BME100 f2013:W900 Group5 L6

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Contents

OUR COMPANY

Name: Lincoln(Grady) Bain
Name: Lincoln(Grady) Bain
Name: Andrew Olson
Name: Andrew Olson
Name: Pedro Giorge
Name: Pedro Giorge
Name: Niko Vlastos
Name: Niko Vlastos
Name: Omar Alsubhi
Name: Omar Alsubhi


PCR Pro by Vidle Industries


LAB 6 WRITE-UP

Computer-Aided Design

TinkerCAD

We used TinkerCAD to make improvements on the PCR test tubes. We made each test tube about 20% longer and labeled the caps of each tube. One row is red with the numbers zero through three and the other row is blue with the same numbers. We also a stamp that will hold the test tubes completely off the ground so that there is no wobbling when working with them.

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Implications of Using TinkerCAD for Design

Using TinkerCAD to design and print out a specialized camera holder would make the design of the experiment optimal. By personalizing the camera holder, the camera being used will be fitted more efficiently, making the possibility of error (e.g. by bumping the camera and shifting it in open space on the general camera holder) less.



Feature 1: Cancer SNP-Specific Primers

Background on the cancer-associated mutation

  • The human genome has 23 chromosomes. The 22nd chromosome contains a pathogenic single nucleotide polymorphism (SNP) known as rs17879961. The rs17879961 nucleotide affects the checkpoint 2 (Chek2) gene. The (Chek2) gene mutation affects the cells’ tumor depressant."


Primer design

  • Forward Primer:

- GGAAGTGGGTCCTAAAAACTCTTACA

  • Cancer-specific Reverse Primer:

- TGCATACATAGAAGATCACAGTGGC


How the primers work

  • The way that the primer works is that it completely binds with that specific mutation to about 100%. However this 100% completion rate will never occur with the non-damaged portion of a DNA sequence. This replication of the damaged one gets amplified by the number of cycles that the machine runs, this being the case, the more prevalent the data sample of damaged DNA, the more likely that the person being sampled has the genetic disorder.


Feature 2: Consumables Kit

The consumables that will be provided the box will go as follows:

  • (1) Pitch black box
  • (1) Micropipette
  • (2) Sets of PCR tubes
  • (1) Cellphone holder
  • (1) Fluorometer
  • (3) Hydrophobic glass plates


The following issues will be addressed with the new and improved functionality of the box and its content:

  • The issue that needed to be addressed was the issue of the light sensitive enzymes"SYBR green" can be degraded with the ambient light from the room which in turn can diminish the amount of fluoresce that is produced by the "SYBR green" dye under the detection of the cell phone megapixel camera.
  • Another issue that was addressed is the neatness and limiting the false positive and the cross contamination associated with working with fluids and being in a dynamic lab environment. The solution would be to keep all of the items that you are using in one localized area and you testing equipment nearby but isolated. WIth two levels in the box; the upper level has a lid which you can open and select the enzyme/aquous solution that you want to work with, close the box and proceed the lower level; the lower level contains the cellphone holder and the fluorometer, and then conduct your expirement and discard. These steps can become second nature and the risk of cross contamination is dramatically reduced and the over functionality is exponentially improved.

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Feature 3: PCR Machine Hardware

The PCR unit will come pre-assembled, to allow for quick start in one's lab.


A major issue found in the OpenPCR machine was that the computer software did not communicate well with the unit. To fix this issue, our software is built into a small computer that is on the PCR unit itself, eliminating the need for external computer systems to communicate with the unit that is already running tests. In addition, due to inconsistent heating among several PCR machines used, we have designed a uniform heating unit in the PCR machine that will more efficiently heat the samples put into the machine; this will also speed up the process of the lab itself.


Feature 4: Fluorimeter Hardware

Essentially the redesigned fluorimeter would be readily and easily included within the system. This is ue to the accessibility of the new and compact design that would enhance the amount of workspace needed to conduct these experiments. The whole purpose of the system is to maximize the total efficiency from every angle and eliminate any errors that could cause faulty results.


A major weakness that was spotted within the fluorimeter was that achieving a picture, and coordinating the lid drop to shield the light was a major problem. What the group decided to do was design a box similar to the one that has been used within the lab. The box would instead have a button that could be pressed to easily take a picture in the dark without having to time it perfectly. What would have to be done is mount a camera on the fluorimeter or where the camera mount was originally designed to be placed. From that vantage point a clear image could be taken, it would however be slightly more costly, however, the improvement and lack of errors would be substantial due to the fact that the use of the fluorimeter for this particular set up was determining a cancer sequence or genome. This really drove the group to proceed with making a full proof device that would function properly and without and troublesome miscommunications as well.

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