Apples in the Tree, Car in the Garage

What is DNA Sequencing? 

DNA sequencing can be used to determine the order of bases within a DNA molecule. There are four DNA bases which include adenine, thymine, guanine, and cytosine. To understand DNA sequencing, you should know that these bases are the building blocks of DNA molecules and be aware of base pairing. Adenine (A) pairs with thymine (T) and cytosine (C) pairs with guanine (G). If these concepts are new to you, certain phrases such as "Apples in the Tree, Car in the Garage" may help you memorize which bases pair with each other. 


DNA sequencing is extremely important in detecting and treating certain diseases and disorders. This is especially true for cancer patients. DNA sequencing may help their doctor determine the type of cancer they have so that the patient will be able to receive more appropriate treatment. Screening newborns for genetic disorders and other issues has become another important use of DNA sequencing. 

I took genetics (GN 311) last semester, so I learned quite a bit about DNA sequencing during the fall. Not only did I learn what DNA sequencing is, but I also had to learn about some of the most important or common uses for DNA sequencing and had to solve certain problems on homework assignments and exams using my knowledge of DNA sequencing and base pairing. We discussed DNA sequencing with regards to genetic testing, mutations, gene mapping, evolution, and many other topics. In my genetics class, we focused on Sanger Sequencing. I do not recall Next-Generation Sequencing (NGS) ever being mentioned. This research project for our GN 312 lab will be the first real application of DNA sequencing that I have been involved in. I look forward to seeing and analyzing collected data in the near future and to helping the rest of the class bring this project together. 

Why DNA Sequencing? 

The purpose of this research project is to obtain data that will contribute to a better understanding of where different bread flavors, aromas, and consistencies come from. To do this, we will be characterizing the phenotypes of the microbial communities growing in our sourdough starters, and then we will be using Next-Generation Sequencing to determine which species of microbes are responsible for the observed phenotypes. We will need to sequence DNA from our sourdough starters and analyze it to be able to make any assumptions about the origins of certain bread characteristics. 


Sanger Sequencing vs NGS

When comparing Sanger Sequencing and Next-Generation Sequencing, the most obvious and important difference between the two is the sequencing volume. While Sanger Sequencing only allows one DNA fragment to be sequenced at a time, NGS makes it possible to sequence millions of DNA fragments at once. This method of sequencing gives us the ability to sequence hundreds of thousands of genes at the same time. This increases the discovery power and provides a much faster way to sequence large numbers of genes. To obtain the same amount of data with the Sanger Sequencing method would be very costly. 


More About NGS & Our Research Project

Illumina sequencing technology will be used in our research project to sequence the DNA from our sourdough starters. This sequencing workflow consists are four steps which include sample preparation, cluster generation, sequencing, and data analysis. After watching a short video about the Illumina sequencing technology, I realized that there are many concepts and steps involved that are fairly easy to understand and actually really fascinating to watch in an animation. However, there were some parts of this animation that left me somewhat confused. The process is definitely complex, but that is understandable seeing as this method is so advanced and efficient. 

Some of the concepts or terms mentioned in this video that I am familiar with include denaturing to make two single-stranded copies, the use of polymerases to form double strands, clonal amplification of fragments, and bases being added or paired to the bases of the template strand sequence. I suppose the most confusing part of the process to me was the binding that occurred between the ends of the strands. Although I do not completely understand every aspect of the process done by the Illumina sequencing technology, the animation video definitely gave me a good idea of what is going to be done with the samples from our sourdough starters. 


Citations

https://www.genome.gov/about-genomics/fact-sheets/DNA-Sequencing-Fact-Sheet
https://www.khanacademy.org/science/ap-biology/gene-expression-and-regulation/biotechnology/v/dna-sequencing
https://www.youtube.com/watch?v=ONGdehkB8jU
https://www.thermofisher.com/us/en/home/life-science/sequencing/sequencing-learning-center/next-generation-sequencing-information/ngs-basics/what-is-next-generation-sequencing.html
https://emea.illumina.com/science/technology/next-generation-sequencing/ngs-vs-sanger-sequencing.html
https://www.youtube.com/watch?v=fCd6B5HRaZ8

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