Physical Sciences and Mathematics Commons^™

Atomistic Simulations And Network-Based Modeling Of The Hsp90-Cdc37 Chaperone Binding With Cdk4 Client Protein: A Mechanism Of Chaperoning Kinase Clients By Exploiting Weak Spots Of Intrinsically Dynamic Kinase Domains, John Czemeres, Kurt Buse, Gennady M. Verkhivker

Mathematics, Physics, and Computer Science Faculty Articles and Research

A fundamental role of the Hsp90 and Cdc37 chaperones in mediating conformational development and activation of diverse protein kinase clients is essential in signal transduction. There has been increasing evidence that the Hsp90-Cdc37 system executes its chaperoning duties by recognizing conformational instability of kinase clients and modulating their folding landscapes. The recent cryo-electron microscopy structure of the Hsp90-Cdc37- Cdk4 kinase complex has provided a framework for dissecting regulatory principles underlying differentiation and recruitment of protein kinase clients to the chaperone machinery. In this work, we have combined atomistic simulations with protein stability and network-based rigidity decomposition analyses to characterize dynamic …

Predicted Suitable Habitat Declines For Midwestern United States Amphibians Under Future Climate And Land-Use Change Scenarios, Brock Struecker, Joseph Milanovich

Biology: Faculty Publications and Other Works

With current declines of vertebrate taxa meeting or exceeding those of historic mass extinction events, there is a growing need to investigate the main drivers of losses. Two of the main drivers of declines are global climate and land-use changes, both affecting multiple groups of taxa. Amphibians are at great risk from these two drivers of change and investigations into the impact of future change could assist with the formation of conservation plans to mitigate losses. Forecasting changes in suitable habitat with ecological niche modeling serves as a useful tool to begin to understand how species may respond to anthropogenic …

Reduced Light Availability Diminishes Mycorrhizal Growth Response Of Invasive Forb, Regina O'Kelley

WWU Honors College Senior Projects

Arbuscular mycorrhizal fungi (AMF) form mycorrhizae, a common, well-studied symbiotic relationship. Controls on the magnitude and direction of plant mycorrhizal growth response (MGR) remain obscured. Specifically, the influence of light availability in the MGR of an invasive forb, spotted knapweed Centaurea stoebe, has not been studied. Greenhouse studies exploring the growth response of knapweed to arbuscular mycorrhizae (AM) often fail to report light intensity levels, which could impact the quality of their data. I conducted a greenhouse experiment studying the MGR in spotted knapweed under shaded and unshaded conditions, designed to approximate light availability in ambient greenhouse and full-sun …

Using Mixed Effects Modeling To Quantify Difference Between Patient Groups With Diabetic Foot Ulcers, Rachel French

Mahurin Honors College Capstone Experience/Thesis Projects

When diabetes progresses, many patients suffer from chronic foot ulcers. In a study described in Matrix Metalloproteinases and Diabetic Foot Ulcers (Muller et al., 2008), sixteen patients with diabetic foot ulcers were examined throughout a twelve week healing period. During this period, levels of matrix metalloproteinases (MMP-1), their inhibitors (TIMP-1), and the extracellular matrix in a wound area were measured at distinct time intervals for each patient. The ratios of these healing components are vital in determining whether a wound will heal or become chronic and never properly heal. Connecting Local and Global Sensitivities in a Mathematical Model for Wound …

A Redescription Of The Ichnospecies Koreanaornis Anhuiensis (Aves) From The Lower Cretaceous Qiuzhuang Formation At Mingguang City, Anhui Province, China, Li-Da Xing, Yuan-Chao Hu, Jian-Dong Huang, Qing He, Martin G. Lockley, Michael E. Burns, Jun Fang

Research, Publications & Creative Work

The Cretaceous bird trackway originally labeled Aquatilavipes anhuiensis, in 1994, had previously been examined, photographed and replicated, but never described or illustrated in detail. However, it has been part of a widening discussion about the distribution of Aquatilavipes and Koreanaornis in China (and Korea). Here we illustrate and formally describe the holotype in detail and assign it to Koreanaornis (Koreanaornis anhuiensis) as informally proposed by previous authors. We also demonstrate that most authenticated reports of Koreanaornis, including the Anhui occurrence, are from the Lower Cretaceous, not from the Upper Cretaceous as previously reported.

Constrained Sequence Alignment, Kyle Daling

WWU Honors College Senior Projects

Constrained Sequence Alignment: A new algorithm designed to help biologists produce better alignment for protein sequences.

Design And Synthesis Of Analogs Of Myo-Inositol, Serine, And Cysteine To Enable Chemical Biology Studies, Tanei J. Ricks

Doctoral Dissertations

Phosphorylated myo-inositol compounds including inositol phosphates (InsPs) as well as the phosphatidylinositol polyphosphate lipids (PIP_ns) are critical biomolecules that regulate many of the most important biological processes and pathways. They are aberrant in many disease states due to their regulatory function. The same is true of the phospholipid phosphatidylserine (PS) which can serve as a marker to begin apoptosis. However, the full scope of activities of these structures is not clear, particularly since techniques that enable global detection and analysis of the production of these compounds spatially and temporally are lacking. With all of these obstacles in …

Ecological And Oceanographic Influences On Leatherback Turtle Behavior And Scyphozoan Jellyfish Distributions In The Gulf Of Mexico, Katrina Aleksa

Dissertations

Leatherback turtles (Dermochelys coriacea) are a wide-ranging, oceanic species that feed exclusively on gelatinous zooplankton. Leatherback have been spotted in the Gulf of Mexico (GoM) for several decades and consistently had a high level of interactions with longline fisheries. However, no quantitative studies have been performed to address the spatiotemporal distribution of these turtles in the GoM. This research determines 1) leatherback movements and high-use areas in the GoM, 2) their association with oceanographic features, 3) the distribution and density of two abundant medusae in the northern GoM and any association with biophysical parameters, and 4) the body …

Heat And Mass Transfer Effects Of Peristaltic Transport Of A Nano Fluid In Peripheral Layer, K. M. Prasad, N. Subadra, M, A. S. Srinivas

Applications and Applied Mathematics: An International Journal (AAM)

This paper deals with a theoretical investigation of heat and mass transfer effects of peristaltic transport of a nanofluid in peripheral layer. By using appropriate methods, the velocity in the core region as well as in the peripheral region, pressure drop, time averaged flux, frictional force, temperature profile, nanoparticle phenomenon, heat transfer coefficient and mass transfer coefficient of the fluid are investigated, using lubrication theory. Effects of different physical parameters like viscosity ratio, mean radius of the central layer, Brownian motion parameter, thermophoresis parameter, local temperature Grashof number as well as local nanoparticle Grashof number on pressure rise characteristics, frictional …

Phylogeography Of An Estuarian Calanoid Copepod; Acartia Tonsa In The Texas Gulf Of Mexico, Nicole J. Figueroa

Theses and Dissertations

The calanoid copepod, Acartia tonsa is one of the most abundant and well-studied estuarian species. However, the idea that this cosmopolitan species has unrestricted dispersal and high gene flow has been challenged. In this study, a more holistic picture of the phylogeography of A. tonsa was developed using the mitochondrial gene cytochrome oxidase one (mtCOI). Multiple new lineages were found in the Texas Gulf of Mexico that are basal to Northeastern Atlantic lineages. Connectivity was also observed between Brazil and the Texas Gulf of Mexico. The revised phylogeny shows a clear pattern of cryptic speciation as the species made a …

Stability Of Equilibria In Quantitative Genetic Models Based On Modified-Gradient Systems, Benjamin J. Ridenhour, Jerry R. Ridenhour

Mathematics and Statistics Faculty Publications

Motivated by questions in biology, we investigate the stability of equilibria of the dynamical system x′ = P(t)∇f(x) which arise as critical points of f, under the assumption that P(t) is positive semi-definite. It is shown that the condition ∫^∞λ₁(P(t)) dt = ∞, where λ₁(P(t)) is the smallest eigenvalue of P(t), plays a key role in guaranteeing uniform asymptotic stability and in providing information on the basis of attraction of those equilibria.

The Effects Of Tension, Curvature, And Lipid Diffusion On The Enrichment Of Ras Proteins In Model Membranes, Nina Daneshvar

Journal of the South Carolina Academy of Science

An intriguing aspect of the cell membrane that provokes study is lipid-anchor enrichment of lipidated proteins on the cell membrane. Specifically, recent in vitro studies involving the enrichment of Ras proteins were done to see how enrichment was affected by changes in membrane curvature. These studies demonstrated the Ras protein’s inclination to the expanded, or outer, leaflet of highly curved membranes. Other research done in vivo, however, provoked further inquiry into Ras protein behavior, since when highly curved protrusions were created in living cells, Ras proteins showed affinity for the inner leaflet. This inspired research to determine the exact mechanism …

Investigating The Toxicity And Accumulation Of 2,4-Dichlorophenoxyacetic Acid (2,4-D) And Glyphosate In Eisenia Fetida, Caitlin Lazurick, Nicole Lidzbarski, Rachel Owings, Jeff Brotherton, Edna Steele

Journal of the South Carolina Academy of Science

Glyphosate, the main ingredient in Roundup^®, is the most widely used herbicide in the world. It is also used in combination with another effective herbicide, 2,4-D, in the formulation called Enlist Duo^®. The EPA approved the use of Enlist Duo^® on certain crops including those genetically modified to be resistant to both herbicides. The predicted significant increase in the use of these herbicides raised concerns from the general public because both compounds have been classified as possibly or probably carcinogenic. Since herbicides are applied directly to vegetation, the safety of organisms that come in contact …

Reef Fish Biodiversity In The Florida Keys National Marine Sanctuary, Megan E. Hepner

USF Tampa Graduate Theses and Dissertations

The biological diversity of reef-fish in the Florida Keys National Marine Sanctuary (FKNMS) from 1999 – 2016 was evaluated in terms of abundance, biomass, species richness, evenness, Shannon diversity, Simpson diversity, and functional diversity, using observations collected by multiple agencies and institutions under the Reef Visual Census (RVC) program. To compare the different diversity indices species richness, Shannon diversity, Simpson diversity, and functional diversity were converted into effective number of species. I examined the seven indices by no-take marine zones, in seven benthic habitat strata, and across the three-distinct geographic subregions in the Florida Keys domain (Upper, Middle, and Lower …

Table Of Contents

Journal of the South Carolina Academy of Science

No abstract provided.

The Effects Of Sports Related Head Impact On Balance And Neurocognitive Functions, Shaquanda D. Ross-Simmons, Michelle L. Vieyra, Abhishek Jain, Keri Weed

Journal of the South Carolina Academy of Science

The goal of this study was to investigate the effects of sports-related head injury on balance, attention, and memory. Reliable differences have been found using measures that directly tap into brain functioning, such as the auditory oddball task combined with EEG recording. We hypothesized that athletes reporting a diagnosed concussion or participation in high-risk sports would have compromised balance and neurocognitive functioning compared to athletes in low risk sports. Forty-five undergraduate participants were identified as either concussed, non-concussed in high-risk sports, or non-concussed in low-risk sports using a survey of athletic history, head trauma and demographics. The Biopac MP36 system, …

Big Data: Computational Biology Opens A New Window On The World's Challenges For Colby Scientists, Kate Carlisle

Colby Magazine

"What makes us 'us' and not a plant? Not a bacteria, or a virus," asks Andrea Tilden, the J. Warren Merrill Associate Professor of Biology and a genomics expert. "Any one genome has six thousand novels worth of information. Computational biology is the tool we use to read them."

Analysis Of Complex Vertebrate Genomes: Computational Challenges And Solutions, Jeramiah J. Smith

Commonwealth Computational Summit

No abstract provided.

Discovery Of Sex-Specific Regions In A Salamander Genome, Nataliya Y. Timoshevskaya, Melissa C. Keinath, Jeramiah J. Smith

Commonwealth Computational Summit

Biological Aspects:

Salamander (Ambystoma mexicanum) has a gigantic genome: ~32,000,000,000 bases (10X of size of human genome)

Sex is determined by a pair of morphologically identical chromosomes:

• ZZ in male
• ZW in female

Object:

• Find (if there are any) genomic differences between chromosomes W and Z

Workflow:

1. Sequencing and de novo assembly of the reference salamander genome
2. Alignment of short sequences from male and female genomes to the reference
3. Coverage analysis

The Lamprey Genome: Illuminating Genomic Change Across Eons And Embryogenesis, Jeramiah J. Smith, Courtney K. M. Waterbury, Melissa C. Keinath, Cody B. Saraceno, Vladimir A. Timoshevskiy, Nataliya Y. Timoshevskaya

Commonwealth Computational Summit

The lamprey genome provides unique insights into both the deep evolutionary history of vertebrate genomes and the maintenance of genome structure/integrity over development. The lamprey lineage diverged from all other vertebrates approximately 500 million years ago. As such, comparisons between lamprey and other vertebrates permit reconstruction of ancient duplication and rearrangement events that defined the fundamental architecture and gene content of all extant vertebrate genomes. Lamprey also undergoes programmatic changes genome structure that result in the physical elimination of ~20% of its genomic DNA (~0.5Gb from a ~2 Gb genome) from all somatic cell lineages during early embryonic development. Here, …

Use Of Hpc To Analyze Changes In Gene Expression During Fruit Fly Spermiogenesis, Sepideh Dadkhah, Douglas A. Harrison, Jeramiah J. Smith

Commonwealth Computational Summit

In the fruit fly, Drosophila melanogaster, JAK/STAT signaling during spermiogenesis is known to play a crucial role in the maintenance of stem cells of the testis. Recent studies in our lab have shown that activation of the JAK/STAT pathway in somatic cyst cells is also required for the later stages of spermiogenesis like individualization.

The main goal of this project is to characterize the events downstream of JAK/STAT signaling in spermiogenesis and more specifically to determine the mechanism by which JAK/STAT activation regulates individualization, a later stage in spermiogenesis where 64 individual spermatids are formed from a 64-interconnected spermatid …

Yeast Cell Cycle And Metabolism Can Be Coupled In Nontrivial Ways., Todd Young

Annual Symposium on Biomathematics and Ecology Education and Research

No abstract provided.

The Behavior Response Of Antlion Larvae To Alternating Magnetic Fields, Lindsey Wagner, Caleb L. Adams

Annual Symposium on Biomathematics and Ecology Education and Research

No abstract provided.

One Tick, Two Tick, Two Pathogens, Oh No! Am I Sick?, Caleb L. Adams

Annual Symposium on Biomathematics and Ecology Education and Research

No abstract provided.

Cnemidophorus Sexlineatus And The Impacts The Environment Has On Its Population At The Braidwood Dunes, Jeremiah Soto

Annual Symposium on Biomathematics and Ecology Education and Research

No abstract provided.

Landscape Genetics Of The California Tiger Salamander: Inferences From Multiple Methods, Samantha Gabrielle Thomas

Masters Theses & Specialist Projects

Landscape genetics is a rapidly growing field of study that compares patterns of gene flow among populations with habitat heterogeneity across a landscape to infer the interaction between dispersal of individuals and their physical environment. Empirical data generated from a landscape genetics study can inform conservation and management strategies, making the field increasing popular. However, concerns have arisen in the literature that the field is expanding faster than the analytic framework that supports it. Multiple methods for generating estimates of the association among habitat types and dispersal (i.e., least-cost paths and resistance surfaces) have been proposed, and there is a …

Marine Reserves Promote Coral Reef Resilience By Mitigating Human Impacts Through The Restoration Of Parrotfish Populations, Increasing Their Reproductive Output And Seeding Neighboring Overfished Reefs, Brian L. Stockwell

Biological Sciences Theses & Dissertations

Coral reefs are some of the most productive ecosystems on the planet, providing fisheries resources for over a billion people with billions of dollars in revenue from tourism for developing nations. Coral reefs are under threat from overfishing and water pollution, resulting in less productive algae dominated reefs. Marine reserves are widely expected to promote the resilience of reefs by protecting and increasing the abundance of herbivorous fishes that can graze on algae, therefore directly or indirectly preventing coral to algal phase shifts. However, the ability of marine reserves to mitigate human impacts, restore herbivorous fish populations and seed nearby …

Life History And Management Methods For Blueline Tilefish (Caulolatilus Microps) From The United States Mid-Atlantic Region, Michael A. Schmidtke

OES Theses and Dissertations

Blueline tilefish (Caulolatilus microps) have recently undergone an increase in landings from waters off the US Mid-Atlantic region (Virginia-Massachusetts). Currently, life history characteristics of blueline tilefish in this area are undescribed. Additionally, appropriate indices of population abundance are not available for this region, necessitating the use of data-limited management methods to set restrictions for harvest of blueline tilefish in this area. This dissertation describes growth and reproductive characteristics of blueline tilefish caught off the coast of Virginia and explores improvements of data-limited management methods that have been applied to blueline tilefish in the US Mid-Atlantic. Blueline tilefish from …

Inventory Of Gulf Of Mexico Oceanic Fauna Data Including Species, Weight, And Measurements From R/V Point Sur (Cruises Dp03 And Dp04) May-August, 2016, April Cook, Tracey Sutton

DEEPEND Datasets

This data set includes the biological and environmental data for all of the species collected during the DP03 (May 2016) and DP04 cruises (August 2016). The main gear type used was a 10-m2 Multiple Opening Closing Net and Environmental Sensing System (MOCNESS). The MOCNESS was fitted with 6 nets which were opened according to the following depth scheme: net 0 from the surface to 1500m, net 1 from 1500-1200m, net 2 from 200-1000m, net 3 from 1000-600m, net 4 from 600-200m, and net 5 from 200m to the surface. Two trawls were conducted at each station sampled to capture diel …

Tropical Cyclones Disrupt The Relationship Between Tree Height And Species Diversity: Comment, Teng-Chiu Lin, Lixin Wang, Chengyang Zheng, Ryan W. Mcewan, Chung-Te Chang, Jyh-Min Chiang, Chung-Hao Chi

Biology Faculty Publications

In a recent report on the patterns of tree species richness in eastern and western North America, Marks et al. (2016) claimed to have identified an operational indicator of environmental harshness (maximum tree height) and concluded that environmental stressors that limit tree height also act as ecological filters on species richness. Marks et al. (2017) attributed the positive association between species richness and maximum tree height to both the direct effects of environmental harshness on species richness and the indirect effects of environmental harshness on species richness as mediated by maximum tree height.

This finding overlooked the fact that many …