PRISM 2018 Project Descriptions - Longwood University

PRISM 2018 Project Descriptions

Faculty Mentor – Dr. Ben Campbell

Concept Sketches as Planning Tools for Practicing Science Teachers

Secondary science teachers typically have extensive background in the content area they are to teach, as well as
significant training in pedagogy. Teachers—especially teachers who are early in their careers—may nonetheless
struggle with the task of actually translating their understanding of both content and pedagogy into appropriate
lessons, activities, and assessments for their students. The concept sketch is one tool that may be effective in
helping teachers articulate their understanding of a concept and develop appropriate curriculum surrounding this
concept. A concept sketch is a simplified sketch illustrating the main aspects of a concept or system, annotated
with concise but complete labels that 1) identify the features, 2) depict the processes that are occurring, and 3)
characterize the relationships between features and processes. With a collaborator at Brigham Young
University, I am developing a series of concept sketches tied to specific Disciplinary Core Ideas from the Next
Generation Science Standards (NGSS Lead States, 2013) in biology, chemistry, physics, and earth and space
sciences. We ultimately plan to position these concept sketches with accompanying materials as unit-planning
devices for practicing teachers. As part of PRISM during 2018, I would like to work with a student to
administer a collection of concept sketches to practicing teachers in Prince Edward County and surrounding
school districts. As part of the administration, we will also conduct post-interviews with the teachers. The data
from this process will provide an opportunity to answer a variety of student research questions.

Faculty Mentor – Dr. Julian Dymacek

Hybrid Distributed Constrained Non-negative Matrix Factorization

Our previous work developed a novel constrained non-negative matrix factorization algorithm and Monte Carlo
Markov chain simulation to identify underlying patterns in mRNA and miRNA gene expression data. Genes can
be associated with quantitative pathology patterns and, using a database of curated gene sets, we can identify
biological processes that are significantly related to a pathology. To keep up with the growing size of available
data sets, we created a distributed system, allowing for a reduction in computation time and an increase in
accuracy. To build on our Prism 2017 work, we propose to modify our system to create a suite of programs that
other labs can use regardless of their equipment. At present, our program is best suited to the hardware in the
Longwood Advanced Computing Lab. While our previous algorithm increases efficiency, each computer in the
distributed system is still an individual unit that has to ask each other computer for results for its piece of the
program. If we can build a constrained shared-memory algorithm, we can increase our efficiency even more by
taking out the push-pull communication between computers. Depending on individual lab setups, the algorithm
can be run using our previous version, the new version, or a hybrid of the two. This gives research groups an
opportunity to optimize efficiency and accuracy using their existing hardware. Understanding the regulatory
networks between mRNA and miRNA in different stages is beneficial for understanding the path of disease
development. These identified genes and pathways may be useful for determining biomarkers for early
detection of disease.

Faculty Mentor – Dr. Catherine Franssen

Efficacy of Aquatic Therapy Techniques in Reduction of Anxiety in Autistic versus Non-Autistic Children

Children with autism struggle with many challenges, particularly with changing environments and new
situations. New methods to help these children build strategies to handle unexpected future experiences are
needed. Therapeutic Recreation faculty have designed a practice-embedded curriculum in which Longwood
University TR students engage with special needs children from at least one neighboring county school in an
aquatic therapy program and a dry lab environment. Dr. Susan Lynch has a decade-worth of anecdotal evidence
for the program’s success, and has partnered with Ms. Kirstin Whitely (assessment of behavioral outcomes) and
me (assay for anxiety-related hormones) to provide quantitative assessment of the program. Currently, my lab is
collecting salivary samples at regular intervals from children participating in aquatic therapy. During the
summer PRISM session, the selected student will work with me to summarize data collected during the 2017-18
academic year. We will then write a feasibility study (for publication in a scholarly journal) that summarizes our
methodology and current survey and saliva data. This first full analysis of the pilot research will provide support
and direction for a 5-year longitudinal study on the aquatic therapy program in place. The PRISM student will
not only develop skills in quantitative reasoning, scientific research, and scientific writing, but will also foster
citizen leadership by playing an integral role in this interdisciplinary, community-engaged project.

Faculty Mentor – Dr. Sujan Henkanaththegedara

An assessment of diversity and structure of vernal pool communities at High Bridge Trail State Park

Vernal pools are highly ephemeral, small aquatic systems that support an array of aquatic species from aquatic
macroinvertebrates to amphibians and turtles. These small pools play a vital role as spring breeding and nursery
grounds for aquatic species and provide ways for them to escape from fish predation of their eggs and larval
stages. Although, coastal vernal pools in Virginia are fairly well studied, vernal pool communities in central
Virginia have received very little attention. Additionally, a recent survey showed that about 20% of historic
sites were lost mainly due to urbanization and development. Such is the case with vernal pools located in the
High Bridge Trail State Park (HBTSP). In spring 2017, we have conducted a short-term preliminary survey of
aquatic organisms in vernal pools at HBTSP and generated the first data set for the diversity of vernal pool
organisms in the park. After a discussion with park officials about the need for an extensive, long-term study to
fully understand this unique and fragile system with park, we plan to start a 5-year study to understand the
diversity and community structure of vernal pool organisms in HBTSP. This PRISM 2018 project will serve as
the first season of the long-term study. We hope to map all the vernal pools in HBTSP, establish sampling
protocols, and collect a comprehensive data set from early spring to mid-summer. This project will provide a
unique opportunity for Longwood faculty and students to develop a long-term collaboration with Virginia State
Park system with mutual benefits.

Faculty Mentor – Dr. Christopher Labosier

High Resolution Mapping of the Urban Heat Island

Extreme heat is the leading cause of weather-related fatalities. Additionally, future climate change projections
suggest that heat waves will become more frequent, more severe, and longer duration. Urban areas can
exacerbate these extreme heat conditions due to a variety of factors including increased absorption of solar
energy, decreased evaporative cooling, and an overall loss in reflective surfaces. This urban area increase in
temperatures, relative to the surrounding rural areas, is termed an urban heat island (UHI). Understanding the
mechanisms by which UHIs develop and manifest themselves is key to adapting to and mitigating their impacts.
Traditionally, UHIs have been examined using satellite-based remote sensing products. While providing some
unique advantages, remote sensing products do not provide information on temporal variability and are limited
in their spatial variability. This project proposes to use a new method of mapping the UHI by using relatively
inexpensive, mobile instrumentation that provides a higher spatiotemporal resolution. This instrumentation
consists of a thermocouple and datalogger to measure temperature and a GPS unit to record location all attached
to a bicycle or automobile. Proposed methods include riding or driving predetermined routes at various times of
day to collect high spatial and temporal resolution temperature and locational data. By mapping the urban heat
island with this high-resolution technique, we seek to (a) contribute to a deeper understanding of the
spatiotemporal variability of urban heat islands and (b) progress towards more climate-resilient urban planning
and design.

Faculty Mentor – Dr. Kenneth Pestka II

Investigation of the dynamics of wooden baseball bats via acoustic and elastic analysis

The mechanical behavior of a baseball bat is governed by its geometry, density and intrinsic elastic properties.
In order to predict and understand the behavior of any wooden system, including baseball bats, all three
components must be well understood. However, wood is an anisotropic material whose material properties are
influenced by a wide range of factors including the growth environment, tree species as well as preparation and
processing conditions. In addition, the elasticity of wood can behave in a nonlinear manner and the vibrational
energy is quickly dissipated due to material damping, making a complete picture difficult to generate. In this
work we plan to model and test wooden baseball bats composed of four different species of wood in order to
improve our understanding of these complex systems. To test the macroscopic behavior of the bats we will
perform acoustic spectral analysis of dynamically excited bats with varying composition and geometry. In
addition, we will also determine the elastic constants of four different wood species used in wooden bat
construction using the method of resonant ultrasound spectroscopy (RUS). We will then utilize the
experimentally determined elastic constants obtained using the RUS method to generate full-scale bat models
using the 3D finite element modeling software Femap with NX Nastran. We will then compare the modeled
bats to the actual bats in order to assess the elastic properties that most significantly affect bat performance and
mechanical behavior.

Faculty Mentor – Dr. Troy Purdom

Monitoring annual training progression with physical testing to prevent overtraining and injury in Division I
athletes

The nature of competitive athletics is to work towards optimal performance, which inherently places themselves
at risk for overtraining. The intense training loads that soccer athletes experience through training bouts and
competitions stress the body. Additionally, periodized changes in training density experienced by Division I
athletes cause variation in various physiological phenotypes which can manifest as decreased performance and
even injury. Structured testing and evaluation is warranted throughout the entire year to show how different
seasonal training programs impact adherence to off-season training and recovery programs. When appropriate
rest is insufficient or detraining is postponed, exposure to overtraining syndrome and eventually injury produce
symptoms which include fatigue, illness, lackluster performance, etc. Recent efforts to track an athlete’s
progress are to monitor heart rate (HR), blood markers (catecholamines, cytokines, cortisol), and incorporate
individual GPS devices. Current methodologies are costly and time consuming to track an athlete’s
physiological status, which burden coaches and athletic departments with the inability to monitor their athletes
appropriately. Ultimately the athletes are put at risk. Efforts using non-invasive methods to effectively evaluate
athletes have yet to be applied to team model. Therefore, the current proposal outlines a non-invasive plan to
effectively track athlete’s status to reduce injury and improve performance.

Faculty Mentor – Dr. Erin Shanle

Investigating the effects of bromodomain cancer mutations on the activity of p300

In eukaryotic cells, DNA is wrapped around histone proteins that regulate gene expression in part through
chemical modifications, such as acetylation. Histone acetylation can serve as binding sites for ‘reader’ proteins
that contain highly conserved regions known as domains. ‘Reader’ proteins recruited to the histone-DNA
complex can act as co-activators for gene expression and promote transcription of neighboring genes. The
protein p300 helps activate gene expression by binding acetylation through its bromodomain (BD) and further
increasing acetylation using the neighboring catalytic core domain. Importantly, p300 is often mutated in cancer
cells but the functional significance of BD mutations has not been fully explored. My previous research
demonstrated that mutations in p300-BD impaired the interaction with histone acetylation, suggesting that these
mutations may affect the neighboring catalytic core and function of p300 in cancer cells. The goal of this
project is to develop a system to test the effects of BD mutations on the catalytic activity of p300 using
CRISPR-Cas9 targeting to a specific location in the genome of human cancer cells. First, mutations in p300 BD
mutations will be made using site-directed mutagenesis of pcDNA3.3-Nm-dCas9-p300-Core, a DNA sequence
that induces expression of enzymatically inactive Cas9 (dCas9) fused to the catalytic core domain of p300.
Next, genomic regions will be identified to develop guide RNA sequences that can target dCas9 fused to wild-
type or p300 catalytic core to that specific genomic region. Finally, RNA levels of the neighboring genes will be
compared in cells expressing normal or mutant dCas9-p300-core proteins.

Faculty Mentor – Dr. Benjamin Topham

A computational study of single molecule electronics

The electronics industry is continually striving to innovate. This typically leads to smaller, more powerful
devices or devices that offer new applications. Making electronic devices out of single molecules has the
potential to reduce the size of electronic device components dramatically and also produce unprecedented
functionality. Device components can be made from single molecules, but the technology is not developed
enough to make viable consumer products. Computational chemistry can play an important role in the
development of single molecule electronic devices by enabling large numbers of molecules to be screened
without needing expensive and sensitive equipment to make the corresponding measurements on actual devices.
We can use computational chemistry to make recommendations for candidate molecules that may have superior
performance. Computational chemistry can also be used to help understand why certain molecules may provide
better performance than others. The primary issue of molecular electronics is the control of transmission of
electrical current through a molecule. We will use computational chemistry to investigate how electron
transmission through a molecular device can be controlled through chemical modification and suggest ways to
design molecules for optimal device performance. We will investigate the effects of various factors on electron
transmission to gain a more complete understanding of single molecule electronic device function.

Faculty Mentor – Dr. Denis Trubitsyn

The effect of Mad2 protein on the morphology of magnetic crystals in Magnetospirillum gryphiswaldense
MSR-1

The proposed study focusses on a group of prokaryotes known as magnetotactic bacteria (MTB). MTB
synthesize crystals of magnetite or greigite inside of their cells and use them to passively orient in earth’s
magnetic field similarly to a compass needle. Bacterial magnetic crystals, termed magnetosomes, are
surrounded by a bi-layer lipid membrane and have unique properties that facilitates their exploitation in
biotechnology and medicine. The morphology of magnetosomes is species specific. Most MTB produce
cuboidal crystals, while some produce elongated magnetosomes, known as bullet- or tooth-shaped. Despite the
progress in research on magnetosome formation, it is still unknown what determines the shape of the crystals. It
has been shown that a mutant strain of Desulfovibrio magneticus which is MRS-1 lacking the expression of
mad2 gene produces less elongated crystals, compared to that of the wildtype strain.

The aim of this project is to investigate the effect of Mad2 protein on the shape of crystals in Magnetospirillum
gryphiswaldense MSR-1, a species of MTB that naturally produces cuboidal magnetosomes. To achieve this
goal, mad2 DNA fragment will be synthesized and cloned on a plasmid that then will be transferred and
integrated in the genome of M. gryphiswaldense MSR-1. The changes in the crystal morphology will be studied
using transmission electron microscopy (done in collaboration). This study will further our knowledge of the
complex processes of magnetosome formation. The elongated crystals have been demonstrated to have a
stronger magnetic response and therefore higher potential to be used in biotechnological and medical
applications.

Faculty Mentor – Dr. Thomas Wears

The Geometry of Curves and Surfaces via Moving Frames

The aim of this project is to use the method of moving frames to study the geometry of curves and surfaces in
two and three-dimensional spaces equipped with a non-Euclidean geometric structure. Building on the study of
the geometry of curves and surfaces in ordinary Euclidean geometry, we will begin by studying the geometry
of curves and surfaces in two and three-dimensional Lorentz-Minkowski space using classical moving frames.
After building a solid foundation based on classical moving frames, we will then introduce the Fels-Olver
moving frame method and use it to investigate the geometry of two and three-dimensional Lorentz-Minkowski
space, comparing the results obtained from the two methods. The project will then culminate by using the Fels-
Olver moving frame method to investigate the geometry of curves and surfaces in three-dimensional non-
Euclidean geometries with large groups of isometries. The geometries under consideration will come from
three-dimensional Lie groups carrying Lorentzian or Riemannian geometric structures and Biannchi-Cartan-
Vranceanu (BCV) spaces. This project will be accessible to any student that is enrolled in (or previously
completed) MATH 361 during the spring semester of 2018.