BME100 f2013:W1200 Group5 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: Dominick Cocciola Name: Hany Arafa Name: Wendy Gray Name: Kristina Roscher Name: Estefania Meza 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] [Instructions: Show an image of your TinkerCAD PCR tube design here] 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.] There are many ways to use TinkerCAD to change how many things are done these days. Withe TinkerCAD, a researcher could upload a 3D image of a smoke detector, for example, and do a complete analysis of the devices flaws. After these flaws are found, he can then redesign the smoke detector in a more practical manner so that all the flaws can be worked out. After the smoke detector is finished, he could then print out the design he has created, have the circuit board and various part of it implemented and put into use. TinkerCAD allows anyone to fully view a device and recreate it how ever they please. 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 A nucleotide is the basic building blocks of nucleic acids. A polymorphism is a common variance in the sequence of DNA. A single nucleotide polymorphism or SNP is a difference in a single nucleotide in the DNA of an individual. The SNP rs17879961 is a cancer associated mutation that is found in the homosapien species and is pathogenic in it's clinical significance. This SNP is located on the 22nd chromosome and the affected gene is called CHEK2, which stands for checkpoint kinase 2. When this gene is active, it inhibits cancer cells from replicating. [Instructions: Use the answers from questions 3, 4, 5, and 7 to compose, in your own words, a paragraph about rs17879961] Primer design Forward Primer: 5' - T G T A A G G A C A G G A C A A A T T T Cancer-specific Reverse Primer: 5' - C A C T A G A A G A T A C A T A C G T C How the primers work: The reverse primer will bind to a complementary cancer-SNP containing template that was taken from a patient sample. The reverse primer only binds to the complementary sequence if it 100% matches just as the forward primer will also bind to its complement given it matches 100%. When the primer does not match the sequence completely, it will not be replicated. This makes it so only the DNA with the cancer-associated SNP will be replicated and any DNA that has the non-cancer allele will not be replicated. [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 [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.] [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.] [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.] [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.]