Labwork (PCR)

Following DNA extractions, it was time for amplification of DNA through Polymerase Chain Reaction (PCR). PCR amplifies the DNA by denaturing, copying, and synthesizing over and over again. Denaturing occurs via temperature, first during the DNA extraction process, and thenĀ again using the Thermocline machine (or PCR machine). The thermocline helps to regulate temperature allowing for PCR to go through its different steps, such as synthesis or denaturing. Synthesis occurs using a special polymerase Taq.

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Following the collection of data and samples, it was time for lab work to begin. The first step of my procedure was DNA extractions. With around 800 plant samples, I quickly realized financially and time wise doing all 800 would not be practical. This led to many discussions on how to subsample. Was it better to do more transects, with fewer plants from each transect? More plants, with fewer coverage of overall transects? How do you account for the difference in densities between transects? Overtime, with more and more discussions, it became clear that sampling more transects would be a better option, even if that meant fewer plants per transect. Additionally, for any transect with ~30 or fewer plants, the entire transect would be sampled. For any plant over that, a subsample would be done using a random number generator to randomly select which plants should be extracted.

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The month of June was predominantly spent on fieldwork and preparation for fieldwork. Preparation included obtaining materials, packing and planning ahead for the visits. There are 5 sites for field work: Presquile National Wildlife Reserve (PWR), Blandy Meadows (BLD-M), Blandy Thistle Thicket (BLD-T), Sky Meadows (SKY), and Greenspring (GRN). For PWR, BLD-M, BLD-T, and SKY, overnight visits were required. We were fortunate enough to have access to research housing for all of these. PWR is an island so that required intensive planning as nothing could be forgotten. Once we arrived at each site, we jumped right into fieldwork. [Read more…]