BME100 s2014:W Group3 L6

BME 100 Spring 2014	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: Joseph Roskop Name: Lorelei Fyfe Name: Ana Kenia Viera Name: Ben Lenschow Name: Adnan Alsharif Name: Group Picture Aloft Technologies 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 a three dimensional modeling software available online. It is used for 3D printing, mapping, and prototype mock-ups among other things. In this lab (April 16th) TinkerCAD was used to illustrate improvements that could be made to the PCR device. In a project prior to this, (March 5th) it was used to design an innovative body monitoring device for a niche market that hadn't previously been addressed. Our Design [Instructions: Show an image of your TinkerCAD design here] [Instructions: A short paragraph describing your design. Why did you choose this design? How is it different from the original OpenPCR design?] While it is a seemingly trivial aspect of its design, the handling of the PCR dramatically effects its marketability so in order to make the device easier to manipulate (and consequently sell), a decision was made emphasizing the need for a more user friendly grip for the heating panel on top of the machine. This will make appropriate compression strength more than just guesswork when a curve is set into the bracket forcing it to click into and out of place. Secondarily, (and less visibly) it was also posited that the construction material could be utilized in such a way as to sequester the heating coils off from its wood casing entirely. This mitigates the obvious fire hazard attributed with housing heating coils inside of a very dry plywood box. Feature 1: Disease SNP-Specific Primers [Instructions: This information will come from the exercises you did in PCR Lab B.] Nucleotide is the chem building blocks that forms DNA "ATCG". Polymorphism is an error in DNA transcription that leads to multiple strands with a duplicate or omitted nucleotide.From the variation rs237025 was found the species Homo Sapiens.The chromosome was located on 6 149721690. The clinical significance of this SNP was listed as other. SNP is associated with sumo4 and TAB2 genes. The diseases linked to this SNP were type I diabetes,Type II diabetes , and rheumatoid arthritis. SUMO4 stands for a small ubiquitia-like modifier 4. The molecular function of this gene is to encode small ubiquitia related modifiers that are attatched to proteins and controls the target proteins' subcellular localization, stability or activity. Allele is an alternative form of a gene that arise by mutation and are found at the same place on a chromosome.The disease- associated allele contains CTG or TTG. Primer design Disease SNP-specific Forward Primer: 5' G T G A A G C A G A T C A G A T T C C G Reverse Primer: 5' G T T C T A A T G A C G T A A G A G T T How the primers work: [Instructions: explain what makes the primers disease-sequence specific. In other words, explain why the primers will amplify DNA that contains the cancer-associated SNP, and will not exponentially amplify DNA that has the non-disease allele.] Feature 2: Consumables Kit The consumables will be placed in a kit that is distributed with each individual PCR unit. It will contain all necessary materials with precise fluid, buffer, and primer quantities premeasured. It will also house the minimum amount of slides and PCR tubes to perform the experiment. The point behind issuing consumable materials in ready-made individual units is to avoid a disorganized scramble and dash for materials. This saves time and effort for all parties involved. ' Feature 3: Hardware - PCR Machine & Fluorimeter The flourimeter will be a part of the PCR machine for our adjustments. The box that houses the heating coils and computer components will serve as our black out box. A small camera inside will take photos of the DNA solution and run the findings through ImageJ software automatically. In our attempt to address the tedious and redundant nature of the flourimeter test, our team has reimagined a device that will allow for all samples to be taken and illuminated with ultraviolet light at once. This will permit the camera's to capture images and simultaneously compare their INTDEN values with one another with a multitude of algorithms. 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 PCR for predicting the disease. 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 a Blackboard quiz. We are doing so for the sake of academic integrity and to curb any temptation to cheat.] Calculations 3 and 4 imply that the PCR method for predicting the disease is pretty unreliable when trying to find if the patient really has the disease. It rarely gives a positive reaction when the patient is actually positive, even though it gives fairly accurate negative readings.