BME100 s2014:T Group2 L6

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Owwnotebook icon.png BME 100 Spring 2014 Home
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
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Name: Bateer Song
Name: Daylin Morgan
Name: Ekanem-Essang Akpan
Name: Hannah Churchill
Name: Alexander Jones
Group 2



Computer-Aided Design


In the beginning each part of the PCR machine was imported to Tinkercad. The files represented were 'Body: Back, Bottom, Side, Side with ports, and Top.

Our Design


In our redesigned OpenPCR machine there is no longer a LCD screen. This screen was considered unnecessary given that all the data is displayed and controlled through the software on the PC it is plugged into. Since this screen was no longer on top nor under the top wood panel it was replaced by a larger well. This allows for a much larger number of PCR's at the same time. Also the lid covering the well and touching the top of the tubes must also be large enough to cover the entire well.

Feature 1: Disease SNP-Specific Primers

rs237025 is a SNP(Single nucleotide polymorphism) mainly found in Homo Sapiens. Which means Humans exhibit this variation most often. A nucleotide is basic unit of nucleic acid. A polymorphism is the presence of two or more phenotypes in a population because of the expression of different alleles of a given gene. rs237025 is seen on the 6:149721690 chromosome. Normally, when a disease is classified, they fall under a certain clinical significance. Basically its general effect on day-to-day. That significance could be palpable, real genuine, or a noticeable effect. rs237025 did not fit any of these categories. Diseases closely linked to rs237025 are diabetes and Vogt-Koyanagi-Harada syndrome, a multi-system disease with dermatological effects.

rs237025 also has the Small ubiquitin-like modifier 4(SUMO4) gene. SUMO4 is a family of genes encode small modifiers that are attached to proteins and control the target proteins’ sub-cellular localization, stability, or activity. rs237025 causes a change of the 'G' allele in the GTG genotype. An allele is any of several forms of a gene, usually arising through mutation, that are responsible for hereditary variation,

Primer design

  • Disease SNP-specific Forward Primer: 5’ T G A A C C A C G G G G A T T G T C A G
  • Reverse Primer: 5’ A G T T T T C T A A T T G A G A A T G C

How the primers work: Primers are single strands of DNA that act as the beginning of DNA synthesis. Primers are set to the beginning and end of the desired DNA fragment that will be amplified. Thus this will keep it from amplifying any non-disease alleles.

Feature 2: Consumables Kit

Our PCR system is packaged in a way that makes it easier for the student to get right down to business doing the experiment. It comes complete with PCR mix, primers, PCR tubes, a micropipetter, pipette tips, and an adjustable phone stand, all packaged neatly in a box. The PCR mix and primers are all pre-measured and pre-sorted in the PCR tubes, allowing the experiment to begin as soon as the box is opened. This makes the experimental more efficient overall. Each PCR tube will also be pre-labeled as well as being covered in foil to prevent too much light exposure; also a time saver on the part of the student. This kit is made to increase the efficiency of the experiment, making it more enjoyable for the student.

Feature 3: Hardware - PCR Machine & Fluorimeter

The PCR was run to test DNA samples. While the flourimeter was used find the specifics of flouresence and the intensity of wavelength.

The PCR machine was redesigned in order to save power and electriciy. This was done my removing the LCD screen from the top of the PCR machine. Once the screen was removed the excess wirieng was removed or diverted to processing. Thus, fewer materials are needed to build the machine, and the price will drop significantly. Including a larger well allows more samples to be taken

Bonus Opportunity: What Bayesian Stats Imply About The BME100 Diagnostic Approach

According to our results for calculations 3 and 4, we realized that the PCR can not predict diseases very accurately, the reliability is kind of low. Especially for positive result. The numerical value we got in calculation 3 is much smaller than 1. Although the value for calculation 4, which present the negative result is pretty close to 1, but it's still not satisfactory enough. Which means the PCR is not able to verdicts patients' situations well such as false positives cases.