BME100 s2014:T Group5 L6
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LAB 6 WRITE-UP
Feature 1: Disease SNP-Specific Primers
The nucleotide is commonly known as the monomer of DNA. Nucleotide is a compound consisting of a nitrogenous base, phosphate group and a sugar. Polymorphism is the occurrence of two distinct phenotypes found in a population, upon which natural selection occurs. An allele is one of numerous forms of a gene. An allele is also located at a specific position on a specific chromosome. The SNP rs23702, is an allele found in humans (homo sapiens). The exact location of it is 149721690. It is associated with the SUM04 And TAB2 genes. The SUM04 is also called the small ubiquitin like modifier 4 gene and functions as a missence and config reference. The SNP is also associated with Type 1 and Type 2 diabetes. The disease containing allele is ATG.
How the primers work: After the DNA is denatured and the temperature is lowered, the disease specific forward primer will bind to the complementary disease containing template at the 3' end. The reverse primer will bind to the complementary strand at the 3' end. The primers will then be used to replicate the specific section of the DNA strands. If the SNP containing template is not present the reaction will not occur as the primer will not be able to bind to the template completely.
Feature 2: Consumables Kit
Along with the PCR, a consumables kit would come with the product. The main goal of the consumables kit is to present all consumables in an organized fashion. There will be 16 empty color-coded PCR tubes. The color coding will help the researcher/scientist distinguish different groups of samples used in the experiment. There will also be pre-labeled tubes with the primers. The tubes containing the SYBR green will be included in the set in black tubes. This will allow no light to reach it since the SYBR green dye is photosensitive. All tubes will also have a white surface for labeling that will hold marker better. The micro pipetter would be included in the kit but packaged in another box within the packaging so it does not break. The kit will also include a pamphlet with the functions of all the materials and PCR tips and tricks. The kit will contain all the materials used in the lab and each material will be labeled and packaged separately to ensure there will not be cross-contamination.
Feature 3: Hardware - PCR Machine & Fluorimeter
The PCR Machine or the Thermal Cycler is used to amplify DNA through the polymerase chain reaction. The machine goes through about 30-40 cycles with three steps that include denaturation, annealing, and extention. The redesigned PCR machine will have bigger holes for the samples to amplify a higher amount of DNA during the process. Also, there will be a LCD screen added to the side of the machine to easily enter the information from the cycles. This would make the PCR process easier since it can be programmed right on the machine instead of having to plug the PCR into a computer.
Bonus Opportunity: What Bayesian Stats Imply About The BME100 Diagnostic Approach
The Bayesian statistics results show that the OpenPCR is not reliable at predicting the particular diabetes we looked at in this experiment. The probability that a patient will develop the disease and get a positive test result after using the PCR and fluorimeter was small and not close to 1. The probability that a patient will not develop a disease and get a negative result was higher than the positive correlation but was still not close to the optimal result of 1. This would not be an optimal method of predicting the diabetes we looked at in this experiment.