb|Name: William Scott<br>Role(R&D Scientist)]] | ||
| [[Image:Funny-monkey-05.jpg|100px|thumb|Name: Andy Son<br>Protocol Planner]] | | [[Image:Funny-monkey-05.jpg|100px|thumb|Name: Andy Son<br>Protocol Planner]] | ||
| [[Image: | | [[Image:404005_4622115081677_1186647743_n.jpg|100px|thumb|Mitch Riggs <br> Open PCR Machine Engineer/ Team Leader]] | ||
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'''We concluded that we would ''Want'' a good system to have:''' | '''We concluded that we would ''Want'' a good system to have:''' | ||
* [Want #1 - | * [Want #1 - Low cost. Nobody wants to pay more than they have to.] | ||
* [Want #2 - | * [Want #2 - Portable and compact. A small portable machine makes use much simpler and hassle-free for use anywhere.] | ||
'''We concluded that a good system ''Must Not Have'':''' | '''We concluded that a good system ''Must Not Have'':''' | ||
* [Must Not Have #1 - | * [Must Not Have #1 - Bad USB connectivity. The whole experiment was dependent on transferring data via USB. If it doesn't work the whole system is compromised.] | ||
* [Must Not Have #2 - | * [Must Not Have #2 - Fire hazard. Dangerous equipment is worse than broken equipment. Safety is #1.] | ||
'''We concluded that a good system ''Should Avoid'':''' | '''We concluded that a good system ''Should Avoid'':''' | ||
* [Should Avoid #1 - | * [Should Avoid #1 - Inaccurate time readout. Accurately estimating time can increase productivity a lot.] | ||
* [Should Avoid #2 - | * [Should Avoid #2 - Slow amplification. Three hours for one batch of DNA is too long to wait in commercial applications.] | ||
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<!-- If your team decided to change any of the machinery/ devices, summarize the new features here and delete the '''We chose keep the devices the same as the original system''' section. --> | <!-- If your team decided to change any of the machinery/ devices, summarize the new features here and delete the '''We chose keep the devices the same as the original system''' section. --> | ||
'''We chose to include these new features''' | '''We chose to include these new features''' | ||
* Feature 1 - | * Feature 1 - We thought we would provide the PCR with an additional flourimeter apparatus (designed like a mini-box that a smart phone can be incorporated into) as well as the necessary chemicals. | ||
* Feature 2 - | * Feature 2 - We would provide an app for smart phone that the user buys. The app would in theory do all the necessary calculations in one easy step (pic->result), basically skipping the image j analysis. | ||
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Latest revision as of 08:23, 16 April 2013
BME 103 Spring 2013 | Home People Lab Write-Up 1 Lab Write-Up 2 Lab Write-Up 3 Course Logistics For Instructors Photos Wiki Editing Help | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
OUR TEAMLAB 3 WRITE-UPOriginal System: PCR ResultsPCR Test Results
* Ave. INTDEN (Patient 91562)= 356035.3 *Ave. INTDEN (Patient 25235)= 452626.3
Bayes Theorem equation: P(A|B) = P(B|A) * P(A) / P(B)
Calculation 3: The probability that the patient will develop cancer, given a cancer DNA sequence.
New System: Design StrategyWe concluded that a good system Must Have:
We concluded that we would Want a good system to have:
[[Image:]]==New System: Machine/ Device Engineering==
KEY FEATURES We chose to include these new features
New System: ProtocolsDESIGN We chose to include these new approaches/ features
Stage one: 1 cycle, 95 degrees Celsius for 3 minutes
New System: Research and DevelopmentBACKGROUND Polymerase Chain Reaction (PCR) is a scientific method that utilizes DNA Polymerase to create a complimentary base strand from a template strand of DNA. Triphosphate nucleotides align with open DNA strands and DNA polymerase works to link the complementary nucleotide bases together growing strands through both condensation and hydroysis reactions. Through these mechanisms it is possible to target specific positions on the template DNA sequence that a scientist intends to amplify(PCR 1). When the PCR process is completed the targeted DNA sequence containing the single-nucleotide polymorphism (SNP) will have manufactured over a billion copies (amplicons). A SNP essentially is a type of gentic variation among organisms which represents a difference in a single nucleotide. For example, a SNP may replace a nucleotide cytosine (C) with a nucleotide thymine (T) in a certain part of an organisms DNA. These SNPs can be utilized as biological markers which in turn can help locate genes that have associative properties that contribute to the formation of harmful diseases. The targeted SNP for this research was rs17879961. This SNP is found in Humans (Homo sapiens) and represents a variation class SNV, which stands for single nucleotide variation. Furthermore, This SNP is a variant of the CHEK2 gene (Checkpoint kinase 2) which if present in a person's genome may increase their risk of developing breast cancer. This SNV signifies a single base change from a Thymine (T) to a Cytosine (C) located on chromosome 22 and its clinical significance is classified as a pathogenic allele. For example, this mutation would alter the normal alelle ATT and the middle position resulting the cancer associated allele ACT.
Primers for PCR Cancer allele forward primer: -> TTGAGAATG[TCA]CGTATGTAT Disease alleles will yield PCR products because the target amplicon is only associated with the cancer DNA sequences. Thus primer annealing will following base pairing rulese when it binds with the template strand. For example, triphosphate nucleotides align with open DNA strands and DNA polymerase works to link the complementary nucleotide bases together growing strands through both condensation and hydroysis reactions. The presence of a primer is required so that polymerase can proceed with directing the new nucleotides in place. Through these mechanisms it is possible to target specific positions on the template DNA sequence that a scientist intends to amplify. When the PCR process is completed the targeted DNA sequence containing the single-nucleotide polymorphism (SNP) will have manufactured over a billion copies (amplicons). Sources:
Our primers address the following design needs
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