BME100 s2014:T Group1 L6

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Owwnotebook icon.png BME 100 Spring 2014 Home
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
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Name: Arianna Moreno
Name: Pritish Char
Name: Chris Joseph Ibarra
Name: Jared Smith
Name: Almoustafa Abbas

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Computer-Aided Design

TinkerCAD is a browser based 3D design tool. It allows for the creation of digital designs to be 3D printed into objects. We used the TinkerCad tool to design our improved PCR component. The changes were made to imporove the weakness found in the PCR machine.

Our Design
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The design we chose was primarily considered to make the PCR machine more convenient and less bulky. This allowed for the implementation of a bigger display which allowed for more information about the processes going on to be shown on the bigger display (blue screen shown on tinkercad image). Also by using the "slide" implementation,it allows for the samples to be easily accessible when compared to the older design of the PCR machine(the gray tray is the sliding drawer). There are also rubber ends at the corners for durability and a handle on each side of the PCR for convenience.

Feature 1: Disease SNP-Specific Primers

Background on the disease-associated mutation

SNP: a single nucleotide polymorphism , nucleotide is the basic building block of DNA, it is A compound consisting of a nucleotide lined to a phosphate group. polymorphism is a common variation in the DNA. SNP is when a single nucleotide differs from two different organisms of the same species. some SNP can have harmful effect on the organism which could causes diesease. genes related diseases such as cancer and diabetes. for example, rs237025; is a C/T variation in chromosome 6 in homosapians. it is linked to the hereditary disease known as diabetes type-1.

Primer design

  • Disease SNP-specific Forward Primer: 5’ A A C C A C G G G G A T T G T C A A T G
  • Reverse Primer: 5’ A G T T T T C T A A T T G A G A A T G C

How the primers work: Primers are complementary DNA sequence for DNA allele, they come in pair, one forward (complementary to the non coding strand) and the reverse primer (complementary to the coding strand). primers bond to the specified allele and the DNA polymerase replicate that specific allele and only that allele because the polymerase can only synthesize molecules with that primer.

Feature 2: Consumables Kit

Consumables Kit:

  • Micropipette
  • PCR Tubes
  • SYBR Green I tubes
  • Micropipette Tips
  • Tube Tray
  • Glass Slides

The MASICS Solutions Open PCR Machine will come with a preassembled consumables kit that contains labeled tubes, PCR mix solutions, primers and micropipettor tips. The items are plastic to ensure cost efficiency. To make every step easier for the user, our consumables kit is color coordinated for each item. Similarly, the tips will be separated (on opposite sides) of the solutions and primers to eliminate any confusion. The PCR also comes with a short and simple step-by-step tutorial displayed on our new display screen and can be looked at whenever necessary.

The problem we had with the consumables previously was that the pipette may have been taking inaccurate measurements because the twisting mechanism was not always precise, we decided that the current pipette was the best fit for our experiments and should not be addressed at this time.

Feature 3: Hardware - PCR Machine & Fluorimeter

Our new design for the PCR machine is a convenient, less bulky design that allows for a bigger, touchscreen display. This way, the screen can display more information for the user to see and understand. We will be implementing a sliding method for the samples that increases the accessibility. The way this works is that the PCR will no longer have a lid but instead have a drawer for the samples that slides in an out of the PCR machine for the user to insert the tubes easily and accurately. In this sliding drawer, we made more holes for the sample tubes. We also made it so that it is much easier to access the inside by reducing the number of screws to remove. Now there are only six screws and once they are removed you can just slide the top right off. Also, for durability, we added rubber ends at the corners of the PCR to absorb any fall damage. Another key component of our machine is the larger base. The larger base allows more surface area for more tubes and faster heat transfer.

The new design for the Fluorimeter consists of a dark, 3D printed plastic design with a small door that simulates a "doggy-door" to take the picture using a smart phone. Because it is 3D printed, the stand and fluorimeter pieces are connected and able to be adjusted.

In our assessment of the original design, our group concluded that the Open PCR top was fragile. We felt that it may have been releasing some of the needed heat for the reaction and we wanted to eliminate this problem so that the reaction could possibly go faster. The machine was not very user friendly as it had a small screen and also only allowed for a few samples. With our new design we fixed this by adding more holes and by taking off the lid design, we were able to expand the screen and make it touch screen.

The fluorimeter's original design let in a lot of light but with our dark plastic 3D printed design, the material will not reflect light and also will not let light enter through any small holes like we had in the cardboard box mechanism. Another problem we had when taking photos was that the system would usually move when constantly lifting and putting down the box. Our design eliminates these problems and makes it easier for the user.

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

The calculations seem to imply that the PCR is not terribly reliable for predicting positives, as the result of calculation three is much less than one. It is however, slightly more effective in predicting negatives, as the result of calculation four was relatively close to one. The results, in conjunction with one another, would imply that the PCR is not a very reliable way of predicting positive results, or negative results.