Using bioinformatics to identify putative ORs in the Photinus pyralis transcriptome

Animals use diverse signals to find mates. Some signals are simple, and are emitted in a single mode, for example, visual or acoustic; while others are really complex, with multiple signal components transmitted simultaneously or sequentially over different modes. When we think about fireflies, we usually immediately think of an image that shines like stars in the night. Fireflies, which fall under the Lampyridae family of insects in the Coleoptera order of beetles, produce a chemical reaction inside their bodies that allows them to light up and they mainly use this ability to find a mate. But in fact, contrary to popular belief, not all firefly species are bioluminescent as adults. The unlighted-adult fireflies are day-active, and females may attract males over long and short distances by pheromones. Pheromones are detected by the firefly’s odorant receptors (ORs), which are heteromultimeric ion channels consisting of an evolutionarily conserved odorant co-receptor (Orco) and a variable non-Orco. Together, they form an OR complex that facilitate odorant binding and signal transduction. Previous work in the lab using a conservative homology-based approach found 27 ORs, including Orco, in Photinus pyralis, which is a lighted species with the most continuous genome assembly in fireflies. However, ORs can be very divergent and thus, missed when searching using conservative parameters. This project sought to develop a more expansive search strategy for ORs using both homology and structure-based predictions. Using this strategy, we identified over 100 putative ORs in the P. pyralis genome. The results of this study will provide a basis for future studies on the expression and evolution of ORs in fireflies.

Surface Roughness Analysis as Relative Dating Technique

When moraines degrade, two distinct changes in their morphology occur: 1) weathering
of boulders on the moraine surface leads to fewer and smaller boulders over time; 2)
initially sharp crests of the moraine become gentle over time as erosion transports
material downhill. These two attributes of moraines, surface roughness and the
sharpness of the crest, are important parameters to characterize the evolution of
glaciated landscapes but they have not been quantified. We established two metrics to
quantify these attributes of moraine morphology using high-resolution elevation data
and compared them against publicly available cosmogenic ages. The surface
roughness of the moraines is proportional to the number and size of the boulders, and
we quantified it by calculating the standard deviation of slope determined from 1-m
LiDAR data. For example, each boulder on the moraine surface produces local slope,
and a large number of boulders on a young moraine should lead to a high variability of
slopes, measured in degrees. Second, we quantified the sharpness of moraine crests
by measuring the maximum curvature along crest-perpendicular transects. Young
moraines tend to have sharp crests resulting in high values of the maximum curvature,
compared to gentle crests of old moraines with low curvature values. We analyzed only
the surfaces of well-dated lateral moraines with five or more cosmogenic ages per
moraine. Preliminary results show a weak negative temporal correlation in the surface
roughness and the sharpness of the moraine crests. However, the correlation is more
apparent at 100,000-yr scale than at 10,000-yr scale, probably because most of the
moraines date to ~16–22 ka. The correlation between these morphologic metrics and
age can be improved by analyzing older moraines from a variety of climate conditions.
This new relative dating technique can be used for mapping glacial landscapes in other
planets, such as Mars.

Feminism vs. Socialism Through the Eyes of the Young Lords

For my research project, I will be presenting a Google Slides presentation on the Young Lords, a Puerto Rican activist group from the late 1960s and early 1970s. In my presentation, I will briefly provide some context and background as to who the Young Lords were, what their priorities were, and how they went about achieving their goals. I then will zero in on the feminism and socialism aspects, what they meant for the group, and how these things worked together and against each other in the 1960s and 70s and how this pertains to today. I will detail how these things differed in a comparative perspective looking both at progress on the island of Puerto Rico and on the mainland United States. Additionally, I will be presenting on some important influential figures in the feminist movement from the Young Lords and why their legacy is so important to research today. My goal is to bring these things together in a way that gives the audience a sense of familiarity with the group and a better understanding of what feminism was in the late 20th century and what it is today, as the word is widely misunderstood. Some of my research materials will include Iris Morales’ Through the Eyes of Rebel Women”, excerpts from Palante, a Young Lords publication from the 60s and 70s, and more.

Deep Brain Stimulation of the Subthalamic Nucleus and its Effect on Gait in Parkinson Disease

Deep brain stimulation (DBS) is a surgical procedure where electrodes are implanted in the brain to modulate specific regions with electricity. This stimulation can alleviate gait disturbances in Parkinson disease (PD). DBS modeling can be used to estimate the spatial extent of stimulation, enabling individualized treatment. Although the standard DBS target for PD is the subthalamic nucleus (STN), a generalized approach may not be optimal for every patient due to the diversity of their symptoms. Better outcomes may be obtained by stimulating regions around the STN.
Forty PD patients who received bilateral STN DBS were included in this study. For each patient, the location of therapeutic stimulation was calculated using tissue activation models built from individualized imaging data and stimulation settings. The volume of tissue activation (VTA) was used to quantify STN and external (non-STN) activation in the lateral-medial, anterior-posterior, and dorsal-ventral directions. The relationship between STN/external activation and symptom improvement (gait, freezing of gait, postural stability, and total gait) was evaluated. A similar analysis was performed for electrode location (the distance between the active contact and STN centroid).
A significant positive relationship between anterior STN activation and total gait improvement was found (p < 0.01). No significant relationships were found for the external activation and electrode location analyses. Results suggest that more anterior STN stimulation may be preferable for patients whose primary symptoms are gait disturbances. Furthermore, VTAs may provide more information about stimulation location than active contacts and highlight the importance of patient- and symptom-specific targeting.

Identification of Novel Microorganisms and Nitrogen Fixing Organisms in Central Pennsylvania

In this project we sought to identify novel organisms from various locations throughout the Bucknell Natural Area. Bacteria were isolated on minimal media (lacking ammonia and nitrate) supplemented with a small amount of yeast extract and sucrose or mannitol. After repeated quadrant streaking, two novel microorganisms were isolated. PCR amplification of the 16S rRNA gene followed by sequencing of the PCR product indicates that one is of the Pantoea genus and the other of the Paenibacillus genus. Once the organisms were isolated, metabolic analyses were conducted using the BIOLOG GenIII plates. We will present the metabolic analysis as well as the results of annotating the genomes of these two organisms. In a second part of this experiment, the community characteristics of the soil samples were assessed using BIOLOG Ecoplates and community DNA was used to assess nitrogen fixing capability by PCR amplification using the nifK and nifH genes.

Exploring How Life History Affects Stress Responses
When an organism encounters a stressful stimulus, the endocrine system activates a physiological stress response through a cascade of hormone signaling, which functions to promote short-term survival by mobilizing and reallocating energy. In vertebrates, glucocorticoids (GCs) are released during the stress response. However, vertebrates vary greatly in their life histories, which in turn may require differentially regulated stress responses. Vertebrate species fall along a continuum of slow to fast life histories. Those with slow life histories tend to have slower growth rates, later maturation, larger size, fewer offspring, and longer lifespans. Alternatively, those with fast life histories tend to have faster growth rates, earlier maturation, smaller size, more offspring, and shorter lifespans. Although quail are classified as having faster life histories compared to other vertebrates, there is still ample variation among quail species. We are developing a comparative quail model to investigate whether stress responses differ based on where a specific quail species falls on the life history continuum. Specifically, we categorized how stress responses differ using three distinct measures. We predict that species with slow life histories will be able to turn off a stress response more rapidly compared to species with fast life histories. Our initial results show that the Blue Scale quail (fast life history) actually recovered more quickly from stressors, in comparison to Chinese Button quail (slow life history). I will discuss interpretations and implications of these results in further detail.

Printing Awareness: Endangered Species and A Piece of the Bigger Picture
In the history of Earth, the planet has gone through five mass extinctions, where at least
60% of the species were wiped out within a million years. Some scientists have stated that the earth is currently going through its sixth mass extinction. Currently, there are over 15,000 endangered species and over 11,000 that are vulnerable due to different anthropogenic disturbances such as habitat loss or pollution. Many studies have shown the effects of these disturbances to animal populations and the resulting implications in the rapid decline of species’ population numbers.
Printing Awareness: Endangered Species and A Piece of the Bigger Picture is a printmaking project that incorporates 24 linoleum blocks to depict the endangered species – reptiles, birds, mammals, mussels – in the state of Pennsylvania. Each block can be a standalone piece, but when all the blocks are placed together, they form the map of the state, highlighting the many endangered species in Pennsylvania. This work is inspired by artists Sue Coe, Asher Jay, Mark Cawood, Banksy, Andy Warhol and their works advocating for animals, as well as Chuck Close’s gridded portraits.
Many people, including artists, have spoken out about the detrimental effects of human
activity on the environment. My printmaking project aims to raise awareness for the numerous endangered species in Pennsylvania, and to give them a spotlight and voice. As humans, we play a role in their endangerment, however we can also play a role in their conservation.

Unveiling the Structure of the Universe for Non-Science Students.
Our research focuses on creating and testing the effectiveness of an introductory astronomy lab activity designed for undergraduate non-science majors. To explore the Hubble Law, the expansion of the universe, and large scale structures, this lab implements the WorldWide Telescope, an interactive multi-perspective visualization tool, analysis of real astronomical data, and tactile models. We conducted a focus group to test the implementation of this new curriculum. Our hope is to fully develop and publish a fun and interesting laboratory experience that can be accessed without economic or social barriers to advanced technological materials.

Effect of Tillage Radish on Mycorrhizal Density in a Regenerative Agriculture System

Traditional agriculture has become dependent on industrial methods, using heavy machines, fossil fuels and synthetic chemicals. However, due to the harm of these methods, a growing movement of regenerative agriculture is emerging. This approach takes advantage of the natural tendencies of organisms in the ecosystem to grow abundant nutritious crops, without the negative effects. The Bucknell Farm follows such a practice, with two main principles being no-till, and the usage of cover crops. Manual tilling in industrial farms loosen the soil to prep for the planting season but have also been shown to induce soil erosion. Cover crops are used to build organic matter, and to retain water in the fields. By planting non-harvested crops during the off-season, these plants help prevent nutrient and water losses. A common cover crop used is the tillage radish, which grows long roots that loosen the soil allowing subsequent crops to develop deeper root systems while using less energy. However, as a member of the Brassicaceae, tillage radish releases chemicals, isothiocyanates, that are known to inhibit the growth of mycorrhizae fungi. These fungi are known to be beneficial in farms, helping crops with water absorption and nutrient collection. Our research looks into whether the tillage radish affects mycorrhizal propagule count in the subsequent growing season. Using the Most Probable Number method (MPN) we investigate if the tillage radish reduces the mycorrhizae populations and if this reduction can be detrimental to the subsequent crop seen by reduced nutrient content.

Analgesic Effects of Mindfulness Meditation

Mindfulness meditation focuses on being aware of the present moment and prior research suggests it can modify the perception of pain. When used as a coping strategy, mindfulness meditation has been shown to increase pain tolerance and threshold. However, most mindfulness techniques focus on a single sense at a time. In other domains, multisensory input enhances perceptual processing, and adding a multisensory component to standard mindfulness meditation might increase the analgesic effects. The present study examined the effects of an added multisensory component to mindfulness meditation on pain perception during a cold pressor test. Three groups, a control group, a mindfulness meditation group, and a multisensory mindfulness meditation group, completed a baseline cold pressor test and a second cold pressor test where pain threshold, tolerance, and intensity were measured. Between the first and second tests, the mindfulness groups were given instructions to practice mindfulness meditation. We hypothesized that while a standard mindfulness technique would increase the duration for acute pain threshold and tolerance, an added multisensory component would show a longer duration for pain tolerance and threshold than a standard mindfulness technique and the control groups. Preliminary results have not supported this hypothesis; thus, we consider alternative explanations for our results.