BME100 f2013:W900 Group11 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
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Name: John Sherman
Name: Diana Terreros
Name: Timothy Millea
Name: student
Name: student
Name: student

Cyber Green


Computer-Aided Design


The TinkerCAD tools we used in this lab were the Capsule by Marrisa, and the Banana by Rob Walch. The use of the Capsules is to indicate the amount of a substance that is in the tube by putting three lines on one side of the tube. These lines were added as a measurement tool. Lastly, the Banana tool was used to connect the tubes together to help keep them organized.

Implications of Using TinkerCAD for Design

One possible way TinkerCAD is used is to redesign objects to work and perform better. One example of this would be redesigning a camera holder. Maybe the camera holder doesnt fit all cameras. TinkerCAD can help one redesign it and create a holder which can transform to the cameras shape. This would allow the product to work and perform better.

Feature 1: Cancer SNP-Specific Primers

Background on the cancer-associated mutation

"rs17879961" is a SNP in the gene CHEK2 in humans. This gene is responsible for stopping tumor growth through preventing runaway mitosis growth. It does this through the production of checkpoint kinase 2, for which it is name. In this pathogenic polymorphism, the protein no longer functions because a thymine base has been replaced with a cytosine base, resulting in an amino acid substitution. This change is indicative of cancer, as the cell no longer checkpoints the cell cycle before mitosis. The SNP's numerical position is 29121087.

Primer design

  • Cancer-specific Reverse Primer: GGTCCTAAAAACTCTTACA

How the primers work: Primers bond to complimentary DNA to begin replication. When temperature within the PCR machine is elevated, double-stranded DNA is "unzipped" into single strands. The primer will then bond to the complimentary strand of DNA, and tac-polymerase will begin replication. The cancer-specific primer is complimentary to the cancer-specific SNP discussed above. It will then bond only to the cancer-specific sequence, and not the normal sequence. If no primer is bonded to DNA, tac-polymerase cannot bond, as the primer is need to begin the reaction because tac-polymerase only works in the 5'-to-3' direction. Therefore, if the DNA is benign, the primer cannot bond and the DNA is not replicated. If it is cancerous, the primer will bond and the PCR process will proceed, amplifying the DNA sample.

Feature 2: Consumables Kit

The consumables will be packages relatively the same way as the ones that we used in the lab. It was very nicely packaged with instructions and multiple supplies. the reason that the boxes were big was because of the supplies in it. It had to have a lot of micropipetting tips and tubes because they are disposable and to avoid contamination you have to throw them away. It is a huge waste to have to throw so many tubes away. our tubes will be made out of a material that can be reusable instead of being thrown away like the other ones. It will be made out of a material that can be washed and disinfected after using them. This way it reduces the size of the packaging because it will have enough tubes to only fill the heating plate. another weakness that the other tubes had were that they were not labeled. the tubes that we will be providing will be labeled for easyer use. there will be mostly clear tubes and some tinted tubes. these tubes will be used for the green dye. this way the dye doesnt get bleached by the lights and stays in perfect condition.

Feature 3: PCR Machine Hardware

the packaging for the PCR machine will be done in the same way, but will be packaged separately from the consumables. There were no major changes to the PCR Machine in terms of physical aspects. It will still be very user friendly and portable. The major problems with it is that it was so time consuming. In the PCR machine that we would make would have a system that would be able to heat and cool the samples at a more rapid rate. This reduces the time that it takes to complete the whole process. Another major weakness is that because it takes so long it is inconvenient to have such a small tray to hold the samples. In our PCR machine, it will be much larger to be able to hold more samples and get the total results faster. This increase in the top size of the PCR machine will also help the hold a better heating and cooling system that will also increase the rate that open PCR is done.

Feature 4: Fluorimeter Hardware

In our system, the fluorimeter will be utilized in the same way, to help detect the concentration of specific DNA in a sample. The slides used with the fluorimeter will remain the same as they did and adequate job in holding the liquid samples in a droplet form in order for it to be analyzed well.

Unlike other fluorimeters, our design will make it easier to adjust and hold the camera phone in place. First of all, the phone holder will be attached to the fluorimeter so that the camera will always be at a constant distance form the fluorimeter without having to constantly adjust. The distance will also be adjustable so it can suit any camera. Another thing that will be better in our design is the camera holder itself. We will make it adjustable in height so that one may position the camera where they want to. The holder will have clamps to hold the phone in place that are adjustable in width. This will make it so that any phone or camera may be used with our product without any difficulties in set up.

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.]