It has been over two months since I began my summer internship in the McGuire lab – I love it! Throughout this internship, I have assisted in various projects in the lab and gained experience working with new tools and techniques. I’ve discovered my love for being out in the field!
As far as the dog urine experiment is concerned, we are planning to synthesize dog urine using data from published literature and urinalysis normative data from ANTECH Diagnostics Lab. The specimen from the lab is obtained from a private dog owner. This project will most likely begin in the upcoming fall semester. Results from this project will give us a better understanding of the impact of urbanization on the ecosystem and improve citywide green infrastructure management.
The green roof assembly project is a survey of the soil microbial communities across different ground-level green infrastructure installations in the city. It has been an active study in our lab for the past five years; 2015 marks the last year we are obtaining soil for comparison and analysis. Fortunately, I was able to partake in soil sampling for its final year. My lab mates and I spent early July soil sampling across ten different green roofs (all of which are on the roof of recreation centers) in NYC: Sunset Park Pool, Brownsville Recreation Center, Chelsea Recreation Center, Lyons Pool, St John’s Recreation Center, St Mary’s Recreation Center, Lost Battalion Hall Recreation Center, Jackie Robinson Recreation Center, Hansborough Recreation Center and Sorrentino Recreation Center. Back in the lab, we conducted DNA extraction and measured the soil's moisture content and the soil pH in water. A few lab mates are currently finishing up on PCR that will undergo shotgun sequencing in the near future. Results from this project will help NYC better confront global issues such as pollution by finding the appropriate plant community to grow on green roofs.
Within these past few weeks, I have been assigned to a yearlong project in collaboration with Nandan from NYC Parks and Recreation and Ranran, a PhD student from Columbia University. We visit eight sample sites in the Bronx twice a month - these sites are green streets and bioswales. They are designed not only to beautify the streets in the city but also to collect stormwater runoff from the streets after a large precipitation event. Our project goal is to determine whether these ground-level green infrastructures are effective in nutrient recycling and capturing water runoff that would otherwise flow into the sewer system. My role is to collect soil to analyze the role of RNA in nutrient recycling. Since RNA is unstable, sieving and immediate flash freezing with liquid nitrogen is done on site. Nandan aims to test soil mineralization and Ranran measures the gas contained in the interstitial spaces of the soil using a soil-gas chamber (also known as soil-gas sampling). My focus for the yearlong Guided Research & Seminar course at Barnard will be an extension of this study.
In the past month, no significant progress has been made towards finding sources of dog urine for our prospective project. Many dog owners declined to donate dog urine since the process of collecting urine is stressful for the dog. Because thirty-five gallons is simply too large to collect manually, we have decided to synthesize dog urine in the lab. We initially planned to research its average composition and synthesize it but failed to find recently published literature on the composition of dog urine. Instead, we plan to use nuclear magnetic resonance spectroscopy to determine the physical and chemical properties of the mere 30 milliliters of dog urine sample that we struggled to collect at the Bideawee dog shelter. From there, we will have the list of ingredients needed for our dog urine recipe.
A familiar lab technique I revisited this past month since general chemistry lab last fall is measuring the pH of a given sample. For a few days, I used a pH probe to measure the pH values of soil samples in water. Measuring the pH, or the soil’s acidity or alkalinity is important because we want to determine the relationship (if any) between soil microbes and the pH of the soil samples. For further analysis, we computed the moisture content of the collected soil samples. We oven-dried a pinch of soil from each sample and compared it with its respective wet weight.
On June 19th, I went on a lab excursion to a one-day conference (Microbes in the City: Mapping the Urban Genome) at the New York Academy of Sciences. I was very excited about this opportunity because the relationship between microbes and human health is poorly studied. The conference successfully tackles the recent discoveries on microbes in urban areas and their relationship with humans and our health. Many findings were fascinating! As a commuting student researcher in the microbial ecology lab, the presentations about the microbiome in urban mass transit, in particular, caught my attention. The various microbial organisms that seep into the cracks of the wooden subway benches grossed me out. I learned that more than 40% of the DNA obtained from sampling in the NYC subway system did not match any currently known species of microbial organisms. We don’t even know what microbes we are coming in contact with. It is safe to bet that I will never sit on the subway benches ever again! Subway poles, however, are supposedly germ-resistant. As quoted by one of my favorite presenters, “you will probably be fine if you like a subway pole.”
In the upcoming weeks, we will be doing soil sampling for the Green Roof Assembly Project. In this project, we aim to create better green spaces throughout New York City to help capture stormwater runoff after a heavy precipitation event. Without the addition of green infrastructures in the city, the water quality will surely be negatively impacted as the runoff combines with raw sewage. For this project, we have been collecting soil samples from nearby parks and recreation centers once a month since 2012. We hope to explore and compare the diversity of microbes among green roofs with different plant communities. Additionally, we hope to explore the differences in the soil and microbes throughout the years. In this past month, my lab mates and I have been working hard to finish DNA extractions and perform PCR (polymerase chain reaction) to amplify a segment of DNA. We will send these DNA samples to another lab for sequencing. We will also be using the PLFA (phospholipid fatty acid) process to measure the microbial biomass and composition. We hypothesize that microbial biomass is directly correlated with the ability of soil to retain water.
On the first day of my summer internship at Barnard College, I walked in Dr. McGuire’s microbial ecology lab not feeling even a little bit nervous since I had been working in the lab the past spring semester. I was already familiar with the work environment and saw a few familiar (and new) faces. Right now, there are multiple research projects going on in the McGuire lab and I have not been officially assigned to a specific project -- I have been working in ones that need an extra helping hand. I spent the first week of my summer internship doing DNA extractions from soil samples collected from Puerto Rico, a technique that isolates microbial genomic DNA, and will later undergo shot-gun sequencing for further analysis.
The research project I am most interested in working on this summer is the investigation of the correlation between dog urine and soil microbe communities in NYC. I hypothesize that while urea from dog urine may benefit soil microbes as a fertilizer at initial application, additional application of dog urine past a certain threshold will negatively affect the water retaining capabilities of ground-level green infrastructures. This has a significant impact on water quality especially after a precipitation event because the unabsorbed stormwater runoff combines with raw sewage which then gets released to the nearest water outlets. Such a phenomenon is especially important in urban areas (i.e. NYC) that are highly populated with pets that urinate outdoors, such as dogs. Results from this research project may lead to increased water quality and educate dog owners on the effects that their pets may have on the environment in which they live in.
In this past week, my lab mate, Jee Min, and I have been researching on facilities that may be interested in donating dog urine for our project. Although we have already secured donation from Bideawee, a dog shelter in the city, a total of 34.6 gallons of dog urine is needed for this project and collecting urine samples from one location is simply not enough. This past week we have also personally visited dog parks in the nearby area, asking owners of pet dogs if they were interested in contributing to our research study. As expected, most initial responses were negative. (Catching dog urine is actually more difficult than expected!) Of the dog owners that were willing to participate, we will be personally collecting the stored dog urine from the household upon contact.
In the upcoming weeks, we hope that facilities and dog owners that we have reached out to will contact and follow up with us. Meanwhile, my other lab mates have been learning how to perform DNA amplification, a technique that increases the number of copies of a particular DNA fragment. With the help and guidance of Dr. McGuire and my fellow lab mates, I hope to take part of this training as soon as I have secured additional locations to collect dog urine from.