Hello! If you haven’t been following along with my blog posts, my name is Siena Parr and I just completed my 3rd week interning at the Dorris Neuroscience Center in La Jolla, California. This week has been a short week, all of the Scripps campus has the 4th of July and the 5th of July off so I only worked Monday-Wednesday this week.
On Monday I learned about Next Generation Sequencing. In next-generation sequencing, DNA strands are fragmented and then ligated with oligonucleotides (one forward strand and one reverse strand). The DNA strands are then denatured and run on a chip. While on this chip the oligonucleotides will attach to matching binding sites and then will be amplified by a PCR. After that, the DNA is denatured again and the original strands are washed away. The remaining strands will then undergo “bridge building”. While doing this, the strands will bend and attach to another matching binding site and form an arch structure. The DNA is amplified again and the process repeats. Once all of the strands have been amplified the reverse strand is cleaved away and you can sequence one copy using fluorescently labeled nucleotides. Once that sequencing is done data analysis is used to generate the entire genomic sequence.
On Tuesday I was taught how to use computer software to track neurons. In order to do this, I would look at a magnified image of a brain where the neurons are visible. I will then label the center of the neuron where the nucleus is located and then map the filaments that branch from the center. Doing this allows us to identify the morphology of different neurons. By comparing the morphology of neurons that are altered to neurons that are not, it is easier to determine what effects gene mutations have on neurons.
This is my gel being imaged, you can see the bands from the ladder, the samples, and the positives and negatives.
This is the machine we run out of E-gels on.
Wednesday was by far my busiest day to date. I started off the morning by helping my mentor with a PCR. After putting the samples in the thermocycler, I went back to tracing neurons to get more familiar with the software. There was another intern who needed to learn how to trace the neurons so I shared my notes with him and let him label the next one. Lunch was provided on Wednesday since it was a lab meeting day (I ate a very good sandwich). In the afternoon I ran my PCR on a gel and imaged it. By imaging the gel you can genotype whichever samples you ran. The pattern on the far left “M” slot of the gel is the ladder. The ladder gives a reference point for the size of unknown DNA fragments. The two samples on the far left provide a reference point for the positive genotype and the negative genotype. If a band occurs in any of the samples next to the positive reference point the genotype is homozygous positive. If a band occurs in any of the samples next to the negative reference point the genotype is homozygous negative. If a band appears for both positive and negative points, the genotype is heterozygous. After imaging my gel I went to my 3rd lab meeting.
This is the corpse flower bud, I don’t know if the name tag is visible but he was named Jack Smellington.
On the 4th of July my fellow intern (Katie) and I decided we didn’t want anything to do with the holiday traffic so we stayed close to home. I got up early and went on a hike. The trails behind my house are really peaceful in the morning but also very steep. I’m learning very quickly that when you live at sea level the only way to really go is up. Our host family invited us to eat dinner with them and we had grain bowls for dinner (they were really good). We all agreed that having grain bowls for holiday dinner is a very California thing but I highly recommend it if you are ever looking for an untraditional holiday choice! On Friday Katie and I went to the San Diego Botanical Garden. They had a corpse flower and a voodoo lily, both of which smell like rotting meat when they bloom. Neither of them was blooming while we were there and I can’t really say I was disappointed. We don’t have many plans for Saturday and Sunday since San Diego is still really busy, we might try and go to the beach sometime.
It is hard to believe that I am already halfway through, the time has gone so fast but that has been it for week #3!
-Siena
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