Natural Sciences

Pennsylvania leads the nation in dam removals, which typically are obsolete milldams eight to fifteen feet in height that span valley bottom widths. There thousands of structures, many of which are in disrepair. Immense amounts of sediment and nutrients that are stored upstream of these dams are eroded after failure or removal, leading to geomorphic and ecosystem damage to downstream waterways. This study focuses on characterizing the sediment in several milldam reservoirs and calculating erosion rates after dam removal (or failure). A key hypothesis evaluated is that sediment grain size determines erosion rate, with finer grained sediment eroding slower than coarser grained sediment. Grain size data was obtained from sieving and the hydrometer method. Erosion rates were determined by change detection with high-resolution LiDAR topographic data. Results will be integrated with ongoing analysis of alternative evaluations for imminent removal of the Roller Mill Dam in the Chiques Creek watershed.

Informal and formal green spaces play a critical role in providing city residents a cleaner environment through helping purify the soil and air, a sense of tranquility and escape, healthier lifestyles through increased exercise, and establishing a firmer connection to nature. Formal green spaces include areas that have been previously incorporated in the layouts of cities, whereas informal spaces are liminal areas that are unkempt. I will be analyzing how formal and informal green spaces are utilized by both people and wildlife in Lancaster City through two different methods: 10 motion-sensored cameras that have been placed around Lancaster City and passive acoustic monitors that detect the presence of various bat species. Through analyzing the data from these two mechanisms, results will show how biodiverse natural spaces are and whether or not they are used by people.

Unnatural amino acids (UAAs) consisting of a vibrational reporter such as a nitrile, azide, or nitro group have the potential to serve as effective, site-specific probes of local protein environments. Specifically the UAA 4-cyano-L-phenylalanine (pCNF) contains a nitrile vibrational reporter that is an effective probe of local environment due to the position and sensitivity of the nitrile symmetric stretch to local environment, in addition to the relative small size of the nitrile group. Additionally, this UAA can be site-specifically incorporated into proteins using the amber codon suppression method. Here, this vibrational reporter UAA was genetically incorporated at multiple distinct sites in the enzyme adenylate kinase (AK), which catalyzes the conversion of two adenylate diphosphate (ADP) molecules to one adenosine monophosphate (AMP) molecule and one adenosine triphosphate (ATP) molecule. Multiple sites were selected to represent a myriad of local solvation states some of which are predicted to change upon nucleotide binding based upon the X-ray crystal structures of apo and nucleotide bound AK. These local environments will be assessed with temperature-dependent infrared (IR) spectroscopy utilizing the correlation of the temperature-dependence of the nitrile stretch of pCNF to local environment.

Reptiles are used heavily in scientific studies but are often misunderstood compared to their mammalian counterparts. To analyze and interpret which handling techniques were most effective at eliciting stress in these studies, a wide search was conducted for sources that studied the effects of handling on reptile stress responses.The 253 studies in the database exhibited a variety of reptiles and conditions that could potentially affect their results such as whether the reptiles in question were captive born or wild caught. We found that the studies were representative of reptile populations and utilized a wide range of handling techniques and unique procedures to elicit stress responses from the reptiles they were studying. Using the database, we built a statistical model including three common handling techniques, which was able to predict a stress response accurately about 85% of the time.

Down Syndrome (DS), a genetic disorder due to an extra copy of chromosome 21, leads to mortality and immunological alterations. We studied the Dp(16)1Yey mouse model gene expression in embryonic liver using RT-qPCR to demonstrate gene dosage imbalance and subsequent immune dysregulation and blood stem cell imbalances observed in DS. We compared transmission rate of the Dp(16)1Yey chromosome to offspring surviving at weaning based on the sex of the carrier parent. The mean rate of Dp+ mice at weaning was 26% with both maternal and paternal carriers, indicating no significant difference, and refuting the theory that maternal phenotypes affect transmission rate and survival of offspring. We found that the average weight percentage of spleens in Dp+ females was significantly higher than in euploid females, indicating the presence of developmental spleen defects. These findings indicate the DS mouse model replicates some phenotypes of the human disease.

Daphnia biogeography is essential in understanding the localization and hybridization of Daphnia species in certain lakes with specific geographical traits. We will analyze the mitochondrial markers of Daphnia species, Mitochondrial NADH dehydrogenase subunit 5 (ND5) and cytochrome c oxidase subunit I (COI), in order to identify the Daphnia species present in the lakes. We hope to overcome DNA analysis issues for the COI loci and obtain genetic information of a wider sample of Daphnia. We will be constructing a phylogenetic tree to illustrate the genetic relationships between the Daphnia samples based on their geographical location and identify hybrids. In the future, we hope that through the findings of this study and the physiochemical properties of the lakes we will understand the distribution of Daphnia species among the lakes.

Outdoor recreation has been increasing yearly, and as a result, the impact on animal populations is rising. Nonconsumptive recreation, which excludes hunting and fishing, has been found to alter the spatial distribution of animal communities, with various hypotheses to explain this. The effects include decreased foraging quality of animal populations, as well as energetic costs as a result of human avoidance and increased vigilance. This research seeks to understand the effects of human recreational activities on the spatial distribution of mammals in forest patches around Lancaster, Pennsylvania. Camera traps were set up within approximately 25 forest patches around Lancaster to collect data on animal abundance and human visitation. Data collected from 2016-2020 was then used to examine the relationship between species abundance and number of recreationists. Altered species distribution as a result of recreation could indicate that current levels of recreation around Lancaster are having a negative effect on wildlife.

The goal of materials chemists is to improve the function and efficiency of matter. Anion exchange is a process in which part of a crystal is substituted with an alternate charged element. Its products could offer new sources of renewable energy, yet anion exchange remains largely unexplored due to the anions being much larger and less mobile. Nonetheless, the Plass lab accepted the challenge: roxbyite nanorods (Cu_2-xS) were produced, and external telluride was allowed to replace the intraparticle sulfide. Weissite (Cu_2-xTe) was successfully generated, and samples were extracted and characterized along the way in order to better visualize the mechanism of exchange. Certain surprises, such as regioselective cores and non-Kirkendall effects, were also observed.

Naegleria fowleri is a thermophilic amoeba found in freshwater across the world and is the causative agent of primary amoebic meningoencephalitis (PAM), a fatal human disease. Historically common in the Southern United States, in recent years N. fowleri has been found as far north as Pennsylvania and Minnesota. In this project, we are evaluating the presence of N. fowleri in thirty samples of freshwater from Lancaster County. It is the goal of this project to optimize molecular methods to detect N. fowleri directly from environmental samples. In pursuit of this goal, DNA was extracted from each water sample and three sets of promising PCR primers specific to N. fowleri were identified from the literature. In the spring semester, we will focus on amplifying and visualizing the genetic material extracted from the samples to evaluate the presence of N. fowleri in Lancaster County waterways.

In partnership with the Hawk Mountain Sanctuary and the Franklin and Marshall College Marshall Fellows Program, I collected videos of wildlife using footage from motion-activated trail cameras to create accessible, educational materials. These videos are to be used at the sanctuary to introduce community members to the conservation techniques and research done on site. The videos, made of real images of animals on the very trails the community members visit, bridge the gap between the academic researchers that utilize Hawk Mountain and the families and hikers that also frequent its trails. The goal is that the videos will also educate and inspire individuals in the community to take action supporting conservation and other science-based initiatives. In addition to the educational materials, a long-term collaboration with Hawk Mountain to allow for wildlife monitoring integrated into education for years to come.

Rabies is a mammalian virus that is spread through scratches and bites and travels from the point of infection to attack the central nervous system. Despite the availability of vaccines, rabies continues to plague human society, especially in Africa and Asia. In the United States, the environmental disruption exacerbates the spread of rabies, with raccoons as the primary vector of rabies. According to the PA Department of Agriculture, southeastern PA is a hot spot for rabies infections. I investigated how environmental disturbance, specifically urbanization, impacts raccoon presence within Lancaster and York counties, as a way to understand rabies risk. I tracked raccoon populations through motion-activated camera traps at 25 locations throughout the region. These locations will be at a variety of urban, suburban, and rural parks. Results will be shown that examine the relationship between urbanization and raccoon populations. This research will benefit wildlife management and public health.

Humans impact wildlife through their use of natural spaces for recreation. Increased hiking can alter temporal behavior of wildlife. I am investigating how human trail use affects temporal activity of native Pennsylvania wildlife. I hypothesize that increased human traffic will cause a temporal shift in wildlife presence and abundance on hiking trails. I predict that fewer wildlife sightings will occur during times of high traffic, leading to increased nocturnality of wildlife. Specifically, raccoons, skunks, opossums, grey foxes, and red foxes will be affected the least due to their already-high levels of nocturnality. Coyotes, deer, and squirrels will be the most affected due to their naturally crepuscular and diurnal activity patterns. I am using motion-activated cameras located near hiking trails throughout Lancaster Conservancy preserves to study presence and abundance of humans and wildlife. Results will be shown which examine the relationship between human trail use and temporal patterns of wildlife.

An useful method of studying local electrostatic environments within protein molecules is by incorporating unnatural amino acids (UAAs) containing chemical bonds with specific features in the infrared spectrum (IR) that change based on local environments. Of the existing UAAs, 4-cyano-L-phenylalanine (pCNF) is a highly useful reporter due to the fact that it is easily synthesized, it is well-studied, and its nitrile stretch appears in a biologically quiet region of the IR spectrum. In this study, pCNF has been genetically incorporated individually into three distinct sites of superfolder green fluorescent protein (sfGFP) which are expected to have unique solvation environments. Temperature-dependent IR spectroscopy was utilized to assess the local solvation environments of these sites. By measuring the nitrile stretching frequency as a function of temperature, the degree to which the incorporated pCNF participates in hydrogen bonding was determined. IR data and X-ray crystal structures from these constructs will be presented.

Hypsibius dujardini is a species of tardigrades, a microorganism that is well known for their morphological structure and their unique ability to survive extreme environmental conditions. Their survival is dependent on anhydrobiosis, a process in which the organism’s metabolism slows to a standstill. Previous studies have indicated that there is a difference in expression of Replication Factor C subunit 2 (Rfc2) and Actd11c05, when a tardigrade is in an anhydrobiotic state and when it is not. This experiment investigates the expression of these genes during periods of desiccation at high and low temperatures. This study lacks significance, but does present trends that suggest Rfc2 is downregulated when the H. dujardini undergoes anhydrobiosis in cold conditions. On the contrary, trends in the collected data also propose that Actd11c05 is upregulated during anhydrobiosis at low temperatures.

Atoms in a solid can be excited by adsorbing energy. The lifetime of the excited states yields information about the atomic interactions in the solid. Mechanisms affecting subsets of the excited ions differently produce heterogeneous decays. Nano-scale ruby is a model system to study these complex populations. The high surface area of the nano-scale host and the energy transfer between ions creates a distribution of ion sub-populations that varies with the Cr3+ concentration. Combustion synthesis is used to create 30 nanometer particles with controlled amounts of Cr3+ ions. The emission of the ions and pairs of ions, after laser excitation, determines the relative populations of the types of ion sites. The ratio of pair-to-single ion sites is found to increase linearly with the Cr3+ concentration, consistent with simulation predictions. Further studies on the energy transfer between the sites will contribute to the understanding of decay dynamics in complex systems.

There are many configurations in which we can pack a unit square with n smaller squares. Mathematicians have tried to study the configuration where the sum of the side lengths of all the little squares is maximal; in particular, Erdös studied the maximum sum possible given such a packing. Since this question is broad, we focus on a more specific case where the small squares do not overlap and they cover the entire unit square (this case is called a tiling). Furthermore, we assume that all the little squares can be tiled with the smallest square in order to make the problem more computationally tractable. We found a relationship between the side length of the smallest square and the sum mentioned above that might help us find the optimal tiling for n=k^2 ± 3 (for which we proved it is sufficient to study the case with the unique smallest square).

Protein ABC is a mitotic protein associated with a degenerative autosomal-recessive nephrocerebellar disorder. While considerable research has been done on identifying genetic mutations in gene ABC associated with this disorder, few studies focus on Protein ABC’s function. Through confocal immunofluorescence microscopy, live-cell imaging, Western blotting and Coomassie staining of proteins co-precipitated with Protein ABC, the Jinks lab has begun to elucidate ABC’s functional role in healthy and patient-derived cells. To elucidate ABC's role, we have continued to optimize live-cell imaging protocol for patient-derived cells. Through developing this model, we also experimentally validated candidate protein interactors with ABC. Another aim is deducing the function of ABC in neuronal differentiation. As neurons are post-mitotic cells, ABC must hold a novel purpose in neurons unlike its established function in mitotic cells. Localization patterns and timelines, gathered using confocal microscopy, suggest a previously unobserved role for ABC in the differentiation of neuronal precursor cells.