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 Name: Brandon Bartels Name: Antonio Moran Name: Robel Yoseph Name: student Name: student The name of our teams company is ChamberS. LAB 6 WRITE-UP Computer-Aided Design TinkerCAD 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. Implications of Using TinkerCAD for Design 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 Primers Background 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 Forward Primer: 5'-AGGTTGCAGTGAGCCAAGAT Cancer-specific Reverse Primer: 5'-CACTAGAAGATACATACGTC 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 Kit Our 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 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.] One of the major weaknesses was that the SYBR dye that is used for the fluorimeter is very light sensitive and becomes bleached when in the presence of light. This means that it has to be covered with tin foil when it is inside of the PCR tubes. Our group redesigned the PCR tubes to be black as apposed to clear. These tubes will make it so that much less light with be able to reach the SYBR dye inside of the PCR tubes causing the dye to not get bleached as easily. Another weakness with the fluorimeter is that it has way too many variables. Its variables include the camera type, the camera stand/alignment, and the distance from the camera lense to the drop. To account for this, our group decided to make the fluorimeter and the camera stand one piece. We made it so that there was an adjustable plate that connects the fluorimeter box to the camera stand. This adjustable plate locks when it is at the desired distance so that it is easy to maintain the correct distance between the camera and fluorimeter throughout the entire course of the lab. The fluorimeter will also have grips on the bottom of it so that it won't slide around as easily. We also corrected for the camera type issue by installing a camera on the fluorimeter itself. Instead of having a stand that holds the camera, we made the stand the camera. There will be a button on the camera that when pushed, will take a picture of the drop on the fluorimeter. When the picture is taken, it will automatically be sent through bluetooth to an app on your phone. The camera also will store up to 100 pictures which can be imported to a computer through the use of a USB cable. 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.]