Nicodemus Wilderness Project
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NWP Global Registry of Apprentice Ecologists - New York, New York, USA

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New York, New York, USA
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sharonlin



Registered: December 2015
City/Town/Province: Corona
Posts: 1
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I am a junior at Stuyvesant High School, in downtown Manhattan. I decided to conduct an Apprentice Ecologist project on behalf of the Nicodemus Wilderness Project in the spring of my freshman year, after learning about a program at my school which allowed student researchers to conduct DNA barcoding experiments and studies, and to contribute to the growing field of urban ecology in the metropolitan area. Teaming up with four other students and two biology mentors, we decided to base our research on the impact of various algal species on the five boroughs of New York City.


As a result, it was necessary for our team to split up and cover different areas of New York. We sampled water and algae from various New York City Parks in Queens, Bronx, Brooklyn, Manhattan, and Staten Island, including Hudson River Park, Central Park, Flushing Meadows Corona Park, Tappen Park, Fort Tryon Park, Bryant Park, Mill Pond Park, and Prospect Park. It took over three months to gather samples from the vast acres we were covering. After we had obtained water and algae in falcon tubes from the various locations, we set to work to tentatively classify the algae sample by their descriptions in order to aid future classification. Many of the samples were similar in appearance, as they all seemed to have been taken from the edges of ponds.


Most of the members in our research group were unable to obtain permission to row to the center of the pond to collect samples, so this was a consequence of our restriction. In addition, many of the samples seemed to be micro algae, as opposed to macro algae, which appears more leaf-life and less moss-like. In addition, many of the samples had water that was cloudy or otherwise filled with dirt and mud, which may have caused the later imperfections in our project. Nevertheless, the majority of the samples did have easily distinguishable features, whether it was the color of the algae or the shape of the organisms.


After our classification, we set to work isolating the DNA. This required an in-depth process in which we hard to partake in hours of lab work after school for four months. The process would begin with the cell lysis, where we would crush the samples in order to break open the cells and release the intercellular components. We then added a detergent to remove membrane lipids to further assist in the DNA extraction. After this step, we added a protease to remove proteins, then an RNase to remove RNA. The salts, reagents, detergents, and proteins were then removed by ethanol precipitation, where we would combine the contents of our now separated cells with ice-cold ethanol and vortex and centrifuge the contents to allow the DNA to aggregate together atop of the rest of the materials, forming a pellet.


This pellet was then removed and further purified by adding additional sodium acetate to remove cellular and histone proteins bound to the DNA. The DNA was then dissolved in a slightly alkaline buffer - our lab group used TE buffer, since we did not have ultra-pure water at hand.


Because our sample would have considerably shrunken to a microscopic level, in order to increase the amount of DNA we had to work with, we performed a polymerase chain reaction (PCR), which involved combining the DNA with Taq polymerase and heating it to 96 °C for about 30 seconds, cooling it to 65 °C for about 40 seconds, and heating it once again to 72 °C for about 15 minutes. The final holding step cools the DNA to 15 °C for an indefinite time in order to keep it at a holding temperature, although multiple cycles of the initial steps were run in order to increase the amount of DNA at hand (typically 20-40 cycles).


After the PCR, we would combine the newly replicated DNA with restriction enzymes in order to divide the long strands into smaller pieces, and then add a small amount of the tracking dye bromphenol blue to the mixture before pipetting it into the agarose gel to begin gel electrophoresis. This process took about 15 minutes, and resulted in a display of the contents of the sample. If we were successful, we kept track of the DNA sample, eventually sending it to the Cold Springs Harbor lab for further testing and barcoding.


After all of our samples had been treated and prepared, we awaited our results. The barcoding results allowed us to match samples to species, eventually discovering that there was a breed of algae in the Manhattan and Brooklyn lakes that had not existed 20 years prior to our research, and had evidently been brought overseas from China or part of Europe. This was exciting for our team, as it meant that we had stumbled upon a case of invasive species in the area, as well as a serious issue for us to report to urban ecologists.


At the Urban Barcode Symposium at the American Museum of Natural History spring of my sophomore year, my team and I presented our finalized research, along with a prepared poster detailing the results of our work. We explained to our audience the importance of taking care of the lakes and public parks, especially for shipping companies and other industries that often deliver goods from one continent to another. We also talked about how cleaning up after yourself and making sure you don't leave behind waste or track out harmful species from parks is important to preserving the ecological vitality of these green spaces in the city.


Our project is ongoing, and we have already gotten support from ecologists from around the city regarding our work. Not only have we been able to share research that can potentially prevent the destruction of these parks and natural resources, but we have also provided a window into the future of our city's ecology - and that of other urban areas around the world. By studying the smallest organisms, we can determine how even small choices - such as not cleaning the helm of a ship or properly watching what species one transports with good - can have a massive impact on the landscape of an area.


This project has definitely taught me a lot about the importance of caring for our natural resources, and it has secured my interest in pursuing a career that helps the environment and those affected by environmental changes. It has taught me that even a seemingly insignificant question can lead to answers no one could have ever expected, and that even small changes can have a massive impact. Most of all, it has taught me the important of preserving our environment and natural land, and reminds me of why I am passionate about research and science. I look forward to continuing my work in these areas, knowing that what I do can and will have an impact on my community's future.
Date: December 31, 2015 Views: 5010 File size: 12.9kb, 187.9kb : 2048 x 1362
Hours Volunteered: 300
Volunteers: 6
Authors Age & Age Range of Volunteers: 16 & 15 to 35
Area Restored for Native Wildlife (hectares): 100
Trash Removed/Recycled from Environment (kg): 30
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