BME100 f2013:W900 Group3 L6

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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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OUR COMPANY

Name: Marissa Kulick
Name: Blake Woods
Name: Shaun Wootten
Name: Bryce Gonzales

Thermo Diagnostics


LAB 6 WRITE-UP

Computer-Aided Design

TinkerCAD

TinkerCAD was is a free online tool used to create simple 3D files that can be saved as .stl which can be used in more advanced programs or even 3d printed. On Nov 20th, we used it to quickly mock up an alteration to the concept of the flourimeter, which we thought was a little to big and bulky. Not only did the program allow us to include a visual document in the report, but it also allowed our team members to more effectively communicate the concepts that were difficult to explain in words.


Above is the redesigned PCR tubes that were both connected and reoriented using TinkerCAD software


Implications of Using TinkerCAD for Design

The redesign of the flourimeter was done using TinkerCAD software. The speed and simplicity at which a 3D technical image can be created allowed for team members to do more in less time. While the mock up wasn't anything that was ready to be printed and utilized as is, it did perfectly illustrate a concept and allow the team to all be on the same page in the redesign. If it was required, it would be possible to create a .stl file with enough precision to 3D print much of the flourimeter turning out a working prototype in less than a day.




Feature 1: Cancer SNP-Specific Primers

Background on the cancer-associated mutation

rs17879961 is a pathogenic mutation found on the 22nd chromosome on the CHEK 2 gene of homo sapiens. SNPs in the CHEK2 gene have been linked to inheritable cancer, as the gene normally produces a protein called checkpoint kinase 2, which functions in tumor suppression.


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 designed sequences of DNA that allow for specificity in reproducing genetic material. The primers will bind around the gene of interest, before (5') desired section of DNA on both strands. Two strands are needed because while the two strands are compliments of each other, they are not identical. In addition, DNA has to be extended in the 3' direction by the primase, and therefore will need to sit over a separate portion of the DNA. By choosing a primer of approximately 20 base pairs, there is enough specificity to ensure that only the gene of interest is extended.



Feature 2: Consumables Kit

Included in the consumables kit will be all plastics, the micropipettor, and reagents. Also added will be labels to our PCR tubes to avoid any confusions and/or mistakes. To avoid human error in regards to the micropipettor, an instructional DVD will be included in the kit, and the instructions will reiterate the importance of watching this instructional video prior to any use of the micropippetor. This will eliminate any air bubble problems or difficulties obtaining all the liquid materials from the PCR tubes.


Feature 3: PCR Machine Hardware


The PCR Machine will be used to log the information recorded during the process. The PCR machine will be used in the experiment to duplicate the DNA to detect the cancerous segment of the DNA by replicating only the cancerous sequence composed in the DNA. The PCR machine will do this by denaturing the DNA at 95 degrees Celsius where the DNA is separated and annealed. After the annealing process begins primers that are predesigned to bind only to specific DNA, the cancerous DNA, attach onto the DNA segments. The DNA then goes through a synthesis where the DNA is heated and cooled and the DNA can stretch completely and then replicate.

The weakness found by the PCR machine is that the machine has to be hooked up to a computer to record and log the data, which could be possibly done easier if we could implement a Bluetooth device into the PCR machine and have the data logged to your smartphone wirelessly. This would also mean on-demand results with the constant stream of data going from the PCR and the smartphone making the system more efficient for the user with logging the data during the experiment.


Feature 4: Fluorimeter Hardware

[Instructions: Summarize how you will include the 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 REALLY awesome and easy to score.]

[Instructions: IF your group has decided to redesign the fluorimeter to address any major weakness discussed by your group or mentioned by others (see the Virtual Comment Board Powerpoint files on Blackboard, Lab Week 12) 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 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.]