BME100 s2014:T Group10 L6: Difference between revisions

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[[Image: BME100_G10Th_Lab6PCRFront.jpg ‎|250px|OpenerPCR Deluxe with integrated whiteboard grid system.]]<br>
[[Image: BME100_G10Th_Lab6PCRFront.jpg ‎|250px|OpenerPCR Deluxe with integrated whiteboard grid system.]]<br>


''[Instructions: A short paragraph describing your design. Why did you choose this design? How is it different from the original OpenPCR design?]''<br>
At The Group 10s of Tomorrow (Ltd.) we strive for excellence, efficiency and extreme people-helping.  Accordingly, we at G10T (Ltd.) have taken it upon ourselves to solve a problem facing those who rely on a system of PCR and Fluorimetry to diagnose patients with various SNPs.  Traditionally, OpenPCR machines only have 16 spaces for PCR tubes.  This means only four patients with three replicates each (along with a positive and negative control) can be thermocycled at one time.  This bottleneck in efficiency increases costs, reduces productivity, increases costs, and most importantly prevents patients from getting quick and accurate diagnoses. <br><br>
At The Group 10s of Tomorrow (Ltd.) we strive for excellence, efficiency and extreme people-helping.  Accordingly, we at G10T (Ltd.) have taken it upon ourselves to solve a problem facing those who rely on a system of PCR and Fluorimetry to diagnose patients with various SNPs.  Traditionally, OpenPCR machines only have 16 spaces for PCR tubes.  This means only four patients with three replicates each (along with a positive and negative control) can be thermocycled at one time.  This bottleneck in efficiency increases costs, reduces productivity, increases costs, and most importantly prevents patients from getting quick and accurate diagnoses. <br><br>



Revision as of 06:45, 24 April 2014

BME 100 Spring 2014 Home
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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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The Group 10s of Tomorrow

Sean-Christopher Bradbury
Thursday Group 10 Member
Suyen Go
Thursday Group 10 Member
Nathaniel Kirkpatrick
Thursday Group 10 Member
Maya Robinson
Thursday Group 10 Member
Lissette Valle
Thursday Group 10 Member

The Group 10s of Tomorrow presents:
OpenerPCR Duluxe


LAB 6 WRITE-UP

Computer-Aided Design

TinkerCAD

TinkerCAD is a 3D imaging software used to create three-dimensional models and designs with ease. Those models can then be printed using a 3D printer. It has pre-built shapes that a person can utilize in combination with other shapes to create any 3D design they can think of. Also, there is an active design community where objects built by others are shared and built upon to make computer aided design more collaborative and easy.


Our Design


OpenerPCR Deluxe now with twice the capacity! OpenerPCR Duluxe with rotated double-wide heated lid! OpenerPCR Deluxe with integrated whiteboard grid system.

At The Group 10s of Tomorrow (Ltd.) we strive for excellence, efficiency and extreme people-helping. Accordingly, we at G10T (Ltd.) have taken it upon ourselves to solve a problem facing those who rely on a system of PCR and Fluorimetry to diagnose patients with various SNPs. Traditionally, OpenPCR machines only have 16 spaces for PCR tubes. This means only four patients with three replicates each (along with a positive and negative control) can be thermocycled at one time. This bottleneck in efficiency increases costs, reduces productivity, increases costs, and most importantly prevents patients from getting quick and accurate diagnoses.

In this landscape of inefficiency we humbly introduce OpenerPCR Deluxe. Its state-of-the art PCR tube system allows for 32 PCR tubes to be thermocycled at one time. This allows for 10 patients with three replicates each, along with one positive and one negative control, to be processed for fluorimetry at once. By increasing the patient capacity by 250%, we alleviated the troublesome bottleneck inherent in the original OpenPCR design.

The educated researcher may ask, "but how will I keep all of those PCR tubes straight?" and they ask a valid question. 16 tubes are hard enough to keep track of, especially when the labels are sometimes removed during thermocycling. How would a researcher be expected to keep tabs on twice that number of tubes? With OpenerPCR Deluxe the researcher does not have to! We have integrated state-of-the-art Whiteboard technology to allow for easy sample labeling.


Feature 1: Disease SNP-Specific Primers

[Instructions: This information will come from the exercises you did in PCR Lab B.]

The disease for the SNP-specific primers derives from the variation of single nucleotide polymorphisms that varies throughout a variation of species. Through this source of genetic specification scientists are able to detect a single has pair mutation simply from a specific locus. Since the loci of a humans genetic code has been conserved during evolution this can serve as a quantitative trait analysis when evaluation the affirmation of a certain disease.

Harbron, Rapley S. "SNP Genotyping." Wikipedia. Wikimedia Foundation, 18 Apr. 2014. Web. 21 Apr. 2014.

[Instructions: Use the answers from questions 3 - 7 to compose, in your own words, a paragraph about rs237025]


Primer design

  • Disease SNP-specific Forward Primer: [Instructions: type the sequence of the forward primer]
  • Reverse Primer: [Instructions: type the sequence of the reverse primer]

How the primers work: [Instructions: explain what makes the primers disease-sequence specific. In other words, explain why the primers will amplify DNA that contains the disease-associated SNP, and will not exponentially amplify DNA that has the non-disease allele.]



Feature 2: Consumables Kit

[Instructions: Summarize how the consumables will be packaged in your kit. You may add a schematic image. An image is OPTIONAL and will not get bonus points, but it will make your report look awesome and easy to score.] The consumables in the improved PCR machine will consist increasing the amount of samples which will elad to also increasing the amount of consumables needed in the process. This will not only make amount of samples larger retains essential data such as negative and positive controls. The PCR machine will consist of:

  • PCR Tubes(32)
  • PCR Reaction Mix(32 with 50 μL each)
  • Template DNA with Primer(32)
    • Positive Control(1)
    • Negative Control(1)
    • Patient 1 DNA with primer (3 replicates)
    • Patient 2 DNA with primer (3 replicates)
    • Patient 3 DNA with primer (3 replicates)
    • Patient 4 DNA with primer (3 replicates)
    • Patient 5 DNA with primer (3 replicates)
    • Patient 6 DNA with primer (3 replicates)
    • Patient 7 DNA with primer (3 replicates)
    • Patient 8 DNA with primer (3 replicates)
    • Patient 9 DNA with primer (3 replicates)
    • Patient 10 DNA with primer (3 replicates)
  • 200μL Micropipeter
  • Disposable Tips

[Instructions: IF your consumables packaging plan addresses any major weakness(es), explain how in an additional paragraph.] The weakness of doubling the tubes that will be tested at one time will be keeping track of which tube is which because there are so many tubes that have to be accounted for. In the midst of tracking the data, tubes will be easily confused and possibly identified as a wrong subject or replicate.The packaging plan addresses weaknesses confusion of the tubes in the rack. Our tube rack will contain clear labels identifying the patients and the replicates.



Feature 3: Hardware - PCR Machine & Fluorimeter

[Instructions: Summarize how you will include the PCR machine and fluorimeter in your system. You may add a schematic image. An image is OPTIONAL and will not get bonus points, but it will make your report look really awesome and easy to score.] The PCR machine will be doubled therefore being able to test more two and a half as much subject compared to the original version. The amount of tubes will be doubled

[Instructions: IF your group has decided to redesign the PCR machine and/or Fluorimeter to address any major weakness(es), explain how in an additional paragraph.]


Bonus Opportunity: What Bayesian Stats Imply About The BME100 Diagnostic Approach

[Instructions: This section is OPTIONAL, and will get bonus points if answered thoroughly and correctly. Here is a chance to flex some intellectual muscle. In your own words, discuss what the results for calculations 3 and 4 imply about the reliability of PCR for predicting the disease. Please do NOT type the actual numerical values here. Just refer to them as being "close to one" or "very small." The instructors will ask you to submit your actual calculations via a Blackboard quiz. We are doing so for the sake of academic integrity and to curb any temptation to cheat.]