BME100 f2013:W1200 Group12 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 | |||||
ChamberS
LAB 6 WRITE-UPComputer-Aided DesignTinkerCAD TinkerCAD is an online tool which allows the user to create and edit existing 3D computer generated objects. In class, we used TinkerCAD to edit PCR tubes. The edits we made were connecting tubes with circles and rows together with lines. The circles are there to allow the tubes to be stacked on top of one another. They are connected by rows, but can be broken apart easily for use in a PCR machine.
As scientists and engineers, we strive to create the best of the best and then improve it. TinkerCAD allows people to take an existing design and make it better. Everyone thinks differently, and when the best and most innovative ideas from different people are applied to a single design, then the result is one of the best product possible. Someone may even take the design we made and make it better in the future.
Feature 1: Cancer SNP-Specific PrimersBackground on the cancer-associated mutation Rs17879961 is an organic molecule, which is a polymorphism expressed in Homo sapiens. Rs177879961 is a single nucleotide polymorphism or SNP, and is known to affect the 22nd chromosome, and is pathogenic in origin. Chromosome 22 is important in the coding and synthesis of many proteins, containing about 500 to 600 genes that are in the body. In chromosome 22 rs17879961 takes affect on checkpoint kinase 2, or CHEK2 for short, which is key in preventing the development of cancerous tumors. Specifically, CHEK 2 inhibits CDC25C phosphatase which acts as a tumor suppressing protein. By altering the coding of the chromosome, rs17879961 leads to a number of disorders concerning the genes in chromosome 22.
Primer design
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 KitOur kit will come in a plastic box with a lid that will lock in place. We have incorporated a special design with the PCR tubes to save space in the box. Also, there will be black plastic PCR tubes so no light can bleach the green dye. The PCR machine itself will come partially assembled to avoid confusion when putting the device together (unlike IKEA products. Also included will be a flowrimiter, glass plates along with an adjustable stand to hold all types of phones. One of the major problems our packaging will be addressing is the bleaching of the green dye. If the green dye is exposed to light for too long, then it will become useless. The black tubes will allow no light to pass through.
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.] [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 HardwareThe fluorimeter will be used in the same way that it was used previously. It will be used to detect the desired DNA and can still be used to detect if somebody has a certain mutation. The main difference is that it will be must more efficient, accurate, and have a much higher convenience level. Having to take a photo with a cellular phone, and then send it to the computer through email was a very high inconvenience and was very time consuming. Now that our new and improved fluorimeter uploads the pictures automatically through the use of bluetooth, the inconvenience will be taken away and the process will be sped up greatly.
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.] |