BME100 f2013:W900 Group13 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: Tyler Angell Name: Reem Gerais Name: Andrew Luc Name: Allison Marley Name: Cory Riecken [Instructions: add the name of your team's company and/or product here] LAB 6 WRITE-UP Computer-Aided Design TinkerCAD Tinkercad is an easy-to-use tool for creating digital designs that are ready to be 3D printed into physical objects. Users are guided through the 3D design process through 'Lessons', which teach the basics before moving on to more complex modeling techniques. In order to improve the PCR tubes, we decided to add labels Instructions: A short summary (up to five sentences) of the TinkerCAD tool and how you used it in lab on November 20t Implications of Using TinkerCAD for Design [Instructions: A short paragraph discussing just one possible way to use TinkerCAD for something practical...like redesigning the OpenPCR machine, fluorimeter, camera holder, printing out some of the smaller plastic items on demand, etc. There are lots of possibilities...pick just ONE.] 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.] In a PCR reaction, primers are one of the most important components in amplifying DNA. Both of the primers are designed to bind only to a specific sequence of the DNA that contains the SNP. When the primers bind to the DNA, it will take nucleotides that are complementary to the sequence of the DNA from the reaction mix and bind them together. This happens in both the forward and reverse directions in order to incorporate both strands of the DNA.If the sequence does not correlate 100% to template of the forward or reverse primer, then the complementary DNA strand will not be formed. This way, the primers will exclude DNA with non-cancer alleles and amplify DNA with the cancer-associated SNP rs17879961. Feature 2: Consumables Kit In our kit, the consumables will be clearly labeled to differentiate between the primers, PCR Mix, and the sample DNA. The tubes in which these materials are packaged will be color-coded and labeled to avoid any confusion that could lead to mistakes in the lab. We will maintain the current micropipettor design and will not be changing the PCR tubes themselves outside of the aforementioned labeling. We will also be making the packaging tubes have a hydrophobic surface on the inside so that the materials do not stick to the inside of the tube. These changes will help prevent human error and will also help prevent excess waste from being left over. [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 [Instructions: Summarize how you will include the PCR machine 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 awesome and easy to score.] This kit will include a redesigned PCR machine that features a latch to seal the PCR lid tight, a durable and heat-proof plastic design, and a removable plate for easy transport of PCR tubes. [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.] 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.]