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 PCR: Who Do you THINK you are? LAB 6 WRITE-UP Computer-Aided Design TinkerCAD TinkerCAD is an 3D modeling software that allows you to easily create models of your designs to be printed on a 3D printer device. After completing tutotorials where you learn how to work on various planes, modify shapes, and scale objects one can then use TinkerCad to its full potential. In this lab, we scaled a cylinder down in order for it to be used as a label on a PCR tube. We then created a new plane to place this cylinder onto the PCR tube and then added numbers to these flattened cylinder labels (an explanation of the labels can be seen below). Implications of Using TinkerCAD for Design In order to improve the PCR tubes, we decided to add red and blue labels and numbers to make each sample identifiable. When we ran the PCR experiment there was some confusion as to what were the primers and the PCR mix, we labeled the tubes with a marker. However, this problem could easily be solved if the PCR tubes had built in labels, so we made this change. There now are red and blue dots on the the tube to determine the primer vs. PCR mix and numbers for various concentrations. Not only can TinkerCad be used for redesigning the fluorimeter. For the fluorimeter we want to create a device that has a stand that is attached to the box and where the fluorimeter and the camera stand are attached at a set distance. To design this, the design capability associated with TinkerCad could easily be employed, making TinkerCad an extremely useful and practical tool for engineers. Feature 1: Cancer SNP-Specific Primers 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] rs17879961 is the title of the gene present in DNA sequences in humans. A nucleotide is a compound consisting of a nucleotide linked to a phosphate group and is the basic structural unit of nucleic acids. A polymorphism is where there is one or more variants of a particular DNA sequence. The species in this variation is rs17879961 is homo sapiens (humans). The clinical significance of this SNP is that is so pathogenic. This SNP (rs17879961) occurs on chromosome 22 out of the typical 23 pairs of chromosomes that humans have. CHEK 2 (Checkpoint Kinase 2) when activated inhibits CDC25C phosphotase, preventing entry into mitosis, and may stabilize the tumor suppressor protein p53, leading to cell cycle arrest in G1. This minuscule change altering CHEK2 has catastrophic affects, it brings a person one step closer to cancer. Primer design Forward Primer: 3'-CACATTCTCAAAAATCCTGG-5' Cancer-specific Reverse Primer: 5'-TGTAAGAGTTTTTAGGACCC-3' 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.] The redesigned PCR machine incorporates a latch in order to keep the heat inside the PCR machine. This will keep the temperature constant to facilitate the PCR reaction in the three processes of denaturing, annealing, and extending. This prevents susceptibility for error, allowing consistent performance. A durable, heat-proof plastic design will minimize cost to allow maximum profit. The addition of the removable plate will allow for easy transport as well as facilitate loading/unloading of the samples. 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.]