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Effects Of Uv Light On Local Stream Frog Behavior, John Buie, Eiichiro Uemura, Candy Hwang, D. Lee, Craig Sutter, Evan Mattiasen, Thomas Vandergon, Rodney Honeycutt, Lee Kats

Featured Research

Amphibian declines have been well documented throughout the world. Several studies have examined whether UV radiation from the sun is a possible contributing cause to declining populations. In Southern California, two closely related species of treefrogs, Pseudacris hypochondriaca and Pseudacris cadaverina, coexist in many perennial streams. P. hypochondriaca is primarily nocturnal while P. cadaverina is known to bask in direct sunlight. The purpose of the study is to determine how the two different species of frogs will react under different types of light emitted by a portable flashlight. The light was emitting either UV radiation or visible light, or …

Assessing Effects Of Symmetry On Motif Finding, Lala Motlhabi

All Theses and Dissertations (ETDs)

Identifying protein DNA binding sites like transcription factor binding sites is a key component of gene regulatory networks. The challenging task of predicting and identifying DNA binding sites both experimentally, and computationally suffers from high false positive due to various contributing factors, including misinterpretation of DNA binding site sequence symmetry. Our study seeks to model and compare the ability of three methods of a motif-finding program, consensus, taking into account orientation to accurately predict variable symmetric/asymmetric true binding site models. The three consensus methods included the c0 method which ignores the complement of a sequence. In this particular experiment it …

Mechanisms Of Copper-Dependent Notochord Formation In Zebrafish, John Gansner

All Theses and Dissertations (ETDs)

The interplay of genes and nutrition during early development profoundly impacts fetal outcome. Copper is an essential nutrient required for the redox activity of many enzymes, and recent work in our laboratory has elucidated the phenotype of copper deficiency in zebrafish, which includes a strikingly distorted notochord. The studies described here establish the specific genetic etiology of this distortion and reveal a number of gene-gene and gene-nutrient interactions critical to notochord morphogenesis. We first demonstrate that the notochord distortion observed in copper-deficient zebrafish results from lysyl oxidase cuproenzyme inhibition. Four lysyl oxidase family members are expressed throughout the developing zebrafish …

Inbreeding Depression And Competition In The Square-Stemmed Monkey-Flower (Mimulus Ringens), Nicholas Griffin

All Theses and Dissertations (ETDs)

Matings between biologically related individuals often produce offspring with reduced fitness, a phenomenon known as inbreeding depression. The magnitude of inbreeding depression can play an important role in determining the overall fitness, and persistence, of populations, and is often considered one of the key factors driving the evolution of mating systems and their associated traits. Recent research has shown that the strength of inbreeding depression is often highly sensitive to environmental conditions, such as the availability of abiotic resources or variation in the strengths of ecological interactions between organisms. In plant populations, drought, plant density, herbivory, and infection by pathogens, …

Analysis Of Dna-Binding Proteins In Yeast Saccharomyces Cerevisiae, Su-Wen Ho

All Theses and Dissertations (ETDs)

Gene expression is an elaborate and finely tuned process involving the regulated interactions of multiple proteins with promoter and enhancer elements. A variety of approaches are currently used to study these interactions in vivo, in vitro as well as in silico. With the genome sequences of many organisms now readily available, a plethora of DNA functional elements have been predicted, but the process of identifying the proteins that bind to them in vivo remains a bottleneck. I developed two high-throughput assays to address this issue. The first is a modification of the yeast "one-hybrid" assay. The second is probing protein …

Novel Algorithms For Structural Alignment Of Non-Coding Rnas, Diana Kolbe

All Theses and Dissertations (ETDs)

Non-coding RNAs are biologically important molecules, with a variety of catalytic and regulatory activities mediated by their secondary and tertiary structures. Base-pairing interactions, particularly at the secondary structure level, are an important tool for identifying and studying these structural RNAs, but also present some unique challenges for sequence analysis. Probabilistic covariance models are effective representations of structural RNAs, with generally high sensitivity and specificity but slow computational speed. New algorithms for dealing with structural RNAs are developed to address some of the practical deficiencies of covariance models. A new model of local alignment improves accuracy for fragmentary data, such as …

The Impact Of Interferon Regulatory Factor 3 On The Immune Response To Herpes Simplex Virus Type I Infection, Vineet Menachery

All Theses and Dissertations (ETDs)

The type I interferon: IFN) cascade is critical in control of herpes simplex virus type I: HSV-1) infection and relies on specific recognition molecules to rapidly signal viral infection via interferon regulatory factor-3: IRF-3) -dependent pathways. The absence of these recognition molecules or the loss of IRF-3 would be predicted to render early recognition pathways inoperative and thus impact viral infection. However, previous results had produced contradictory results in terms of the role of IRF-3 during HSV-1 infection. In this study, infected IRF-3-/- immune cells were found to support increased HSV-1 replication compared to control cells. In addition, IRF-3 deficient …

The Function And Regulation Of Senescent Stromal-Derived Osteopontin, Ermira Pazolli

All Theses and Dissertations (ETDs)

Our understanding of tumors as complex organs has increased our appreciation for each component of the tumor microenvironment and its respective contribution to tumorigenesis. Fibroblasts found within a tumor actively participate in the growth, progression and metastasis of cancer cells. Senescent fibroblasts, which are permanently arrested yet metabolically active, accumulate in tissue over time where they may promote the proliferation and malignant conversion of preneoplastic cells in older individuals. I have examined the relationship between senescent fibroblasts and preneoplastic keratinocytes and identified the secreted multifunctional protein osteopontin: OPN) as a critical stromal mediating factor. RNAi-directed reduction of stromal OPN leads …

Genetic Influences On Preterm Birth, Jevon Plunkett

All Theses and Dissertations (ETDs)

Preterm birth: PTB) is a leading cause of mortality and disease burden globally; however, determinants of human parturition remain largely uncharacterized, making prediction and prevention of difficult. Genetic studies are one way in which we can attempt to better understand this disorder. We first sought to develop a model for the genetic influences on PTB to facilitate gene discovery. Study of standard measures of familial aggregation, the sibling risk ratio and the sibling-sibling odds ratio, and segregation analyses of gestational age, a quantitative proxy for preterm birth, lend support to a genetic component contributing to birth timing, since preterm deliveries …

Characterization Of The Role For Nmnat, Kinase Cascades, And Purines In Axonal Degeneration, Craig Press

All Theses and Dissertations (ETDs)

Axonal degeneration is a prominent feature of many neurological disorders including Parkinson's disease: PD), motor neuron disease, inherited, diabetic, and drug-induced peripheral neuropathies. It is now thought that axonal degeneration is an active process, due in large part to studies of the Wlds mutant mouse, which undergoes delayed Wallerian degeneration in response to axonal injury. Wlds mice have slower disease progression in numerous models of neurodegenerative diseases. The Wlds mutation results in the production of a chimeric protein that containing nicotinamide mononucleotide adenylyltransferase 1: Nmnat1). Increased expression of Nmnat isoforms are sufficient for axonal protection in vitro and in vivo. …

Phylogenetics And Phylogeography Of Moray Eels (Muraenidae), Joshua Reece

All Theses and Dissertations (ETDs)

This dissertation describes the evolutionary history of Moray eels: Muraenidae). Moray eels are apex predators on coral reefs around the world, but they are not well studied because of their cryptic habitats and occasionally aggressive behaviors. I provide the first molecular phylogeny of moray eels with widespread taxonomic and geographic coverage, including 44 species representing two subfamilies, eight genera, and all tropical ocean basins. Phylogenetic relationships among these taxa are estimated from portions of mitochondrial loci cytochrome b and cytochrome oxidase subunit 1, and portions of the nuclear loci RAG-1 and RAG-2. I test four sets of contrasting phylogenetic hypotheses …

The Role Of The Clock Gene Bmal1 In Female Fertility And Parturition, Christine Ratajczak

All Theses and Dissertations (ETDs)

Successful reproduction is essential for survival of species. For humans, reproductive problems can cause large emotional and medical burdens. Evidence in both humans and rodents indicates that circadian rhythmicity is important for supporting reproductive function. A molecular clock orchestrates circadian rhythmicity. Impairment in fertility and parturition are observed in female mice expressing a mutant form of Clock, suggesting critical roles for clock genes in reproduction. Since the clock gene Bmal1, but not Clock, is necessary for the generation of circadian rhythmicity, exploring the role of Bmal1 in reproduction may yield a better understanding of the importance of the molecular clock …

Conservation Of The Intracellular Bacterial Community Pathogenic Pathway In Urinary Tract Infection, David Rosen

All Theses and Dissertations (ETDs)

Urinary tract infections: UTIs) affect 13 million women annually in the United States. Uropathogenic Escherichia coli: UPEC) is the predominant etiologic agent of UTI; however, several other uropathogens, including Klebsiella pneumoniae, are also significant causative agents. In a murine cystitis model, UPEC utilize a multistep pathogenic pathway in which they invade and form intracellular bacterial communities: IBCs) within bladder facet cells. Type 1 pili, adhesive fimbriae, are necessary for UPEC binding and invasion of urothelial cells and formation of IBCs. UPEC ultimately disperse from the IBC, many with filamentous morphology, and proceed to infect other host urothelial cells. This work …

The Mechanisms And Roles Of Neural Feedback Loops For Visual Processing, Debajit Saha

All Theses and Dissertations (ETDs)

Feedback pathways are widely present in various sensory systems transmitting time-delayed and partly-processed information from higher to lower visual centers. Although feedback loops are abundant in visual systems, investigations focusing on the mechanisms and roles of feedback in terms of micro-circuitry and system dynamics have been largely ignored. Here, we investigate the cellular, synaptic and circuit level properties of a cholinergic isthmic neuron: Ipc) to understand the role of isthmotectal feedback loop in visual processing of red-ear turtles, Trachemys scripta elegans. Turtle isthmotectal complex contains two distinct nuclei, Ipc and Imc, which interact exclusively with the optic tectum, but are …

Examination Of Molecular Recognition In Protein-Ligand Interactions, Yat Tang

All Theses and Dissertations (ETDs)

This dissertation is a compilation of two main projects that were investigated during my thesis research. The first project was a prospective study which identified and characterized drug-like inhibitors of a prototype of bacterial two-component signal transduction response regulator using computational and experimental methods. The second project was the development and validation of a scoring function, PHOENIX, derived using high-resolution structures and calorimetry measurements to predict binding affinities of protein-ligand interactions. Collectively, my thesis research aimed to better understand the underlying driving forces and principles which govern molecular recognition and molecular design. A prospective study coupled computational predictions with experimental …

Transient-State Kinetic Studies Of The Mechanisms Of Dna Unwinding And Translocation Of The E. Coli Recbc And Recbcd Helicases, Colin Wu

All Theses and Dissertations (ETDs)

This thesis presents mechanistic studies of the E. coli RecBC and RecBCD helicases using transient-state kinetic approaches to understand the relationship between DNA unwinding and ssDNA translocation. RecBC initiates unwinding from duplex DNA ends with pre-existing 5'-(dT)6 and 3'-(dT)6 ssDNA tails using a series of repeated rate-limiting steps with a rate of 345 ┬▒ 8 bp/sec and an average kinetic step-size of ~4 bp: 20 mM Mops-KOH, pH 7.0 at 25°C, 30 mM NaCl, 10 mM MgCl2, 5% glycerol, 1 mM 2-mercaptoethanol) while RecBCD unwinds these same DNA substrates with a rate of 745 ┬▒ 18 bp/sec using a more …

Design, Synthesis And Characterization Of Synthetic Ion Receptors As Biologically Functional Ion Carriers And Channels, Carl Yamnitz

All Theses and Dissertations (ETDs)

The study of proteins and natural molecules that transport cations and anions across biological membranes has been a major focus of biochemistry and cellular biology for more than a century. The function of ion transporters is vital for all known forms of life. Natural and synthetic transporters can have applications as antimicrobial agents, in nerve impulse transduction and cell signaling. The current work was performed to further the understanding of a diverse array of novel and previously-studied synthetic molecules as membrane-active ion transporters. In the process, important facets such as ion binding capacity, aggregation behavior, ion transport functionality, and antimicrobial …

Fcs Analysis Of Pore Formation By The Human Protein Bax In Lipid Membranes, Olena Ivashyna

All Theses and Dissertations (ETDs)

Bax is a pro-apoptotic member of the BCL-2 protein family and its paramount function during apoptosis is to form pores in the mitochondrial outer membrane: MOM). In a simplified apoptosis model, upon apoptotic stimulation, Bax is activated via an unresolved mechanism, translocates to the MOM, where it changes conformation, inserts into the membrane as a monomer, and finally undergoes in-membrane oligomerization to form a pore. Once the Bax pore is formed, cytochrome c and other mitochondria-resident proteins escape into the cytoplasm where they activate the cascade of caspases, which dismantle the cell. To date, the structure of the inactive cytoplasmic …

The Role Of Aerobic Glycolysis In The Resting Human Brain, Sanjeev Vaishnavi

All Theses and Dissertations (ETDs)

The human brain accounts for 2% of total body weight, though it consumes 20% of the body's energy supply. Most of this energy is provided by the complete oxidation of glucose to carbon dioxide and water, though some fraction of glucose undergoes aerobic glycolysis without concomitant oxidative phosphorylation. Elevation in neuronal activity increases aerobic glycolysis due to the disproportionate increase in blood flow and glucose utilization greater than oxygen consumption. Since aerobic glycolysis produces significantly less energy than complete oxidation of glucose, its role in cellular activities has been overlooked, though its presence in the resting brain has been known …

Impact Of Second Messenger Modulation On Activity-Dependent And Basal Properties Of Excitatory Synapses, Chun Yun Chang

All Theses and Dissertations (ETDs)

Cognitive processing in the central nervous system relies on accurate information propagation; neurotransmission is the fundamental mechanism underlying network information flow. Because network information is coded by the timing and the strength of neuronal activity, synaptic properties that translate neuronal activity into synaptic output profoundly determine the precision of information transfer. Synaptic properties are in turn shaped by changes in network activity to ensure appropriate synaptic output. Activity-dependent adjustment of synaptic properties is often initiated by second messenger signals. Understanding how second messengers sculpt synaptic properties and produce changes in synaptic output is key for elucidating the interplay between network …

Regulation Of Human T-Cell Leukemia Virus Type 1 Infection And Replication, Gunjan Choudhary

All Theses and Dissertations (ETDs)

Retroviruses have evolved complex mechanisms to regulate their cellular tropism and gene expression. It is generally accepted that productive infections proceed via interactions between viral envelope molecules and specific receptors on the host cell surface. Currently, there is no known receptor for HTLV-1, though a number of factors that enhance entry have been identified. In an effort to identify a cellular receptor or attachment factor for HTLV-1, we carried out a retroviral cDNA library screen, in which cDNA from permissive HeLa S3 cells was introduced into poorly susceptible NIH 3T3 cells. These cells were selected after infection with HTLV-1 envelope …

The Hematopoietic Compartment Regulates Osteoblast Differentiation And Apoptosis During Cytokine Treatment, Matthew Christopher

All Theses and Dissertations (ETDs)

Adult hematopoiesis normally occurs in bone marrow, where hematopoietic stem cells: HSC) reside within a specialized microenvironment. At steady state, hematopoiesis state is regulated such that immature hematopoietic stem and progenitor cells: HSPC) are restricted to the bone marrow and are rarely observed in peripheral blood. Under certain circumstances, however, this regulation is loosened and significant numbers of HSPC are released to the circulation, a process termed "mobilization." Mobilization can be induced pharmacologically by a wide range of agents. Of these, the best characterized and most widely used mobilizing agent is Granulocyte-colony stimulating factor: G-CSF). G-CSF is widely used clinically …

P38 Phoshporylates Rb On Ser567 By A Novel, Cell Cycle-Independent Mechanism That Triggers Rb-Hdm2 Interaction And Apoptosis, Rachel Delston

All Theses and Dissertations (ETDs)

The retinoblastoma protein: Rb) inhibits both cell division and apoptosis, but the mechanism by which Rb alternatively regulates these divergent outcomes remains poorly understood. Cyclin dependent kinases: Cdks) promote cell division by phosphorylating and reversibly inactivating Rb by a hierarchical series of phosphorylation events and sequential conformational changes. The stress-regulated mitogen activated protein kinase: MAPK) p38 also phosphorylates Rb, but it does so in a cell cycle-independent manner that is associated with apoptosis rather than with cell division. Here, we show that p38 phosphorylates Rb by a novel mechanism that is distinct from that of Cdks. p38 bypasses the cell …

Brain Insulin Action Regulates Hypothalamic Glucose Sensing And The Counterregulatory Response To Hypoglycemia, Kelly Diggs-Andrews

All Theses and Dissertations (ETDs)

The brain is the primary organ that senses blood glucose levels and initiates a stress response when blood glucose levels are too low: hypoglycemia). Insulin-dependent people with Type 1 diabetes: T1DM) have an impaired ability to sense hypoglycemia and an impaired ability to activate this counterregulatory response: CRR) to hypoglycemia. As a result, T1DM are at a greater risk of experiencing insulin induced severe hypoglycemic episodes, which can result in seizures, brain damage, or even death. Since hypoglycemia is a major barrier that limits intensive blood glucose control, important research initiatives are needed to prevent or reduce the burden of …

Use-Dependent Plasticity Regulates Sleep Need In Drosophila Melanogaster, Jeffrey Donlea

All Theses and Dissertations (ETDs)

Although the necessary functions of sleep have not been identified, sleep has been shown to play an important role in the consolidation of memories. Recent studies have shown that, in addition to playing a strong role in sleep regulation, the circadian clock also influences processes associated with learning and memory. Thus, the neural circuits that control circadian rhythms are uniquely positioned to play an important role in coordinating interactions between sleep and memory. Drosophila melanogaster exhibit increased sleep following several days of social experience and require sleep to consolidate long-term memories: LTM) after Courtship Conditioning, an associative memory assay. We …

Local And Systemic Consequences Of Reducing Notch Signaling In Skin Keratinocytes, Shadmehr Demehri

All Theses and Dissertations (ETDs)

Notch is a transmembrane receptor that mediates short-range signaling between neighboring cells. Notch signaling has been implicated in various cellular and developmental processes essential in the life of metazoans. Specifically, Notch signaling plays a critical role in mammalian skin. Removal of Notch alleles in skin keratinocytes has been associated with an array of phenotypes with varying severity based on the identity and number of remaining Notch receptors. Phenotypes include carcinogenesis: in the case of Notch1 loss), transformation of hair follicles to epidermal cysts and neonatal lethality, the latter seen in the absence of all Notch signaling. Although these phenotypes were …

Experimental Evolution Of Burkholderia Cenocepacia Biofilm Populations, Steffen R. Poltak

Doctoral Dissertations

Many biofilm populations are known for their exceptional biodiversity but the relative contributions of the forces that could promote this diversity are poorly understood. This uncertainty pervades in the well-established communities found on many natural surfaces and in long-term, chronic infections. Here we describe the parallel evolution of cooperative communities derived from a clone of Burkholderia cenocepacia during approximately 1500 generations of biofilm selection. This long-term evolution was enabled by a new experimental method that selects for daily cycles of colonization, biofilm assembly, and dispersal. Each of six replicate biofilm populations underwent a common pattern of adaptive morphological diversification, in …

Effects Of Physical And Chemical Disturbance On Stream Ecosystem Structure And Function, Elena M. Traister

Doctoral Dissertations

A variety of natural and anthropogenic disturbances influence the structure and function of stream ecosystems. While past investigations have focused on the response of community indicators to stream disturbances, functional indicators may also be helpful for assessing stream ecosystem health. To date, few studies have compared the response of structural and functional indicators to ecosystem-level disturbances. I separately measured the effects of long-term acidification, a large-scale avulsion, and the individual and combined effects of physical streambed disturbance and altered refugia availability on stream structural and functional metrics.

I found that acidification was associated with changes in macroinvertebrate communities including reduced …

Updated Life History And Population Structure Assessment Of Spiny Dogfish, Squalus Acanthias, In The Gulf Of Maine, Walter Bubley

Doctoral Dissertations

Spiny dogfish (Squalus acanthias) are considered to be the most abundant shark species in the Western North Atlantic, but recently there was a decline in biomass estimates following a nearly ten-fold increase in fishery landings. Because fishing pressure has been shown to affect population dynamics in targeted species, an update of previous life history parameters is warranted to effectively manage the population. Although updated and accurate life history parameters are important, it is crucial that these parameters are applied to the correct populations, especially when there is evidence of population structuring in the Western Atlantic. This comprehensive study addressed the …

Conjecturing In Dynamic Geometry: A Model For Conjecture-Generation Through Maintaining Dragging, Anna Baccaglini-Frank

Doctoral Dissertations

The purpose of this research is to study aspects of the impact of Dynamic Geometry Systems (DGS) in the process of producing conjectures in Euclidean geometry. Previous research has identified and classified a set of dragging schemes spontaneously used by students. Building on these findings, the study focuses on cognitive processes that arise in correspondence to particular dragging modalities in Cabri. Specifically, we have conceived a model describing what seems to occur during a process of conjecture-generation that involves the use of a particular dragging modality, described in the literature as dummy locus dragging. In order to accomplish this goal, …