BME100 s2014:W Group6 L6

BME 100 Spring 2014	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 Elizabeth Burkett Rose Among the Thorns Matthew Warren The Handy Man Samuel McCollum Man in Charge Frederick Sebastian WetWare Master [Instructions: add the name of your team's company and/or product here] LAB 6 WRITE-UP Computer-Aided Design TinkerCAD TinkerCAD is a user-friendly 3D design tool that allows users to make a 3 dimensional representation of their idea. Instead of using a pre-existing design, we used simple shapes that we could easily manipulate to alter the design of the PCR machine. We made these shapes to look like the basic designs we wanted to implement on our improved PCR machine. Our Design The new design allows for faster heating/cooling and therefore more accurate results. The box itself will be made out of wood-plated rubber as these materials are non heat conductive. The circuit boards will also be redesigned to assist with the faster heating/cooling. There will also be a new ventilation system to make the cooling process of the PCR test faster. Additionally, there will be a total of three heating trays hence increasing efficiency. With the new modifications the total time required to conduct a PCR test will decrease. Feature 1: Disease SNP-Specific Primers Background on the cancer-associated mutation Nucleotides are monomers (or the building blocks) of DNA, and when certain nucleotides have variations they are called polymorphism. This variation comes about due to the change a DNA makes. rs237025 is a type of polymorphism, more specifically it is a Single Nucleotide Polymorphism (SNP). It is found in homo sapiens (human beings) and specifically located on the 6th chromosome: 149721690. The genes that are associated with this polymorphism are SUM04 and TAR2 which are in turn associated with Type I and Type II diabetes, as well as coronory heart disease. The gene SUM04 is an acronym that stands for Small Ubiquitin-like Modifier 4. This gene works primarily in protein coding of small ubiquitin-like modifiers. An allele is a variation of a gene that finally determines the phenotype, and the three bases that have a disease associated allele contains the sequence ATG. Primer design Disease SNP-specific Forward Primer: 5' ATGATTGCTATGTGT 3' Reverse Primer: 3' TACTAACGATACACA 5' How the primers work: DNAs are made of a double helix structure and when they separate to replicate themselves, the primers will only bind themselves to the exact site on the DNA that has their complementary nucleotide bases. When the primers "realize" that the sequence they need to bind to is not perfect, they will not bind hence, the DNA amplification fails. 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 BioMed Testing Corp. also supplies each purchase of a Thermal Cycling and PCR package with a consumables kit, containing the following regents: SYBR GREEN 1 dye in disposable plastic tubes, variable tube size and quantity option provided. • Standard PCR reaction mix containing DNA polymerase and dNTPs in disposable tubes. • Calf thymus DNA, variable tube size, DNA concentrations and quantity of tubes option provided. • Tubes for final reaction mix, sized to fit the patented BioMed tube trey. • Tubes containing Buffer solution and demarcated by the letter B pasted to the top of the tube, variable tube sizes and quantities provided. • Tubes with distilled water for dilution, variable tube size and quantity option provided. • One standard sized container of disposable pipette tips • One courtesy biohazard disposal kit (we are not liable for contagion outbreaks) • A sharps container for disposing of glass slides. Note: Micropipettes are not included. [Instructions: IF your consumables packaging plan addresses any major weakness(es), explain how in an additional paragraph.] Other consumables packages send light-sensitive reagents (the SYBR GREEN 1 dye) with a cheap and minimally effective reflective covering. BioMed Testing Corp. packages all light-sensitive reagents in tubing with a reflective coating over every surface, maximizing the accuracy of the fluorometry results. Additionally, the consumables kit list shows that BioMed supplies both a biohazard disposal kit and a sharps container. This is a part of our growing dedication to safety, minimizing potential harm to the consumer or to the environment. Of course, all tubes are color-coded based on their contents and identifiable based on a complementary and intuitive key relating each color to the corresponding reagent. Feature 3: Hardware - PCR Machine & Fluorimeter The new PCR and fluorimeter machine will The PCR machine will incorporate a fluorimeter in order to analyze amplified DNA samples, thus enabling the detection of disease. This can be done by [Instructions: Summarize how you will include the PCR machine and 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 awesome and easy to score.] [Instructions: IF your group has decided to redesign the PCR machine and/or Fluorimeter to address any major weakness(es), 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 PCR for predicting the disease. 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 a Blackboard quiz. We are doing so for the sake of academic integrity and to curb any temptation to cheat.]