Digital Commons Network^™

Retrospective Barrier Placements For A Skunk Rabies Epizootic In Nw Wyoming, C. Ramey, K. Mills, R. Mclean, R. Engeman, J. Fischer

Wildlife Damage Management Conference

Striped skunks (Mephitis mephitis) are the most important reservoir of rabies on the Great Plains. In August, 1988 a skunk rabies epizootic proceeded from the "index case" west of Cowley, WY. By 1991, epizootic had reached nearly all areas in the Shoshone River Basin (SRB), and it ended in 1993. This area and the remainder of the SRB had been previously considered rabies-free. The USDA's Wildlife Services (WS) cooperated with state and local officials in a rabies monitoring and control program starting in 1990. Using information from the literature, signs, tracks, and radio-telemetry of normal and rabid skunks, …

Natural Ice-Nucleating Bacteria Increase The Freezing Tolerance Of The Intertidal Bivalve Geukensia Demissa, Alexander M. Mccorkle

Biology Honors Papers

Instead of avoiding freezing, freeze tolerant invertebrates actively initiate controlled ice nucleation at relatively high sub-zero temperatures in extracellular compartments. Most produce proteinaceous ice-nucleators in their hemolymph, however the intertidal bivalve mollusc Geukensia demissa lacks this ability. Instead it utilizes at least one strain of ice-nucleation active (INA) bacteria, Pseudomonas fulva, present in seawater, to induce crystallization in the pallial fluid that fills its mantle cavity. In this study, two additional INA bacteria strains were isolated from the palial fluid of Geukensia demissa: Psychrobacter sp. and Shewanella sp. The ice-nucleation activity of both strains was characterized and Psychrobacter was found …

A Comparative Ecological Study Of Two Sister Species Of Darters In Kentucky, Etheostoma Kantuckeense And Etheostoma Lawrencei, Bjorn Victor Schmidt

Masters Theses & Specialist Projects

Etheostoma kantuckeense and E. lawrencei are former members of the wide ranging E. spectabile species complex. Etheostoma kantuckeense is endemic to the Barren River Basin in Southern Kentucky and Northern Tennessee, while E. lawrencei occurs in the Green River, Salt River, and Cumberland River Basins of Central and Eastern Kentucky. Isolation of populations within these drainages has allowed for a relatively recent evolutionary divergence, leading to slight differences in morphology. This study was conducted to address if geographical isolation has led to measurable differences in the ecology of these two species. In particular, habitat preference across three spatial scales and …

Fisheries Research Report No. 184 - Macroscopic And Microscopic Description Of Snapper (Pagrus Auratus) Gonads From Shark Bay, Western Australia, Michael C. Mackie, Gary Jackson, Nadia E. Tapp, Jeffrey V. Norriss, Adrian Thomson

Fisheries Research Reports

Since 1997, research on snapper (Pagrus auratus, Sparidae) in the inner gulfs of Shark Bay has focussed on providing biological information required for the management of the regionally important recreational fishery. A major component of this research has been a comprehensive investigation of snapper reproductive biology to determine size and age at maturity, the timing of the spawning season and to estimate batch fecundity. This research has necessitated a review of the macroscopic staging system used for P. auratus in Western Australian waters and the development of a more detailed microscopic system to allow accurate analyses of histological material. Based …

The Regulation Of Epithelial Sodium Channels In Mammalian Taste Receptor Cells, Arian F. Baquero Gonzalez

All Graduate Theses and Dissertations, Spring 1920 to Summer 2023

Nutrient recognition is one of the main physiological roles of the gustatory system. In mammals, it is well established that the taste of sodium salts is primarily mediated by sodium influx through the epithelial sodium channel. The epithelial sodium channel is a sodium-specific ion channel that is expressed across a wide range of transporting epithelia such as colon, kidney, and taste. In addition to its role as a salt taste receptor, sodium influx through the epithelial sodium channel is important systemically for maintaining sodium balance and blood pressure. Following our earlier work on the endocrine regulation of salt taste at …

Application Of Electrified Fladry To Decrease Risk Of Livestock Depredation By Wolves (Canis Lupus), Nathan J. Lance

All Graduate Theses and Dissertations, Spring 1920 to Summer 2023

Wolf (Canis lupus) predation on livestock can cause economic and emotional hardships for livestock producers, complicating the balance of wolf conservation with other human interests. New management tools that decrease risk of predation may offer additional flexibility or efficiency for both livestock producers and management agencies. I examined 1) the efficacy of electrified fladry compared to fladry at protecting a food source from wolves in captivity, 2) the efficacy of electrified fladry for reducing wolf use of pastures and preventing depredations, and 3) the applicability of electrified-fladry. In captivity I tested the reaction from 15 groups (46 wolves) …

Engineering An Anaerobic Derivative Of The Obligately Aerobic Thermophile Thermus Thermophilus Hb27 For The Purposes Of Studying Thermophilic Aerobic Respiratory Chain Proteins, Prajit Limsirichai

Biology Honors Theses

The thermophilic bacterium Thermus thermophilus (Tth) is an obligate aerobe with many important biotechnological applications and products. Thermostable proteins isolated from Thermus species have proven important in understanding adaptation to thermophilic environments. Thermophilic adaptations of respiratory electron transport chains (ETC) are not well characterized. Conventional homology-based, genetic, and biochemical techniques are limited in their ability to identify thermophilic Tth homologues of mesophilic respiratory ETC proteins due to the lack of a mutable facultative platform. We are attempting to generate this platform by increasing glycolytic flux through metabolic engineering techniques. Based on physiological studies, Tth HB27 demonstrates a low affinity for …

Joint Multiple Testing Procedures For Graphical Model Selection With Applications To Biological Networks, Houston N. Gilbert, Mark J. Van Der Laan, Sandrine Dudoit

U.C. Berkeley Division of Biostatistics Working Paper Series

Gaussian graphical models have become popular tools for identifying relationships between genes when analyzing microarray expression data. In the classical undirected Gaussian graphical model setting, conditional independence relationships can be inferred from partial correlations obtained from the concentration matrix (= inverse covariance matrix) when the sample size n exceeds the number of parameters p which need to estimated. In situations where n < p, another approach to graphical model estimation may rely on calculating unconditional (zero-order) and first-order partial correlations. In these settings, the goal is to identify a lower-order conditional independence graph, sometimes referred to as a ‘0-1 graphs’. For either choice of graph, model selection may involve a multiple testing problem, in which edges in a graph are drawn only after rejecting hypotheses involving (saturated or lower-order) partial correlation parameters. Most multiple testing procedures applied in previously proposed graphical model selection algorithms rely on standard, marginal testing methods which do not take into account the joint distribution of the test statistics derived from (partial) correlations. We propose and implement a multiple testing framework useful when testing for edge inclusion during graphical model selection. Two features of our methodology include (i) a computationally efficient and asymptotically valid test statistics joint null distribution derived from influence curves for correlation-based parameters, and (ii) the application of empirical Bayes joint multiple testing procedures which can effectively control a variety of popular Type I error rates by incorpo- rating joint null distributions such as those described here (Dudoit and van der Laan, 2008). Using a dataset from Arabidopsis thaliana, we observe that the use of more sophisticated, modular approaches to multiple testing allows one to identify greater numbers of edges when approximating an undirected graphical model using a 0-1 graph. Our framework may also be extended to edge testing algorithms for other types of graphical models (e.g., for classical undirected, bidirected, and directed acyclic graphs).

Bromeliads As A Breeding Site For The Dengue Vector Aedes Aegypti, Eva B. Shultis

Independent Study Project (ISP) Collection

Dengue Fever is a major public health concern in tropical and subtropical climates worldwide, including the city of Cairns, Australia, which is currently suffering a severe outbreak. The most important vector of the Dengue virus is the predominantly urban mosquito Aedes aegypti (L.), which lays its eggs in both artificial and natural containers, including the ornamental bromeliad plants found in many household gardens. The ability of larvae to develop to adulthood inside bromeliads has become controversial, however, and bromeliad enthusiasts frequently refuse to have their plants treated with insecticide. The aim of this study was to determine the conditions under …

Fisheries Research Report No. 187 - Management And Monitoring Of Fish Spawning Aggregations Within The West Coast Bioregion Of Western Australia, Michael C. Mackie

Fisheries Research Reports

Final FRDC Report – Project Number 2004/051

Objectives

1. To identify species that aggregate to spawn within the WCB and to describe (e.g. location, size, timing, nature) the aggregations of key demersal species such as pink snapper and dhufish.

2. To investigate the biology, ecology and fishery for Samson fish with emphasis on the sports fishery targeting deep water spawning aggregations west of Rottnest Island.

3. To establish methods and protocols for monitoring fish aggregations within the WCB.

4. To review relevant information and provide advice on the impact of aggregation fishing and the management of aggregating fish species in …

Microarray And Cdna Sequence Analysis Of Transcription During Nerve-Dependent Limb Regeneration, James R. Monaghan, Leonard G. Epp, Srikrishna Putta, Robert B. Page, John A. Walker, Chris K. Beachy, Wei Zhu, Gerald M. Pao, Inder M. Verma, Tony Hunter, Susan V. Bryant, David M. Gardiner, Tim T. Harkins, S. Randal Voss

Biology Faculty Publications

Background

Microarray analysis and 454 cDNA sequencing were used to investigate a centuries-old problem in regenerative biology: the basis of nerve-dependent limb regeneration in salamanders. Innervated (NR) and denervated (DL) forelimbs of Mexican axolotls were amputated and transcripts were sampled after 0, 5, and 14 days of regeneration.

Results

Considerable similarity was observed between NR and DL transcriptional programs at 5 and 14 days post amputation (dpa). Genes with extracellular functions that are critical to wound healing were upregulated while muscle-specific genes were downregulated. Thus, many processes that are regulated during early limb regeneration do not depend upon nerve-derived factors. …

Genic Regions Of A Large Salamander Genome Contain Long Introns And Novel Genes, Jeramiah J. Smith, Srikrishna Putta, Wei Zhu, Gerald M. Pao, Inder M. Verma, Tony Hunter, Susan V. Bryant, David M. Gardiner, Timothy T. Harkins, S. Randal Voss

Biology Faculty Publications

BACKGROUND: The basis of genome size variation remains an outstanding question because DNA sequence data are lacking for organisms with large genomes. Sixteen BAC clones from the Mexican axolotl (Ambystoma mexicanum: c-value = 32 x 10(9) bp) were isolated and sequenced to characterize the structure of genic regions.

RESULTS: Annotation of genes within BACs showed that axolotl introns are on average 10x longer than orthologous vertebrate introns and they are predicted to contain more functional elements, including miRNAs and snoRNAs. Loci were discovered within BACs for two novel EST transcripts that are differentially expressed during spinal cord regeneration and skin …

Abundance And Distribution Of Two Species Of Squilla (Crustacea: Stomatopoda: Squillidae) In The Northern Gulf Of Mexico, Jennifer L. Wortham

Gulf and Caribbean Research

Stomatopods (mantis shrimps) are predatory benthic crustaceans. Mantis shrimp in the genus Squilla are frequent bycatch animals unintentionally collected in conjunction with the shrimp fishery in the Gulf of Mexico (GOM). Their carcasses are discarded instead of being retained for human consumption, fish meal, or other protein-based food products. The size, depth, salinity, and temperature distributions of these species, as well as their abundance based on gender, were examined to gain biological information that would be necessary if a fishery were to develop in the GOM. I collected samples (n = 2,854) of Squilla empusa and Squilla chydaea in the …

Birds Of The Great Plains: Family Vireonidae (Vireos), Paul A. Johnsgard

Birds of the Great Plains (Revised Edition, 2009) by Paul Johnsgard

Black-capped Vireo
White-eyed Vireo
Bell Vireo
Gray Vireo
Yellow-throated Vireo
Solitary Vireo
Red-eyed Vireo
Philadelphia Vireo
Warbling Vireo

Birds Of The Great Plains: References, Paul A. Johnsgard

Birds of the Great Plains (Revised Edition, 2009) by Paul Johnsgard

A 21-page bibliography, including REGIONAL AND STATE REFERENCES and REFERENCES ON INDIVIDUAL SPECIES. Approximately 400 entries, through 1979.

An updated list of references will be found at the end of the new essay "Three Decades of Change in Great Plains Birds."

Birds Of The Great Plains: Family Parulidae (Wood Warblers), Paul A. Johnsgard

Birds of the Great Plains (Revised Edition, 2009) by Paul Johnsgard

Black-and-white Warbler
Prothonotary Warbler
Swainson Warbler
Wonn-eating Warbler
Golden-winged Warbler
Blue-winged Warbler
Tennessee Warbler
Nashville Warbler
Northern Parula
Yellow Warbler
Magnolia Warbler
Cape May Warbler
Black-throated Blue Warbler
Yellow-rumped Warbler (Myrtle and Audubon Warblers)
Black-throated Green Warbler
Cerulean Warbler
Blackburnian Warbler
Yellow -throated Warbler
Chestnut-sided Warbler
Bay-breasted Warbler
Pine Warbler
Prairie Warbler
Palm Warbler
Ovenbird
Northern Waterthrush
Louisiana Waterthrush
Kentucky Warbler
Mourning Warbler
MacGillivray Warbler
Conunon Yellowthroat
Yellow -breasted Chat
Hooded Warbler
Canada Warbler
American Redstart

Birds Of The Great Plains: Family Strigidae (Typical Owls), Paul A. Johnsgard

Birds of the Great Plains (Revised Edition, 2009) by Paul Johnsgard

Screech Owl
Great Horned Owl
Burrowing Owl
Barred Owl
Great Gray Owl
Long-eared Owl
Short-eared Owl
Saw-whet Owl

Birds Of The Great Plains: Family Turdidae (Thrushes, Bluebirds, And Solitaires), Paul A. Johnsgard

Birds of the Great Plains (Revised Edition, 2009) by Paul Johnsgard

American Robin
Wood Thrush
Hermit Thrush
Swainson Thrush
Veery
Eastern Bluebird
Mountain Bluebird
Townsend Solitaire

Louisiana Agriculture Winter, 2009

Louisiana Agriculture

No abstract provided.

Enzymatic Quantification Of Phytate In Animal Manure, Zhongqi He, Heidi W. Waldrip, C. Wayne Honeycutt, M. Susan Erich, Zachary N. Senwo

United States Department of Agriculture-Agricultural Research Service / University of Nebraska-Lincoln: Faculty Publications

Phytate (inositol hexaphosphate) has been identified as a major organic phosphorus (P) form in soil, animal manure, and other environmental samples. Although a number of methods are available for quantitative isolation and determination of phytate, they are time-consuming and not amenable to routine analysis. We developed a simple, rapid method for enzymatic determination of phytate in animal manure. Animal manure was extracted by H₂O, 1M hydrochloric acid (HCl), 0.1M sodium acetate (NaOAc, pH5.0) with or without 0.05M ethylenediaminetetraacetate (EDTA), and 0.25M or 0.5M sodium hydroxide (NaOH)–0.05M EDTA. Extracts were diluted (1/10–1/150) and adjusted to pH5.0 in sodium acetate …

A Locus-Based Paradigm For Generating Systems Biological Inferences From Large Scale Functional Genomics Datasets, Ajish Dominic George

Legacy Theses & Dissertations (2009 - 2024)

Genomics data is growing at a exponential rate. The ability to integrate new results with existing knowledge about genomic biology is rapidly becoming the limiting factor as there no universal language with which to describe genomic functional elements. To integrate and compare new and existing genomic data, we define our basic functional unit of a genome to be a locus -- a set of positional coordinates along any genome with an arbitrary amount of functional annotations attached. The locus concept enables addressing genomic elements and annotations at any level of granularity from entire swaths of chromosomes to single base-positions. We …

Study Of Seasonal Influences On Algal Biodiversity In The River Yarqon (Central Israel) By Bio-Indication And Canonical Correspondence Analysis (Cca), Sophia Barinova, Moti Tavassi

Turkish Journal of Botany

In our research conducted in the River Yarqon during 2003-2006, we identified 313 taxa of algae and cyanobacteria belonging to 8 taxonomical divisions. Out of these 313 taxa, 268 taxa (85.6%) were indicators of environmental conditions that characterised the river water as alkaline with medium mineralisation. In the rainy and dry seasons the algal taxonomic compositions were very different, with prevailing diatoms in the winter and cyabobacteria and greens in summer. Bio-indication shows that the taxonomic preference for the self-purification process was more intensive during the rainy season, while the low level of river water in the dry season stressed …

Unionoida (Mollusca: Margaritiferidae, Unionidae) In Arkansas, Third Status Review, John L. Harris, William R. Posey Ii, C. L. Davidson, Jerry L. Farris, S. R. Oetker, J. N. Stoeckel, B. G. Crump, M. S. Barnett, H. C. Martin, J. H. Seagraves, M. W. Matthews, R. Winterringer, C. Osborne, Alan D. Christian, N. J. Wentz

Journal of the Arkansas Academy of Science

We analyzed stream inventories, phylogeographic studies, community and population estimates, life history and reproductive biology research, and suitable habitat investigations conducted from 1997-2008, as well as the Arkansas Natural Heritage Commission mussel database, to update the conservation status for all native freshwater unionoid bivalves thought to occur in Arkansas. Prior to this study, Harris et al. (1997) reviewed the distribution and status of 75 freshwater mussels considered native to Arkansas and ranked 22 species as endangered, threatened or special concern. We now recognize 85 mussel taxa in Arkansas; however, some of those have yet to be described or their nomenclature …

Optimization Strategies For Electrospun Silk Fibroin Tissue Engineering Scaffolds, Kristopher Kubow

Selected Works

No abstract provided.

Productive Replication Of Malacosoma Neustria Nucleopolyhedrovirus (Manenpv) In Md203 Cell Line, İsmai̇l Demi̇r, Nurten Gürel, Remzi̇ye Nalçacioğlu, İkbal A. İnce, Zi̇hni̇ Demi̇rbağ

Turkish Journal of Biology

A plaque-purified genotypic variant, derived from a field isolate of the Malacosoma neustria nucleopolyhedrovirus (ManeNPV) from Turkey was characterized based on in vitro replication properties in a cell line, Md203 derived from Malacosoma disstria. The life cycle of ManeNPV was studied based on the cytopathic effects (CPEs), polyhedral inclusion body (PIB) formation, budded virus (BV) production, viral DNA replication and polyhedrin protein expression in ManeNPV-infected Md203 cells. Infection of Md203 cells with ManeNPV resulted in cytopathic effects within 24 and 36 h post infection and most cells detachted from the bottom of the culture plate on the fourth day. Typical …

First Approaches To Standard Protocols And Reference Materials For The Assessment Of Potential Hazards Associated With Nanomaterialss, Gordon Chambers, Hugh Byrne, Iseult Lynch, Micheal Riediker, Hans Bouwmeester, Hans Marvin, Alan Casey, Markus Berges, Martin Clift, Teresa Fernandez, Lise Fjellsbo, Lucienne Juillerat, Gert Roebben, Christoph, Klein, Qinglan Wu, Vince Hackley, Jean-Pierre Kaiser, Wolfganag Kreyling, Michael Garner, Peter Hatto,, Kenneth Dawson

Articles

All new technologies have an inherent risk, which is typically assessed alongside the development of applications of the technology. This is also the case for nanotechnology: a key concern in the case of engineered nanomaterials (ENMs) is that due to their very small size, NMs can reach areas such as the cell that are inaccessible to other materials, such as implants and drugs. As a result of their large surface area, NMs may be more reactive than other larger materials. The large physical and chemical variability of NMs, and the fact that small changes can have large consequences, mean that …

Comparative Susceptibilities Of Six Insect Cell Lines To Infection By Malacosoma Neustria Nucleopolyhedrovirus (Manenpv), İsmai̇l Demi̇r, Nurten Gürel, Remzi̇ye Nalçacioğlu, Zi̇hni̇ Demi̇rbağ

Turkish Journal of Biology

In this study, 6 lepidopteran cell lines derived from Trichoplusia ni (Tn5), Lymantria dispar (LdElta), Bombyx mori (Bm-5), Spodoptera frugiperda (Sf21), Spodoptera exigua (Se-1), and Choristoneura fumiferana (Cf-124T) were investigated for susceptibility to Malacosoma neustria nucleopolyhedrovirus (ManeNPV) isolated in Turkey. Infection of Malacosoma disstria (Md203) cell line by ManeNPV was used as a control. In ManeNPV-Md203 infection, polyhedral inclusion bodies (PIBs) were detected at 36 h p.i. and observed in all infected cells by 120 h p.i., and the infectious virus titer increased 10^3-fold. At 24 h p.i., the efficient replication of viral DNA was detected. In this study, we …

Microarray And Cdna Sequence Analysis Of Transcription During Nerve-Dependent Limb Regeneration, J. R. Monaghan, L. G. Epp, S. Putta, Robert B. Page, J. A. Walker, C. K. Beachy, W. Zhu, G. M. Pao, I. M. Verma, T. Hunter, S. V. Bryant, D. M. Gardiner, T. T. Harkins, S. R. Voss

Biology Faculty Publications (Archived)

Background: Microarray analysis and 454 cDNA sequencing were used to investigate a centuries-old problem in regenerative biology: The basis of nerve-dependent limb regeneration in salamanders. Innervated (NR) and denervated (DL) forelimbs of Mexican axolotls were amputated and transcripts were sampled after 0, 5, and 14 days of regeneration. Results: Considerable similarity was observed between NR and DL transcriptional programs at 5 and 14 days post amputation (dpa). Genes with extracellular functions that are critical to wound healing were upregulated while muscle-specific genes were downregulated. Thus, many processes that are regulated during early limb regeneration do not depend upon nerve-derived factors. …

Population Density, Circulating Testosterone And Dawn Chorus Behaviour In White-Throated Sparrows (Zonotrichia Albicollis), Simon Richard Hall

Theses and Dissertations (Comprehensive)

An integrative approach to biological research has facilitated the study not only of specific phenomena, but of the connections between these phenomena. A particularly striking example is that of the relationships between testosterone, social behavior, and social context. Increased levels of testosterone increase the frequency of aggressive behaviors and reduce the quality of parental care in many songbird species, and these changes in behavior can affect the surrounding social environment. Different social contexts, population density as a readily studied example, affect the cues that control the release of testosterone into the bloodstream. The distinct tan-stripe and white-stripe phenotypic morphs of …

Trichomycetes From Lentic And Lotic Aquatic Habitats In Ontario, Canada, D. B. Strongman, Merlin M. White

Biology Faculty Publications and Presentations

Fungi and protists make up an ecological group, trichomycetes, that inhabit the guts of invertebrates, mostly aquatic insects. Trichomycetes are reported herein from arthropods collected in lotic habitats (fast flowing streams) and lentic environments (ponds, ditches, seeps, and lakes) from 11 sites in Algonquin Park and 6 other sites in Ontario, Canada. Thirty-two trichomycete species were recovered, including 7 new species: Legeriomyces algonquinensis, Legeriosimilis leptocerci, Legeriosimilis whitneyi and Paramoebidium umbonatum are described from mayfly nymphs (Ephemeroptera); Pennella digitata and Glotzia incilis from black fly and midge larvae (Diptera), respectively; and Arundinula opeongoensis from a crayfish (Crustacea). Legeriomyces rarus Lichtw. & …