BME100 s2014:W Group3 L6

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BME 100 Spring 2014 Home
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Lab Write-Up 1 | Lab Write-Up 2 | Lab Write-Up 3
Lab Write-Up 4 | Lab Write-Up 5 | Lab Write-Up 6
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Contents

OUR COMPANY

Name: Joseph Roskop
Name: Joseph Roskop
Name: Lorelei Fyfe
Name: Lorelei Fyfe
Name: Ana Kenia Viera
Name: Ana Kenia Viera
Name: Ben Lenschow
Name: Ben Lenschow
Name: Adnan Alsharif
Name: Adnan Alsharif
Name: Group Picture
Name: Group Picture


Aloft Technologies


LAB 6 WRITE-UP

Computer-Aided Design

TinkerCAD


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


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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. The material to be used will be a chemically treated polymer compound that has a high level of heat resistance.


Feature 1: Disease SNP-Specific Primers

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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: Primers define the region that will be amplified. Primers are DNA sequences that arrange a nucleotide sequence (specific) in both forward and reverse directions. The forward and reverse are complementary to one another because the primers will bind to its complementary sequence and the template strand will find each other. In other words, DNA sequence amplify these complementary nucloutide to join together and add new nucleotides to extend the strand. The cancerous strand is what allow the pathogenic DNA to amplify. The non-cancer allele will not amplify because the primers would not be complementary to the target DNA sequence.



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.

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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. Further more, it was posited that a more flame retardant material than plywood could be used to house the heating unit. Polymers and various alloys were discussed as possible improvements to the PCR's original design.



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