BME100 f2013:W1200 Group11 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 TEAM Name: Angelina Ledesma Name: Shayan Naeini Name: Nitish Peela Name: Meera Doshi Name: Nathan Dacasin LAB 6 WRITE-UP Computer-Aided Design TinkerCAD [Instructions: A short summary (up to five sentences) of the TinkerCAD tool and how you used it in lab on November 20th] During this lab, TinkerCAD was able to assist us in making changes to the micropipette tubes. TinkerCAD is a 3D design website that helps in changing products design by using various types of workplaces and innovative designs. The original design of the eight Eppendorf tubes was very confusing and difficult to determine the solution that each of the tubes contained. In order to fix this, our group decided to label each of the tubes with a number in order to avoid cross contamination. The main tools used was the change in workplace, which changed the sides of the tubes in order to place a number on the surface. We were also able to change color of the number tubes to make them all consistent in a set of eight. 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.] TinkerCAD can be used for numerous practical reason in Biomedical Engineering ranging from redesigning PCR Machine by putting a better display with a all in one PCR computer program within itself or making new fluorimeter that has a sliding camera holder. The camera holder will allow the phone to be at a constant distance away from the slide without having to move the phone constantly. To illustrate this on TinkerCAD, different types of shapes can be added for the camera holder allowing it to extend to and away from the slides as well as vertically to provide the ideal picture of the machine. 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] rs17879961 was the cancer-associated mutation that was studied in the lab. This specific mutation is an SNP or single nucleotide polymorphism. Nucleotides are organic molecules that mainly act as monomers for nucleotides found in RNA and DNA. Polymorphism is when several phenotypes are all located within the same population. Rs17879961 is a pathogenic SNP that is found in the 22nd of 23 chromosome found in Homo Sapiens. This specific gene was affected by a Checkpoint Kinase 2 or CHEK 2. The Checkpoint Kinase 2 is a cell cycle regulator that suppressed tumors specifically stabilizing the protein p53, stops cell cycle progress when DNA is impaired, and phosphorylates the BRCA 1. Primer design Forward Primer: 5’-ACTCACTTAAACCATATTCT Cancer-specific Reverse Primer: 5’-GGTCCTAAAAACTCTTACAC 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.] Primers start by recognizing the "target sequence", which is the cancer oriented SNP known as rs17879961. This specific cancer reverse primer will locate the complementary target sequence in the cancer SNP template to bind together. Remember that, the primer needs to find a matching target sequence to properly bind together. The forward primer like reverse primer must find a complementary sequences to be able to bind together. The sequence must correlate exactly to the forward and reverse primer templates in order for the complementary DNA strand to be formed. Feature 2: Consumables Kit Packaging of materials can be carried out in a way that effectively prevents a major problem encountered throughout the process: bleaching of the SYBR green dye. The tubes used to contain this dye should be covered with a light-blocking foil that can be removed manually when necessary. This will minimize contact between the dye and light, ensuring that the SYBR green dye remains potent. Additionally, packaging can be made more compact by stacking pipette tip trays atop one another, rather than having a collection of many trays that take up unnecessary space. These pipette tip trays should be placed in a shatter-resistant, cohesive container that will keep the trays intact even when dropped. [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 An inconvenience encountered during the use of the given PCR machine hardware was having to hook up the PCR machine to the computer in order to display results. This frequently caused problems due to additional materials being needed and a lack of quality in the cable connecting the PCR machine and the computer. Insead, it would be much more convenient to simply be able to view the results on the PCR machine itself. In order to accomplish this, the PCR machine hardware would have to be redesigned in order to include a large screen and display system programmed to take in instructions and show completion of the cycles. Also, the LED display could be improved. Overheating in the PCR machine system caused the LED display to burn out and stop working. Designing and implementing a better cooling system with fans within the machine could help users avoid this problem. [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 The fluorimeter is still necessary in order to analyze the fluorescence of the drop of the SYBR/PCR sample and find out if it is similar to a cancer sequence. A cell phone camera with a timer is used to get the initial picture and in order for it to align with the drop of SYBR/PCR, it is placed on a stand that keeps the phone perpendicular to the table. The bottom of the stand is permanently attached to the block ensuring that the phone camera is always exactly 10 centimeters away from the drop of SYBR/PCR. Finally, a big black box is used to block out any external light and ensure that the picture is clear/accurate. One of the main problems with the original design is that the stand was always moving around and a ruler had to continually be used to measure the distance between the stand and the box. In order to remedy this, the stand was attached to the box at a set distance away from it so the phone wouldn't move over the course of the experiment and the results would be accurate. Another problem was that the phone was never perfectly perpendicular and always fell over. The phone never stood properly and caused a lot of problems because it kept falling over. Whenever a button was pressed on the phone, the picture got out of focus because it kept moving around. In order to remedy this, a clamp will be introduced on the new version so the phone will be held in place and will always be centered with respect to the drop. Whenever a button is pressed on the phone, the phone will not move and will never go out of focus. With the box and the stand being a permanent 10 centimeters away, and the phone being secured on the stand, the process will be substantially smoother and easier as the phone will not tip over, the light conditions will be consistent, the distance will always be constant, and the phone will never go out of focus because it will be held in place and it will not move around. Thus, a reliable and accurate measurement of fluorescence in the drop of PCR/SYBR will be taken with every trial. [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.]