Advanced Science Research

Morgan Amoils

Project title: Validating RNA-Seq results on the top differentially expressed genes upregulated in oncogenic GNAS R201C pancreatic ductal organoids

Abstract: Pancreatic ductal adenocarcinoma (PDAC) has a very high mortality rate because it is usually diagnosed at a late stage when there is a lack of curative treatment options. It, therefore, becomes important to detect the disease earlier on. One way this can be achieved is by monitoring the lesions that come before invasive PDAC, such as intraductal papillary mucinous neoplasms (IPMNs). Investigating the genetics behind IPMNs has shown that a mutation to a gene known as GNAS has been associated with IPMNs, yet the role that GNAS plays in IPMN development still remains largely unknown. The goal of my research was to uncover the role of GNAS by investigating which genes show an increase in expression in the presence of GNAS. I accomplished this through the use of biologically accurate models known as organoids, grown with and without mutated GNAS. After analyzing and validating the changes in gene expression, my results indicate that a gene known as EYA4 shows an increase in expression when GNAS is mutated. While it is still unclear how GNAS contributes to IPMN development, EYA4 could potentially act as a novel treatment if the development of the cancer is slowed when EYA4 is inhibited.

ANDREW CHEN

Project title: The impact of COVID-19 on 3rd through 8th grade student achievement across the nation

Abstract: The COVID-19 pandemic caused disruptions to the U.S. education system, especially for marginalized students. There is limited evidence on the disproportionate impacts of COVID-19 on achievement by race, socioeconomic status, and grade level. There is also a gap in research conducted at the school level needed to effect remedial policies. I used school-level test data from Northwestern Evaluation Agency’s Measures of Academic Progress (NWEA MAP) to examine variations in achievement and growth during the pandemic by grade, subject, term, school poverty level, and district segregation levels. Standardized mean difference effect sizes were calculated to compare achievement over the years across grades and school poverty levels, and regressions were conducted on the interaction between school poverty and segregation on Black and Hispanic student achievement. My results show increased socioeconomic achievement gaps with disproportionate impacts on Black and Hispanic student achievement in high-poverty and highly segregated schools. Academic growth within the same school year significantly decreased by a larger percentage in reading than in math. However, consistent with prior evidence, scores decreased during the pandemic more in math than in reading and more in lower grades and higher-poverty schools. Using prior recovery initiatives as a benchmark, new initiatives designed to counter decreases in test scores during COVID-19 (e.g., remedial tutoring) will need to be ~2-4 times more effective than past reading interventions, and ~3-4 times more effective than past math interventions, in order to return to pre-pandemic spring testing levels.

Lucas Libshutz

Project title: Increasing the resolution of Cassini VIMS spectra

Abstract: In the early 2000s, NASA sent Cassini to explore the outer reaches of the solar system. Onboard Cassini, the Visual and Infrared Mapping Spectrometer (VIMS) observed Titan, a moon of Saturn. Titan has many similarities to Earth, such as lakes, dunes, and an atmosphere. Yet, the combination of Titan’s thick atmosphere and the low resolution of VIMS makes it extremely difficult for accurate identification of surface compounds. However, systematic instrument drift caused the peak sensitivity wavelength value of each VIMS channel to shift. In other words, there was an increasing gap between the wavelengths VIMS was measuring and those it was designed to measure. My goal was to develop and implement a technique to leverage this behavior to create a higher-resolution spectrum of Titan’s equatorial dunes. I organized the data into an SQL database, as the publicly available NASA database is not consolidated into one volume. I also determined the best filter and correction pair to remove outliers and remove the effect of the atmosphere. After applying the shift to all spectra, I increased the resolution of VIMS fivefold, and reduced the effect of the atmosphere. However, there still remains atmospheric influence on the dataset, and the current resolution increase is not enough to resolve narrow spectral features. In the future, I plan to implement a more efficient SQL querying technique, along with a more comprehensive atmospheric model. This technique can be applied to any other body observed by VIMS.

joshua luo

Project title: Single-molecule Investigation of the Interaction between MeCP2 and chromatin

Abstract: While DNA is responsible for genetic information, other things can affect the expression of DNA, such as methyl-CpG binding protein 2 (MeCP2). MeCP2 binds to chemical tags on DNA, and when bound to these tags, MeCP2 regulates DNA expression. However, MeCP2 has never been studied on chromatin, which is significant, as MeCP2’s behavior on chromatin is a more accurate representation of MeCP2’s behavior in the human body. To address this, I observed the behavior of individual MeCP2 molecules on chromatin via optical tweezers. By observing MeCP2 with this method, I unexpectedly found that MeCP2 bound to nucleosomes over DNA. This was unexpected because MeCP2’s usual binding site is methylated DNA. However, this result suggests that MeCP2 must somehow navigate through nucleosomes to reach methylated DNA (its usual binding site). To further investigate this, I found that once MeCP2 bound to all nucleosomes, MeCP2 then began to bind to methylated DNA. I also found the specific subunit of MeCP2 that was responsible for MeCP2 nucleosome binding. From these results, I can deduce that nucleosomes play a vital role in MeCP2 DNA repression, providing a new and compelling angle for future disease intervention.

ARJUN SHARMA

Project title: Does primary care availability mediate the relationship between rurality and lower life expectancy in the United States?

Abstract: Rural counties in the United States have lower mean life expectancy than their urban counterparts and comprise the majority of primary care provider (PCP) shortage areas. Increased PCP availability has been associated with improved health outcomes in prior studies. However, the association between increased PCP availability and life expectancy in PCP shortage rural areas is unknown. This study evaluates whether PCP availability casually mediates the relationship between rurality and lower life expectancy using county-level data. The results show that PCP density mediates 5% of the relationship between rurality and life expectancy in all counties and 10% of the relationship in rural counties. PCP density was found to mediate a portion, but not a majority, of the relationship between rurality and life expectancy. Increasing PCP density in rural counties with PCP shortages to the threshold of being a non-shortage county (>1 physician/3500 population, as defined by the Health Resources and Services Administration) would be expected to increase mean life expectancy in the county by 26 days and increasing it to the standards recommended by a Secretarial Negotiated Rulemaking Committee would be expected to increase mean life expectancy by 65 days. From a policy perspective, understanding how PCP density may be increased in rural areas may be of benefit to rural health, and improving PCP access may be considered as part of a multi-pronged approach toward improving rural life expectancy.

MAYA SMITH

Project title: Evaluating an AAV gene therapy in a bovine model of maple syrup urine disease

Abstract: Maple syrup urine disease (MSUD) is a rare genetic disease that affects an enzyme, the branched-chain alpha-ketoacid dehydrogenase complex (BCKDHA), and its ability to break down specific substances in the body properly. These substances are amino acids, specifically branched chain amino acids (BCAAs), which are leucine, isoleucine, and valine. MSUD can be fatal and does not have a cure. Because of this, I investigated the effectiveness of a promising treatment for genetic diseases: gene therapy. The goal of this study was to evaluate the effectiveness of the adeno-associated virus (AAV) gene therapy for MSUD by measuring BCAA levels, neurotransmitters, and vector genomes of the therapy. Doing this helped us determine the efficacy of the gene therapy in hopes of finding an effective and non-invasive treatment for patients with MSUD. BCAA levels were measured to determine the activity of the BCKDHA enzyme. Quantitative PCR (qPCR) was conducted to track the concentration of vector genomes to determine whether the vector was spreading throughout the cow’s body, and whether it continued to move into new cells after cell division. The concentration of vector genomes decreased as the cow grew, and the BCAA levels were higher than normal. This means that the gene therapy was not as effective as it could be because vector genomes did not spread throughout the body and BCAA levels were still higher than normal. The treatment was determined to be effective in decreasing BCAA levels. In the future, a higher dose of gene therapy may help achieve this goal.

ANNIKA Spaet

Project title: Water retention of small-scale green roofs with edible vegetation

Abstract: Green roofs (GRs) are roofs that are partially or completely covered with vegetation that can reduce the effects of climate change. GRs have many environmental benefits including water retention, which reduces runoff – the harmful draining away of excess liquid into larger bodies of water. GRs are increasingly being used to grow edible vegetation, such as peppers. However, there have been conflicting studies on how much water GRs with peppers can retain as compared to GRs with Sedum (a succulent popular in GRs). In this study, water retention was compared among three different vegetation types: two Sedum setups, two pepper setups, and one unvegetated (bare) setup. There was not a statistically significant difference for water retention between the different vegetation types, and the peppers wilted by the end of the study and did not produce food. These results indicate that Sedum should be used in future GRs because it can retain high amounts of water and provide many benefits other than water retention.

Stephanie wang

Project title: Loneliness and well-being in mid and late adolescents: The role of resilience, hope, and wisdom as protective factors 

Abstract: Loneliness is associated with worsening mental and physical health as well as higher mortality rates. However, there are factors that protect some people from the negative effects of loneliness. The three protective factors chosen in this study are resilience, hope, and wisdom. My goal is to examine whether these three factors protect against loneliness by mediating the relationship between loneliness and well-being among mid and late adolescents. By studying protective factors, researchers could have a better understanding of developing effective loneliness prevention and intervention strategies. The sample (N = 181) was recruited from six high schools in New York, and they completed measures of loneliness, well-being, resilience, hope, and wisdom. Statistical analysis, including Pearson correlation, hierarchical multiple regression, and regression-based multiple mediation modeling with a bootstrapping approach, was carried out. The results showed a moderately strong negative correlation between loneliness and resilience, loneliness and hope, and loneliness and wisdom. Loneliness inversely predicted well-being directly and indirectly, through resilience, hope, and wisdom as mediators. Specifically, hope accounted for the most additional variance in well-being above the effect of loneliness. This indicated the importance of goal-oriented personal resources in combating loneliness. Since resilience, hope, and wisdom are found to be significant protective factors against loneliness, future interventions on loneliness among adolescents may be more effective if they incorporate strategies to enhance these three traits.

2023 ASR Symposium Program

2023 Symposium recording and poster session

"At the beginning of high school, I knew I wanted to do STEM in the future, but I had no idea what it would be really like, and I didn't know what field I wanted to pursue. With ASR, I got the chance to actually see what STEM would be like in the real world, and I really loved it! The work I did in ASR was the most meaningful work I did in high school since I got to focus on what I was really interested in, and it gave me a lot of research skills that I utilize now in college for both research and classes."

Alex Lyons '21

"ASR is just as much about training you how to think and study as about how to be a scientist. Besides introducing you to the world of science and how it is done, ASR also continuously pushes you to improve yourself, to study and manage your time more efficiently. ASR is about learning how to tackle seemingly impossible challenges; it teaches you how to break them down into tangible and achievable pieces and work on them one at a time. Ultimately, ASR will leave you with a problem-solving approach that will stick with you even after you leave the program."

Yuqiao Zou '22

"ASR was a powerful influence on both Annika’s education and her life’s goals; the class provided a combination of timely, relevant knowledge on a topic that’s critical to society and can impact our future. The subject matter of the class had a game-changing effect, prompting her decision to make science the focus of her career. As parents, we highly recommend this class as we watched it build our daughter's character and confidence while broadening her understanding and perspective on current events."

Jon and Becky Spaet, parents of annika '23

"Although the School has many strong disciplines, ASR was by far the most beneficial experience our son [Alex] had at CGPS. Due in large part to the talented and dedicated faculty, the program literally changed the course of his young life. He learned how to best approach complex and long-term projects, developed self reliance and resilience, and discovered and pursued his intellectual passion. We couldn’t recommend this program more!"

Josefina and Gregory Lyons, parents of alex '21

"We are so grateful for Mr. Yashin and the ASR program.  It has been an incredible all around experience for our son that has also served to benefit him in all of his classes. We have seen a noticeable improvement in his communications and writing skills which has made him a confident presenter in and out of ASR.  Lastly, his interaction with both Mr. Yashin and his project mentor has been invaluable as he has been exposed to and learned things that he likely would not have been exposed to until college."

Jill and Jeff Libshutz, parents of lucas '23

"ASR is hard work, but it pays off in spades. We have seen tremendous growth in Arjun. In his research journey, he progressed from knowing very little about healthcare and struggling to understand journal articles to authoring a published paper on the subject. The structure of the program facilitates growth as it pairs individual responsibility with mentoring and support. He has learned to organize his time and pace his work to meet commitments. Research isn't always easy, and Arjun has faced his share of setbacks, but learning to cope with them is an important skill he has acquired, and this experience has made him resilient. In addition to the domain knowledge he has accumulated, the process of writing a lengthy review article and scientific paper and going through numerous revisions and presentations has led to a strong improvement in his writing and presentation skills. The close-knit community where the students help and support each other is a highlight of his experience and has reinforced in him that success is not an individual effort but a team sport. If you are curious about science and desire to make an impact, ASR provides an ideal platform to realize your ambitions.

Arjun had the opportunity to join other selective schools but was drawn by the unique opportunity at CGPS to conduct college-level scientific research on a topic of his choosing in the ASR program. We can confidently say that the mentorship and support that ASR provided enabled him to advance his research much further than he might have been able to at other schools. Judging by the remarkable growth in his skills, knowledge, and confidence in a relatively short time by being part of ASR, we feel that we made the right decision."

Roopali and Ushane Sharma, parents of arjun '23