BME100 f2013:W1200 Group1 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: Chloe Kwon Name: Jeff Miles Name: Casey Weinstein Name: Nima Afzalian Name: Mario Gonzalez 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] TinkerCAD is an easy to use 3D design website. It allows users to manipulate any design within different workplanes and utilize the wide variety of tools and shapes to carefully add precise details to the design. In this lab, TinkerCAD was used to modify a set of eight Eppendorf tubes used in a PCR machine. In order to make the tubes more effective and easy to use, numerical labels would be added to each tube to keep the different samples organized and filters would be incorporated to each tube to avoid cross-contamination with the other samples. [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.] TinkerCAD can be used for something practical in Biomedical Engineering, such as redesigning the OpenPCR machine to incorporate a camera holder. The current model of the OpenPCR machine does not have an attached camera holder, which makes getting accurate pictures of the sample very difficult. TinkerCAD would allow an attached camera holder to be added to the OpenPCR machine that would enable a camera or a phone to easily and accurately take pictures at the exact same distance and height each time. The multiple tools and views in workplanes in TinkerCAD allows the attached camera holder to be designed in a precise manner to make the OpenPCR machine a better device. 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] The cancer-associated mutation that was studied in lab was rs17879961, which is a SNP standing for single nucleotide polymorphism. A nucleotide is an organic molecule that serves as the monomer of nucleic acids such as DNA and RNA. Polymorphism is when two or more different phenotypes exist in the same population of a species. rs17879961 is found in the the species homo sapiens. This SNP is considered pathogenic, which means that is causes a disease. It is found on chromosome number 22. Typically, humans have 23 pairs of chromosomes. The gene affected from a SNP is called CHEK2. This stands for Checkpoint Kinase 2. CHEK2 is a cell cycle checkpoint regulator and putative tumor suppressor that stabilizes the tumor suppressor protein p53. Primer design Forward Primer: 5’-TGTAAGGACAGGACAAATTT Cancer-specific Reverse Primer: 5’-GGTCCTAAAAACTCTTACAC How the primers work: [Instructions: Explain what makes the cancer sequence specific to the SNP 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.] In order to reduce the chance of potential contamination, all consumables will be packaged individually. Also, each consumable will have a designated spot within a styrofoam cutout to reduce the chance of breaking during transportation and shipment. An instrucion booklet will also be included in the kit in order to tech the user how to properly use and dispose of each piece. To minimize confusion, each component will be separately labeled, with a corresponding color and letter in the instructions booklet. 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.] The PCR machine will be incorporated into our system in the same way that is it already used. Similar to the setup in class, the PCR machine will be used solely to heat and cool the samples, allowing for the DNA contained within the Eppendorf tubes to multiply rapidly. Our PCR machine will heat and cool the samples to the same temperatures as the current one because this has been established to be most successful at multiplying DNA, however, it will be significantly more efficient. Our modified PCR machine will be more efficient than the one used in class and will improve on its major weaknesses. One problem that our machine addresses is the fact that the current model must be programmed via computer. The redesigned PCR machine will be programmable from the machine itself, removing the need for time consuming and challenging computer programming. Another problem with the original machine is that a user cannot easily see when the heating plate is in direct contact with the Eppendorf tubes. To solve this problem, our redesigned machine would would have a clear lid with a pressure sensor. This would allow the user to ensure that the samples don't spill over and that the heating plate is in direct contact with the samples. An additional improvement is that the the heating plate would be larger and the Eppendorf tubes would be smaller. Rather than the current 16 well plate, a 96 well plate would be incorporated as to allow more samples to be tested at one time, eliminating the need of having to run countless PCR processes. Another drawback of the current machine is that the complete process takes hours. We noticed that there was a fair amount of open space inside the PCR machine. This open space would be filled by making a larger and more powerful heating/cooling system, which would effectively allow the temperatures to change much more rapidly and would significantly reduce the time needed for the PCR process. Lastly, we would add our brand name to the side walls of the PCR machine. 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.] Similar to the fluorimeter used in lab, our redesigned fluorimeter will be used to shine a beam of blue light through the drop of sample containing DNA. Then pictures of the drop will be taken in complete darkness. However, the fully upgraded and redesigned fluorimeter will consist of the fluorimeter with LED light, an automated closing lid, and a built in camera that works in sync with the lid. This setup will result in more accurate and higher quality photos. It would also ensure that all pictures are the exact same. As previously mentioned, the improved fluorimeter would improve on a few of the weaknesses of the current model. One major problem is that it is hard to keep the phone in place and at the same distance away from the sample drop and beam of light. Our new fluorimeter improves on this weakness by including an adjustable clamp that holds the phone ins the same position. This is the most basic model our company would sell. The upgraded model with built-in camera and an automated lid would ensure that ideal pictures are taken every time and that pictures are only taken when the lid is completely placed. With a simple press of a button, the lid would shut and a perfect picture would be taken when the lid is completely lowered. This eliminates the possibility of user error. 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.] Bayesian statistics is a method to determine the reliability of detecting cancer SNPs and predicting cancer. The equation for Bayesian statistics is: P(A|B)=P(B|A)*P(A)/P(B). Calculation 3 asks what is the probability that the patient will develop cancer, given a cancer DNA sequence. Because the P(A|B) value for this calculation is very small and less than one, it is not accurate at all. Calculation 4 asks what is the probability that the patient will not develop cancer, given a non-cancer DNA sequence. Because the P(A|B) value for this calculation is also very small and less than one, it is not accurate at all either. Thus, the reliability of CHEK2 PCR for predicting cancer is not good and should not be used. The calculations may not have produced reliable results because of human error using the OpenPCR machines. Many of the trials were not completed to full term, which threw out samples and may have skewed the overall data with a smaller amount of trials than expected. In order for the CHEK2 PCR to actual be a reliable predictor for cancer, the values of P(A|B) for calculation 3 and 4 should be very close to one instead of being such small numbers.