Field Trip II – Point Reyes

We travelled up north to the southern end of Point Reyes to Leemantour Beach to find the purple variants of the Coastal Lupines. The drive up was really picturesque, as we drove by the ocean and then into a redwood forest (Samuel Taylor State Park). We spotted a deer out in the wild probably out to mate with another deer. When we stepped foot on the beach, we saw humpback whales in the distance feeding on krill and plankton. We noticed that there were a bunch of birds concentrated on where the whales are at because when the whales feed, they might release some fish up for the birds to eat. We also found the purple lupines! What’s pretty epic about them is that the plate that is on the beach was originally where Santa Monica is so it’s like a whole new different population! I’m curious now to find if the genes for this lupines and the lupines down south in SoCal are similar. We stopped by Samuel P Taylor State Park to find another plant, but we couldn’t find them.

 

DNA Barcoding II

The next week, we ran two gel electrophoresis on our fish DNA, one for our gDNA and one for our PCR product. The agarose block was prepared for us already (well for the first one) and all we had to do was pipette our sample into the wells and run the gel electrophoresis for about 10 minutes at 145V. To prepare out samples, we pipetted 2 microlitres of loading dye on a piece of parafilm and pipetted 3 microlitres of our DNA onto it. We repeated this step for our PCR product BUT we reused our old agarose gel by melting it and letting it cool and set. After determining which PCR worked, we did an Exosap PCR Clean up. We first made a master mix per table consisting of water, buffer, Exo and SAP, and then we pipetted our PCR product into a PCR tube and pipetted 12.5 microlitres of our master mix in the tube. After this, we put the tubes in a thermocycler and ran the program and after it’s done, we put it in the freezer.

For my gel electrophoresis, only 2/3 of my fish samples worked. This is probably because I only realized till the end of the first lab that I was using the pipette wrong so I probably have the wrong volumes used.

 

DNA Barcoding

Introduction

On the 6th September, we extracted the DNA from our raw fish that we collected. The purpose was to find out if the raw fish we got was actually what is was advertised to be by analyzing the fish DNA.

Methods

We cut up our raw fishes into tiny pieces, weighing approximately 2mg and labelled screwcap microfuge tubes. We used a commercial DNA extraction kit for this extraction. We pipetted 100 microlitres of extraction solution into each tube and then added another 25 microlitres of tissue preparation solution. We then added the fishes into the microfuge tubes that has their label (i.e. salmon in the tube labelled as salmon). We used a disposable pipette tip to smash the fish in the tube and left it out for around 10 minutes at room temperature. After that, we moved it to a heat block for 3 minutes (95 degrees celcius). Once we removed it, we added 100 microlitres of neutralizing solution and used a vortex machine to mix it up. We then left it in ice while we prepared our master mix (a mixture of water, PCR rxmix, forward and reverse primer). We diluted our fish samples by pipetting 18 microlitres of purified water in a microcentrifuge tube and then another 2 microlters of our fish DNA. In a PCR tube, we added 2 microlitres of our DILUTED fish DNA and 18 microlitres of our master mix and started out PCR.

The next week, we ran two gel electrophoresis on our fish DNA, one for our gDNA and one for our PCR product. The agarose block was prepared for us already (well for the first one) and all we had to do was pipette our sample into the wells and run the gel electrophoresis for about 10 minutes at 145V. To prepare out samples, we pipetted 2 microlitres of loading dye on a piece of parafilm and pipetted 3 microlitres of our DNA onto it. We repeated this step for our PCR product BUT we reused our old agarose gel by melting it and letting it cool and set. After determining which PCR worked, we did an Exosap PCR Clean up. We first made a master mix per table consisting of water, buffer, Exo and SAP, and then we pipetted our PCR product into a PCR tube and pipetted 12.5 microlitres of our master mix in the tube. After this, we put the tubes in a thermocycler and ran the program and after it’s done, we put it in the freezer.

Sushi Collection

On 5th September (Tuesday), I went down to Nijiya market, a Japanese supermarket located in Japantown to get some sashimi for the upcoming project. I bought a chirashi don which contained three types of raw fish – salmon, spanish mackerel and yellowtail. It also contained raw squid, which is not a fish. The purpose of this is to extact the DNA out of the fishes and see if they are really what they are advertised to be.

Field Trip 1 – Half Moon Bay

On Wednesday (30/8/17), we drove down two beaches located in Half Moon Bay, in search of a plant, the California Lupines. They are characterized by their palm shape leaf-bush and are found near the coasts. The plan is to extract the DNA and compare it to that of the Lupines found in the North, in Marin County. We also learned about the invasive species, ice plants.

 

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