BME100 f2013:W1200 Group6 L6: Difference between revisions
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The | The PCR machine is newly improved and will be able to test more samples at once. The machine will run more smoothly and will be able to run cycles simultaneously on the open PCR program. This will make the machine more time efficient and it will allow hospitals to do more tests at once for a high demand of samples. | ||
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[[Image:Fluorup3.png|500px|]] | [[Image:Fluorup3.png|500px|]] | ||
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A weakness when using the open | A weakness when using the open PCR machine is that it was not fast enough and that it did not do enough PCR tests at once. Also, it only took 16 samples for 2 hours. So what we decided to do was to add more sample holders on the machine. We accomplished this by making a double open PCR machine that can hold two separate sets of samples. This way the machine will be doing double the work in only half of the time. This can also help separating your samples. Next, the machine had to be connected to a computer to access the information on the PCR Machine. To fix that we added a USB port. A USB flash drive can be plugged in directly to the PCR machine. When the machine says complete on the LED screen, all information is transferred onto the flash drive. This flash drive can be plugged into any computer to have the information readily available.<br><br> | ||
==Feature 4: Fluorimeter Hardware== | ==Feature 4: Fluorimeter Hardware== |
Revision as of 23:02, 26 November 2013
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 COMPANYLAB 6 WRITE-UPComputer-Aided DesignTinkerCAD TinkerCAD is an online site that allows the user to create 3D designs easily. By combining and manipulation basic shapes, any design can be created. There are special tools and shapes that allow the user to create precise details. Once designed, it can be sent to a 3D printer to get a physical model by using a standard STL file.
We used TinkerCAD to modify a set of tubes used in PCR.
Feature 1: Cancer SNP-Specific PrimersBackground on the cancer-associated mutation A genome is an organism's entire genetic makeup. The human genome is composed of billions of base pairs. When the genome is copied to make a new cell it is not always perfect because a single base pair may: get deleted, added, or substituted. An example of this is when one DNA sequence is CTAAGTA and the other DNA sequence is CTAGGTA (this sequence should be CTAAGTA). The two DNA sequences seem identical; however, they differ at one nucleotide position. Variation or mutation in a single base pair creates a single nucleotide polymorphism (SNP). Our DNA is actually made up of millions of SNPs; this accounts for the many differences (e.g. physical characteristics, development of diseases or our systems’ response to pharmaceutical drugs) we have to each other. Furthermore, the SNP rs17879961 is linked to a high risk of cancers to homo sapiens. It commonly occurs on chromosome number 22 with a clinical significance of a pathogenic allele (i.e. it is in the human gene checkpoint kinase 2 or also called CHEK2). The CHEK2 gene provides codes for making proteins called checkpoint kinase 2. Checkpoint kinase 2 is stimulated when the dsDNA is damaged for whatever reason (e.g. disturbance of homeostasis). Ultimately, it acts as a tumor suppressor by inhibiting cancer cells from rapidly dividing and affecting healthy cells. Primer design
How the primers work: Feature 2: Consumables Kit
We will use a cardboard box with a styrofoam block in the inside to safely protect the materials. The micropipette, primer and mix will be held in place so that it will not move during packaging. Also, there will be plastic baggies to hold the tubes so that the kit is neatly organized and nothing gets mixed around. On the side of the styrofoam box will be the instructions manual. The outside of the box will have pictures that will demonstrate its uses and make it look professional.
Feature 3: PCR Machine Hardware
Feature 4: Fluorimeter HardwareThe fluorimeter will be using its same methods when its incorporated in the system design. It will still detect DNA in the our system and transmit light that will detect a fluoresence for a concentration of DNA. Though the added changes to the Fluorimeter will make it more effecient and easier to use. Such as adding grips and connecting the cradle to the fluorimeter box.
Bonus Opportunity: What Bayesian Stats Imply About The BME100 Diagnostic Approach
Calculation 4 tests specificity. It analyzes the probability that the patient will not develop cancer, given a non-cancer DNA sequence. Our result from calculation 4 was larger than calculation 3, but still not close to 1. So, a non-cancerous DNA would often still return a positive result.
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