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Post by Zoë and Modupe (ARISE student researchers)

Before we could even begin sampling at the Gowanus, we had to determine the best method for DNA collection and extraction. To do this, we tested the sidewalks right in Metrotech center. Each day we altered a different variable in the collection process, with the goal of increasing DNA yield. To prepare for swabbing, we packed a box with the needed supplies: the frame, swabs, gloves, ethanol and napkins (to clean the frame) and a marker for labeling. Once we were ready, we headed outside to begin swabbing. Because of the natural variety in the sidewalks, we were careful to choose areas right next to each other and of similar appearance. We took turns swabbing the sidewalk, stopping at the halfway point of each trial to re-dip the swab in the elution fluid. After we had collected all of the samples for a given day, we went to the lab for culturing and DNA extraction — and next the DNA quantification and analysis. Over the weeks we tested two elution fluids (aimes fluid and 0.15M NaCl + 0.1% Tween 20), two frame sizes (20×20 cm. and 30×30 cm), three swabbing surfaces (concrete, slate, and cobblestone), and swabbing times from two minutes to six. Based on the DNA quantification results, we determined to ideal mechanism:

• Swabbing Procedure: Swab the concrete inside a 30×30 cm. frame for 3 minutes, pausing at 1:30 to re-dip the swab. Use the amies elution fluid and swab vigorously, making sure to cover the whole area.

Determining the Baseline

Post by Zoë and Modupe (ARISE student researchers)

After establishing the method for DNA collection, we could start to determine the baseline DNA levels for areas surrounding the Gowanus Canal. We chose to focus on 9th street, because 9th street between the Gowanus and 2nd avenue is a commonly flooded area. Thus, we collected samples from along 9th street in three locations — before 2nd avenue, after 2nd avenue, and after 3rd avenue. We compared the DNA yield in these three locations to understand if there is a difference between the microbial composition in areas in and out of the flood zone. We found significantly less DNA yield in the location inside the flood zone, than either of the two areas farther from flooding. As of now we are not sure of why we are getting these results — we are planning to run qPCR and sequence the DNA from all three locations to look for further differences.

Project Overview

Post by Zoë and Modupe (ARISE student researchers)

The ultimate goal of this research is to study the impact of flooding on the microbiome of urban surfaces in NYC by collecting and sequencing DNA from these surfaces before and after flooding. To do this, a baseline measure of the microbial composition of these surfaces is necessary. This particular research is a preliminary stage which aims to establish the baseline by optimizing the DNA collection and extraction procedures. The procedures determined to produce the highest DNA yield will be used to measure and characterize the baseline microbiome of NYC urban surfaces. This baseline will then be used in the next phase of the project by comparing it with the microbiome of recently flooded surfaces. Overall, this research will contribute to a better understanding of the possible effects of flooding on the city’s microbiome, which can help motivate interventions to protect the health of NYC residents.

Who Are We?

Our names are Zoë Cappella Cooper and Modupe Oridota. We are New York City high school students. Zoë will be a senior at the Bronx High School of Science and Modupe is a rising junior at Medgar Evers College Preparatory School . This summer we have been working in Dr. Silverman’s lab on this research project. We are part of the ARISE (Applied Research Innovations in Science and Engineering) program at NYU. Through this program we interviewed and were then matched with a lab. Both of us are interested in environmental engineering, which is why we have spent the summer in Dr. Silverman’s laboratory working on this particular research project.