Digital Commons Network^™

Profiling Condition-Specific, Genome-Wide Regulation Of Mrna Stability In Yeast, Wendy Olivas, B. Foat, S. Houshmandi, H. Bussemaker

Biology Department Faculty Works

The steady-state abundance of an mRNA is determined by the balance between transcription and decay. Although regulation of transcription has been well studied both experimentally and computationally, regulation of transcript stability has received little attention. We developed an algorithm, MatrixREDUCE, that discovers the position-specific affinity matrices for unknown RNA-binding factors and infers their condition-specific activities, using only genomic sequence data and steady-state mRNA expression data as input. We identified and computationally characterized the binding sites for six mRNA stability regulators in Saccharomyces cerevisiae, which include two members of the Pumilio-homology domain (Puf) family of RNA-binding proteins, Puf3p and Puf4p. We …

Yeast Puf3 Mutants Reveal The Complexity Of Puf-Rna Binding And Identify A Loop Required For Regulation Of Mrna Decay, Wendy Olivas, S. Houshmandi

Biology Department Faculty Works

The eukaryotic Puf proteins regulate mRNA translation and degradation by binding the 3' untranslated regions of target mRNAs. Crystal structure analysis of a human Puf bound to RNA suggested a modular mode of binding, with specific amino acids within each of eight repeat domains contacting a single nucleotide of the target RNA. Here we study the mechanism by which the yeast Puf3p binds and stimulates the degradation of COX17 mRNA. Mutation of the predicted RNA-binding positions of Puf3p to those found in Puf5p demonstrated that a single amino acid change in Puf3p abolished detectable binding to COX17. Since this amino …

Plant Ontology (Po): A Controlled Vocabulary Of Plant Structures And Growth Stages, Pankaj Jaiswal, Shulamit Avraham, Katica Ilic, Elizabeth Kellogg, Susan Mccouch, Anuradha Pujar, Leonore Reiser, Seung Rhee, Martin Sachs, Mary Schaeffer, Lincoln Stein, Peter Stevens, Leszek Vincent, Doreen Ware, Felipe Zapata

Biology Department Faculty Works

The Plant Ontology Consortium (POC) (www.plantontology.org) is a collaborative effort among several plant databases and experts in plant systematics, botany and genomics. A primary goal of the POC is to develop simple yet robust and extensible controlled vocabularies that accurately reflect the biology of plant structures and developmental stages. These provide a network of vocabularies linked by relationships (ontology) to facilitate queries that cut across datasets within a database or between multiple databases. The current version of the ontology integrates diverse vocabularies used to describe Arabidopsis, maize and rice (Oryza sp.) anatomy, morphology and growth stages. Using the ontology browser, …

Analysis Of Genotypic And Phenotypic Differences In Desmognathus Quadramaculatus Across The Southern Appalachians, Deborah Susan Merritt

Theses, Dissertations and Capstones

Populations of Desmognathus quadramaculatus were compared for genotypic and phenotypic differences across 5 states in the Southern Appalachians. Series consisting of 10 salamanders each were collected from West Virginia, Virginia, Tennessee, North Carolina and Georgia. Salamanders were assessed for genotypic differences by using allozyme (proteins with polymorphic loci) electrophoresis staining for 13 loci of the muscle, liver and stomach tissue. Nei’s genetic distance was used to score genetic variation between populations. Phenotypic differences were assessed by comparing 10 external morphological measurements between populations. Mahalanobis’ distance was used to score morphological differences between populations. Both genetic and morphological differences were correlated …

Fecycle: Attempting An Iron Biogeochemical Budget From A Mesoscale Sf6 Tracer Experiment In Unperturbed Low Iron Waters, Robert Michael Mckay, P. W. Boyd, C. S. Law, D. A. Hutchins, E. R. Abraham, P. L. Croot, M. Ellwood, R. D. Frew, M. Hadfield, J. Hall, S. Handy, C. Hare, J. Higgins, P. Hill, K. A. Hunter, K. Leblanc, M. T. Maldonado, C. Mioni, M. Oliver, S. Pickmere, M. Pinkerton, K. Safi, S. Sander, S. A. Sanudo-Wilhelmy, M. Smith, R. Strzepek, A. Tovar-Sanchez, S. W. Wilhelm

Biological Sciences Faculty Publications

An improved knowledge of iron biogeochemistry is needed to better understand key controls on the functioning of high-nitrate low-chlorophyll (HNLC) oceanic regions. Iron budgets for HNLC waters have been constructed using data from disparate sources ranging from laboratory algal cultures to ocean physics. In summer 2003 we conducted FeCycle, a 10-day mesoscale tracer release in HNLC waters SE of New Zealand, and measured concurrently all sources (with the exception of aerosol deposition) to, sinks of iron from, and rates of iron recycling within, the surface mixed layer. A pelagic iron budget (timescale of days) indicated that oceanic supply terms (lateral …

Effects Of Nitric Oxide Inhibitors And Scavengers On Gravitropism In Arabidopsis Thaliana, Kristin Russell, Jennifer Jacobi, Jacob Elmore

Opportunities for Undergraduate Research Experience Program (OURE)

No abstract provided.

Bioactive Glass Coatings For Adherence To Bone Tissue, Wesley Trueblood

Opportunities for Undergraduate Research Experience Program (OURE)

The purpose of the experiments for this research project was to determine whether certain compositions of borate-based glasses are bioactive and can be used to bond titanium pins to bone. Two different major experiments were done. The first experiment was done to determine the bioactivity of the glass. The second experiment was done to simultaneously determine the bioactivity of the glass and determine whether or not the glass would bind to titanium and bone.

The majority of the research consisted of working with different compositions of borate-based glass, making glass pins, and coating titanium pins with the glass. The making …

Lead Tolerant Bacteria Could Be The Future Of Bioremediation, Kendra Waltermire

Opportunities for Undergraduate Research Experience Program (OURE)

The contamination of soil, sediment, and water by toxic metals is a major problem worldwide, both environmentally, and economically. Microorganisms that are resistant to lead are rare in nature. Lead is toxic to most microorganisms and only a few have developed mechanisms to survive in this toxic environment In this study, bacteria found in soil and water with high concentrations of soluble lead are isolated and characterized. I grew and isolated bacteria that are resistant to the lead found in the solid medium. A gram stain was used to characteristically determine the bacteria that were isolated. Four isolated bacteria were …

Quest For The ‘Holy Grail Bird’. Discovery Of The Ivory-Billed Woodpecker Brings Arkansas Unprecedented Attention, Aldemaro Romero Jr., Jim Bednarz

Publications and Research

No abstract provided.

Introduction – Regional Monitoring Programs, Richard L. Hutto, C. John Ralph

Biological Sciences Faculty Publications

There is increasing interest in the initiation of regional or statewide monitoring programs that are less extensive than national efforts such as the Breeding Bird Survey. A number of regional programs have been in existence for a decade or more, so the papers in this section represented an effort to bring together the collective experience of the people who had developed these programs, and to hear about the benefits and drawbacks of their particular designs. Speakers reviewed why they felt there was a need for a regional monitoring effort, examined the designs and response variables associated with their regional monitoring …

Monitoring For Adaptive Management In Coniferous Forests Of The Northern Rockies, Jock S. Young, John R. Hoffland, Richard L. Hutto

Biological Sciences Faculty Publications

Monitoring can and should be much more than the effort to track population trends; it can be a proactive effort to understand the effects of human activities on bird populations. It should be an integral part of the adaptive management process. With this in mind, the Northern Region Landbird Monitoring Program has a dual focus: (1) to monitor long-term bird population trends, and (2) to study bird-habitat relationships and management effects. By conducting permanent, longterm monitoring transects every other year, we are free to use the intervening years to study the effects of specific management activities. The coordination and funding …

Fire On The Mountain: Birds And Burns In The Rocky Mountains, Natasha B. Kotliar, Victoria A. Saab, Richard L. Hutto

Biological Sciences Faculty Publications

No abstract provided.

Diving In Two Marine Lakes In Croatia, Eric Klos, John H. Costello, Sean Colin, William M. Graham

Arts & Sciences Faculty Publications

We describe the diving methods used for in-situ observations of the scyphozoan medusa, Aurelia sp., in two marine lakes on the island of Mljet, Croatia. Both lakes have a strong pycnocline at approximately 15 m. During this study (May, 2004) surface temperature was about 20o C; bottom temperature about 10o C. Visibility was 15 m to 30 m. Tide and currents were negligible. A dense resident population of Aurelia sp. and a predictable environment made this an ideal study site. Aurelia was most abundant in mid-water around the pycnocline. There were several dive objectives: specimen collection for laboratory analysis, population …

Prophylactic Efficacy Of Crushed Garlic Lobes, Black Seed Or Olive Oils On Cholinesterase Activity In Central Nervous System Parts And Serum Of Lead Intoxicated Rabbits, Maged M. Yassin

Turkish Journal of Biology

The effect of lead on cholinesterase activity in various central nervous system (CNS) parts and in serum, and the potential of crushed fresh garlic lobes, black seed and olive oils to combat lead poisoning in rabbits were assessed. Oral administration of lead acetate elevated BLL compared to control and sodium acetate groups. This increase was a function of the experimental time. Treatment of animals with crushed fresh garlic lobes, black seed or olive oils lowered BLL, with garlic was the most effective. Lead caused progressive decrease in the activity of acetylcholinesterase in different brain regions and spinal cord allover the …

Gene Expression Maps: The Cartography Of Transcription, Scott F. Gilbert

Biology Faculty Works

No abstract provided.

Ego-1, A Putative Rna-Directed Rna Polymerase, Promotes Germline Proliferation In Parallel With Glp-1/Notch Signaling And Regulates The Spatial Organization Of Nuclear Pore Complexes And Germline P Granules In Caenorhabditis Elegans, Valarie E. Vought, Mitsue Ohmachi, Min-Ho Lee, Eleanor M. Maine

Biology - All Scholarship

Caenorhabditis elegans EGO-1, a putative cellular RNA-directed RNA polymerase, promotes several aspects of germline development, including proliferation, meiosis, and gametogenesis, and ensures a robust response to RNA interference. In C. elegans, GLP-1/Notch signaling from the somatic gonad maintains a population of proliferating germ cells, while entry of germ cells into meiosis is triggered by the GLD-1 and GLD-2 pathways. GLP-1 signaling prevents germ cells from entering meiosis by inhibiting GLD-1 and GLD-2 activity. We originally identified the ego-1 gene on the basis of a genetic interaction with glp-1. Here, we investigate the role of ego-1 in germline proliferation. Our data …

Soil Microbial Community Dynamics In Florida Scrub Ecosystem, Maria Albarracin

Electronic Theses and Dissertations

Pyrogenic ecosystems are maintained by fires which vary in frequency, seasonality, and intensity. Florida oak-saw palmetto scrub ecosystem is characterized by fires occurring at intervals of 10-20 years. Diverse factors as private land acquisition and development has created a patchy distribution of scrub ecosystems and also interrupted the natural fire cycle. The effects of fire over plant regeneration and fauna habitat utilization of the scrub have been well characterized in previous research. In the present paper the objective is to characterize the short- and long-term fire effects on the soil microbial community. Fire effects were studied in a chronosequence, comprising …

Effects Of A Shore Protection Project On Loggerhead And Green Turtle Nesting Activity And Reproduction In Brevard County, Florida, Kelly Brock

Electronic Theses and Dissertations

Marine turtle reproductive success is strongly correlated with the stability and quality of the nesting environment. Because females show fidelity to key nesting beaches, the management and physical characteristics of these beaches directly affect future generations of marine turtles and may be essential for the recovery of these threatened and endangered species. The impacts of beach restoration on loggerhead turtles (Caretta caretta) and on green turtles (Chelonia mydas) were investigated. Previous studies concerning beach nourishment projects have focused on loggerhead turtles. I compared data between nourished and non-nourished areas and between loggerhead and green turtles. I found, at one season …

Expression Of Gal/Galnac Lectin Of Entamoeba Histolytica In Transgenic Chloroplasts To Develop A Vaccine For Amebiasis, Seethamahalakshmi Chebolu

Electronic Theses and Dissertations

Amebiasis, also defined as invasive intestinal and extra intestinal amebiasis, is caused by Entameoba histolytica, an invasive protozoan parasite. World Health Organization (WHO) has reported that approximately 50 million people are infected each year causing an estimated 40 to 100 thousand deaths annually. Entameoba histolytica ranks only second to malaria as a protozoan cause of death. Amebiasis occurs world wide but people living in Central and South America, Africa and Asia are the majority to suffer from morbidity and mortality. The enteric parasite has no zoonotic reservoirs and insect vectors for its transmission and infects humans and non-human primates. Therefore, …

Juvenile Green Turtle (Chelonia Mydas) Foraging Ecology:Feeding Selectivity And Forage Nutrient Analysis, Eliza Gilbert

Electronic Theses and Dissertations

For the endangered green turtle, Chelonia mydas, a fundamental component of recovery and conservation is an understanding of its foraging ecology. Foraging optimality models suggest animals will select resources of high quality over those of low quality. For green turtles, this behavior is important, as sufficient quantities of nutritionally adequate forage items are necessary for growth and reproduction. One intrinsic element in the understanding of green turtle foraging ecology is to identify and document the availability and quality of forage resources preferred by green turtles. The objectives of this study were: 1) determine whether juvenile green turtles showed a feeding …

The Uptake Of Amino Acids By Microbes And Trees In Three Cold-Temperate Forests, Adrien C. Finzi, Sean T. Berthrong

Scholarship and Professional Work - LAS

Amino acids are emerging as a critical component of the terrestrial N cycle, yet there is little understanding of amino acid cycling in temperate forests. This research studied the uptake and turnover of amino acid N by soil microbes and the capacity of forest trees to take up the amino acid glycine in comparison to NH₄⁺ and NO₃⁻. This research was conducted in three temperate forests located in northwest Connecticut, USA. The three forests differed in soil parent material and canopy tree species composition. At all three sites, amino acids were released from soil organic …

Diverse Spatial, Temporal, And Sexual Expression Of Recently Duplicated Androgen-Binding Protein Genes In Mus Musculus, Christina M. Laukaitis, Stephen R. Dlouhy, Richard D. Emes, Chris P. Ponting, Robert C. Karn

Scholarship and Professional Work - LAS

Background

The genes for salivary androgen-binding protein (ABP) subunits have been evolving rapidly in ancestors of the house mouse Mus musculus, as evidenced both by recent and extensive gene duplication and by high ratios of nonsynonymous to synonymous nucleotide substitution rates. This makes ABP an appropriate model system with which to investigate how recent adaptive evolution of paralogous genes results in functional innovation (neofunctionalization).

Results

It was our goal to find evidence for the expression of as many of the Abp paralogues in the mouse genome as possible. We observed expression of six Abpa paralogues and five Abpbg paralogues …

Descriptive Ecology Of A Turtle Assemblage In An Urban Landscape, Conner C. A, B A. Douthitt, Travis J. Ryan

Scholarship and Professional Work - LAS

We studied turtle populations inhabiting a canal and a lake (both man-made) within a heavily disturbed, urban setting. Six aquatic and semi-aquatic turtle species were collected in both habitats: spiny softshell turtle (Apolone spinifera), painted turtle (Chrysemys picta), common snapping turtle (Chelydra serpentina), common map turtle (Graptemys geographica), common musk turtle (Sternotherus odoratus) and red-eared slider (Trachemys scripta). While G. geographica was the most common species in the canal habitat, T. scripta was most common in the lake habitat. We describe patterns of sexual size dimorphism and sex ratios for the three most abundant species (G. geographica, T. scripta and …

Cortactin Regulates Cell Migration Via Activation Of N-Wasp, Jennifer Kowalski, C. Egile, S. Gil, S. B. Snapper, R. Li, S. M. Thomas

Scholarship and Professional Work - LAS

Cortactin is an actin-associated scaffolding protein that regulates cell migration. Amplification of the human gene, EMS1, has been detected in breast, head and neck tumors, where it correlates with increased invasiveness. Cortactin can regulate actin dynamics directly via its N-terminal half, which can bind and activate the Arp2/3 complex. The C-terminal portion of cortactin, however, is thought to have limited function in its regulation of the actin polymerization machinery. In this report, we identify a role for the cortactin C-terminus in regulating cell migration and, more specifically, actin dynamics. Overexpression of either full-length cortactin or cortactin C-terminus is sufficient to …

Of Looks, Laws And Lawns: How Human Aesthetic Preferences Influence Landscape Management, Public Policies And Urban Ecosystems, Loren B. Byrne

Arts & Sciences Faculty Publications

No abstract provided.

Changes In Antioxidative Enzymes Of Young And Mature Leaves Of Tomato Seedlings Under Drought Stress, Serpi̇l Ünyayar, Fazi̇let Özlem Çeki̇ç

Turkish Journal of Biology

The effects of exogenous abscisic acid (ABA) on antioxidant enzymes of young and mature leaves of 4-week old Lycopersicon esculentum cv. Ailsa Craig and ABA-deficient mutant, notabilis, were investigated under drought stress. Although ABA induced increases in ascorbate peroxidase (APX), glutathione reductase (GR) and catalase (CAT) activities in drought-stressed young leaves of notabilis, CAT activities remained unchanged in both ABA-treated young and mature leaves of Ailsa Craig under drought. Superoxide dismutase (SOD) activity did not substantially increase in notabilis or Ailsa Craig in all treatments. APX activity significantly increased in ABA-, drought- and drought+ABA- treated young leaves of notabilis. These …

Identification Of Neuronal Enhancers Of The Proopiomelanocortin Gene By Transgenic Mouse Analysis And Phylogenetic Footprinting, Flavio S. J. De Souza, Andrea M. Santangelo, Viviana Bumaschny, Marıa Elena Avale, James L. Smart, Malcolm J. Low, Marcelo Rubinstein

Faculty Publications - Department of Biological & Molecular Science

The proopiomelanocortin (POMC) gene is expressed in the pituitary and arcuate neurons of the hypothalamus. POMC arcuate neurons play a central role in the control of energy homeostasis, and rare loss of function mutations in POMC cause obesity. Moreover, POMC is the prime candidate gene within a highly significant quantitative trait locus on chromosome 2 associated with obesity traits in several human populations. Here, we identify two phylogenetically conserved neuronal POMC enhancers designated nPE1 (600 bp) and nPE2 (150 bp) located approximately 10 to 12 kb upstream of mammalian POMC transcriptional units. We show that mouse or human genomic regions …

Aerodynamics Of The Hovering Hummingbird, Douglas R. Warrick, Bret W. Tobalske, Donald R. Powers

Faculty Publications - Department of Biological & Molecular Science

Despite profound musculoskeletal differences, hummingbirds (Trochilidae) are widely thought to employ aerodynamic mechanisms similar to those used by insects. The kinematic symmetry of the hummingbird upstroke and downstroke has led to the assumption that these halves of the wingbeat cycle contribute equally to weight support during hovering, as exhibited by insects of similar size. This assumption has been applied, either explicitly or implicitly, in widely used aerodynamic models, and in a variety of empirical tests. Here we provide measurements of the wake of hovering rufous hummingbirds (Selasphorus rufus) obtained with digital particle image velocimetry that show force asymmetry: hummingbirds produce …

Calmodulin-Dependent Kinase Kinase/Calmodulin Kinase I Activity Gates Extracellular-Regulated Kinase-Dependent Long-Term Potentiation, John M. Schmitt, Eric S. Guire, Takeo Saneyoshi, Thomas R. Soderling

Faculty Publications - Department of Biological & Molecular Science

No abstract provided.

Preservation Of Eumelanin Hair Pigmentation In Proopiomelanocortin-Deficient Mice On A Nonagouti (A/A) Genetic Background, Andrzej Slominski, Przemyslaw M. Plonka, Alexander Pisarchik, James L. Smart, Virgine Tolle, Jacobo Wortsman, Malcolm J. Low

Faculty Publications - Department of Biological & Molecular Science

No abstract provided.