BME100 f2013:W1200 Group7 L6

From OpenWetWare
Jump to navigationJump to search
BME 100 Fall 2013 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
Wiki Editing Help


Name: Ambar Khare
Name: Carlee Farhar
Name: Thalia Lebratti
Name: Matthew Campion
Name: Zack Silverman



Computer-Aided Design


What is TinkerCad and How we Used it:

In this lab, we used Tinkercad which is basically a browser-based 3D modeling program that lets people design whatever is on their mind. It is intuitive with several tutorials and easy to use for all ages. People can tweak an existing product or create a completely new model. The design can be saved and the file can be used to 3D print it.

In this lab, we used Tinkercad to create a better design for the tubes that holds solution in the PCR. We changed it by connecting all the tubes for stability sort of like an accordion style and users can expand tubes for use or collapse it for storage. Also, the tubes are pre-labeled for efficiency and recognition.

An image of your TinkerCAD PCR tube design:

Implications of Using TinkerCAD for Design

Open PCR can be use to create or redesign a product. A practical sense for Tinkercad in relation to our lab would be redesigning the fluorometer camera setup. In our previous two labs, the camera setup was inefficient because the fluorometer didn’t have a place to hold the camera in place and so each time it was difficult to position the camera at the set distance. There could have been different camera angles that could have flawed our results. Additionally, the fluorometer device couldn’t be adjusted to a certain amount of height which could be a problem since people have cameras that are different sizes. We could use Tinkercad program to redesign this product by having an attachment to the device that has a place for people to put a camera. Or better yet, we can make a built in camera that is always facing the fluorometer at the slide level.

Another implication for using the Tinkercad program is that it only is used to tweak physical features. If we wanted to change something internally of a PCR machine, it wouldn’t show in the 3D model at all.

Feature 1: Cancer SNP-Specific Primers

Background on the cancer-associated mutation

What is rs17879961?

rs17879961 is a type of SNP which stands for single nucleotide polymorphism. A nucleotide is a subunit of nucleic acids like DNA or RNA. It is composed of a nucleotide base (A-T, G-C), five-carbon sugar, and a phosphate group. Polymorphism is when there are two or more differences existing in a population of species. From this, we can conclude that rs17879961 is a type of mutation which is found in homosapiens and extremely pathogenic. Humans have 46 chromosomes in their body and on chromosome number 22 is where this SNP is located. This type of SNP is significant over time in increasing the risk of breast cancer. The gene that rs17879961 affects is called the CHEK2 gene which stands for checkpoint kinase 2. Because SNP causes a mutation in this gene, it can lead to breast cancer. Basically the mutation this causes is the deletion of a single nucleotide at position 1100 at the CHEK2 gene. Deletion in this position causes production of a nonfunctional version of CHK2 protein. Without any healthy version of this protein, cells can’t regulate cell division leading to DNA damage. After a while, cells start to uncontrollably divide leading to cancerous tumors.

Primer design

  • Forward Primer: 5’ – T G T A A G G A C A G G A C A A A T T T
  • Cancer-specific Reverse Primer: 5’ – G G T C C T A A A A A C T C T T A C A C

How the Primers Work:

Primers are an essential part of the DNA replication process. The reverse primer bonds to complementary cancer-SNP. It will only bond to the strand that compliments it, so only DNA containing the cancer association will be replicated.

Feature 2: Consumables Kit

As previously mentioned, one of the problems with the kit was that it was that it made the experiment very time-consuming to run. Pipetting was also very tedious. The tubes in the packaging are stacked in our new design, making it much easier to access the tubes, ultimately making the experiment easier. The tubes not being pre-labeled made things much more difficult. The redesigned tubes are now labeled with 1A, 2A, 3A, 4A, 1B, 2B, 3B, 4B, etc. for greater ease of experimentation. The tubes were also redesigned with an accordion-like structure, making them able to be folded in for a more compact form of storage. These packaging changes will make the experiments that the scientists run much easier.

Feature 3: PCR Machine Hardware

The PCR machine will be used to target DNA replication in our system.

The aspect of the PCR machine that we have decided to redesign is the software and the display errors. The external software and transmission causes communication errors and can alter the results. Placing the software as an internal component rather than an external one, should also fix the display errors as well and improve the reliability of the PCR machine. The first time we used the machine half of the replications failed and and it took over 3 hours for 12 replications when it should have been more than that. This should hopefully improve the reliability as well as the speed of receiving results.

Feature 4: Fluorimeter Hardware

When using the fluorimeter a few issues were noted. The first was when the stand holding the sample was moved the drop of solution on top slid along the glass surface. This could be fixed by increasing the sturdiness and adding wheels so it could be transported more smoothly. Also, to insure consistent distance for the camera, a stand would be connected at the optimal distance for the camera to sit.

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

Calculation 3 was the probability of patients with cancer testing positive meaning a positive predictive value. The percent value for this calculation was small (close to 0) and has low specificity (probability of person without the disease will test negative). This tells us that the PCR diagnostic test resulted in some patients being positive for cancer but they are however non-cancerous patients and that this test is not good with testing cancer patients. Calculation 4 was the negative predictive value. This value was slightly above .5 and this was the probability that a patient without cancer will test negative. This had a somewhat sensitivity (probability that a person with the disease being tested will test positive) and would be a somewhat a good test for testing with patients without cancer.