BME100 f2013:W900 Group14 L6

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BME 100 Fall 2013 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: Austin Davis
Name: Andrew Cable
Name: Rachael Brard
Name: Omar Eltohamy

PCR Beginnings


Computer-Aided Design


The tinkerCAD tool is an online modeling program that allows the user to depict physical concepts in 3 dimensional space. These concepts can then be printed using a 3D printer. We used the program to imagine modifications to the PCR tubes used in the OpenPCR. The tubes we designed were all connected for more efficient transportation of the tubes. The modified tubes also had indicated labeling sites on each tube to remind the user that they should label their tubes for sake of better organization.

Implications of Using TinkerCAD for Design

It is very easy to use TinkerCAD to design practical items. A camera holder for the lab would be a perfect example of an item that needs to be redesigned on TinkerCAD. It has a simple rectangular shape and would be easy to mold on the design website. This apparatus was chosen because it failed multiple times throughout the lab. The smartphones used in the lab were too top-heavy to be held with the existing camera holder, so a more stable design for the holder is needed. The design on TinkerCAD could have a completely altered shape, or just one side of the camera rack could be extended to prevent the camera from falling. A simple edit to the design of a camera holder on TinkerCAD would greatly improve the results in the lab.

Feature 1: Cancer SNP-Specific Primers

Background on the cancer-associated mutation

The SNP rs17879961 is a pathogenic variation of the CHEK2 gene in humans, it is one of 25 SNPs associated with a high risk of breast cancer, as well as one of three SNPs that are closely associated with a risk of lung cancer, especially as brought on by tobacco use. It most commonly appears on the 22nd of the 23 pairs of chromosomes in humans, as causes an inhibition in CDC25C phosphotase, interfering with the mitosis stabilizing protein, p53, which results in an interruption of the cell cycle.

Primer design

  • Forward Primer: A-C-T-C-A-C-T-T-A-A-A-C-C-A-T-A-T-T-C-T
  • Cancer-specific Reverse Primer: G-G-T-C-C-T-A-A-A-A-A-C-T-C-T-T-A-C-A-C

How the primers work:
Primers are enzymes that bond to complementary, opposite ends of a desired gene sequence, following its denaturing into two separate strands, allowing for a translation enzymes, usually DNA Taq Polymerase to bond to the these points as well, and then copy the desired section of DNA.

Feature 2: Consumables Kit

The consumables will be packaged with all of the kit's necessary components. Included will be PCR tubes in a sealed container, a separate holder for the PCR tubes, the PCR mix, a micropipet with extra tips, sample solutions for micropipetting practice and an instruction manual. The packaging plan addresses that students using the micropipets may have little to no experience, so extra micropipet tips and practice solutions are provided. The instruction manual would have separate instructions for the practice solutions. The solution in the PCR tube would change to a certain color when the correct volumes of two solutions were combined. This would allow students to check their micropipetting work before they begin the lab.

This is an example of how our consumables kit would be packaged. Our kit would have an additional manual and small bottles of solutions.

Feature 3: PCR Machine Hardware
The PCR machine is an integral part of the system in our experiment. As of its current use as well as composition, it is perfect as it is. The Open PCR machine contains a LCD display at the top, helping to indicate how long the system will take to complete one circle, and the total allotted time for the entire procedure. It contains a circuit board at the bottom to help with the LCD display and the store the information of the entire process. The power supply of the machine is located on the left hand side at the back of the machine, where it's connected to the heater. This is already a convenient place for it, as it protects that integral component from harm. It also has a conveniently placed cooling fan next to the heater, helping to counter the heat that will arise from the use of the machine. Lastly, it has a sample holder and heating lid, having a good place to put the samples and be used to hold the Open PCR machine. Overall, it is already an excellent model with no possible need for changes. It also comes at quite the price of $599, a solid price for a form of machinery that is able to perform it's job with its multiple aspects. The only possible suggestion would be a heater that provides more energy, or a circuit board with a stronger chip to hold more data for more PCR cycles.

Feature 4: Fluorimeter Hardware

The fluorimeter operates by subjecting a liquid sample containing a fluorescent agent to very mild ultra-violet radiation, activating the fluorescent agent to produce a visible light, indicating its presence and activation. Such agents, particularly SYBR Green require the presence of complete strands of DNA, containing both halves of the double helix so it can bond to these molecules and be subsequently activated. It will come pre-assembled with the package, and provide a convenient means of determining whether or not one possesses the gene of interest.

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 CHEK2 PCR for predicting cancer. Please do NOT type the actual numerical values here. Just refer to them as being "less than one" or "very small." The instructors will ask you to submit your actual calculations via e-mail. We are doing so for the sake of academic integrity and to curb any temptation to cheat.]