Biology Commons^™

Mycodb, A Global Database Of Plant Response To Mycorrhizal Fungi, V. Bala Chaudhary, Megan A. Rúa, Anita Antoninka, James D. Bever, Jeffery Cannon, Ashley Craig, Jessica Duchicela, Alicia Frame, Catherine Gehring, Michelle Ha, Miranda Hart, Jacob Hopkins, Baoming Ji, Nancy C. Johnson, Wittaya Kaonongbua, Justine Karst, Roger T. Koide, Louis J. Lamit, James Meadow, Brook Milligan, John C. Moore, Thomas H. Pendergast Iv, Bridget J. Piculell, Blake Ramsby, Suzanne Simard, Shubha Shrestha, James Umbanhowar, Wolfgang Viechtbauer, Lawrence Walters, Gail W. T. Wilson, Peter C. Zee, Jason D. Hoeksema

Biological Sciences Faculty Publications

Plants form belowground associations with mycorrhizal fungi in one of the most common symbioses on Earth. However, few large-scale generalizations exist for the structure and function of mycorrhizal symbioses, as the nature of this relationship varies from mutualistic to parasitic and is largely context-dependent. We announce the public release of MycoDB, a database of 4,010 studies (from 438 unique publications) to aid in multi-factor meta-analyses elucidating the ecological and evolutionary context in which mycorrhizal fungi alter plant productivity. Over 10 years with nearly 80 collaborators, we compiled data on the response of plant biomass to mycorrhizal fungal inoculation, including meta-analysis …

Towards A Better Understanding Of Antiviral Rnai In Caenorhabditis Elegans: Function Characterization Of Loss Of Antiviral Rnai Alleles 1026a And 1026d, Drake Leonard

Honors Capstones

No abstract provided.

An Analysis Of Environmentally-Persistent Free Radical Formation On Surrogate Soil Systems Containing Iron(Iii) And Copper(Ii) And The Potential Remediation Effects Of Laccases, Andrew Paul Mullet

Honors Capstones

No abstract provided.

Linking Trophic Interactions In Above- And Below-Ground Systems, Savannah Bennett

Theses, Dissertations and Culminating Projects

This study explored trophic interactions among herbivores, plants, and soil communities. Two experiments were conducted such that the below-ground effects of an above-ground herbivore, as well as the above-ground impacts of soil biota could be examined. The first project investigated the effects of gypsy moth (Lymantria dispar L.) herbivory on soil communities associated with oak trees (Quercus rubra L.). The goal of this study was to compare soil biota from defoliated oak trees with soil communities from undefoliated trees. The abundances of bacteria, bactivorous nematodes, and herbivorous nematodes were compared between a defoliated sampling site and an undefoliated site in …

Characterization Of The Ubiquitination Of Icer, A Potential Anti-Cancer Protein, In Human Melanoma Cells, Joseph J. Bulatowicz Iii

Theses, Dissertations and Culminating Projects

Inducible cAMP Early Repressor (ICER) is a transcriptional repressor that regulates the expression of cAMP inducible genes. ICER has recently garnered attention because of cAMP’s implication in oncogenesis. ICER is shown to be downregulated in melanomas by the means of the ubiquitin-proteasome pathway. It is marked for degradation by ubiquitination on its lysine residues. By rescuing ICER levels in cancer cells, it is hypothesized that it may be possible to reverse the adverse progression of melanoma tumor growth. One possible way of rescuing ICER is by making it unavailable for ubiquitination by altering its ubiquitination sites. Special mutant ICERs that …

A Novel Solution To Targeting Prosthetic Joint Infection, Christopher Chen

Theses, Dissertations and Culminating Projects

Prosthetic arthroplasty may be a life changing event for better or worse. The integrity of bone cartilages such as the lateral and medial meniscus found between the femur and tibia may degrade over time due to natural causes which may eventually result in bone on bone exposure causing excruciating pain. Prosthetics are used to replace the cartilage and bone damage using femoral and tibial component and a plastic spacer. A small percentage of all orthopedic replacement surgeries may lead to infections. These infections are caused by biofilm forming bacteria which allows bacteria to attach to abiotic surfaces and mature as …

Warmer Temperatures On American Kestrel (Falco Sparverius) Breeding Grounds Associated With Earlier Laying And Successful Reproduction, Marisa Del Corso

Theses, Dissertations and Culminating Projects

The American Kestrel (Falco sparverius) recently has been discovered to be in decline and the reason is still unknown. Many studies have shown climate’s effect on migratory birds, but the relationship between climate and kestrel ecology has received little attention. This study sought to determine whether the climate in northwestern New Jersey and kestrel reproductive efforts have changed over the course of 20 years as well as determining whether these two factors are related. Monthly temperature, rainfall, and snowfall data were obtained from online databases. Breeding variables, including percentage of nest boxes used, clutch and brood size, percentage of successful …

Settling Patterns Of Chrysaora Quinquecirrha Polyps On Common Vinyl Construction Material : Potential Implications For Jellyfish Blooms And Coastal Development In Barnegat Bay New Jersey, Alexander Lawrence Soranno

Theses, Dissertations and Culminating Projects

Coastal development in estuaries is altering abiotic and biotic factors that encourage the propagation of populations of Chrysaora quinquecirrha. Extensive coastal development results in the proliferation of vinyl bulkheads and plastic floating docks in the Barnegat Bay estuary system. The purpose of this study was to determine if the increase in artificial vinyl substrate can affect density of C. quinquecirrha polyp recruitment. Oyster shell and vinyl settling plates were submerged at ten sites in Barnegat Bay for six, two-week periods during the summer of 2014. Polyps showed a greater affinity for settling on vinyl plates (0.337 polyps/cm2) than oyster shell …

Interaction Of Asic And Bk Channels In Human Glioma And Its Role In Cell Migration And Proliferation, Carola M. Springer

Theses, Dissertations and Culminating Projects

Acid sensing ion channels (ASICs) and large conductance calcium and voltage-activated potassium (BK) channels are expressed through out the nervous system. Studies have showed that ASICs can act as endogenous regulators of BK channels in a pH dependent manner. At physiological pH 7.4 ASIC blocks BK channels, when pH is reduced, ASIC channels are activated and the inhibition of BK is relieved (Petroff et ah, 2008). Our previous studies suggest that pH-dependent relieve of BK inhibition by ASICs increases cell proliferation in glial cells. Extracellular acidosis has been associated with cerebral trauma and brain cancer known as glioma (Andersen et …

A Study Of Small Mammal Populations In The Rockaway River Wildlife Management Area, Jefferson Township, Nj, Alexis Rose Levorse

Theses, Dissertations and Culminating Projects

Small mammal populations within the state of New Jersey have not been as thoroughly studied as avian, amphibian and reptile populations. The state list of species of special conservation concern includes very few mammals proportionally, and of those mammals that are listed only a handful are ground dwelling small mammals. This study sampled the small mammal population at the Rockaway River Wildlife Management Area in Jefferson Township, New Jersey and compared the sample to a similar study in Stokes State Forest. Pitfall traps were installed in four different kinds of habitats within the management area and the captures collected and …

Neuronal Glutamate Transporter Eaac1 Regulates Motor Activity And Anxiety In Mice, Kelsey Fleming

Biological Sciences

Obsessive Compulsive disorder (OCD) is a neuropsychiatric disorder characterized by the onset of recurrent thoughts, anxiety, and repetitive motor behaviors. The molecular basis of OCD remains elusive, but recent meta-analysis and genome-wide association studies (GWAS) suggest the existence of a genetic association between polymorphisms in the gene coding for excitatory amino acid carrier 1 (EAAC1) and OCD. It is also known that the Cortico-Striatal-Thalamo-Cortical (CSTC) pathway shows patterned hyperactivity in patients with OCD. EAAC1 is the primary neuronal glutamate transporter in the brain and is abundantly expressed in the cortex and the striatum, two regions that are part of the …

Depression In Thermal Performance Of Age-Structured Spirodela Polyrhiza Due To The Presence Of Rhopalosiphum Nymphaeae, Mitchell Matis, Chad Brassil, Colby J. Tanner

UCARE: Research Products

Thermal performance curves are keys components of population ecology. We performed this study to determine the effects of aphids on duckweed age-structured models across temperature. Results show a depression in birth rates and maturation of rates of duckweed in the presence of aphids. Regression analysis shows that this depression in maturation and birth is directly proportional to aphid growth rates across temperatures. This hints of the idea of modeling duckweed and aphid growth via nested thermal performance curves.

The Effect Of Interspecies Signaling On Stenotrophomonas Maltophilia Growth., Zachary Ethan Dickinson

College of Arts & Sciences Senior Theses

Cystic fibrosis (CF) is a genetic disorder that effects over 70,000 people worldwide, and is particularly prevalent in those of Caucasian descent. CF increases susceptibility to chronic infections of the lungs and GI tract, often leading to decreased quality of life and early death to afflicted individuals. No cure is available, and so treatment is limited to treating the frequent infections that afflict CF patients. Several species of bacteria are commonly implicated in these infections, including Stenotrophomonas maltophilia. Infections of this species is of particular interest as it has been shown to be highly antibiotic resistant. This is a concern …

Antibiotic Resistant Bacteria In Natural Environments Within Kentucky., Steve Tran

College of Arts & Sciences Senior Theses

Rates of antibiotic resistance in bacteria are rapidly rising; this is, in part, due to overuse of antibiotics resulting in a great burden on the U.S. healthcare system. With the rise of resistant bacteria, a large-scale outbreak of antibiotic resistant bacterial infections may also occur. Research on developing antibiotics has also decreased. Thus healthcare is at a great disadvantage in the arms race against bacteria. The environmental reservoirs of antibiotic resistance are currently being explored in Kentucky, in which bacteria have been collected from a broad spectrum of natural environments to analyze their antibiotic resistant capabilities and their interactions with …

Syndecan-1 Tagged Liposomes As A Theranostic Nanoparticle For Pancreatic Adenocarcinoma., Wenyuan Yin

College of Arts & Sciences Senior Theses

Theranostic nanoparticles are emerging as a novel mechanism for detecting and treating cancer. Due to the difficulties in detection and treatment of pancreatic cancer, these particles could serve within this unique niche. In this study, a Syndecan-1 ligand was utilized to increase tumor specificity of fluorescent dye encapsulated liposomes which were evaluated as a potential theranostic nanoparticle for pancreatic adenocarcinoma. Their diagnostic capabilities and specificity to pancreatic adenocarcinoma were determined in vitro using immunocytochemistry and in vivo using multi-spectral optoacoustic tomography (MSOT). Immunocytochemistry showed that liposomes preferentially bound and released their contents into cells expressing high levels of Insulin-Like Growth …

The Role Of Intermediate Filament Proteins In Retinal Degeneration And Regeneration, Alexandria Aruck

Renée Crown University Honors Thesis Projects - All

More than 30 million Americans are blind or visually impaired due to injury or disease. Retinitis pigmentosa is a genetic disease that initially causes death of rod photoreceptor cells and is followed by the progressive degeneration of the retina, the light sensing tissue of the eye, ultimately leading to blindness. Retinitis pigmentosa leads toretinal gliosis, a process in which a specialized neuroglial cell that is specific to the retina, known as Müller glia, undergoes hypertrophy and migration as a reaction to retinal stress or damage. I am investigating the mechanisms that are responsible for this type of degeneration in the …

Molecular Mechanisms Regulating Pathogen Defense: The Role Of Jmj3 In Arabidopsis Thaliana, Nelson Trysler

Renée Crown University Honors Thesis Projects - All

The Raina lab studies plant-pathogen interactions through genetics and molecular biology by using the model organism, Arabidopsis thaliana. A group of genes in A. thaliana, the Jumonji gene family, regulates gene expression by epigenetic mechanisms. Jumonji genes influence histone demethylation. Previous research in the Raina lab has shown that some Jumonji (JMJ) genes play a role in immune signaling in A. thaliana in response to pathogens. My project is to characterize JMJ3 gene, and see if there was any role that JMJ3 played in pathogen defense in A. thaliana.

The goal of my study was …

Understanding The Role Of Sog-4 And Sog-6 In The Glp-1/ Notch Signaling Pathway, Micheline Laing

Renée Crown University Honors Thesis Projects - All

Notch signaling is a highly conserved signaling mechanism that is important for many developmental processes in animals. In the roundworm, Caenorhabditis elegans (C. elegans), GLP-1 signaling, a form of Notch signaling, is necessary for mitotic proliferation of the germline. glp-1(ts) mutants display a sterile phenotype at 20 °C. Previously, 14 extragenic suppressors were found that rescued the embryonic and germline temperature sensitive defects caused by improper functioning of GLP in a glp-1(ts) mutant. These mutations were mapped to six genes. These genes are referred to as suppressors of glp-1 or sog mutants. The current study serves to determine the …

Improving The Nutrient Content Of Agriculture Crops Through Community Ecology, Margo Malone

Renée Crown University Honors Thesis Projects - All

Agriculturists continually look for ways to improve the nutrient content of crops without decreasing yield or economic benefits. Mutualistic relationships have the potential to enhance the nutrient content without sacrificing the production needs of the farmer. Mutualisms occur when two or more species interact and both members of the association benefit. An exceedingly important and often overlooked mutualism is the one formed between arbuscular mycorrhizal fungi (AMF) and plants. This interaction has been shown to be a critical component of most ecosystems, yet our understanding of these relationships is still limited. We know that in exchange for photosynthetically derived carbon, …

Estrogens Regulate Metabolic Substrate Concentrations In Brains Of Young Adult Female Rats: A Multiple Memory Systems Approach, Ella D'Amico

Renée Crown University Honors Thesis Projects - All

As the most potent circulating form of estrogen in most young adult female mammals, estradiol has extensive effects on physiological functioning. Estradiol effects are especially notable with the drop in the hormone observed when a woman transitions into menopause, with accompanying changes not only in overall physiology but also in brain functions. Recent research reveals the complex effects estradiol has on regulating learning and memory that vary by type of cognitive task among other variables. In particular, increased estradiol levels improve performance on hippocampus-dependent tasks, but impair performance on striatum-dependent tasks through direct actions on these different memory systems. Estradiol’s …

The Effects Of Large Herbivores On Soil Organic Matter Quality In Terrestrial Ecosystems, Adrian Alvarez

Renée Crown University Honors Thesis Projects - All

Understanding the factors that control the natural fluxes of carbon into and out of terrestrial ecosystems is of paramount importance to forecast and adapt to climate change. Soil respiration – the release of carbon dioxide from roots and soil micro-organisms– is considered to be the largest terrestrial source of carbon dioxide. Microbial respiration, the least understood component of soil respiration, is to a great extent determined by soil organic matter quality, reflecting the relative fractions of labile and recalcitrant soil carbon. The goal of this research was to examine how herbivory affects soil organic matter quality across a wide range …

Structure-Guided Site-Directed Mutagenesis Of The Bacterial Atp Synthase’S Epsilon Subunit, Mariam Bhatti

Renée Crown University Honors Thesis Projects - All

Adenosine triphosphate (ATP) contains energy-rich phosphoanhydride bonds that provide the energy needed for many cellular processes. F-type ATP synthase is found in bacteria, chloroplasts, and mitochondria, having a conserved function to catalyze the synthesis and hydrolysis of ATP. ATP synthase is a membrane bound rotary motor enzyme, with coupled rotation between it’s two distinct complexes F_o and F₁. In bacteria and chloroplasts, the ε-subunit’s C-terminal Domain (εCTD) has a distinct regulatory function that is absent in mitochondria. Determining the inhibitory interactions of ε is important in understanding it’s physiological functions and for potential targeting of ε’s bacteria-specific …

Lactate As A Memory-Enhancing Metabolite Across The Lifespan In Male Fischer 344 Rats, Brooke Hamling

Renée Crown University Honors Thesis Projects - All

Aging is often associated with cognitive decline, including problems with working memory and difficulties forming new memories. These deficits can be directly linked to the hippocampus, an area of the temporal lobe of the brain that is engaged during spatial working memory. Age-related declines may be influenced by changes in important modulatory pathways that impact hippocampal function, including regulation of the metabolite lactate. When astrocytic stores of glycogen are hydrolyzed, lactate is released into the extracellular space where it can be taken up by neurons and used as fuel during moments of activation. We previously found that the extracellular concentration …

Estrogen's Effects On Oxidative Stress Levels In Glial Cells, Jacob J. Dirkman

Theses and Dissertations

A decrease in astrocyte function and viability has been linked to many neurodegenerative diseases, including schizophrenia, major depressive disorders, Alzheimer’s disease, and Amyotrophic Lateral Sclerosis (ALS). Previous research indicates that some estrogens may have a positive effect on neuron and astrocyte viability. Estrogens’ effects on the brain are of interest as estrogens are commonly prescribed as hormone replacement therapy to reduce the symptoms of menopause in women. Unfortunately, these effects on are not completely understood. The goal of the project was to discover if estrogen has any protective effect on astrocytes exposed to oxidative stress. We measured the oxidative stress …

An Investigation Into The Adiponectin Receptor Levels In Cardiac, Liver And Skeletal Muscle Of Mature Rats., Jacqueline Sippel

College of Arts & Sciences Senior Theses

Both obesity and diabetes are domestic and international health problems. Adiponectin is a protein secreted from adipocytes and other tissues such as muscle which influences carbohydrate and lipid metabolism. For this reason, Adiponectin is a primary target for therapeutic treatment of metabolic diseases. Adiponectin interacts with receptors termed AdipoR1 and AdipoR2, which are structurally similar to G protein-coupled receptors except with a reverse membrane topology. The aim of this study is to determine the levels of AdipoR1 and AdipoR2 within cardiac, skeletal, and liver tissue samples of mature non-obese rats. The objective of determining potential differences in the tissue levels …

Habitat Effects On Blood Adiponectin Isoforms In Black Bears., James-Dean Wood

College of Arts & Sciences Senior Theses

No abstract provided.

Movement Patterns Of The Cave Salamander (Eurycea Lucifuga) In Sauerkraut Cave, Kentucky., Paige N. Wilson

College of Arts & Sciences Senior Theses

The Cave Salamander, Eurycea lucifuga, is a common but poorly understood species of salamander that inhabits limestone features and karst systems across the eastern and midwest United States. As a species that can bridge the gap between subterranean and epigean environments, E. lucifuga may behave as a top predator and act as a significant facilitator in the flow of energy from the outside environment into the dark zone. The goal of this study was to document the seasonal movements of a local population of cave salamanders in Louisville, Kentucky, and the relationship between those movements and abiotic factors. Secondarily, …

Selection Of Food Patches By Sympatric Herbivores In Response To Concealment And Distance From A Refuge, Miranda M. Crowell, Lisa A. Shipley, Meghan J. Camp, Janet L. Rachlow, Jennifer S. Forbey, Timothy R. Johnson

Biology Faculty Publications and Presentations

Small herbivores face risks of predation while foraging and are often forced to trade off food quality for safety. Life history, behaviour, and habitat of predator and prey can influence these trade-offs. We compared how two sympatric rabbits (pygmy rabbit, Brachylagus idahoensis; mountain cottontail, Sylvilagus nuttallii) that differ in size, use of burrows, and habitat specialization in the sagebrush-steppe of western North America respond to amount and orientation of concealment cover and proximity to burrow refuges when selecting food patches. We predicted that both rabbit species would prefer food patches that offered greater concealment and food patches that …

Using Rad‐Seq To Recognize Sex‐Specific Markers And Sex Chromosome Systems, Tony Gamble

Biological Sciences Faculty Research and Publications

Next‐generation sequencing methods have initiated a revolution in molecular ecology and evolution (Tautz et al. 2010). Among the most impressive of these sequencing innovations is restriction site‐associated DNA sequencing or RAD‐seq (Baird et al. 2008; Andrews et al. 2016). RAD‐seq uses the Illumina sequencing platform to sequence fragments of DNA cut by a specific restriction enzyme and can generate tens of thousands of molecular genetic markers for analysis. One of the many uses of RAD‐seq data has been to identify sex‐specific genetic markers, markers found in one sex but not the other (Baxter et …

Spa47 Is An Oligomerization-Activated Type Three Secretion System (T3ss) Atpase From Shigella Flexneri, Jamie L. Burgess, Heather B. Jones, Prashant Kumar, Ronald T. Toth Iv, C. Russell Middaugh, Edwin Antony, Nicholas E. Dickenson

Biological Sciences Faculty Research and Publications

Gram-negative pathogens often use conserved type three secretion systems (T3SS) for virulence. The Shigella type three secretion apparatus (T3SA) penetrates the host cell membrane and provides a unidirectional conduit for injection of effectors into host cells. The protein Spa47 localizes to the base of the apparatus and is speculated to be an ATPase that provides the energy for T3SA formation and secretion. Here, we developed an expression and purification protocol, producing active Spa47 and providing the first direct evidence that Spa47 is a bona fide ATPase. Additionally, size exclusion chromatography and analytical ultracentrifugation identified multiple oligomeric species of Spa47 with …