PCR - Spring 2024

Contents.

AP Biology

Analyzing Cheese Mold Growth when Treated with Shiitake Fungi and Lion’s Mane Fungi 10

Calcium and its Effect on Duckweed Growth 10

Different Duckweed Species’ Effect on Lead Concentration 11

Duckweed’s Potential for Reduction of Heavy Metal Toxicity in Water 11

Effect of pH on Duckweed 12

Effects of Anabaena variabilis on Lemna minor Surface Area Growth and Ammonia Levels 12

Effects of Sodium Chloride on Saccromyes cervisae Metabolism and Ethanol Production 13

How do Common, Unhealthy Artificial Sugars Impact Cell Repair in Yeast Digestion? 13

How does pH Affect Lemna minor (Duckweed) Growth? 14

How pH Levels Affect the Growth of Lemna minor 14

How do Varying Levels of Zinc Affect the Growth Rate of Duckweed? 15

How does Varying Water Disturbance Affect the Growth of Lemna minor? 15

Impact of pH on Ethanol Production During Yeast Fermentation 16

Light Intensity’s Affect on the Growth Rate and Photosynthetic Efficiency of Duckweed (Lemna minor) 16

Measuring the Effect of pH Levels 3, 5, 7, and 9 on the Proliferation of S. cerevisiae Yeast Cells 17

Measuring The Effect of Varied Sugar Concentrations on Ethanol Production via Yeast (Alcoholic) Fermentation with Saccharomyces cerevisiae 17

Observing the Effects of Varying Caffeine Concentrations on Daphnia magna Heart Rate 18

Optimizing the Ethanol Tolerance of Saccharomyces cerevisiae with Potassium Chloride 18

The Effect of Lemna minor on Decreasing Nitrogen and Phosphate Concentration in Contaminated Water 19

The Effect of Lemna minor on a Salt-Diluted Aqueous Environment 19

The Effect of Varied Microplastic (Polyethylene) Concentrations on Yeast Cell Survivability 20

The Impact of Caffeine on the Fermentation Rate of Yeast 20

Yeast Cell Growth Under Varying Conditions of Materials and UV 21

AP Statistics Exploring the Relationship Between the Frequency of Exercise and Reported Stress Levels Among Students 35

Contents.

Belize Global Programs

How Did the Protection of Mexico Rocks Affect the Populations of Overfished Species? 37

The Population of Apex Predators and the Impact on Abundance of Fish 38

The Abundance of Parrotfish at Ambergris Caye After the Protection of Mexico Rocks 38

Independent Research

Characterizing D(n)-tuples of Polygonal Numbers 39

Improving Liquid Cancer Biopsy through Computer-Aided Microfluidic Device Design Based on the Tubular Pinch Effect and Dean’s Flow 39

Clubs

Pingry Robotics Club 40

Science in the Pingry Community: About FYI Sci 41

Editor’s Note.

Welcome to the 2024 Research Week edition of the Pingry Community Research (PCR) Journal. We are excited to showcase Pingry’s top scientific talent, both in terms of research skills and knowledge of scientific concepts and discoveries.

The PCR journal provides students the opportunity to publish novel research. Through a written medium, students demonstrate their in-depth understanding of complex, collegiate-level scientific topics, and their applications in research at Pingry.

This research week edition of PCR serves as a written complement to the in person poster presentations occurring throughout research week. Readers can preview abstracts, figures, and summaries reflecting the research conducted in advanced courses and extracurriculars, such as AP Biology, Independent Research Teams (IRT), and the Methods in Molecular Biology Research Class, among others.

Through the PCR journal, we hope to spark intellectual curiosity and promote scientific inquiry amongst the next generation of Pingry researchers.

Dive into the wonders of Pingry Research through this special edition of PCR: Pingry’s foremost journal of scientific research.

Melinda Xu (V), Editor-in-Chief

Elbert Ho (V), Editor-in-Chief

Evan Xie (VI), Former Editor-in-Chief

Annabelle Shilling (VI), Former Editor-in-Chief

Editorial Staff.

Editors-in-Chief:

Melinda Xu (V), current Elbert Ho (V), current Evan Xie (VI), former Annabelle Shilling (VI), former

Head Layout Editor:

Sriya Tallapragada (V)

Head Copy Editor:

Carolyn Zhou (V)

Head Cartoon Editor:

Sophia Lanao (IV)

Faculty Advisor:

Mr. Maxwell

Copy Editors:

Alexander Recce (V)

Christian Zhou-Zheng (IV)

Edward Huang (IV)

Jingjing Luo (V)

Sofia Wood (V)

Layout Editors:

Carolyn Zhou (V)

Christian Zhou-Zheng (IV)

Jingjing Luo (V)

Sophia Lanao (IV)

Julia Ronnen (IV)

AP Biology

Analyzing Cheese Mold Growth When Treated With Shiitake Fungi and Lion’s Mane Fungi

by Jiya Desai (V), Parth Patel (V), Sriya Tallapragada (V)

This research explores the impacts of shiitake fungi (Lentinula edodes) and lion’s mane fungi (Hericium erinaceus) on mold growth in cheddar cheese, a field of study with significant economic and food safety implications. Our experiment aims to fill the lack of research on the interaction between fungi and cheddar cheese mold growth, using inoculation to measure and compare fungi growth accurately. Results from our trials demonstrate that cheddar cheese inoculated with shii-

take fungi shows statistically significantly greater mold growth than cheese treated with lion’s mane fungi, indicating differential influences of the two fungal species on mold growth in the cheese. This finding contributes to the understanding of mold growth dynamics in cheese and provides insights into effective mold management strategies, potentially benefiting food safety and preservation practices within the culinary industry.

Calcium and its Effect on Duckweed Growth

by Britney Alfieri (VI), Jack Buckley (V), Greta Reinhardt (V)

Lemna minor, better known as duckweed, is a small aquatic plant that comprises a fundamental component of many organisms’ habitats and diets and plays roles in bioremediation and livestock feed. Since L. minor is commonly used for research, we chose to use the plant for our research due to its rapid growth and vast environmental adaptability. Calcium is an essential nutrient in plants like L. minor because it plays a key role in the structure of plant cell walls and cell membranes and coordinating responses to developmental and environmental challenges in its role as an intracellular messenger. Studies have shown that when too much calcium is present in the environment, cells suffer from toxicity, resulting in decreased growth. However, the effect of calcium

on L. minor surface area has yet to be extensively studied. Our studies aim to evaluate the relationship between L. minor growth and calcium concentration to examine further whether excess calcium will prevent germination. This experiment establishes the connection between L. minor size and calcium concentration, which can be used to determine calcium’s potential negative effect in the natural environment, and we conclude that the growth of L. minor can be optimized by reducing the amount of calcium that L. minor is exposed to. Our findings can be utilized in fields like agriculture, where L. minor can be used as a food source, or environmental protection, where L. minor can be used to clean bodies of water.

Different Duckweed Species’ Effect on Lead Concentration

by Eshaan Golchha (VI), Charles Levine (VI), Sebastian Talarek (VI)

The present study investigated the effect that two distinct duckweed species, Lemna minor and Spirodela polyrhiza, had on the lead concentration in water. The objective was to determine the most effective duckweed species in lowering lead concentration in stagnant water, with the ultimate goal of implementing duckweed as a large-scale water filtration system to save animal habitats and protect human populations. In experimental trials, duckweed was placed in conicals containing water with an initial lead level of 50 ppm. After 7 days, pH strips were used to measure the lead levels and compare the difference in lead concentrations between the conicals of each duckweed species. Results showed that

S. polyrhiza removed more lead from the water than L. minor, meaning that S. polyrhiza was more effective at lead filtration. Analyzing the RGB data for each of the testing strips, we determined that the green value had significant fluctuations showing differing lead concentrations (higher green value means lower lead concentration). Our experiment ended with the following green values: control (130-140), L. minor (155-165), and S. polyrhiza (185-195). Our research shows that S. polyrhiza could be a potential option for largescale water filtration in the future, but further research has to be conducted to compare it to other duckweed species and to test other heavy metals.

Duckweed’s Potential for Reduction of Heavy Metal Toxicity in Water

by Savannah Dibre (V), Graham Houghton (V), Owen Murphy (V)

Pollution of waterways is a consequential problem with widespread impacts on wildlife ecosystems, drinking water supplies, and public health. This study examines the potential implementation of duckweed as a method to extract heavy metal pollution from contaminated water in a cost-effective manner. Duckweed was introduced to contaminated water samples to assess its effectiveness at removing metal impurities and improving overall water cleanliness. The results of the experimental trials, as measured by light wave spectrophotometry, indicated that duckweed was effective at reducing metal contamination by an average of 12.6% in contaminated samples, which is a statistically significant result (p-value = 4.81%). Overall, these are important findings, as duckweed is inexpensive and only requires a viable food source to grow and isolate metal impurities in water samples.

Credit: Google Images (Duckweed)

Effect of pH on Duckweed

by Mari Finkelstein (V), Julia Haidri (VI), Julia Woodbury (V)

Lemna minor (duckweed) is used to clean pollutants out of water. In order to use duckweed most effectively and achieve the best results, it is important to understand the conditions in which duckweed grows best. Measuring the growth of duckweed at different pH levels shows what environment duckweed thrives in, allowing for duckweed to be used efficiently. To determine the most effective pH for duckweed to grow in, we placed duckweed in five different pH values, along with Miracle Gro (duckweed fertilizer), and measured the change in surface area every 6 days.

Through two trials, our results concluded that a neutral pH 7 is the optimal value for duckweed to grow. Our results also concluded that the further away from neutral pH level the water is—pH 2 and 12 in this case—the larger the decrease in surface area is and the less effective it will be at removing pollutants from water. The importance of these results is that those who are trying to remove pollutants from our oceans and rivers should attempt to neutralize the pH of the water to have the most toxins removed.

Effects of Anabaena variabilis on Lemna minor Surface Area Growth and Ammonia Levels

by Samuel Gonzales (VI), Nicolas Rodriguez-Lopez (V), Keira Troy (V)

Anabaena variabilis, a cyanobacterium found in freshwater ponds, is capable of forming symbiotic relationships with aquatic plants through nitrogen fixation. We hypothesized that Anabaena could form a relationship with Lemna minor (duckweed), an aquatic, rapid-growing flowering plant, though few studies regarding these interactions have been conducted. Duckweed’s rapid growth, paired with Anabaena’s nitrogen-fixing abilities, holds promise for environmental applications ranging from wastewater treatment to helping provide insight into aquatic nutrient cycling. Duckweed and Anabaena samples were independently gathered and cultured before being integrated into 6-well Falcon plates with ratios that we determined in preliminary trials. Duckweed samples that received around 1 mL of Anabaena for every 70 mm2 of Duckweed surface area demonstrated significant growth as opposed to their control counterparts, which received 0 mL/70 mm2. ImageJ analysis indicated an average increase in surface area of 67.2% for the 1 mL/70 mm2 treatment and a 19.7% increase for the control. However, although the 1 mL/70

mm2 seemed to optimize duckweed growth the most, Anabaena treatments that slightly varied didn’t produce significantly different results. A decrease in ammonia levels was also observed, with values reducing from an initial 1 part per million (ppm) to values ranging between 0 and 0.25 ppm. Our research suggests that a symbiotic relationship between Duckweed and Anabaena can be established, which may contribute to duckweed growth and ammonia filtration for the specific Duckweed-to-Anabaena ratios tested.

Credit:

Google Images (Anabaena variabilis)

Effects of Sodium Chloride on Saccharomyces cerevisiae Metabolism and Ethanol Production

by Uma Menon (V), Ziv Shah (V), Hansen Zhang (VI) Credit: Google Images (Yeast)

In our study, we aimed to find the optimal concentration of NaCl (table salt) for Saccharomyces cerevisiae (yeast) metabolism. Several studies have been conducted on the effects of either high or low NaCl concentrations on yeast metabolism, yet none have attempted to find an optimal one. We measured the ethanol produced by yeast in tubes with various concentrations of NaCl over the course of several days. We found that a concentration of 15 mM was optimal for ethanol production. Our experiment confirmed that some NaCl is needed to maintain an osmotic balance, and extremely high concentrations are ineffective in the process of yeast metabolism. This was also the first study to find optimal concentrations rather than just examine

the effects of NaCl, and similar studies could help optimize biofuel production in the future.

How do Common, Unhealthy Artificial Sugars Impact Cell Repair in Yeast Digestion?

by Malcolm Adedjouma (V), Rafferty Harris (V), Kayla Kerr (V)

Researching the impact of various sugars on the digestive system, we ask the question: how do common, unhealthy artificial sugars impact cell repair in yeast digestion? Due to its affinity to sugars and its efficacy against gastrointestinal diseases, yeast was chosen to replicate the enzymes present in stomach acid. We tested various sugars (fructose, glucose, maltose, sucrose, and aspartame) to recreate an environment where stomach enzymes break down natural and artificial sugars. From the experiments, we found varying levels of CO2 production in the yeast fermentation. When comparing CO2 production levels of different types of sugars (glucose, fructose, sucrose, and maltose), fructose resulted in the highest level of CO2 production. These results are supported by our ANOVA test because the p-value in the Water Displacement and Calculated CO2 vol-

ume was below 0.05, providing statistical significance. When comparing CO2 production levels at different levels of aspartame, 4 grams of aspartame with 2 grams of yeast produced the most CO2. According to our data, however, there was a downward trend in CO2 production with increased levels of aspartame. After performing an ANOVA test on the aspartame trials, these results were supported because the p-values in Water Displacement and Calculated CO2 production were higher than 0.05, indicating that there is no statistical difference in the data. Overall, fructose appears to be the best sugar to enhance yeast fermentation, so it may be the easiest sugar for the stomach to digest. These conclusions can advance our understanding of how consuming sugars can impact our digestion and help us make informed adjustments to our eating habits for better health.

How Does pH Affect Lemna minor (Duckweed) Growth?

by Alexis Bartoli (VI), Michael Caratzola (VI), Ronald DeMyers (VI)

The purpose of this experiment is to determine the pH at which Lemna minor (duckweed) grows the most. We did this by filling 4 wells each of 6 different solutions of varying pH before growing the duckweed in them for seven days. Our experimental solutions had pH levels of 3, 5, 9, and 11, and used distilled water and a salt solution as controls. We then used ImageJ to analyze the photos we took of the well plate over the course of the experiment. ImageJ works by finding any green in the image and measuring it against a set measurement of the diameter of the well plate. We then averaged the growth for the four wells of each solution to find the total growth over the seven days. Our data from the

final day of trial one was inconsistent with the rest of our data, so we decided to remove this data from our conclusion. We found that there was no statistically significant difference between the total growth in the pH 5, 7, 11, and salt solutions. The duckweed grew the worst in the pH 3 and 9 solutions. After the first trial was concluded, we attempted a second trial, which had to be scrapped because the duckweed was photobleached and dead at the end of the trial. We concluded that while there was no statistically significant difference between the solutions with the best growth, there are pH levels, namely pH 3 and 9, in which duckweed grows significantly less.

How pH Levels Affect the Growth of Lemna minor

by Isabella Fuentes (VI), Neil Srikanth (VI), Theo Strelecky (VI)

This study investigates the growth adaptability of Lemna minor, commonly known as duckweed, in varying pH levels. Duckweed has the potential to be a more sustainable and cost-friendly alternative for water purification in bodies of water, so we tested the reliability of duckweed with four trials spanning over different durations, ranging from five to thirty days. We filled microwells with varying pH levels and placed duckweed in each well. The control group was the set of wells with a pH of 7, the optimal pH level for duckweed. Several trials were conducted, and after each, a computer program, ImageJ, was used to see the change in the number of green pixels in each well using before and after photos. The results highlight the importance of nutrient provision, as the absence of Miracle-Gro compromised growth in the initial trial. Furthermore, challenges related to algae competition arose, prompting the introduction of copper sulfate to mitigate interference. In our findings, Lemna minor strug-

gles to thrive in pHs outside of neutral levels, suggesting potential limitations in utilizing duckweed for water filtration, emphasizing the importance of considering environmental factors and potential competitors in practical applications.

Credit: Google Images (Duckweed)

How do Varying Levels of Zinc Affect the Growth Rate of Duckweed?

by Mia Cuiffo (V), Tobin Huang (V), Rebecca Novofastovsky (V)

Lemna minor (duckweed) can be used to remove pollutants, like zinc, from contaminated bodies of water. Zinc is commonly released into environments from mining and other industrial processes and can harm both the duckweed and its surroundings. Our research aims to develop natural pollution reduction processes that utilize duckweed without harming it by understanding what the threshold is for the amount of zinc L. minor can remove before its growth is compromised. We test zinc concentrations of 0.0M, 0.25M, 0.50M, 0.75M, 1.0M, and 1.25M. Two well plates were used for each concentration. The first trial lasted 5 days, with three measurements taking place. The second trial lasted 14 days, with six measurements taking place. The Java program ImageJ was used to calculate the surface area of the L. minor at each measurement. At 0.25M of

zinc, L. minor experienced the highest positive change in growth. At 0.50M and 0.75M of zinc, L. minor experienced minimal growth in surface area, indicating that the zinc did not stunt nor stimulate growth. At 1.0M and 1.25M of zinc, the L. minor began to die and experienced the greatest amount of negative change in surface area. Therefore, 0.25M of zinc was determined to be the most suitable concentration for duckweed growth. After performing statistical analysis through an ANOVA analysis, the results were deemed statistically significant. This information can be used to implement L. minor in zinc-polluted bodies of water commonly found around the world. 0.25M of zinc is the threshold L. minor can withstand while also stimulating its growth, as higher concentrations begin to cause harm to the plant and lower concentrations do not have a significant effect.

How does Varying Water Disturbance Affect the Growth of Lemna minor?

by Dylan Blekicki (V), Becca Kirschner (V), Katia Krishtopa (VI)

Our experiment seeks to gain further knowledge on how organisms are affected by environmental change; specifically, on how the growth of Lemna minor (duckweed), a common solution to the absorption of metals in polluted water, is affected by freshwater distubrance. Our group attempted to answer the question of how freshwater disturbances affect the growth of Lemna minor (duckweed). We set up three groups of duckweed: one control, one with one bubbler, and one with two bubblers. The bubblers were used to simulate a water-disturbed environment with different levels of disturbance. Over 3 weeks, we monitored and measured the water’s oxygen levels and the duckweed’s growth to determine

the effects of water on the duckweed’s growth. In the end, the duckweed grown in water with no disturbances had a higher growth rate compared to the duckweed grown in water with disturbances. Therefore, we conclude that duckweed with no bubblers has no resistance to its growth while duckweed with disturbances does, meaning that duckweed thrives in still water and cannot tolerate any water disturbance. Duckweed serves as an aid to pollution, but our experiment demonstrates that it cannot be employed in bodies of freshwater that are not still. Finally, our results confirm that aquatic organisms that experience changes in flow rates in bodies of water can be negatively impacted by the sudden change in water flow.

Impact of pH on Ethanol Production During Yeast Fermentation

by Brooke Hannon (V), Sarina Lalin (VI), Neil Riener (V)

In desiring to research the environmental impact of the yeast industry, we formulated our research question: how does pH impact ethanol production during yeast fermentation? The relationship between yeast and pH was selected because extreme pH levels cause chemical stress to yeast cells, limiting their ability to ferment. This is significant as ethanol, a byproduct of yeast fermentation, is a renewable energy source that can reduce environmental impact. In examining this process, we can observe the effects of specific pH levels on the production of ethanol by yeast. We attempted to answer our research question by evaluating the ethanol production when 0.5 grams of yeast was fermented with 1 gram of sucrose (added to aid the fermentation process) in different pH solutions (4pH - 10pH) over 72 hours.

The solutions were placed in a test tube with an airlock, and after 0 minutes (initial), one hour, 24 hours, 48 hours, and 72 hours, the ethanol production was measured using a Brix refractometer. Our results concluded that pH 7 is most successful for yeast cells producing ethanol, with pH 10 yielding similar results. We found that pHs 4 and 9 were the least effective for producing ethanol. Based on our ANOVA test, the p-value of ethanol production is less than the significant value of 0.05. This means that the observed difference is not due to chance, and the null hypothesis can be rejected. These results aid our understanding of the relationship between yeast fermentation byproducts and pH levels, furthering our insight into yeast’s impact on renewable energy.

Light Intensity’s Effect on the Growth Rate and Photosynthetic Efficiency of Duckweed (Lemna

minor)

by Milligan Clark-Schoeb (VI), Jonathan Mitchell (V), Kennedy Sharperson (VI)

Light’s influence on duckweed physiological processes can aid in the development of more efficient and sustainable methods for wastewater treatment, while also enhancing the potential for utilizing duckweed as a renewable and eco-friendly biofuel feedstock. Our question was how does varying light intensity affect the growth rate and photosynthetic efficiency of duckweed (Lemna minor)? This experiment can provide valuable insights into duckweed growth processes and light’s influence on all plants’ photosynthetic processes. For our experiment, we looked at duckweed growth under three light intensities; covered, partially covered, and uncovered. We calculated the mass of the tray the duckweed

was in, the duckweed solutions, and the fronds. We left three different trays under an LED light for 3 days. After this growth period, we measured the mass of the tray, nutrient solution, and seeds. To calculate the growth of the duckweed, we subtracted the original mass of the tray and nutrient solution from the final mass of the growth tray. We found that all trays decreased in mass from their initial measurements, regardless of the amount of light they had been exposed to. The results of our experiment yielded poor outcomes, as all trays showed a decrease in mass, proving our experiment unsuccessful, and providing evidence to support

Measuring the Effect of pH Levels 3, 5, 7, and 9 on the Proliferation of S. cerevisiae Yeast Cells

by Devan Gambello (VI), Kate Marine (VI), Maisy Webster (VI)

This experiment seeks to determine the optimal pH for S. cerevisiae yeast cell proliferation. Yeast, particularly S. cerevisiae, is a model organism for basic biological research, as the mechanisms underlying yeast cell proliferation are similar to cellular processes. Examples of similar processes in yeast and humans include cell cycle regulation, providing the potential to obtain insights into the formation of diseases such as cancer. Our methods included filling twelve conical tubes with solutions of pH 3, 5, 7, and 9 – three tubes for each level – and adding to each 1 milliliter of proofed S. cerevisiae. We then continued to monitor the

cells each day for a week, taking a direct cell count for each tube using a hemocytometer. We compared the number of yeast cells before and after feeding each tube 0.1 grams of glucose. This was done to determine which pH allowed for the most cell proliferation. Our results showed that yeast cells can proliferate better in a basic pH environment, as the cells in the tubes of pH 5 consistently yielded the highest growth rates. These results suggest that pH plays a critical role in regulating yeast cell proliferation and that the pH 5 environment may provide the ideal conditions for cancer cells to grow and proliferate as well.

Measuring the Effect of Varied Sugar Concentrations on Ethanol Production Via Yeast (Alcoholic) Fermentation with Saccharomyces cerevisiae

by Aviv Cohen (VI), Valentyn Kurylko (V), Brennan McVey (VI)

Anaerobic fermentation of carbohydrates by yeast and bacteria leads to the production of alcohols and acids. Specific alcohol molecules, ethanol, isopropanol, and butanol, are produced by fermentation. Yeast, a single-cellular organism, serving as a catalyst for alcoholic fermentation, reacts with sugar (carbohydrates) and produces ethanol. The following experiment tests the relationship between sugar concentration and ethanol produced via yeast fermentation, specifically the effect of varying sugar concentration on yielded ethanol production. The group’s conducted research helped understand the trend of ethanol production as it changed with var

ied sugar concentration (i.e. whether it follows a linear or exponential growth trend or no such growth) and whether there is such a relationship between sugar concentration and ethanol production. Our research concludes that ethanol production increases as sugar concentration increases, following a linear growth trend. Understanding the effect of varied sugar concentration helps us to understand potential inhibitory levels of concentrations that hamper the reaction with Saccharomyces cerevisiae and optimal sugar concentrations for industrially produced goods and additives that utilize this process on a daily basis.

Observing the Effects of Varying Caffeine Concentrations on Daphnia magna Heart Rate

by Daniel Lanao (V), Sophia Odunsi (VI), Leila Souayah (V)

Despite being invertebrates, Daphnia magna have cardiovascular systems comparable to humans. The vagus nerve plays an essential role in heartbeat regulation and is a primary part of the parasympathetic nervous system in D. magna, making the organisms ideal for studying chemical effects on the human heart rate. Past research has shown that D. magna heart rate increases with monosodium glutamate (MSG) consumption, and these results can apply to humans; therefore, by using D. magna, we can find generalizable results on heart rate related to caffeine consumption.

We hypothesized that the heart rate of D. magna would increase as the concentrations of caffeine increased. To prove this hypothesis, we kept cultures of D. magna and fed them a yeast-water solution. Then, we divided them into four chambers, fed each group a different concentration (0 mg/L, 50 mg/L, 100 mg/L, and 150 mg/L) of caffeine, and counted their heart rate after seven hours under a microscope. By studying the rate of change of the heart rate of D. magna, we can discern how caffeine affects human heart rates at a milligram-per-liter level.

Optimizing the Ethanol Tolerance of Saccharomyces cerevisiae with Potassium Chloride

by Sienna Patel (V), Katharine Shea (V), Annika Shekdar (VI)

Ethanol, a byproduct of Saccharomyces cerevisiae (yeast) fermentation, is an essential substance used in industries such as the automotive and pharmaceutical sectors. Recent studies have shown that ethanol production is limited due to its toxicity to yeast cells, indicating that alternative methods are needed to optimize ethanol production and increase the ethanol tolerance of yeast cells. The optimization of ethanol production is essential for industries reliant on ethanol, such as those in fuel and beverage production, because it decreases the cost and resources that go into ethanol distillation while maximizing ethanol output. We have conducted an experiment in response to this question by testing the effects of various potassium chloride levels in yeast fermentation to optimize ethanol concentrations. First, a control group with 0mM and experimental groups with 30mM, 40mM, and 50mM of potassium chloride were added to test tubes, all containing the same amount of yeast growth media and active yeast. The initial ethanol levels of the tubes were

measured, and subsequent measurements were taken at 24, 48, and 72 hours. By altering potassium chloride levels, we sought to determine if potassium chloride could increase the ethanol tolerance of yeast cells, ultimately leading to increased ethanol production. Our results actually show that the addition of potassium chloride has a deleterious effect on ethanol tolerance, and we accepted our second alternative hypothesis. Our future steps include trying different chemicals to optimize ethanol tolerance and increase efficiency throughout the ethanol distillation process.

Credit: Google Images (Yeast)

The Effect of Lemma minor on Decreasing Nitrogen and Phosphate Concentration in Contaminated Water

by Jack Goodwin (VI), Alex Rudnik (VI), Ellie Solomon (V)

The aquatic plant Lemma minor, more commonly known as duckweed, can remove nitrate and phosphate from polluted aquatic environments. The research conducted in this experiment aimed to determine what concentration of duckweed would most effectively remove the toxins from the water. Experimental parameters involved varying concentrations of duckweed within a constant volume of water and recording the nitrate concentration and the phosphate concentration for each concentration before and after the experi-

ment. In the study, a nitrogen probe and phosphate test tablets were used to record results. The water used was contaminated from the industrial region of the Raritan River. The experimental protocol was replicated across four trials. Results indicated a proportional decrease in nitrate and phosphate concentrations when increasing duckweed concentration. These findings could help prove that duckweed is a natural and sustainable remedy for cleaning contaminated ecosystems.

The Effect of Lemna minor on a Salt-Diluted Aqueous Environment

by Emma Davidkhanian (V), Andre Masache (VI), Anika Paul (V)

Duckweed, Lemna minor, is a plant known for its versatility and its ability to depollute bodies of water, making it a key factor in the de-pollution process of freshwater bodies across North America. Approximately 97% of the Earth’s accessible water is filled with salt and other extraneous factors that turn it non-drinkable, causing thousands to not have access to any clean source of water. Research has proven that the addition of duckweed in aqueous environments can potentially de-pollute it, we decided to scrutinize the effects of Duckweed on the salinity of the water. To start our experiment, we placed duckweed in three test groups of masses; 0.5g, 0.75g, and 1g, adding a constant amount of saltwater to each tube. After calculating the average salinity before and after with a Brix Meter, our research revealed that the vials with larger amounts of duckweed had slightly lower salinity levels than the tubes with less duckweed, After three trials, there was a demonstrated decrease in salinity levels after larger

masses of duckweeds were added to the beakers.

Credit: Google Images (Duckweed)

The Effect of Varied Microplastic (Polyethylene) Concentrations on Yeast Cell Survivability

by Maggie Ellsworth (VI), Aanya Shah (VI), Coco Simon (VI)

This study investigates the impact of polyethylene (PE) plastic on yeast cell survivability, utilizing Saccharomyces cerevisiae (yeast) as a model organism. The research aims to examine the effects of pervasive microplastic pollution on cells, with potential implications for the health of humans, animals, and broader ecosystems. The specific question being addressed is the effect of polyethylene exposure on yeast cell survivability, which we measured by exposing yeast cells to various concentrations of polyethylene before using a hemocytometer to count cells. The results suggest that

polyethylene exposure does not significantly impact yeast cell survivability, as indicated by minimal variation in cell viability across different concentrations of polyethylene. However, limitations in cell counting accuracy and viability assessment methods were encountered, indicating the need for further refinement in experimental procedures. Addressing these limitations and refining the experiments will contribute to a better understanding of the potential ecological ramifications of microplastic pollution in the environment.

The Impact of Caffeine on the Fermentation Rate of Yeast

by Emily Gao (VI), Ananya Sanyal (VI), Rohan Variankaval (VI)

A common stimulant, such as caffeine, yields undetermined effects on organisms like yeast, which are commonly used to study cellular processes. Prior research suggests that yeast perceives caffeine as a stressor and inhibits the growth of the cultures through interference with DNA repair mechanisms and the cell cycle. A deeper understanding of the interactions between these compounds can expand their usages beyond their current scope. This experiment explores the effect of varying caffeine concentrations on the fermentation rate of yeast. It is expected that adding more caffeine to the yeast mixture will negatively affect the amount of carbon dioxide produced and measured in a given time frame. To answer this question, two trials were conducted to determine the relationship between caffeine and the fermentation rate of yeast. The first trial used water heated to 35 degrees Celsius and 6 solutions of 100ml of water combined with varying amounts of caffeine powder ranging from 0mg to 1000mg in intervals of 200mg. Each solution was mixed with 0.8g of sugar and 1g of yeast. Following a 36-hour observation period, there were negligible gas productions from all six solutions, suggesting that the

sugar-to-yeast ratio needed to be adjusted in all flasks to prompt yeast fermentation. Further research led to a second trial with water instead heated to 37 degrees Celsius, and significant increases in the quantities of sugar and yeast, to 6g and 3g, respectively. After 50 minutes of observation, all 6 flasks exhibited measurable amounts of carbon dioxide production. From 0mg to 1000mg, increasing in 200mg intervals, the amount of carbon dioxide produced was as follows: 130mL, 90mL, 80mL, 70mL, 50mL, and 40mL. A chi-square analysis of these results determined that we reject the null hypothesis that there is no statistically significant correlation between caffeine concentration and the rate of fermentation. The fermentation process is inhibited by caffeine, and it is an indirect linear relationship, where carbon dioxide production decreases as caffeine concentration increases. Conclusive evidence of caffeine’s effect on yeast allows for further research on its other uses. We now can expand our studies to other organisms and can consider using caffeine to kill off unwanted strains of parasitic protozoa, which effectively choke out algae in unbalanced ecosystems.

Yeast Cell Growth Under Varying Conditions of Materials and UV

by Sloane Mandelbaum (V), Ella Tabish (V), Marcus Wilson (VI)

Exposure to UV radiation can lead to life-threatening health issues for humans, such as skin cancer, premature aging, and immune system suppression. To prevent skin damage, a variety of clothing materials can create a barrier between human skin cells and UV radiation. The goal of our experiment is to determine which clothing material (cotton, nylon, or polyester) is most effective at protecting Saccharomyces cerevisiae (yeast) cells, which are commonly used to mimic skin cells, from UV rays. While changing the material covering the petri dish containing yeast cells, we exposed each group of yeast cells to a constant amount of UV light, which was measured by a constant period of time. For example, one group was exposed to UV light with a polyester material placed over the petri dish, and another test group had a cotton material placed over the petri dish that was exposed to UV light. After testing all five of our test groups and incubating

our plates, the yeast cell colonies of each test group were compared. We also ran an ANOVA test on our data to discover that the between-groups variance was statistically greater than the within-groups variance. Thus we can reject our null hypothesis, which stated that no matter the material of the clothing scrap present over the petri dish of yeast cells, the percentage of growth of the yeast cells will remain unchanged with all differences being due to chance. Our results revealed that polyester, followed by rayon, followed by cotton were the most effective materials at protecting yeast cells from UV light exposure. These results indicate that when humans are spending time in the Sun, they should choose to wear clothing articles made of polyester fabric over the other fabrics tested to help best prevent skin cancer and the various other life-threatening impacts of UV light exposure on humans.

Methods in Molecular Biology Research (I & II)

Research I

by By Sasha Bauhs (V), Thomas Davis (V), Sophia Deeney (VI), Noor Elassir (VI), Ria Govil (V), Thomas Goydan (VI), Miles Kelly (VI), Kayla Kerr (V), Siyara Kilcoyne (VI), Katia Krishtopa (VI), Sarina Lalin (VI), Mia Libretti (VI), Julia Oussenko (V), Krish Patel (V), Will Pertsemlidis (V), Ally Smith (VI), Sriya Tallapragada (V), Mason Vance (VI), Leon Zhou (VI)

Our Molecular Biology Research project is an adaptation of the Biochemistry Authentic Scientific Investigation Laboratory (BASIL) program. The project goal is to determine the function of BASIL proteins with known structures (Fig. 1), primarily carboxylesterases and lipases. First, we used the plasmid DNA of our proteins to transform our proteins into E.Coli cell cultures. Colonies were grown on media containing ampicillin or kanamycin to select for the transformed bacteria. Subsequently, autoinduction was used to express proteins and gel electrophoresis was conducted to confirm expression. Following con-

firmed expression, computational modeling and bioinformatics tools such as DALI and PyMol were used to predict function and structure based on both sequence and active site alignments; all proteins were determined to be some form of hydrolase. Then, we lysed our cells, performed nickel-column chromatography to purify our proteins, and confirmed purification using SDSPAGE. We are currently designing in-vitro assays to establish the function of our proteins and further characterize the protein. By determining the function of novel proteins, we can further understand their applications in the real world.

Figure 1: Target proteins with UniProt IDs listed

Research II

by Britney Alfieri (VI), Madeline Alfieri (VI), Daniela Karnaugh (VI), Alex Rudnik (VI), Coco Simon (VI), Javi Trujillo (VI)

The BASIL (Biochemistry Authentic Scientific Inquiry) curriculum has allowed the students in Methods in Molecular Biology Research to conduct novel research on specific proteins with predicted structures and unknown functions. In Research 1, the same proteins have been tested for many years, many of which have yet to yield significant and precise results. The Research 2 students are using AlphaFold, an artificial program that predicts the structure of proteins, to investigate the enzymatic function and structure models of ten new proteins (Fig. 1) with the goal of identifying candidate proteins for use in the Research 1 curriculum. A combination of laboratory and computational techniques were used to investigate these unidentified proteins. First, plasmids containing the proteins of interest were transformed into BL21(DE3) E. coli bacterial cells to express the proteins. Au-

toinduction was then used to induce protein expression in the bacterial cells, and the results were quantified using gel electrophoresis. To characterize the proteins structurally, three homologs were chosen for each AlphaFold protein to identify their possible functions using the computer programs PyMOL, Foldseek, Brenda, Blast, and Dali. In the future, trial purification will be performed during which the expressed proteins from E. coli will be isolated and purified. Ligand prediction and assay design will then be conducted to predict substrate binding, and experiments will be designed to test enzyme function. Finally, largescale protein purification and enzyme activity assays will be conducted, followed by mutagenesis, where amino acids will be mutated to determine enzyme activity and to test function.

Figure 1: Target proteins with UniProt IDs listed

Accelerated Molecular Dynamics

by Ethan Liu (V), Laura Liu (VI), Katharine Luo (IV), Alex Wong (V), Hansen Zhang (VI), Christian Zhou-Zheng (IV), Dr. Chu

Molecular dynamics (MD) is an important computational tool for simulating complex systems in many fields of scientific research, such as theoretical physics, computational chemistry, molecular biology, and materials science. Upon dividing complex systems into smaller subunits or particles, MD simulates the movement of each particle based on the laws of physics and the particle’s interactions with its surroundings.

Our research has two different parts: one focusing on the computational side of interacting particle simulations, and the other with an emphasis on oscillations and spring networks. The interacting particle group uses two different Newtonian propagation schemes, the Velocity Verlet

method and the Runge-Kutta method, to measure its accuracy. The spring oscillations group utilizes a constant acceleration propagator to predict the behaviors of undriven damped harmonic oscillators, testing with analytical results, energy methods, and the fast Fourier transform. We also study resonance behavior by simulating steady-state amplitudes for driven damped oscillators at various driving frequencies. Our goal is to construct a robust MD scheme such that it can be performed on most personal computers using consumer hardware such as GPUs; this can be applied to a wide variety of physical systems in molecular biology, nanoscience, astronomy, fluid dynamics, and quantum physics.

Artificial Collagen

by Ria Govil (V), Daniel Hall (IV), Sarina Lalin (VI), Annabelle Shilling (VI), Theo Strelecky (VI), Ella Tabish (V), Carolyn Zhou (V), Dr. Haven

Collagen is the most abundant protein in the human body and it plays an important structural and functional role in many physiological and pathogenic processes. At the molecular level, collagen is made up of three polypeptide chains that form a secondary triple helical structure, which then self-assembles in a lateral staggered association to create fibrils with a unique 67 nm gap-overlap repeat; known as D-period. The unique conformity and behavior of the collagen molecule arise from the repeating Glycine-X-Y pattern in its primary structure.

The ultimate goal of our project is to create a collagen mimetic peptide that can model the physical and chemical properties of natural collagen. Our designed collagen peptide, FACT-152 (Fragment of A Collagen Trimer), did not work, so this year, we are using a pre-existing plasmid design named V-F877 to start optimizing protein expression in bacteria.

Currently, collagen is most commonly purified from animals for use in the medical field. This process is expensive, tedious, and

often results in a high degree of variation. Generating collagen mimetic peptides that successfully replicate human collagen could provide a safer and more cost-effective alternative. We plan to provide

critical research on these foundational steps to deepen our knowledge of collagen’s structure and determine the best methods of creating viable artificial collagen that can be used as a biomaterial.

Figure 1. Hierarchical Organization of Collagen Structure (A. Collagen Fibrils under an Electron Microscope, B. Staggered and Intertwined arrangement of triple helices within a fibril, C. Different stages of Fibrillogenesis from the Primary Structure (Bottom))

Coral

by Emily Gao (VI), Chloe Huang (IV), Eshaan Jain (V), Aarav Sonthalia (V), Rohan Yadav (V), Ms. Mygas

Coral polyps have a symbiotic relationship with zooxanthellae, photosynthetic dinoflagellates that help corals absorb nutrients from their environment. Zooxanthellae are responsible for providing the coral with the requisite nutrients for survival and typically assist the process of photosynthesis (NOAA).

Zooxanthellae play a major role in protecting and maintaining coral reefs; however, when there is a depleted amount of zooxanthellae present in the coral reefs, the coral begins to bleach and stress (NOAA). Our research team aims to extract and understand zooxanthellae, so we can design a solution that will prevent premature coral reef death and increase coral reef longevity. If we can

uncover patterns and trends in the change of zooxanthellae during horizontal transfer among individual corals housed near each other, we can make inferences about how global warming affects coral reefs in our oceans. To uncover these trends, we will take samples of coral and extract the zooxanthellae. We will then fingerprint their DNA to record the various species of zooxanthellae in the coral. Once we establish a baseline library of zooxanthellae identities and quantities, we will develop further questions and parameters for measuring zooxanthellae community dynamics.

Thus far, the Coral group has designed a process for tank maintenance. We first measured a

tank size and depth that would be habitable for our coral, then began developing a procedure to form a habitable system. Our weekly procedures for tank maintenance include checking the pH level to confirm the accurate acidity of the water and checking the salinity to ensure that there is sufficient salt in the water—our desired salinity is around 35 ppt. Based on the salinity of the tank water, we then change the water with a newly created saltwater substance. Our group’s first batch of coral unfortunately died due to double acclimatization after we switched our tank, but we have received a few species of coral dinoflagellates upon which we are

testing our DNA extraction procedures to ensure they work when we test our next batch of coral.

Drover

by Ethan Chan (V), Keira Chen (VI), Matt Dicks (V), Connor Francis (V), James Kotsen (V), Nick Meng (VI), Alexander Recce (V), Victoria Xie (IV), Dr. Jolly

The integration of an unmanned aerial vehicle (UAV, or drone) and an unmanned ground vehicle (UGV, or rover) into a single autonomous system (a drover) allows for unique capabilities and visual perspectives that have many possible applications such as in replacing dangerous wildfire surveying techniques. Our project Drover uses a drone to pathfind in unknown areas which the rover traverses on the ground. The system can map unexplored terrain while identifying obstacles, and autonomous communication allows the drone and rover to enter areas that are too dangerous or too small for humans to enter.

We propose a cooperative pathfinding protocol called Long-term Direction, Short-term Correction (LDSC), where the drone’s global view allows it to dictate paths (long-term) for the rover, while the rover uses LIDAR to identify smaller objects in its path and dodge them (short-term). The drone’s path-planning ability involves turning images into path-planning ability involves turning images into node maps and applying the A* search algorithm. Photogrammetry, a 3D reconstruction technique, is combined with other computer vision techniques to analyze larger terrain features using

aerial drone photos. Previous Drover research included using photogrammetry to perform autonomous estimation of annual solar power output for residential roofs. Roof geometry, such as slant angle, is difficult to obtain manually and Drover’s autonomous methods allowed for efficient and accurate solutions.

Drover is focused on accessibility, low-cost, and scalability. We use budget, consumer-grade hardware and open source software for centimeter-accurate pathfinding. Current research involves using photogrammetry for high-accuracy rover pathfinding in familiar terrain in combination with real-time drone image segmentation for applications such as trash pickup.

Credit: Google Images

Figure 1: Drone

Figure 2: Rover

Figure 4: A*

Figure 6: Photogrammetry scan of the front of the school

Figure 3: System Diagram

Figure 5: Roof Detection

Figure 7: A* Pathfinding used on elevation map created from photogrammetry of front of school

Fluorescent Fish

by Ethan Boroditsky (VI), Katherine Jung (IV), Nataly Ruiz (V), Ziv Shah (V), Annika Shekdar (VI), Leon Zhou (VI), Dr. Fried

Understanding the molecular mechanisms underlying bioluminescence and fluorescence could significantly impact various fields of biology, from enhancing our understanding of ecological interactions to developing new fluorescent tags. Since the discovery of the Japanese fluorescent freshwater eel (Anguilla japonica) as the first fluorescent vertebrate in 2013, additional fluorescent marine organisms, such as species of scorpionfish, algae, and plankton, have been identified. Our current

project focuses on inducing luminescence in a luciferase protein derived from dinoflagellate algae. We have successfully transferred our protein plasmid into E. coli cells and achieved moderate success in expressing our protein. This protein requires the binding of the co-factor molecule luciferin. Therefore, in the future, we aim to purify our protein and attempt to induce fluorescence through luciferin binding.

GenerARTive AI

by

Bogdan Kuzmanov (V), Jingjing Luo (V), Rennick Mirliss (IV), Alessio Pasini (IV), Saniya Tariq (VI), Melinda Xu (V), Dr. Unal

As neural network architectures and machine learning techniques are increasingly applied to various scientific fields, such as healthcare, biology, and engineering, their integration into humanities and the arts has encountered challenges. While numerous studies have already addressed image creation and classification through machine learning algorithms, the GenerARTive AI project seeks to approach these tasks from an architectural and artistic perspective. In particular, we aim to answer the following question: how can we develop assistive tools for artwork classification using visual design principles?

This year, we began by training an EfficientNet convolutional neural network for single-label classification of our art dataset. Subsequently, we adjusted the model’s hyperparameters and data set for multi-label classification. We obtained the initial dataset from Istanbul Technical University, and the images were labeled with nine different architectural visual design principles: color, symmetry, regular, isolation, asymmetric, progressive, shape, crystallographic, and flowing. Our team is collaborating with Mr. Joseph Napolitano’s

Theatrical Design &Technology course at Pingry to expand the dataset by creating new artwork, composed of digital, photographic, and physical media.

In the future, we plan to employ transformer machine learning architectures to better classify the images we have acquired and created. We will then compare the accuracies with our current model. We also hope to implement image generation from natural text input related to the visual design principles by applying more advanced machine learning algorithms.

Credit: Google Images

Metagenomics

by Graham Houghton (V), Verna Mae Lange (VI), Sriya Tallapragada (V), Ella Wunderlich (V), Julian Zassenhaus (IV), Ms. Farrell

Metagenomics is the study of genetic material taken from populations of organisms. By performing metagenomic analysis of DNA from the Pingry composter, we aim to understand how the microbial community of the composter responds to changes in environmental conditions. In doing so, we hope to gain practical insights into the biological mechanisms that drive the composting process.

From the 2019-20 school year through the present day (April 2023), DNA from 39 compost samples has been isolated and sequenced successfully. Compost samples were collected approximately once per month, both at the distal end (finished compost) and 10 feet from the distal end (approximate midpoint of the composting process). To further characterize the composter environment, we used a HOBO data logger to measure the computer’s internal temperature. The data logger was placed at the beginning of the compost stream and naturally passed through it for a period of about 80 days, recording the temperature every hour. A second data logger was added to the composter during the 2021-2022 school year at a 30-day offset from the original to provide simultaneous internal temperature data at different locations within the composter. These temperature readings, over time and at various locations in the composter, were digitized and statistically analyzed in comparison to the relative bacterial abundance of each sample. An additional measurement of pH was recorded for fresh samples of compost. These measurements were also digitized and statistically analyzed in comparison to the relative bacterial abundance of each sample.

After collection, samples are dried in a desiccator for several days. Each sample is then processed; 0.250 g of the sample is stored at -20° for up to eight months. In April 2023, the DNA of samples from the 2022-2023 school year was extracted using a

Qiagen Power Soil Pro Kit. The samples’ purity was tested using agarose gel electrophoresis and then spectroscopy. Samples with a purity reading between 1.8-2.0 for A260/280 were used; others were deemed unfit for NGS (next-generation sequencing) and discarded. The sample purification and assessment process took approximately one week, with 2-3 hours in the lab each day, and purified DNA samples were stored in microcentrifuge tubes at -80°. Samples were then diluted with distilled water to a concentration of 20ng/µL, per Genewiz’s instructions at Azenta Life Sciences. The processed, evaluated, and diluted samples were then transported to Azenta Life Sciences in South Plainfield, NJ, for next-generation sequencing. The metagenomics services offered by Azenta assess genetic material from only the bacteria and archaea kingdoms, using the 16S rRNA gene, sequenced on the V3 and V4 regions of RNA. In approximately three weeks, Azenta provided results of their analysis, outlining relative bacterial abundance in each sample from genus to species. Data was used from the taxon order, since that information yields minimal unidentified results, but still retains enough specificity to inform the mechanisms for energy consumption in the identified bacterial groups. Visual data on the relative abundances of different types of bacterial orders is demonstrated in Figure 1; percentages are also included in Azenta’s data report.

The results from Azenta were imported into a spreadsheet model, comparing the relative abundance of bacterial orders to previously outlined measurements of temperature and pH, using statistical significance tests and trend analysis.

Preliminary analysis of all data reveals differences between microbial communities present at different stages of the decomposition process. The analysis also reveals that several characteris-

tics in the composter environment, such as temperature, pH, and amount of raw material added, correlate in varying degrees to the abundance of specific bacterial orders. The data provides a

natural history of the composter’s functionality, which will be translated into practical recommendations.

Pathogens

The Pathogens IRT group is performing experiments to confirm the interaction between the antibacterial viral protein 77ORF104 and its host target protein, Staphylococcus aureus helicase loader DnaI. Future investigations will confirm the mechanism by which this antibacterial pro-

tein inhibits DNA replication, thereby killing the Gram-positive pathogen S. aureus, one of the most common hospital-acquired infections. Not only is this infection dangerous due to its abundance, but it is also becoming more resistant to methicillin, which is the last resort for treatment.

by Isabelle Chen (V), James Draper (IV), Kate Marine (VI), Lauren Poprik (VI), Coco Simon (VI), Divya Subramanian (VI), Aanvi Trivedi (IV), Dr. Hood

Figure 1. Relative abundance of bacterial orders in samples from October 2020 to January 2022

PETase

by Jules Amorosi (VI), Sari Berman (IV), Siyara Kilcoyne (VI), Sloane Mandelbaum (V), Sebastian Talarek (VI), Sofia Wood (V), Dr. D’Ausilio

The United States of America only recycles about 32% of its total waste, sending nearly 150 million tons of trash to landfills each year. There, it takes up to 450 years to fully biodegrade. Often, it ends up invading oceans or forests, where it poses a serious threat to native species. Polyethylene terephthalate (PET) is one of the most widely used plastics globally, but only 9% of the 56 million tons of PET produced annually is recycled. It is necessary to find an efficient way to recycle plastic to mitigate the damage done to our planet. Our team works with PET depolymerase (PETase), an enzyme with the unique ability to break PET polymers into monomers, which can then be reassembled into new plastic. This nuanced method is called “biochemical recycling” and has become an increasing focus of research—however, it requires optimization before it can be implemented commercially. Because the severity and pervasiveness of plastic-related damage to the environment is growing, the scientific community is eagerly seeking to improve the efficiency and thermostability of PETase through mutation. Our goal is to identify and investigate various mutations and assess the change in efficiency and thermostability that each offers. After researching mutations that demonstrate promise for accomplishing these two goals through scientific literature, we obtained various PETase mutations through our partnership with Deerfield Academy. Deerfield created these mutations using site-directed mutagenesis, a common method to induce mutations, utilizing a primer to confer a mutation in double-stranded plasmid DNA. To replicate the mutated plasmid, we transform it into NEB 5-alpha cells and grow colonies on LB-AGAR plates with ampicillin. We harvest the colonies using inoculation loops before miniprepping: lysing the cells and discarding all contents besides the mutated plasmid. Then, we transformed the mutated DNA into

BL21 cells and induce protein expression with autoinduction to create copies of the mutated PETase enzyme. Finally, we perform cell lysis and purification to obtain the pure enzyme. Along the way, we performed gel electrophoresis to ensure our protein is present throughout the process. To determine the efficacy of mutant PETase, we plan to use a PCL-clearing assay. This assay would allow our enzyme to degrade PCL (more commercially available than PET) through a clearing halo that we can measure. A larger clearing halo would prove greater efficiency. This experiment will allow tangible results of whether, and how efficiently, our PETase mutants are capable of degrading PET/PCL plastic. By comparing the degradation rate to our Wildtype PETase, we will find out which mutant is the most efficient. We are currently performing this assay with a PETase mutant containing a signal peptide, allowing our enzyme to exit the cell to break down the plastic. If successful, we can clone signal peptides onto our other mutants to test them as well. In the coming months, we want to make more progress researching and documenting the effects of mutation on PETase activity, which will further our understanding of the enzyme, and will contribute to the global effort to make recycling more efficient and widely used.

Figure 1: PETase

SmartHeart

by Elbert Ho (V), Vinav Shah (V), Arjun Subramanian (IV), Albert Wu (IV), Evan Xie (VI), Alan Zhong (VI), Dr. Jolly

Atherosclerosis is a chronic disease of the arteries, affecting nearly half of all Americans between the ages of 45 and 84. In this disease, Cholesterol ester transfer protein (CETP) converts lipoproteins from high to low density, which accumulate in the walls of blood vessels. No existing drugs target the mechanism of CETP, which is a major contributor to atherosclerosis, so we use diffusion methods to generate new molecules based on existing inhibitors of the CETP protein. Initially, we converted the molecules, represented as SMILES (Simplified Molecular-Input Line-Entry System) strings, to a lower-dimensional latent vector using an autoencoder model. We then created a noise scheduler, sampling from an isotropic Gaussian distribution to generate noise to corrupt the latent vector. A neural network was trained to denoise the vector, generating a molecule after being run through the autoencoder in reverse. Produced molecules were screened using molecular docking simulations, selecting structures with the highest predicted binding affinity to maximize effectiveness. Filtered molecules were then screened for efficacy, producing 110 molecules with pIC50 greater than 7. Molecules were also assessed using QED (Quantitative Estimate of Drug-Likeness) and SAS (synthetic accessibility scores). Ultimately, the molecules that we generated performed as well as or better than molecules currently in clinical trials. Diffusion methods therefore show viability for novel drug discovery to combat atherosclerosis.

VirF

by Mia Cuiffo (V), Daniela Karnaugh (VI), Katia Krishtopa (VI), Tingting Luo (IV), Krish Patel (V), Anika Sinha (VI), Dr. Hood, Dr. D’Ausilio

Shigella is a pathogen that is a leading cause of bacterial foodborne illness worldwide. The virulence cascade of shigellosis requires a specific protein within the AraC superfamily of transcription factors, namely VirF. Other members of this superfamily, such as ToxT, are also involved in the virulence cascades of other viruses, like Vibrio cholerae. While VirF does not have a solved structure, ToxT notably contains a notable binding pocket within its structure where a small fatty acid attaches to inhibit DNA binding. We wish to solve the structure of VirF and de-

termine whether or not VirF operates similarly to ToxT, and therefore discover whether VirF can be inhibited in a similar manner to ToxT using a fatty acid. Therefore, we are working to express, purify, and ultimately crystallize VirF in order to examine its structure and use biochemical property testing to assess VirF for any homologous function to ToxT. This work would help to reveal the mechanism of transcriptional regulation in S. dysenteriae and could lead to the development of novel treatments for Shigella-related illnesses.

Figure 1: SDS PAGE Gel electrophoresis showing cells before Cell Lysis (lysate) and the results after Lysis (supernatant). Lanes labeled “I” show cell cultures grown in autoinduction media with overexpression of VirF, shown by a protein band with the predicted VirF size of ~ 50 kDa. Lanes labeled “C” show control cultures, lacking expression of the VirF plasmid. The lysate lanes contain excess extracellular material in contrast to the supernatant lanes, suggesting that cell lysis successfully dissolved the cell membrane and removed insoluble proteins alongside other miscellaneous

Is Euthanasia Morally Permissible?

by Malcolm Adedjouma (V), Sasha Bauhs (V), William Brisson (IV), Dr. Ward

Euthanasia, commonly referred to as “assisted suicide”, is defined by Merriam-Webster as “the act or practice of killing or permitting the death of hopelessly sick or injured individuals (such as persons or domestic animals) in a relatively painless way for reasons of mercy.” The controversy surrounding the process of euthanasia led us to our research question: Is euthanasia morally permissible? The two most common forms of euthanasia are active and passive. Active euthanasia is when a lethal dose of a drug is administered to the patient to ensure a quick and peaceful death. Passive euthanasia involves the intentional withholding of life-sustaining treatments, such as a ventilator or life support systems. The main stakeholders in cases involving euthanasia are the family, doctors and the patient themselves. We found that both the principles of deontology and consequentialism could be used to argue a case for or against euthanasia. These principles can be applied when considering whether it is right for a doctor to end a patient’s life, even though doctors have a duty to do no harm (but also have the duty to fulfill the wishes of their patient). One must also consider the potential impact on the patient’s loved ones. When analyzing this topic, we focused on the case of Terri Schiavo. After experiencing a severe cardiac arrest in 1990, Terri Schiavo suffered significant brain damage due to the lack of oxygen in her brain and was left in a comatose state. Soon after, she was deemed to be in a persistent vegetative state, and, for the next 15 years, she showed little to no signs of recovery. Her husband petitioned to remove her feeding tube, advocating for pas-

sive euthanasia. On the other hand, her parents believed that Terri would have wanted to continue life-prolonging measures and sought to wait for her awakening. This case exemplifies the con-

Credit: Sophia Lanao (IV)

Jane Austen & Friends

by Sarina Lalin (VI), Carolyn Zhou (V), Dr. C. Madere

This research project aims to analyze the role of female characters in romantic comedies and how these stories facilitate female writers in the public sphere. The romantic comedy genre is particularly fascinating because it was one of the earliest areas in which women’s stories could be featured and focused on. By studying Austen’s predecessors, works, and later adaptations, we want to carefully examine the role of women in romantic comedies to understand why this genre was particularly attractive to female authors. We hope to compare different types of works, including novels, short stories, and movies, and eventually create a catalog on a web-

site to analyze and connect the different pieces.

So far, we have finished reading The Female Quixote by Charlotte Lennox, a parody of Miguel de Cervantes’ Don Quixote and inspiration for Austen’s Northanger Abbey. We worked through this long novel methodically, with weekly discussions used to recap and document the plot points and themes we saw relating to women and romance. We are planning on integrating more works by Austen like Northanger Abbey and Emma to connect this novel and films like Clueless, which offer a modern interpretation of Jane Austen’s writing.

Lyric Analysis

by Izzy Berger (III), Hannah Castiglione (IV), Gabby DeLorenzo (IV), Ashley Gao (IV), Marc Gautier (IV), Tanya Puranik (IV), Julia Ronnen (IV), Max Ruffer (IV), Kirsten Thomas (V), Aanvi Trivedi (IV), Dr. Cottingham

The Lyric Analysis group is examining how different artists from a variety of genres, including rap, pop, and country, express commentaries on racism through their lyrics. During our examination of songs such as “Your Best American Girl” by Mitski and “Blacker The Berry” by Kendrick Lamar, we noticed a similarity in their

anti-racism messages despite the difference in the expression of those messages. Our future research will dive deeper into how artists from various genres use their lyrics to make statements, connecting the message of anti-racism to other messages that we can observe in their songs.

The Ethics of Section 230

by Jaxon Beal (III), Jeremy

Betz

(VI), Eddy Chen (VI), Roger Wang (III)

Our HIRT looks at the ethics of Section 230 of the 1996 US Communications Decency Act, examining the value of protecting social media

companies from liability, the responsibility of companies to address certain types of speech and the ethics of how free speech is defined.

AP Statistics

Exploring the Relationship Between the Frequency of Exercise and Reported Stress Levels Among Students

by Daniela Henriques (VI), Katia Krishtopa (VI), Alex Rudnik (VI), Avery Santomassimo (VI), Mehr Takkar (VI)

This study investigates whether stressed Pingry students can effectively alleviate tension through physical activity and discern if this connection positively impacts productivity, academic success, and overall well-being. We collected data on students’ exercise habits and stress levels via an anonymized survey with randomly selected participants, which collects data on average weekly exercise hours (explanatory variable) and stress

levels (response variable) during the school year. The null hypothesis assumes beta = 0, with the alternative hypothesis being beta < 0, representing the slope of the true regression line predicting stress from exercise. After the results are determined, statistical analysis will inform the findings to share with the Pingry community.

Credit: Sophia Lanao (IV)

Financial Modeling with Geometric Brownian Motion

by Chelsea Peng (VI), Coco Simon (VI)

This project evaluates the effectiveness of Brownian Motion compared to historical stock market data. Stochastic calculus allows the modeling of random systems such as financial markets. “Stochastic components” in such models are randomly determined, with a random probability distribution that may be statistically analyzed but is impossible to predict precisely. Brownian Motion is often a component in the differential equations of stochastic calculus, representing the unpredictable aspect. The Brownian motion model imitates prices in a continuous-time setting and is independent of past movements.We are analyzing the application and limitations of this stochastic (random) model, focusing on the Dow Jones Industrial Average (DJIA) to evaluate its accuracy in predicting stock market trends. Stochastic elements reflect factors that influence the value of a derivative, like time, volatility of the underlying asset, interest rates, and other market conditions.

We begin by tracing the historical context of stochastic calculus, highlighting the contributions of Louis Bachelier and Albert Einstein in laying the foundation for modern financial modeling. Geometric Brownian Motion (GBM) is then introduced with options pricing and then examined through the lens of the Markov property, emphasizing its “memoryless” nature. To test this, Python simulations were coded using the DJIA Index, based on Brownian Motion across the periods 1900-2000 and 2000-2015. These models were then compared to the historical data of the DJIA to evaluate predictive validity. The research also examines the model’s inherent limitations, aiming to provide insights into the extent to which GBM can be a reliable tool for financial forecasting. This comparison will enable a nuanced understanding of the utility and shortcomings of this model for economic predictions and stock market analysis.

Martingale Roulette Betting Strategy Under a House Limit

by Sarah Gu (VI), Nicholas Meng (VI), Kain Wang (VI)

This paper dissects the Martingale betting strategy in American roulette, in which the gambler doubles their bet following every loss, and evaluates its efficacy under realistic casino-implemented restrictions: specifically, house limits. The Martingale’s behavior under such a limit is examined through mathematical calculation and

simulation of expected payout and waiting time. After this, the Martingale is compared theoretically and realistically to its counterpart in which the gambler doubles their bet following every win, the Reverse Martingale, as well as the less aggressive Fibonacci betting strategy, in which the bets are based on the Fibonacci sequence.

Belize Global Programs

How Did the Protection of Mexico Rocks Affect the Populations of Overfished Species?

by Monroe Russell (VI), Avery Santomassimo (VI), Ziv Shah (V), Melinda Xu (V)

Ambergris Caye is an island off of mainland Belize, home to the largest barrier reef in the Northern Hemisphere. The Belize Barrier Reef runs parallel along the length of the island, separated by a lagoon. It is home to over 200 species, including fish that depend on the reef for habitat and to act as a natural wave breaker, slowing the erosion process. Due to global warming and human activities, the health of the reef is slowly declining. Overfishing has created a significant problem for the biodiversity of reef organisms as healthy fish populations are linked to the overall health of the coral, driving the need for marine protected areas (MPAs).

The first official effort to protect the reef was in 1987, when Hol Chan, in the southern section of the Belizean reef, became an MPA. Parts of Hol Chan were declared no-take areas, where no extraction of any kind was allowed. The other zones were regulated to promote sustainable fishing practices. In 2015, Mexico Rocks, a northern section of the reef, was also declared a MPA. It was separated into a general-use area and a no-take zone, just like Hol Chan. We hypothesize that the protection of Mexico Rocks as an MPA will protect the populations of overfished species. We chose to look at this effect through two fish: the black grouper and the stoplight parrotfish. We predict that both species would display a big jump in abundance since they are hunted and overfished in unprotected zones.

The protection of Mexico Rocks will reduce the amount of overfishing of these populations.

The Reef Environmental Education Foundation (REEF) hosts a citizen science program allowing participants to complete fish surveys at any sight in the world and upload the findings to their database. The REEF database was launched in 1993 and includes over 250,000 surveys at 15,000 sites around the world by over 16,000 volunteers, ranging from novice snorkelers to proficient divers. Our group snorkeled several sites, including Mexico Rocks, Playa Blanca, and Tres Cocos, and completed a survey using the Tropical Western Atlantic Survey sheet available through the REEF organization. While snorkeling, we identified and marked the various species and noted their numbers. After completing the snorkel and verifying our findings with guidebooks, we uploaded our data to the REEF database.

Credit: Belize Global Program

The Population of Apex Predators and the Impact on Abundance of Fish

by Britney Alfieri (VI), Emma Davidkhanian (V), Brennan McVey (VI), Kirsten Thomas (V)

Ambergris Caye, off the coast of San Pedro, Belize, is the world’s second-largest reef, housing 230 km of marine life. With abundant sunlight, nutrients, warm water, and prosperous microhabitats, Ambergris Caye can maintain an extremely high level of biodiversity, providing a habitat to over 700 species of marine life.

We formed conclusions about the relationship between apex predator abundance and prey fish population in Ambergris Caye using data from the Reef Environmental Education Foundation Volunteer Fish Survey Project (REEF VFSP),

one of the world’s largest marine life databases. We used data gathered at Hol Chan, which has been protected by the government since 1987, and Mexico Rocks, protected since 2015. We predicted that there would be an increase in prey fish abundance in these nature reserves over time, resulting in a corresponding increase in apex predators. We looked at blue-striped grunts, French grunts, sharp-nosed puffers, yellowtail snappers, schoolmasters, coney groupers, and Nassau groupers for our prey fish. For our apex predators, we looked at nurse sharks, southern stingrays, spotted eagle rays, and great barracuda.

The Abundance of Parrotfish at Ambergris Caye After the Protection of Mexico Rocks

by Jules Amorosi (VI), Nathan Goldberg (VI), James Kotsen (V), Casey McKeon (V), Lauren Poprik (VI)

The country Belize is a natural hub for an abundance of marine species and coral reefs. Ambergris Caye is an island of Belize adjacent to the largest barrier reef in the northern hemisphere. Providing habitats for over 500 species of fish and other marine creatures, the reefs in Ambergris Caye offer immense biodiversity in the Belizean ecosystem and protect against coastal erosion. However, overfishing and global warming are threatening these reefs. In particular, increasing ocean temperatures are causing coral bleaching, a loss of habitat for marine species, and, ultimately, a decrease in biodiversity. Marine Protected Areas (MPAs) have been established to decrease the negative impact of human

activity on coral reefs by regulating human interactions with the reef. In 2015, the reef complex Mexico Rocks was established as a MPA. The establishment of Mexico Rocks as a MPA could increase biodiversity in neighboring sites, so we studied the change in biodiversity of Ambergris Caye after the addition of Mexico Rocks as a MPA. Parrotfish are a keystone species, playing a crucial role in the ecosystem. They eat algae off coral, keeping it clean. Additionally, moray eels and reef sharks rely on parrotfish for food. Without parrotfish, the biodiversity of the whole reef would suffer. We hypothesize that the addition of Mexico Rocks as a MPA has increased the number of parrotfish in nearby reefs since

Independent Research

Characterizing D(n)-tuples of Polygonal Numbers

by Christian Zhou-Zheng (IV), Sounak Bagchi, Dr. Simon Rubenstein-Salzedo )

Diophantus of Alexandria (ca. 250 CE) studied integer sets {x1, x2, …} with the property that the product of any two of them is one less than a perfect square, which are called Diophantine tuples. For sets where the product of any two elements is n less than a perfect square, they are determined to have the property D(n). Vibrant results have been found when working with Diophantine tuples, invoking tools from across the subfields of number theory; our concern is a 1977 study

by Hoggatt and Bergum [and subsequent generalizations regarding the connection between Diophantine tuples and Fibonacci numbers, as well as the lesser-known Lucas numbers. We attempt to characterize the properties of D(n)-tuples with respect to another family of numbers, the polygonal numbers, which are the numbers represented by the count of dots in the shape of a regular polygon of varying side lengths.

Improving Liquid Cancer Biopsy through Computer-Aided Microfluidic Device Design Based on the Tubular Pinch Effect and Dean’s Flow

by Alexander Recce (V)

A blood test, called a liquid biopsy, is being developed by several research groups for the early detection of cancer. The key challenge in this process is enrichment, or isolation, of the small number of cancer cells in blood serum from other cells. This study uses numerical simulations to design devices that advance state of the art techniques in the enrichment of circulating cancer cells. In particular, the lift forces acting on neutrally buoyant, small, spherical particles in a Poiseuille flow bounded by a wall are modeled using numerical computation. Specifically, we explore the influence of the Reynolds number, distance to the wall, and particle size on these lift forces, building upon previous research on the Segre-Silberberg effect. By validating the mechanism in which particles concentrate at specific positions within the fluid, we confirm the

existence of the Segre-Silberberg effect. Subsequently, we apply a customized 3D model of a filtration device to investigate the Segre-Silberberg effect and Dean’s effect in a nonPoiseuille flow, which can be applied in liquid cancer biopsy. Our results demonstrate that this flow pattern could potentially be used to separate cancer cells from the mean flow. Finally, we apply the flow separation mechanisms in microfluidic design through a rapid 3D design and computational fluid dynamics (CFD) verification cycle. The popular spiral microfluidic design does not demonstrate strong flow separation pattern in our tests, while the sinusoidal design shows much more promise with further research.

Club Spotlights

Pingry Robotics Club

by Jesse Busch (IV), Keira Chen (VI),

Alex Delorenzo

(III),

Matt Dicks (V), Sia Ghatak (V), Som Ghatak (III), Ryan Hao (III), James Kotsen (V), Laura Liu (VI), Aadi Stewart (IV), Alan Zhong (VI), Christian Zhou-Zheng (IV), William Zhou-Zheng (III)

The Pingry robotics team builds two robots to complete specific tasks in time-constrained competitions to win points. We compete in FTC (FIRST Tech Challenge) and FRC (FIRST Robotics Competition) along with mentoring the middle school FTC team.

In this year’s FTC competition, points are scored by placing hexagonal “pixels” on a slanted backboard. Our robot has a spinning set of wheels to intake the pixels and place them into a compartment. Once the pixels are aligned, the compartment goes up the slides and flips so that the pixels can come out downward at the same angle as the backboard. Many parts of our robot, specifically much of the vertical slides and claw, were custom-designed and 3-D printed. We experimented with different materials, ultimately settling on PETG for strength to better protect our robot from breaking during competition. During the autonomous period of the match (the first 30 seconds), the robot drives itself using sensors and cameras which help it move and score, and during the tele-operated period (the remaining 2 minutes), our drivers use gamepads to control the robot. While autonomous, our robot uses computer vision to determine which of three QR codes on a sleeve of a custom-designed game element are facing it and then drives to different places and puts the pixel on different parts of the backboard, depending on the cone. Additionally, we have a plane launcher that shoots a paper plane over a set of rods and

lands around 6 feet from where we shoot it. The challenge is to ensure that it can make it over the rods and the field walls while landing as close as possible. Finally, our robot hangs on the set of horizontal rods by lifting the slides, grabbing on with the hooks, and then retracting the slides.

In this year’s FRC competition, points are scored by shooting orange disks, called notes, through two different areas; the amp is around 4 feet, and the speaker is around 8 feet. To achieve this, we have a set of rotating wheels that pivot out of our robot, since we have to stay within certain size parameters for starting. Then, the robot gets pushed up a ramp and out of our four-wheeled outtake, which can shoot across the entire Pingry Middle School! To change the angle that we shoot, we have an adjuster that allows us to score into both the amp and the speaker. Our robot is also exceptionally fast, as we have special wheels and motors. At the end of the match, robots must climb onto and hang from a piece of chain. To do this, we have a strong climber with high torque that grabs onto the chain and pulls up, bringing our whole robot with it.

Throughout the past few years, we have been using our skills and experience from FTC and FRC to help those around us. We have embraced Pingry’s values of intellectual engagement, discovery, and innovation to help us continue building amazing robots.

Credit: Pingry Robotics

Science in the Pingry Community: About FYI SCI

by Sophia Odunsi (VI), Sriya Tallapragada (V)

FYI Sci, previously Project 80, is a student-driven science club at Pingry dedicated to sharing science with the community through videos, blog posts, and presentations. Sophia Odunsi (Form VI, President) and Sriya Tallapragada (Form V, Vice President) run the club this year with faculty advisor Ms. Mygas.

FYI Sci has always been a major part of Research Week; club members run scientific demonstra-

tions, such as strawberry DNA extraction, elephant toothpaste, science trivia, and an egg drop competition. Be on the lookout for this year’s fun and science-filled research week! In addition, please check out our website (https://students. pingry.org/fyisci/) and social media (Insta: @fyi. sci), as we will update it throughout the week.

FYI Sci is looking forward to another successful Research Week and welcomes new members!

Credit: FYI Sci

PINGRY COMMUNITY RESEARCH

Develop your scientific literacy while learning about current research at Pingry.

Email:

Melinda Xu (V): mxu2025@pingry.org

Elbert Ho (V): eho2025@pingry.org

Mr. D. Maxwell: dmaxwell@pingry.org

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