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Limnological Analyses Of Cutler Reservoir And Dingle Marsh With Respect To Eutrophication, J. D. Abbott, Deb Collins, Colin Cook, Dan Lamarra, Ryan Leonard, Ben Marret, Justin Stout, Gilbert Rowley, Jeremy Rowley, Wayne A. Wurtsbaugh

Watershed Sciences Faculty Publications

Cutler Reservoir is located in Cache county, Utah and was created for the purposes of irrigation, water storage and flood control. High nutrient loading to Cutler has raised concerns about the health of this system and has resulted in it being listed on the state's 303(d) list of impaired waters. The TMDL plan being drafted for Cutler lists dissolved oxygen and phosphorous as the key issues of concern. The underlying problem created by nutrient loading is eutrophication. If Cutler is to remain as a valuable source of recreation, wildlife habitat, and water for the Cache Valley we must understand the …

Thin Wire Nucleate Boiling Of Water In Sustained Microgravity, Justin P. Koeln, Heng Ban, John R. Dennison

All Physics Faculty Publications

The advancement of small satellite technology relies on the development of effective thermal management systems that can be made smaller, safer, and more robust. This paper presents the results and analysis of a nucleate boiling experiment in sustained microgravity aboard the Space Shuttle Endeavor (STS-108). Bubble growth and departure were observed from a single and a braid of three 0.16 mm diameter and 80 mm long nickel-chromium resistive wires. Analysis showed that the braided wire provides a unique surface configuration to enhance the onset of boiling. The braid of wires was also observed to produce several bubble explosions; this is …

Advances In Nuclear Magnetic Resonance For Drug Discovery, Robert Powers

Robert Powers Publications

Background—Drug discovery is a complex and unpredictable endeavor with a high failure rate. Current trends in the pharmaceutical industry have exasperated these challenges and are contributing to the dramatic decline in productivity observed over the last decade. The industrialization of science by forcing the drug discovery process to adhere to assembly-line protocols is imposing unnecessary restrictions, such as short project time-lines. Recent advances in nuclear magnetic resonance are responding to these self-imposed limitations and are providing opportunities to increase the success rate of drug discovery.

Objective/Method—A review of recent advancements in NMR technology that have the potential of …

Effects Of Feeding Wet Distillers Grains Plus Solubles On Feedlot Manure Value, Virgil R. Bremer, Terry J. Klopfenstein, Galen E. Erickson, Richard K. Koelsch, Raymond E. Massey, Judson Vasconcelos

Nebraska Beef Cattle Reports

Feeding wet distillers grains plus solubles (WDGS) improves the fertilizer value and net value of feedlot manure for all feedlot sizes. The net fertilizer value of feedlot manure increased 375% to 550% since 2006. Valuing manure at 2008 fertilizer nutrient prices and feeding 20% or 40% WDGS instead of feeding a corn-based diet improved profitability by $7 to $17 per steer finished ($4 to $11 per ton of manure).

Characterization Of A Novel 53bp1-Dependent Mechanism That Promotes Non-Homologous End Joining Of Deprotected Telomeres By Increasing Chromatin Mobility, Nadya Dimitrova

Student Theses and Dissertations

When a double-stranded break (DSB) occurs in mammalian genomes, the local chromatin is altered through the modification of histones (notably the phosphorylation of H2AX) and the binding of DNA damage response factors (e.g. MDC1, 53BP1). Although several lines of evidence have pointed to a role for some of these factors in DSB repair through non-homologous end-joining (NHEJ), the mechanism of their contribution has not been established. To study the regulation of NHEJ, we have used as a model system dysfunctional telomeres, which are uncapped by the removal of the shelterin component, TRF2. As a consequence of TRF2 loss, deprotected chromosome …

Biophysical Characterization Of Structure And Dynamics Of Nuclear Pore Complex Components, Martin Kampmann

Student Theses and Dissertations

The Nuclear Pore Complex (NPC) mediates nucleo-cytoplasmic transport in all eukaryotes and is among the largest cellular assemblies of proteins, called nucleoporins (nups). The details of NPC architecture, dynamics, and mechanism are still unknown. NPCs can be dissected biochemically into distinct subcomplexes. One of the best-characterized subcomplexes, the Nup84 complex, consists of seven nups and was proposed to form a membrane-coating module of the NPC. I optimized the isolation of the heptameric complex from budding yeast and analyzed its structure by negative-stain electron microscopy (EM). My data confirm the previously reported flexible Y-shape. I solved the three-dimensional structures of two …

Architecture Of A Coat For The Nuclear Pore Membrane, Kuo-Chiang Hsia

Student Theses and Dissertations

Nuclear pore complexes (NPCs) reside in the nuclear membrane and mediate macromolecules exchange between the nucleus and cytoplasm. Although the protein components of NPCs, termed collectively nucleoporin, have been identified, how nucleoporins arrange in NPC, however, is still an enigma. NPC is a highly symmetric protein complex, which contains an eight-fold rotational symmetry across the center of the pore and a two-fold symmetry in the plane of the nuclear envelope. In addition, according to electron microscopic reconstruction model, NPC can also be considered schematically as a series of concentric cylinders. A peripheral cylinder coating the nuclear pore membrane contains a …

Cell Size Control And Asymmetric Cell Fates In Start Of The Saccharomyces Cerevisiae Cell Cycle, Talia, Stefano Di

Student Theses and Dissertations

Understanding the molecular and biophysical mechanisms that couple the process of cell growth to cell division is one of the major challenges of modern cell biology. Saccharomyces cerevisiae (budding yeast) has been an important model organism to study the coupling between cell growth and cell division. The insights obtained from studies of this unicellular organism have been pivotal for related studies in animal systems. The classical picture that emerged from studies in budding yeast was that cell cycle commitment in G1, at a point called Start, requires growth to a critical cell size. This deterministic model did not address how …

The Role Of Adult Stem Cells And Tumor Necrosis Factor In Peripheral Neuropathy, Prabhjot Singh Dhadialla

Student Theses and Dissertations

Peripheral neuropathies are a significant cause of morbidity and mortality, with a population prevalence of 2,400 per 100,000 (2.4%) that increases in the elderly to 8,000 per 100,000 (8%)(C. N. Martyn and R. A. Hughes, 1997). The variations in symptom distribution and etiologic attribution have resulted in the classification of over 100 types of peripheral neuropathy with specific patterns of development and prognoses. In the first study, we use a mouse model of hereditary peripheral neuropathy that results in hind-limb paralysis to investigate the therapeutic efficacy of adult, adipose derived stem cells (ADSC). The paralyzed mice that received ADSC transplantation …

Analysis Of Cellular Factors Involved In Adeno-Associated Virus Type 2 Entry, Cameron Dale Bess

Student Theses and Dissertations

The study of virus-host interactions has not only produced insights relevant to both preventative drug design and the emerging field of gene therapy, but it has also served as a valuable tool to the field of cell biology. The biological roles of many pathogen recognized cell-surface receptors have yet to be determined, yet are being exploited by pathogens to facilitate their entry and infection. Specifically a small family of sugar modified membrane protein known as heparan sulfate proteoglycans, have been shown to be a critical determinant in the efficiency of infection of many important pathogens. Adeno-associated virus type 2 (AAV) …

Population Dynamics In A Model Closed Ecosystem, Doeke Romke Hekstra

Student Theses and Dissertations

For almost any species in any environment, it is nearly impossible to predict its fitness from molecular knowledge. If fitness is not to be a mere tautology, reproducible measurements of the survival and reproduction of populations are needed over many generations. Laboratory microbial ecosystems afford the short time and length scales required for such measurements. Their conventional implementations, batch cultures with period refreshment of growth medium or chemostats with continuous refreshment, have a number of disadvantages, such as the introduction of additional frequencies, selection for surface growth and the distortion of chemical interactions. In closed ecosystems free energy is instead …

The Neural Circuitry Of Social Behavior In C. Elegans, Evan Z. Macosko

Student Theses and Dissertations

Most animal species, from simple invertebrates to complex mammals, require behavioral mechanisms to communicate with and respond to conspecifics, whether to mate, to assess predatory danger, or evaluate the nutritional quality of the surrounding environment. Understanding the molecular and cellular underpinnings of these social behaviors remains a central challenge in neurobiology. I used the nematode C. elegans as a model system to study the genetics and neural circuitry that underlie social behavior. First, I evaluated the behavioral responses of C. elegans to a nematode extract (deathmone), which served as a model for alarm pheromones in other animal species (chapter 2). …

Mechanism Of Signal Transduction By The Staphylococcus Aureus Quorum Sensing Receptor Agrc, Elizabeth A. George Cisar

Student Theses and Dissertations

Bacteria use receptor histidine kinases to sense extracellular cues and convert them into intracellular signaling events that allow them to respond to their environment. In Staphylococcus aureus, each individual cell must sense the size of its overall population in order to synchronize virulence factor expression with the entire population. This task is carried out by the accessory gene regulator (agr) quorum sensing system. The agr autoinducing peptide (AIP) pheromone activates the AgrC receptor histidine kinase, resulting in downstream modulation of virulence factor expression. As S. aureus is a dangerous pathogen, understanding virulence regulation is of great interest, and the agr …

Fibrin Formation And Dissolution In The Progression Of Amyloid-Beta Pathology In Alzheimer's Disease, Justin Paul

Student Theses and Dissertations

Alzheimer's disease (AD) is a neurodegenerative disorder that leads to profound cognitive decline and eventually death. There are no effective long-term treatments or preventative measures available, and as the incidence and prevalence of the disease are increasing, new insights and tractable therapeutic targets are sorely needed. Genetic evidence indicates that a major cause of AD is the production of the amyloid-β (Aβ) peptide, which is proteolytically derived from the amyloid-β precursor protein. The Aβ peptide can oligomerize and be deposited as extracellular plaques in the brain and blood vessels, but the mechanism of how it leads to neuronal death is …

Novel Interactions Of The Hormone Leptin Revealed By Pet Imaging In Rodents And Rhesus Macaques, Robert Richard Flavell

Student Theses and Dissertations

Leptin is a polypeptide hormone, secreted principally by adipose tissue, which functions as an afferent signal in a feedback loop to maintain body weight and energy homeostasis. In addition to its well documented effects on food intake and energy expenditure, leptin modulates the function of many other physiological systems in mammals, through actions in the central nervous system and periphery. Remarkably, despite extensive studies on leptin receptor expression, the physiological biodistribution of the hormone remains essentially unknown. In order to characterize the distribution leptin in mammals, we have developed methodologies to radiolabel the hormone and visualize its biodistribution using positron …

Regulated Histone H3 Proteolysis During Mouse Embryonic Stem Cell Differentiation, Elizabeth M. Duncan

Student Theses and Dissertations

The association of genomic DNA with histone proteins in the three-dimensional structure known as chromatin is the central framework for "epigenetics," which is defined as inherited phenotypes governed by differences that cannot be explained by changes in DNA sequence. In recent years, studies have shown that regulated changes in the chemical and physical properties of chromatin often lead to dynamic changes in many cellular processes, including development and differentiation, by affecting the accessibility of the genomic information stored in the DNA. The cell uses many different mechanisms to regulate chromatin in order to establish, maintain, and propagate patterns of gene …

Regulation Of The Heterochromatin Protein 1 By Phosphorylation Of Histone H3 And The Hp1 Hinge Domain, Holger Dormann

Student Theses and Dissertations

Chromatin, a polymer formed from DNA, histones, and associated proteins, is the physiological form of genetic information in all eukaryotic cells. Posttranslational modification of histones, such as acetylation, methylation, and phosphorylation, regulates various DNA-dependent processes, ranging from transcription to replication, DNA repair, and apoptosis. A key mechanism by which histone modifications exert these effects is by recruitment of specific binding partners (effector proteins), that in turn direct downstream functions. Insight into the underlying mechanisms are of great importance for a full understanding of chromatin structure and function. One of these effector proteins, Heterochromatin Protein 1 (HP1), plays important roles in …

Studies Of G-Protein Coupled Receptors Incorporated Into A Novel, Nanoscale, Membrane-Mimetic System, Sourabh Banerjee

Student Theses and Dissertations

From first principles of phospholipid — apolipoprotein A-I (apo A-I) interactions, we hypothesized that the amino acid sequence of apo A-I derived from a different species may exhibit improved properties compared to human apo A-I for the purpose of incorporation of G protein-coupled receptors (GPCRs) into homogeneous discoidal lipoprotein particles. We generated apolipoprotein A-I DNA derived from zebrafish (Danio rerio) using molecular cloning techniques and optimized a heterologous bacterial expression system, and protein purification and labeling scheme for obtaining high-yields of pure zebrafish apo A-I. We demonstrated that zebrafish apo A-I forms stable, homogeneous discoidal lipoprotein particles, which we termed …

The Role And Fate Of Branch Site-U2 Snrna Interaction During Pre-Mrna Splicing, Duncan Smith

Student Theses and Dissertations

Many details of the conformational dynamics underlying transitions during premRNA splicing, particularly during the catalytic phase, remain unclear despite our deep knowledge of spliceosome composition. The complex assembly phase that precedes catalysis, and the involvement of several motifs in multiple interactions along the splicing pathway, exacerbate the difficulty of accessing splicing catalysis experimentally. snRNAs likely form some or all of the spliceosomal active site. We attempted to establish an snRNA-only splicing system as a means to bypass assembly and recapitulate splicing catalysis. Our approach, however, yielded a 2'-3' bondforming ribozyme activity in a linker region in our fused snRNA construct; …

Specification And Function Of Early Hair Follicle Stem Cells, Jonathan Nowak

Student Theses and Dissertations

In adult skin, multipotent epithelial stem cells (SCs) reside in a quiescent niche associated with each hair follicle termed the "bulge" and are essential for cyclic bouts of hair growth. Bulge stem cells can also contribute to sebaceous glands and the intefollicular epidermis when it is injured. While hair follicles begin to develop during embryogenesis, niche architecture becomes pronounced postnatally at the start of the first hair cycle. Whether SCs exist or function earlier is unknown. To determine if a stem cell population exists during follicle development, I conducted embryonic pulse-chase experiments to identify putative stem cells based on slow-cycling …

Regulation Of Apoptosis By Xiap Ubiquitin- Ligase Activity, Andrew James Schile

Student Theses and Dissertations

Virtually all animal cells have the known ability to self-destruct by undergoing apoptosis, a morphologically distinct form of programmed cell death. The proper regulation of apoptosis is critical for both development and tissue homeostasis, and inhibition of apoptosis contributes to the development and progression of cancer. Inhibitor of Apoptosis Proteins (IAPs) can bind to and inhibit caspases, the key executioners of apoptosis. Because IAPs are frequently over-expressed in human tumors, they have become major pharmacological targets for developing new cancer therapeutics. Many IAPs contain RING domains that function as E3 ubiquitin-ligases to regulate the abundance of IAPs themselves and their …

Peak Mitotic Cyclin Permits Mitotic Exit, Benjamin Drapkin

Student Theses and Dissertations

In eukaryotes, DNA replication, mitosis, and cytokinesis are all regulated by Cyclin-dependent kinase (Cdk). Cyclin/Cdk complexes promote replication origin firing and mitotic entry, and conversely, inhibit pre-replication origin loading and exit from mitosis. Cyclin synthesis and degradation, Cdk phosphorylation and Cdk inhibitors are controlled such that Cdk activity oscillates once per cell cycle. Little is known about the quantitative relationship between the level of Cdk activity and the occurrence, rate, and coordination of cell cycle events. We have addressed this question in Saccharomyces cerevisiae by introducing titrated levels of undegradable mitotic B-cyclin (Clb2kd) in cells prior to release of a …

Transcriptional Regulation Of Adipocyte Function, Kivanç Birsoy

Student Theses and Dissertations

The increased white adipose tissue mass associated with obesity is the result of both hyperplasia and hypertrophy of adipocytes. While adipocyte development and transcriptional processes are well studied in vitro, regulation of in vivo genes (such as leptin), the identity of the adipocyte progenitor cells and the development of the adipose organ have not been defined invivo. In this thesis, firstly KLF4 was discovered to be an essential early regulator of adipogenesis. KLF4 together with Krox20 cooperatively transactivates C/EBPβ, suggesting that KLF4 and Krox20 are part of an immediate early transcriptional network. This network is upregulated in a lipodystrophic animal …

Regulation Of Immunoglobulin Gene Diversification By Noncoding Rna's, Grace Teng

Student Theses and Dissertations

Small regulatory RNAs supplement the canonical pathways of gene regulation through diverse mechanisms of transcriptional, post-transcriptional, and post-translational silencing. These mechanisms range from "classical" RNA interference (RNAi), to gene repression by microRNAs (miRNAs), to maintenance of genomic stability by repeatassociated small RNAs. Here, I describe the contribution of miRNA-mediated regulation to a specific case of gene expression that requires significant somatic alteration of the genetic code. B lymphocytes perform somatic hypermutation (SHM) and class switch recombination (CSR) of the immunoglobulin locus to generate an antibody repertoire diverse in both affinity and function. These somatic diversification processes are catalyzed by activation-induced …

Regulation Of Gene Expression In Trypanosoma Brucei, Tim Nicolai Siegel

Student Theses and Dissertations

The protozoan parasite Trypanosoma brucei is one of the most divergent well-studied eukaryotes and many discoveries of general interest have been made in T. brucei. Atypical for a eukaryote, in T. brucei genes transcribed by RNA polymerase II (RNA pol II) are arranged in polycistronic transcription units (PTUs). mRNAs are separated post-transcriptionally by coupled splicing and polyadenylation reactions. During the splicing reaction a 39 nt 'sliced-leader' is added to every mRNA, a process termed trans splicing. The arrangement of generally unrelated genes in PTUs has lead to the assumption that little gene regulation occurs at the level of transcription initiation …

Physiological Effects Of Estradiol In The Mouse Hippocampal Formation, Joanna L. Spencer

Student Theses and Dissertations

At several points in a woman's life, changes in circulating estradiol are associated with disturbances in mood and cognitive function. To determine the biological basis of these behavioral changes, researchers have concentrated on the hippocampal formation, a medial temporal lobe structure involved in the regulation of mood and cognition in humans. It is now clear that estradiol increases the substrates of hippocampal synaptic plasticity, including dendritic spine density, synapse density, and synaptic protein expression. In some cases, these changes are associated with alterations in mood and hippocampal-dependent learning and memory. The upstream mediators of these estradiol effects remain unknown, but …

Dissecting The Development And Function Of C. Elegans Glia With Mutations Of The Mls-2 And Vab-3 Genes, Yoshimura Satoshi

Student Theses and Dissertations

The past decade has produced much evidence that glia, the major cellular component of vertebrate nervous systems, play active integral roles in a variety of processes including neuronal migration, synaptogenesis, and modulation of synaptic activity. Yet, many aspects of glia-neuron interactions remain obscure partly because manipulation of glia can result in neuronal death, hampering attempts to study glial cells in vivo. Moreover, a comprehensive understanding of glia differentiation is not yet achieved, although several key molecules in the process have been discovered. C. elegans possesses glia-like cells that are morphologically reminiscent of vertebrate glia. In this thesis, I show that …

A Model Of The Production Of Spontaneous Otoacoustic Emissions In The Tokay Gecko, Michael Gelfand

Student Theses and Dissertations

The role of the ear is to detect sound. Many ears, however, can also generate sounds and transmit them into the environment. These sounds, known as spontaneous otoacoustic emissions, are the most striking proof of the existence of an active process within the ear. This active process originates in hair cells, the sensory receptors of the inner ear; by augmenting the energy contained in sound, it improves both the sensitivity and the frequency selectivity of hearing. Under certain conditions, the active process generates spontaneous oscillations, which then produce spontaneous emissions. Little is known about the process by which the spontaneous …

Biochemical And Genetic Studies Of Beclin 1 Function In Autophagy, Yun Zhong

Student Theses and Dissertations

Beclin 1 is a mammalian autophagy protein and has important functions in development, tumor suppression and neurodegeneration. Beclin 1 exists in a protein complex with Vps34, which is a class III phosphatidylinositol (PtdIns) 3-kinase and mediates multiple vesicle trafficking pathways including autophagy and endocytosis. However the precise role of Beclin 1 in autophagy regulation is not well understood and information is lacking regarding the function of Beclin 1 in neuronal development and degeneration. In a study that combines mouse genetics and biochemistry, three novel Beclin 1 interaction proteins Atg14L (yeast Atg14-like), Rubicon (RUN domain and cysteine-rich domain containing, Beclin 1-interacting …

Biochemical Analysis Of The Protein-Protein Interactions Involved In Karyopherin-Mediated Transport Across The Nuclear Pore Complex, Jaclyn Tetenbaum-Novatt

Student Theses and Dissertations

Nucleocytoplasmic transport occurs through the nuclear pore complex (NPC), which in yeast is a highly symmetric ~50 MDa complex consisting of approximately 30 different proteins. Small molecules can freely exchange through the NPC, but macromolecules larger than ~40 kDa such as proteins, mRNAs, and ribosomal subunits must be aided across by shuttle proteins (karyopherins, or Kaps). Kap-mediated transport involves FG-nups, a family of NPC proteins. While much has been learned about the mechanism of nucleocytoplasmic transport, many details are still unknown; perhaps among the most important missing details is the binding kinetics of almost all the transport relevant interactions, due …