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Carbon Dioxide Expulsion By Ceanothus Spinosus In Response To Predawn Sunlight, Eian Carter, Jon Pauwels, Brittany Wilkins

Featured Research

In our experiment we studied the respiratory qualities of green bark ceanothus (Ceanothus spinosus). Plants are generally thought to undergo respiration during the night, building up carbon dioxide stores that are released in response to light. In resprouts with large root crowns, such as C. spinosus, we expected to see large amounts of carbon dioxide released right after dawn. This can be shown with the use of a portable gas exchange system. In C. spinosus, we compared normal respiration rates, based on carbon dioxide expulsion, to values obtained at predawn. We were able to show that …

The Effect Of Hydraulic Lift In Quercus Agrifolia On The Health Of Venegasia Carpesioides, Kelly Donovan, Brittany Wagner

Featured Research

Hydraulic lift was studied in live and dead Quercus agrifolia (Coastal Live Oak) in order to test its impact on surrounding Venegasia carpesioides (Canyon Sunflower). Hydraulic lift causes soil moisture to rise around the base of deep-rooted plants where neighboring plants can utilize this excess water. We predicted that the hydraulic lift of the Coastal Live Oak would increase soil moisture, causing higher stomatal conductance and higher water potential in nearby plants. Pvalues of .5258 and .6392 indicated there were no significant differences in soil moisture or in stomatal conductance of the Canyon Sunflowers. A p-value of .0378 showed a …

Annual Report October 1, 2006 - September 30, 2007 Endangered Species Act Section 10(A)1(B) Permit For The Incidental Take Of The Barton Springs Salamander (Eurycea Sosorum)

KIP Data Sets and Technical Reports

Table of Contents Summary of Compliance 2 Summary of Salamander Status/Biological Data 14 Pool Maintenance and Management Activities 21 Barton Springs Improvements Master Plan Short-Term Projects 25 Literature Cited 32 Open Access - Permission by Publisher See Extended description for more information.

Accurate Docking Is Achieved By Decoupling Systematic Sampling From Scoring, Jianwen Feng

All Theses and Dissertations (ETDs)

This dissertation discusses two main projects from my thesis work. The first project focuses on the development of a small molecule docking program, SKATE, for drug discovery. The second project focuses on the critical analysis of the thermal stability of a mini-protein, FSD-1. SKATE is a novel approach to small molecule docking. It removes any inter-dependence between sampling and scoring to improve docking accuracy. SKATE systematically and exhaustively samples a ligand's conformational, rotational and translational degrees of freedom, as constrained by a receptor pocket, to find sterically allowed poses. A total of 266 ligands were re-docked to their respective receptors …

Systemic Levels Of G-Csf And Il-6 Determine The Angiogenic Potential Of Bone Marrow Resident Monocytes, Alyssa Gregory

All Theses and Dissertations (ETDs)

Recent studies have demonstrated the efficacy of hematopoietic cell-based therapies in promoting therapeutic angiogenesis for a wide variety of vascular syndromes, however the cell populations responsible and the mechanisms involved are poorly understood. Using a mouse model of hindlimb ischemia, we previously showed that an adoptive transfer of donor monocytes significantly enhanced revascularization. Monocytes are a widely heterogeneous cell population and differences in the ability of various monocyte subsets to mediate revascularization have not been previously investigated. Using the hindlimb ischemia model we demonstrate that an adoptive transfer of inflammatory: CX3CR loGr-1+), but not resident: CX3CR1hiGr-1-) monocytes, significantly enhances revascularization …

A Quest For Meaning In Spontaneous Brain Activity - From Fmri To Electrophysiology To Complexity Science, Biyu He

All Theses and Dissertations (ETDs)

The brain is not a silent, complex input/output system waiting to be driven by external stimuli; instead, it is a closed, self-referential system operating on its own with sensory information modulating rather than determining its activity. Ongoing spontaneous brain activity costs the majority of the brain's energy budget, maintains the brain's functional architecture, and makes predictions about the environment and the future. I have completed three separate studies on the functional significance and the organization of spontaneous brain activity. The first study showed that strokes disrupt large-scale network coherence in the spontaneous functional magnetic resonance imaging: fMRI) signals, and that …

Medial Temporal Lobe Structure And Function, Meghana Karnik

All Theses and Dissertations (ETDs)

Medial Temporal Lobe Structure and Function by Meghana Sunil Karnik Doctor of Philosophy in Biology and Biomedical Sciences: Neuroscience) Washington University in St. Louis, 2009 Professor John G. Csernansky, Chairperson My main goal was to examine the relationship between brain structure and function, specifically medial temporal lobe structure and episodic memory, in various groups of subjects who had schizophrenia, were at risk for schizophrenia because of genetic and disease influences, or who were healthy, in order to explore the influence of genetic and disease influences on brain structure-function relationships. Most of what is known about the neural structures thought to …

The Role Of Astrocyte Activation In Infantile Neuronal Ceroid Lipofuscinosis, Shannon Macauley-Rambach

All Theses and Dissertations (ETDs)

Infantile neuronal ceroid lipofuscinoses: INCLs), or Batten Disease, is an inherited neurodegenerative lysosomal storage disorder affecting the central nervous system: CNS) during infancy or childhood. Hallmark pathological changes include accumulation of autofluorescent material, neuronal loss, cortical thinning, and brain atrophy, which ultimately lead to cognitive deficits, motor dysfunction, seizure activity, and blindness. INCL is the result of mutations in the CLN1 gene leading to a deficiency in the lysosomal enzyme, palmitoyl protein thioesterase 1: PPT1). A mouse model of INCL, the PPT1-deficient: PPT1-/-) mouse, was recently created by a targeted disruption in the CLN1 gene. The phenotype of the PPT1-/- …

A Role For The Ecdysone Response Gene E93 In Imaginaling Patterning During Metamorphosis, Xiaochun Mou

All Theses and Dissertations (ETDs)

Drosophila melanogaster E93 is an early ecdysone response gene that encodes a pipsqueak domain transcription factor. E93 is induced by ecdysone at the end of larval development, and directs the death and elimination of several larval tissues during metamorphosis. Although E93 has been considered a dedicated regulator of larval cell death, I have found that E93 is also widely expressed in imaginal tissues during metamorphosis, where it is required for the proper patterning of many adult structures. Our working hypothesis is that E93 functions in imaginal tissues as a metamorphosis-specific cofactor that determines the pupa-specific action of numerous other transcription …

Structural Rna Homology Search And Alignment Using Covariance Models, Eric Nawrocki

All Theses and Dissertations (ETDs)

Functional RNA elements do not encode proteins, but rather function directly as RNAs. Many different types of RNAs play important roles in a wide range of cellular processes, including protein synthesis, gene regulation, protein transport, splicing, and more. Because important sequence and structural features tend to be evolutionarily conserved, one way to learn about functional RNAs is through comparative sequence analysis - by collecting and aligning examples of homologous RNAs and comparing them. Covariance models: CMs) are powerful computational tools for homology search and alignment that score both the conserved sequence and secondary structure of an RNA family. However, due …

Historical And Geographic Context For The Evolution Of Climate Niche Breadth In Temperate Plants, Brad Oberle

All Theses and Dissertations (ETDs)

In order to predict how species will respond to global climate change, scientists must understand the relationships between traits, fitness, environments and distributions. Niche theory provides a useful framework. Niche breadth describes the range of environmental conditions necessary for population growth. Among these conditions, climate is especially important. Climate niche breadth in turn may reflect a confluence of different forces. This dissertation presents a series of projects that assess the relative roles of historical, geographic and population processes that contribute to climate niche breadth in temperate plants. The first project evaluates the predictive power of a classical hypothesis. If gene …

Coordinate Interstitial Deletions Of Retinoblastoma (Rb1) And Neurobeachin (Nbea) Genes On Chromosome 13 In Mgus And Multiple Myeloma, Julie O'Neal

All Theses and Dissertations (ETDs)

ABSTRACT OF THE DISSERTATION Coordinate interstitial deletions of Retinoblastoma: RB1) and Neurobeachin: NBEA) genes on chromosome 13 in monoclonal gammopathy of undetermined significance: MGUS) and multiple myeloma By Julie O'Neal Doctor of Philosophy in Biology and Biomedical Sciences: Molecular and Cellular Biology) Washington University in Saint Louis, 2009 Assistant Professor Michael H. Tomasson, Chair Numeric or structural chromosomal abnormalities are detected in nearly all patients with plasma cell dyscrasias, including primary amyloidosis, monoclonal gammopathy of undetermined significance: MGUS) and multiple myeloma: MM). Chromosome 13 deletions, most frequently monosomy 13, are detected in 10- 20% of MM cases by routine cytogenetics …

Identification And Characterization Of A Xylosylphosphotransferase Of Cryptococcus Neoformans, Morgann Reilly

All Theses and Dissertations (ETDs)

Cryptococcus neoformans is an environmental yeast and an opportunistic pathogen capable of causing a meningoencephalitis in human hosts. The organism produces an extensive polysaccharide capsule that is unique among pathogenic fungi and absolutely required for its virulence. Work in the Doering laboratory on the capsule and other glycoconjugates of C. neoformans has focused on the identification of glycosyltransferases, enzymes that catalyze the transfer of a sugar moiety from an active donor to a specific acceptor, creating a particular linkage. Previous work demonstrated that xylose residues, derived from the nucleotide sugar UDP-xylose, are necessary for cryptococcal virulence. An assay to detect …

Flap Endonuclease 1 Ensures Telomere Replication And Stability, Abhishek Saharia

All Theses and Dissertations (ETDs)

Telomeres, protein-DNA structures that distinguish the end of a chromosome from a bona fide DNA double strand break, are integral to genomic stability. High fidelity replication of telomeres is indispensable for their stability. Telomere replication is a challenging task that is completed through the coordinated actions of telomere binding proteins and DNA replication and repair proteins in ways that are not well understood. This work focuses on delineating the function of one DNA replication and repair protein, Flap Endonulcease 1: FEN1), in telomere replication and maintenance. I demonstrate that FEN1 is essential for the efficient replication of telomeres through its …

Role And Regulation Of Escrt-Iii In Multivesiculr Body Biogenesis, Soomin Shim

All Theses and Dissertations (ETDs)

Endosomal sorting complex required for transports: ESCRT) machinery responsible for multivesicular body: MVB) biogenesis is essential for receptor downregulation, viral budding and cytokinesis. ESCRT-III is a large polymer built from related ESCRT-III proteins that is thought to help generate intralumenal vesicles: ILVs) within the MVB. How ESCRT-III functions is poorly understood. Although ESCRT-III assembles on the endosomal membrane, its components are predominantly soluble in the cytoplasm. I found that the transition between these two states is controlled by autoinhibitory domains within ESCRT-III proteins, which I identified by structure/ function analysis in four human ESCRT-III proteins - Charged multivesicular body protein2A: …

Targeting The Dimerization Of Erbb Receptor Tyrosine Kinases, Rob Yang

All Theses and Dissertations (ETDs)

The epidermal growth factor receptor: EGFR) is a membrane receptor tyrosine kinase whose over-activation has been implicated to cause many human cancers. Novel strategies to inhibit the activation of EGF receptors other than the conventional antibody-based and tyrosine kinase inhibitors are virtually non-existent but could provide benefits both in the laboratory and clinical settings. In an effort to expand the current approaches, this thesis focused on targeting the homodimerization of the EGF receptors themselves and the heterodimerization of EGF receptors with the related ErbB2 receptor. Three sub-projects were completed in the process. The first project explored the feasibility of inhibiting …

Hiv-1 Envelope-Induced Signaling Mediates Actin Cytoskeleton Rearrangements Necessary For Fusion And Entry, Brooke Harmon

All Theses and Dissertations (ETDs)

Human immunodeficiency virus type-1: HIV-1) initiates infection by direct fusion of the virus membrane with the plasma membrane of the target cell. This fusion event is a multi-step process mediated by the envelope: Env) surface subunit gp120 and the transmembrane subunit gp41 which anchors gp120 into the viral membrane. First the surface subunit gp120 binds to the primary receptor CD4. This interaction promotes actin cytoskeletal rearrangements in the target membrane that bring the chemokine coreceptor, CCR5 or CXCR4, into close proximity for binding and induces conformational changes in gp120 that allow it to couple to the coreceptor. Formation of the …

Runx1 In Primitive Hematopoiesis And Characterization Of Hematopoietic Stem Cells In A Mouse Chronic Inflammatory Arthritis Model, Yunglin Ma

All Theses and Dissertations (ETDs)

Hematopoietic cells are essential for growth and survival throughout adult life. Two different aspects of hematopoiesis are addressed in this dissertation. I. The regulation of primitive hematopoiesis by Runx1 and TGF-beta signaling. Primitive hematopoiesis, occurring exclusively in the yolk sac, is characterized by its transient nature. As the primitive hematopoiesis declines in the yolk sac, definitive hematopoietic progenitors generated in the yolk sac and/or embryo take over in blood cell production. Whether the transition from primitive to definitive hematopoietic program reflects a mere shift in hematopoietic sites or whether it is an actively regulated process is currently unknown. Runx1 is …

Characterization Of Ligand-Induced Conformational Changes In The Egf Receptor, Katherine Yang

All Theses and Dissertations (ETDs)

ABSTRACT OF DISSERTATION Characterization of ligand-induced conformational changes in the EGF receptor by Katherine S. Yang Doctor of Philosophy in Biochemistry Washington University in St. Louis, 2009 Professor Linda Pike, Chairperson The epidermal growth factor: EGF) receptor is a classical receptor tyrosine kinase that mediates cellular processes such as proliferation, migration, and differentiation in response to growth factor stimulation. Crystal structures of the EGF receptor suggest that its activation is associated with extensive conformational changes in both the extracellular and intracellular domains. However, evidence of these structural dynamics in intact cells has been lacking. This thesis describes the characterization of …

Regulation Of Bax/Bak-Dependent Cell Death Program, Hyungjin Kim

All Theses and Dissertations (ETDs)

Mammals have evolved an intricate regulation of a genetically programmed apoptotic cell death that involves mitochondria. Diverse apoptotic signals converge on mitochondria, which causes the release of cytochrome c into the cytosol to activate Apaf-1. This initiates caspase activation, which results in irreversible cellular demise. The BCL-2 family proteins constitute a critical checkpoint in mitochondrion-dependent apoptosis. Multidomain proapoptotic BAX/BAK promotes mitochondrial outer membrane permeabilization, whereas anti-apoptotic BCL-2/BCL-X_L/MCL-1 protects mitochondrial integrity and prevents cytochrome c release. The proapoptotic activity of BAX/BAK is triggered by BH3-only molecules: BH3s) which are upregulated by upstream death signals. However, how these subfamilies interact …

Calling Cards For Dna-Binding Proteins, Haoyi Wang

All Theses and Dissertations (ETDs)

Organisms respond to their environment by altering patterns of gene expression. This process is orchestrated by transcription factors, which bind to specific DNA sequences near genes. In order to understand the regulatory networks that control transcription, the genomic targets of all transcription factors under various conditions and in different cell types must be identified. This remains a distant goal, mainly due to the lack of a high-throughput, in vivo method to study protein-DNA interactions. To fill this gap, I developed transposon "Calling Cards" for DNA-binding proteins. I endowed DNA binding proteins with the ability to direct the insertion of a …

The Evolution And Regulation Of Dna-Binding By The Nickel-Dependent Transcription Factor Nikr, Erin Benanti

All Theses and Dissertations (ETDs)

Transition metal homeostasis is critical for all cells to balance cellular metal requirements with metal availability. One common homeostatic mechanism in bacteria is metal-dependent transcriptional regulation. The Ni2+-dependent transcription factor NikR is a member of the ribbon-helix-helix: RHH) family of DNA-binding proteins and is widespread among bacteria and archea with vastly different nickel physiologies. The goal of this thesis was to better understand basic aspects of cellular transition metal homeostasis by examining the activity and regulatory properties of NikR family members from different bacterial species. One organism that exhibits a prominent and well-defined nickel physiology is Helicobacter pylori, making it …

Mechanisms Of Feedback In The Visual System, Adam Eggebrecht

All Theses and Dissertations (ETDs)

Feedback is an ubiquitous feature of neural systems though there is little consensus on the roles of mechanisms involved with feedback. We set up an in vivo preparation to study and characterize an accessible and isolated feedback loop within the visual system of the leopard frog, Rana pipiens. We recorded extracellularly within the nucleus isthmi, a nucleus providing direct topographic feedback to the optic tectum, a nucleus that receives the vast majority of retinal output. The optic tectum and nucleus isthmi of the amphibian are homologous structures to the superior colliculus and parabigeminal nucleus in mammals, respectively. We formulated a …

Identification And Characterization Of Novel Astroviruses, Stacy Finkbeiner

All Theses and Dissertations (ETDs)

Approximately 1.8 million children die from diarrhea annually, and millions more suffer multiple episodes of nonfatal diarrhea. Despite the availability of improved molecular diagnostics to detect the known viral agents, the etiology of a large proportion of diarrheal cases is unknown. In fact, it is estimated that no causative agent can be identified in up to 40% of sporadic cases or in gastroenteritis outbreaks. Detection of novel or unexpected viruses is the first step in identifying agents that could potentially close the diagnostic gap and pave the way for the development of more comprehensive preventative measures and better treatments. This …

Barton Springs Salamanders, Spring Discharge And Dissolved Oxygen An Update To Dr-07-07 Bss&Abs Salamander Data Report 2006 And Sr-04-06 Some Water Quality Threats To The Bbs At Low Flows, Martha Turner

KIP Data Sets and Technical Reports

An evaluation of salamander counts, spring flowrates, and dissolved oxygen concentrations was completed to update previously collected data. Originally, this evaluation was used to recommend a pumping limit for sustainable yield to the Barton Springs Edwards Aquifer Conservation District. The primary purpose of the current evaluation was to verify correlations between flow, dissolved oxygen, and surface count data of the endangered Barton Springs Salamander. Significant correlations provide the statistical basis for setting thresholds for Barton Springs flows related to a water quality parameter commonly used in aquatic life support. The pattern previously observed in Barton Springs Pool, with salamander counts …

Genetic Variation Within The Daphnia Pulex Genome, Abraham Eaton Tucker

Doctoral Dissertations

Genetic variation within the diploid Daphnia pulex genome was examined using a high quality de novo assembly and shotgun reads from two distinct D. pulex clones. Patterns of variation and divergence at single nucleotides were examined in physical and functional regions of the genome using comparative assembly output and available annotations. Additionally, mitochondrial genomes of the same D. pulex clones were assembled and compared for patterns of divergence, and substitutional biases. Intron presence/absence polymorphisms were identified computationally and verified experimentally. Finally, gene duplicate demographics were examined for patterns of divergence and estimates of gene birth rates.

Modeling Congenital Disorders Of Glycosylation In Caenorhabditis Elegans: Genetic Influences And Structural Consequences Of N-Linked Glycosylation, Weston Booth Struwe

Doctoral Dissertations

The attachment of oligosaccharides to the amide nitrogen of asparagine side chains in proteins is a fundamental process occurring in all metazoans. This process, known as N-glycosylation, is complex and is achieved by the precise interactions of various cellular components. The initial stage of N-glycosylation occurs in the endolasmic reticulum and is preserved among eukaryotes. Glycans are further developed in the Golgi and the structural complexity depends greatly on the animal species, tissue and developmental stage. Oligosaccharides are unique biomolecules because unlike DNA or proteins, no primary sequence exists nor is its' synthesis template driven. A major goal of glycobiologist …

Photosynthetic And Oxidative Stress In The Green Alga Dunaliella Tertiolecta: The Effects Of Uv-B And Uv-A Radiation, Priya Sampath Wiley

Doctoral Dissertations

The penetration of ultraviolet-B (UV-B; 290-320 nm) into the biosphere has increased in response to decreased stratospheric ozone. As a consequence, significant attempts have been made to elucidate the effects of UV-B radiation on primary producers such as phytoplankton and plants. Considerably less effort has been devoted to describing the role played by ultraviolet-A (UV-A; 320-400 nm) radiation, which is not attenuated by stratospheric ozone. The present work details the independent and combined effects of UV-B and UV-A radiation on photosynthetic and oxidative stress responses using the unicellular green alga Dunaliella tertiolecta as a model organism. A UV-B spectral profile …

Gonadotropin Releasing Hormone In Agnathans, Scott Ira Kavanaugh

Doctoral Dissertations

Hagfish and lampreys are the only two representatives of Agnathans among extant vertebrates. The regulatory hypothalamic neurohormone, gonadotropin-releasing hormone (GnRH), regulates reproduction in all vertebrates through the hypothalamic-pituitary-gonadal axis. Most vertebrates have at least two forms of GnRH in the brain. In hagfish the primary amino acid structure of GnRH has not been identified as yet, however, indirect methods have shown an immunoreactive GnRH or a GnRH-like peptide in the brain of hagfish. In addition concentrations of brain immunoreactive-GnRH have been correlated with reproductive stages in the Atlantic hagfish ( Myxine glutinosa). Therefore the objective of the first study was …

Tracking Diet And Movement Of Atlantic Bluefin Tuna (Thunnus Thynnus) Using Carbon And Nitrogen Stable Isotopes, John Logan

Doctoral Dissertations

Atlantic bluefin tuna (ABFT; Thunnus thynnus) are important top predators in pelagic ecosystems. Understanding their diet and movements is necessary for proper management, but existing methods are costly and logistically challenging. Naturally occurring stable isotopes have been used to study diet and movement in many aquatic ecosystems and offer a novel approach for studying these large pelagic fishes.

Lipids, which have lower carbon isotope values than protein, can affect isotope analyses of bulk tissue. Both chemical and mathematical corrections were used to address lipid effects on ABFT and the prey. All chemical extraction methods altered nitrogen isotope values. Mathematical corrections …