BME100 f2013:W900 Group9 L6

BME 100 Fall 2013	Home People 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 Photos Wiki Editing Help
OUR COMPANY Name: Allison Lind Name: Julianna A. Brunner Name: Neel J. Patel Name: Callie M. LaMarche Name: student LAB 6 WRITE-UP Computer-Aided Design TinkerCAD TinkerCAD is a free online tool used to create 3D models. TinkerCAD was used to optimize the rendering of the current PCR tubes. The software allows making changes to shape, color, text, etc. Common usage of the TinkerCAD software is to create a design of a 3D object which can then be sent to a 3D printer. What our group did to improve the PCR tubes was we added labels to each separate tube to make sorting easier. We also added a small mechanism on the lid of the tubes for a vacuum pipe to be inserted. This way the PCR tubes can be air tight. Implications of Using TinkerCAD for Design TinkerCAD can be used to create and modify virtually anything, including the camera holder used to keep smartphone cameras steady in the experiment. For example, TinkerCAD can modify the dimensions of the slot for the phone, allowing custom holders to be printed for any brand or type of smartphone. The angle of the slot can be modified as well, in order to keep the phone at a perfect 90° angle to the table. Feature 1: Cancer SNP-Specific Primers [Instructions: This information will come from the Week 9 exercises you did in lab. Your notes should be in a pdf file that is saved on Blackboard under your group.] Background on the cancer-associated mutation [Instructions: Use the answers from questions 3, 4, 5, and 7 to compose, in your own words, a paragraph about rs17879961] Primer design Forward Primer: [Instructions: write the sequence of the forward primer] Cancer-specific Reverse Primer: [Instructions: write the sequence of the forward primer] How the primers work: [Instructions: explain what makes the primers cancer-sequence specific. In other words, explain why the primers will amplify DNA that contains the cancer-associated SNP rs17879961, and will not exponentially amplify DNA that has the non-cancer 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 Kit will be packaged much like it already is. There will be sterilized, ordered tips in a sealed rack that are ready for use. Along with the tips, the micropipettor is accurate as is and will have no changes made to the actual device. The goal is to keep the new devices as simple to use as the ones that are already use, so the consumer has no issues adjusting. The only difference in the Consumables Kit is the material of the tips. The tips will still be made of plastic, but they will be covered in a hydrophobic material on the inside to ensure all the liquid is being released while pipetting. This will give the already accurate devices an even smaller margin for error. As for the issue of waste, there is not much that can be done without sacrificing the sterility of the tips. The tips will still have to be changed after each use. [Instructions: IF your consumables packaging plan addresses 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.] Feature 3: PCR Machine Hardware The Open PCR (picture shown above) is a machine that uses heating and cooling cycles to multiply DNA strands. The DNA heats to 95 degrees Celsius, separating the double helix structure of the DNA. Then, it cools down to 57 degrees Celsius to attach the primers to the beginning of the desired strand. The final step of the cycle reheats the DNA to 72 degrees Celsius. This attaches the DNA polymerase, an enzyme which attaches the complimentary bases to the template DNA strand, to the primer, replicating the DNA. After 35 cycles of replicating, there is an abundance of the desired strand of DNA, outnumbering the initial DNA. The PCR machine is a vital tool to have in lab because when working with DNA it is not easy to receive DNA from the desired target. This means that even a small amount of DNA would be sufficient enough to test with and to attain accurate results with. The PCR machine allows labs to run tests efficiently yet still attain correct results. [Instructions: IF your group has decided to redesign the PCR machine 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.] 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.] The biggest variable that can cause error is the camera angle. Since there are multiple phones out there with different placements of their cameras, the results could be altered based on the angle the camera makes with the Fluorimeter. To ensure this doesn't happen, the new Fluorimeter will have an adjustable stand on the bottom to raise or lower the height of the actual hardware to fit the cell phone's camera height. This allows for any camera to have a perfectly level view with the drop and the blue light, which will give accurate results. 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.] Bayesian statistics are useful in determining whether or not results are conclusive. In this experiment, Bayesian stats can be used to figure out how reliable the PCR procedure was at determining whether a patient had cancer or not.