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In order to gain large qualities of the DNA of interest, DNA and primer amplification is necessary. DNA and primer sequences can be amplified through polymerase chain reaction. In order to look at a particular SNPs, restriction enzymes for that SNP should be amplified using PCR-restriction fragment length, RFLP, also called cleaved amplified polymorphic sequencing, CAP. In the case that there is not a specific digestion enzyme that exists for a particular trait of interest, there is a way to create one. These enzymes are called derived cleaved amplified polymorphic sequences, or dCAPS. These reactions cut and amplify a specific single polymorphism (SNP). A dCAP is used on a mismatched PCR primer to make or get rid of a restriction site based on the particular genotype of the SNP being looked at. The primer used to create a dCAP is mismatched to create the restriction site of interest and the differing alleles are mutated. Primers used do not overlap or mutate the SNP. The restriction enzyme will cut at one site, so if the DNA sequence is cut into two fragments then both strands of DNA contain the allele. However, in the case that the individual is heterozygous, the restriction enzyme will cut only on one strand of DNA resulting in three strands of DNA. Additionally, if the DNA is homozygous for the other allele, there will be no cuts made (J. Laney, dCAPS Primer Design PowerPoint. Moodle.1, 1-16 (2018)).

DNA sequencing is a helpful tool in determining the exact nucleotide sequence of a particular genome. The Sanger Method is a particular way this can be achieved. This method feeds off of DNA replication occurring naturally within a cell. The DNA needs a primer to begin the process but can be stopped with the addition of a dideoxynucleotide. The reason the process is stopped when a dideoxynucleotide is added is due to the missing OH group on the 3’ end. Therefore, a fragment of DNA can be sequenced with a large amount of the DNA sequence of interest, a large amount of primers, DNA polymerase, an excess of nucleotides, and a small amount of one of the dideoxynucleotides. Due to the ratio of high normal, deoxynucleotide, to low dideoxynucleotides, there will be termination of the sequence at many different places. This process can also be done with all of the nucleotides labeled with different florescent dyes. If the fragments were then run on a gel, the piece of DNA could be sequenced. The use of capillaries is a technological way of doing this (J. Laney, Sequencing Slides. Moodle.1, 1-17 (2018)).

In this experiment, dog DNA was extracted and amplified through polymerase chain reaction (PCR). The DNA was then sequenced and analyzed using the Sanger Method. Excitability and size were chosen as traits to further analyze. By creating primers for dCAPS, the specific alleles for each trait were determined. The DNA was then dissolved with the digestive enzyme and ran on the gel for analysis. We had hypothesized that excitability and size are traits where heterozygous alleles exhibit codominance. Due to error in selection of the proper primer for creating our dCAPS, only the DNA marker was present on our gel. Therefore, no conclusion to our hypothesis was made. 

In the unknown lab, we started by gram-staining our unknown organism. This is a way of testing for the presence of a thick polysaccharide wall. Gram positive organisms have this thick wall, while gram negative organisms do not. To gram stain, first 4-5 drops of crystal violet are added onto the organism. Then after 60 seconds it is washed off with sterile water, and 4-5 drops of iodine is added for 60 seconds. Then hydrogen peroxide is added and left on for 10 seconds. Then 4-5 drops of safran is added for 60 seconds. Once that is done, the organism is observed under a microscope. The gram positive organisms appear purple, and the gram negative organisms appear pink. Gram negative organisms consist of non-fermenters and enteric bacteria. Gram positive organisms consist of staphococci and strepococci. Oxidase tests are done on gram negative bacteria to distunguish between non-fermenters and enteric bacteria. Positive tests appear for non-fermenters. Catalase tests are done on gram positive tests to distinguisg between staphococci and strepococci. Positive tests appear for staphococci. 

In the respirartory system, the air travels into the oral and nasal cavities. In the nasal cavity there are conchea and meatus. Continuing from the nasal cavity to the larynx and trachea, there is the nasopharynx, oropharynx, and laryngealpharynx. The larynx is protected by thyroid cartiage and the trachea is protected by cricoid cartilage. From there the air enters the primary bronchi. The primary bronchi split off into secondary brochi, and the secondary bronchi split off into tertiary brochi. The tertiary bronchi break off into brochioles, where there are aveoli sacs. Oxygen and carbon dioxide exchange into and out of the blood occur here. 

When a fat molecule is broken down, it is turned into acyl-CoA. The acyl-CoA is transported into the mitochondria and goes through beta-oxidation. The result of this process is acetyl-CoA, which can enter into the citric acid cycle (CAC). The acetyl-CoA is reduced and reduced electron carriers, ATP, and carbon dioxide are produed. The reduced electron carriers are used in oxidative phosporylation. They are passed down protiens builit into the inner mitochondrial membrane. This process creates a proton gradient in the inner membrane space. The protons flow through a protein, ATPsynthase, which produces ATP. 

In the unknown lab, we started by gram staining our organism. This is a way of testing for the presence of a thick polysaccharide wall. Gram positive organisms have this thick wall, while gram negative organisms do not. To gram stain, first 4-5 drops of crystal violet are added onto the organism. Then after 60 seconds it is washed off with sterile water and 4-5 drops of iodine is added for 60 seconds. Then hydrogen peroxide is added for 10 seconds. Then safran is added for 60 seconds. Once that is done, the organism is observed under a microscope. The gram positive organisms appear purple and the gram negative organisms appear pink. Gram negative organisms consist of non-fermenters and enteric bacteria. Gram positive organisms consist of staphococci and strepococci. Oxidase tests are done on gram negative bacteria to distunguish between non-fermenters and enteric bacteria. Positive tests appear for non-fermenters. Catalase tests are done on gram positive tests to distinguisg between staphococci and strepococci. positive tests appear for staphococci. 

Modern gene therapy tools have the potential to treat diseases through gene editing. Deadly diseases in the human genome could be eliminated or minimized. However, the technology could easily become abused. Therefore, countries have been banning research on gene editing for ethical and safety reasons. The goal of this study was to gain perspective about the opinions students have on gene editing. For our project, we surveyed 40 students attending the Univeristy of Massachusetts (UMass) Amherts about the ethics of gene therapy. The survey consisted of 10 questions, and the results were assembled into pie charts. The study showed that most people were neutral or agreed that using gene therapy to genetically modify genes to prevent lethal or genetically linked diseases was ethical. The majory also agreed that gene editing is not ethical when used for self-satisfaction and that people would use this technology for selfish purposes if it was normalized. 

Modern gene therapy tools have the potential to treat diseases through gene editing. Deadly diseases in the human genome could be eliminated or minimized. However, the technology could easily be abused. Therefore, countries have been banning research on gene editing to maintain safety and for other ethical reasons. The goal of this study was to gain perspective about the opinions students have on gene editing. For our project, we surveyed 40 students attending the Univeristy of Massachusetts Amherts about the ethics of gene therapy. The survey consisted of 10 questions, and the results of these surveys were assembled into pie charts. The results showed that most people were neutral or agreed that using gene therapy to genetically modicy genes is ethical. The majory also agreed that gene editing is not ethical when used for self-satisfaction and that people would use this technology for selfish purposes if it was normalized. 

We conducted a survey taken by 40 students at UMass Amherst, which collected their thoughts about how gene therapy should be used and regulated in the medical field, pertaining to ethics. The survey consisted of 5 questions. Answer options included: strongly agree, somewhat agree, neutral, somewhat disagree, and strongly disagree. The data was collected and condensed into pie charts.