BME100 f2013:W900 Group4 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 COMPANY Name: Elliott Tejada Name: Sierra Headrick Name: Philip Terzic Name: student Name: student Name: student ACUSpeed PCR LAB 6 WRITE-UP Computer-Aided Design TinkerCAD The TinkerCAD tool is a program that was used in lab on November 20th that allowed people to create files compatible for 3D printing. What TinkerCAD does is provides users with shape, number, and letter templates that are to be combined in a grid that makes an object in three dimensional space. Operators of TinkerCAD are exposed to a whole new world of design that that can be used as practice for a more complex and developed way of creating 3D objects that may be printed. It allows users to group objects together to make a solid figure, put a hole in another figure, or a variety of other options with the accompanied settings provided to make them possible. In the lab session on November 20, 2013, groups were given a file on TinkerCAD to search for and modify. The objects were the PCR tubes, however they were not connected or labeled. Each group did their own modification along the lines of labeling and connecting the tubes. Implications of Using TinkerCAD for Design Practical uses for TinkerCAD range from myriad uses for different professions. Students in labs may use TinkerCAD as an introduction to the 3D printing process for the preparation for their profession. With the knowledge of the program, those students and others with knowledge of the system may use if for their own leisure use to practice their own ideas. A research lab in need of a more reliable camera stand for a fluorimeter, an openPCR machine, or even the box used to block out light for the fluorimeter may use TinkerCAD to construct those objects for their own use or for the use of engineering the object as an improvement for the disbursement into the public. Feature 1: Cancer SNP-Specific Primers Background on the cancer-associated mutation With the use of the NCBI database of the complete human genome sequence, the cancer-associated sequence "rs17879961" was evaluated. This sequence is contained in the section for genetic variations in single nucleotides. In other words, it is a variation in the basic building block of nucleic acid; nucleotides are composed of a nitrogenous base, a sugar and a phosphate group. The variation type is referred to as a "polymorphism" which occurs when different forms or phenotypes exist in the same population of a species. The sequence "rs17879961" is found in the Homo Sapiens species and the nucleotide that is affected is clinically significant due to the fact that it contains a pathogenic allele--that for the cancer substitution. In this case, the polymorphism occurs on the 22nd chromosome out of the 23 chromosomes that humans possess. Going further into the actual gene that is affected in the "rs17879961" sequence, it is called CHEK2 which stands for "checkpoint kinase 2." Based on the NCBI database's information on checkpoint kinase 2, the damage that occurs to the DNA stops the progression of the cell cycle prior to mitosis in a cell that stabilizes the tumor supressor "protein p53" which is linked to the predisposition for the cancers: sarcomas, breast cancer and brain tumors. Primer design Forward Primer: T G T A A G G A C A G G A C A A A T T T Cancer-specific Reverse Primer: T G G G T C C T A A A A A C T C T T A C 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 [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 The PCR kit will function similarly to how it functioned in our previous experiment, in that it will be responsible for producing and amplifying new DNA strands. It contains a power supply, a cooling fan, an LED display for easy reading, a circuit board for information storage, and a heat lid to prevent condensation. The PCR machine denatures the DNA, then anneals and elongates the strands to provide more copies, which can then be used for analysis. The machine runs multiple cycles of the DNA strands found from the Consumables Kit for a exponentially increasing DNA sample, although this process does have some aspects that can be improved. Our PCR would be augmented so that the number of sample tubes that can be processed is higher, and therefore more experiments can be run during the same time interval. Also, the cooling and heating systems could be improved by making them more potent. Thus, the time required for the cycle would further increase, because the period required for specific heat up and cool down would be decreased. When we ran the PCR machines in lab, the time to prepare the specific temperature was a major factor that consumed our time. These solutions would both decrease the time it would take to run the cycles for the experiment. 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.]