Biology Commons^™

A Holistic Approach To Mima Mound Prairie Restoration, Kristin R. Anicito

EWU Masters Thesis Collection

"Invasive winter annual grass (IWAGs) abundance has increased throughout much of the western United States, with serious consequences for biodiversity and ecosystem function. While a variety of tools have been used to control IWAGS, they often fail to achieve the goal of creating a self-sustaining native plant community. Therefore, a major goal of my thesis has been to explore and test restoration approaches that might help realize such plant communities. These approaches include ecologically based invasive plant management (EBIPM) and assisted succession. EBIPM is a holistic approach that aims to restore ecological functions damaged by IWAGs with a combination of …

Assessment Of The Hatchery Kokanee (Oncorhynchus Nerka) Release Program In Lake Roosevelt 2009 -- 2012, Alix O. Blake

EWU Masters Thesis Collection

This study determined which kokanee stock performed best in Lake Roosevelt, WA: Lake Whatcom, Meadow Creek, or F1 mixed stock. The F1 mixed stock was created by collecting eggs from Lake Whatcom, Meadow Creek and non-marked kokanee that returned to Hawk Creek and raising them to the residualized smolt stage at the Spokane Tribal hatchery for release back into Lake Roosevelt. Fall spawning run data (2009 – 2012) were analyzed to assess the percentage and sex ratios of each stock returning to spawn in Lake Roosevelt. We had record returns of hatchery kokanee in 2009 (n = 8,895) and 2010 …

Use Of Magnetic And Olfactory Cues For Orientation By A Fossorial Rodent, Thomomys Talpoides, Dustin J. Cousins

EWU Masters Thesis Collection

"Fossorial, or below ground, living provides shelter from the elements and some predators, but comes at a cost with respect to metabolic requirements of movement and reduced, or altered, sensory cues. I examined the ability of the North American pocket gopher, Thomomys talpoides, to use magnetoreception and olfaction in navigation and foraging. Magnetoreception was tested using three manipulative experiments: 1) field homing of displaced animals, 2) nest location in an 8-arm maze, and 3) movement through a complex labyrinth. Homing results, analyzed by V-test, indicated that the gophers displaced from their burrow systems relied on magnetic cues for homing orientation. …

Predation, Turbidity, And Other Factors Influencing Juvenile Salmonid Survival In The Lower Snake River, Devin M. Sontag

EWU Masters Thesis Collection

"The object of this study was to quantify consumption rates of juvenile salmonids by three introduced species, smallmouth bass (Micropterus dolomieu), walleye (Sander vitreus) and channel catfish (Ictalurus punctatus). Consumption information is crucial because the construction of the Snake River hydrosystem has created a series of reservoirs, which have altered the river 's flow regimes, riparian vegetation, and turbidity. Further, several non-native fishes have been introduced as sport fish into the Lower Snake River. This combination of physical alterations and new biological interactions with introduced species has reduced the survival of anadromous salmonids in the Lower Snake River. Currently all …

Disruption Of Ephrin-A5 In Developing Xenopus Laevis Embryos By Shrna, Sarah C. Engmark

Senior Honors Theses and Projects

Eph receptors are the largest class of receptor tyrosine kinases (RTKs) that participate in bidirectional cell signaling with their cell surface ephrin ligands during the development of vertebrate embryos. Ephrin-A5 is one ligand that interacts with the EphA4 receptor, but is present much earlier than EphA4 in developing Xenopus laevis embryos. This raises the question why ephrin-A5 is expressed so early and suggests that it may have a role in embryonic development and tissue differentiation independent ofEphA4. This project attempted to study ephrin-A5's function using a short hairpin RNA (shRNA) knockdown approach. A vector encoding shRNA of the ephrin-A5 mRNA …

Does Ecosystem Disturbance Alter The Capacity Of Dissolved Organic Matter To Mitigate The Impact Of Copper To Hyalella Azteca?, Kelly Livingstone

Theses and Dissertations (Comprehensive)

The potential for aquatic ecosystem recovery as a result of dissolved organic matter (DOM) protecting against metal toxicity has become a significant area of research in environmental toxicology. It is a well-characterized relationship that DOM binds free metal ions in a concentration-dependant manner, making them unavailable for toxic action and a reduction in toxicity is seen. Less understood is source variability and how the upland terrestrial environment influences the protective quality of DOM. The aim of this study was to examine the influence of land disturbance (logging, fire, smelter emissions) on DOM quality by comparing the protective capacity of different …

Mechanisms Of Nitrogenous Waste Excretion During The Complex Life Cycle Of The Sea Lamprey (Petromyzon Marinus), James M. Neal Mr.

Theses and Dissertations (Comprehensive)

Sea lampreys (Petromyzon marinus) are a phylogenetically ancient jawless fish, with a multi-staged life cycle characterized by a prolonged suspension-feeding larval stage, which is followed by metamorphosis into parasitic lampreys that feed on the protein-rich blood of fishes. The switch from a nutrient poor to protein-rich diet in the sea lamprey is associated with an increased capacity to deaminate excess amino acids and to excrete ammonia and urea following metamorphosis. The focus of this thesis was to determine if changes in nitrogenous waste transporter protein abundance facilitate ammonia and urea excretion during different stages of the sea lamprey …

Smb Myosin Heavy Chain Knockout Enhances Tonic Contraction And Reduces The Rate Of Force Generation In Ileum And Stomach Antrum, Qian Huang, Gopal J. Babu, Muthu Periasamy, Thomas J. Eddinger

Biological Sciences Faculty Research and Publications

The role of SMA and SMB smooth muscle myosin heavy chain (MHC) isoforms in tonic and phasic contractions was studied in phasic (longitudinal ileum and stomach circular antrum) and tonic (stomach circular fundus) smooth muscle tissues of SMB knockout mice. Knocking out the SMB MHC gene eliminated SMB MHC protein expression and resulted in upregulation of the SMA MHC protein without altering the total MHC protein level. Switching from SMB to SMA MHC protein expression decreased the rate of the force transient and increased the sustained tonic force in SMB^(−/−) ileum and antrum with high potassium (KPSS) but not …

The Conservation Status Of The World’S Reptiles, Tony Gamble

Biological Sciences Faculty Research and Publications

Effective and targeted conservation action requires detailed information about species, their distribution, systematics and ecology as well as the distribution of threat processes which affect them. Knowledge of reptilian diversity remains surprisingly disparate, and innovative means of gaining rapid insight into the status of reptiles are needed in order to highlight urgent conservation cases and inform environmental policy with appropriate biodiversity information in a timely manner. We present the first ever global analysis of extinction risk in reptiles, based on a random representative sample of 1500 species (16% of all currently known species). To our knowledge, our results provide the …

A Transgenic Minipig Model Of Huntington's Disease, Monika Baxa, Marian Hruska-Plochan, Stefan Juhas, Petr Vodicka, Antonin Pavlok, Jana Juhasova, Atsushi Miyanohara, Tetsuya Nejime, Jiri Klima, Monika Macakova, Silvia Marsala, Andreas Weiss, Svatava Kubickova, Petra Musilova, Radek Vrtel, Emily M. Sontag, Leslie Thompson, Jan Schier, Hana Hansikova, David S. Howland, Elena Cattaneo, Marian Difiglia, Martin Marsala, Jan Motlik

Biological Sciences Faculty Research and Publications

Background: Some promising treatments for Huntington's disease (HD) may require pre-clinical testing in large animals. Minipig is a suitable species because of its large gyrencephalic brain and long lifespan. Objective: To generate HD transgenic (TgHD) minipigs encoding huntingtin (HTT)1–548 under the control of human HTT promoter. Methods: Transgenesis was achieved by lentiviral infection of porcine embryos. PCR assessment of gene transfer, observations of behavior, and postmortem biochemical and immunohistochemical studies were conducted. Results: One copy of the human HTT transgene encoding 124 glutamines integrated into chromosome 1 q24-q25 and successful germ line transmission occurred through successive generations (F0, F1, F2 …

Suppression Of Chemically Induced And Spontaneous Mouse Oocyte Activation By Amp-Activated Protein Kinase, Ru Ya, Stephen M. Downs

Biological Sciences Faculty Research and Publications

Oocyte activation is an important process triggered by fertilization that initiates embryonic development. However, parthenogenetic activation can occur either spontaneously or with chemical treatments. The LT/Sv mouse strain is genetically predisposed to spontaneous activation. LT oocytes have a cell cycle defect and are ovulated at the metaphase I stage instead of metaphase II. A thorough understanding of the female meiosis defects in this strain remains elusive. We have reported that AMP-activated protein kinase (PRKA) has an important role in stimulating meiotic resumption and promoting completion of meiosis I while suppressing premature parthenogenetic activation. Here we show that early activation of …

Fungi Isolated From Niedźwiedzia Cave In Kletno (Lower Silesia, Poland), Rafał Ogórek, Agnieszka Lejman, Krzysztof Matkowski

International Journal of Speleology

Niedźwiedzia Cave is the most beautiful cave in Poland, discovered in a block of Cambrian marbles. It is the most important part of the reserve established in 1977. The cave is located within the Kłodzko Valley, in Śnieżnik Mt. Massif, in Kleśnica Stream Valley and was discovered in 1966 while working in a quarry. The study aimed at first mycological evaluation of the air and the rocks in Niedźwiedzia Cave. Nine species of filamentous fungi and a yeast species were isolated from the air sampled in the cave, whereas from the rocks - nine species of filamentous fungi and two …

Exploring The Sulfide Tolerance Of Ectosymbiotic Niphargus Amphipods From The Frasassi Caves, Central Italy, Jan Bauermeister, Karoline Assig, Sharmishtha Dattagupta

International Journal of Speleology

Two species of the crustacean amphipod genus Niphargus inhabit the sulfidic groundwaters of the Frasassi caves in central Italy, and both harbor filamentous, sulfide-oxidizing Thiothrix ectosymbionts. As sulfide is toxic to most aerobic organisms, it appeared possible that the ectosymbionts could help their Niphargus hosts with detoxification processes. In this study, mortality due to sulfide was compared between Niphargus individuals with ectosymbionts and individuals whose ectosymbionts had been killed by antibiotic treatment. Both Frasassi-dwelling Niphargus species revealed exceptionally high tolerances to sulfide compared to other amphipod species studied so far. Niphargus individuals without viable ectosymbionts tolerated sulfide levels exceeding those …

Environmental Effects On The Biomechanics And Motor Physiology Of Elastically Powered Movements In Chameleons, Christopher Van Anderson

USF Tampa Graduate Theses and Dissertations

Environmental temperature exhibits profound effects on the activity and ecology of ectotherms through its impact on muscle contractile physiology. While the performance of locomotor behaviors powered by muscle contraction directly decreases by at least 33% over a 10°C drop in body temperature, chameleons are known to feed, presumably with high performance, at body temperatures where sympatric lizard species remain inactive. I propose that ballistic movements that are powered by the recoil of preloaded elastic and collagenous tissues are less thermally dependent than movements that rely on direct muscular power. Despite the reduced thermal sensitivity of the elastic-recoil powered movement, I …

Family Matters: An Analysis Of Genetic Relatedness Of Tetraclita Rubescens (The Pink Volcano Barnacle) Over Several Spatial Scales At Monterey And Bodega Bay, California, Kelly N. Chang

Scripps Senior Theses

Inbreeding involves the mating of closely related individuals at a higher frequency than at random; this can decrease the average fitness of populations and individuals by reducing the presence of heterozygotes and augmenting the expression of deleterious genes. Since marine invertebrates exhibit widespread dispersal, their potential for inbreeding is often disregarded. The adult sessile state of barnacles creates the potential for inbreeding as a result of necessary copulation between neighboring individuals. Depending on the degree of mixing that occurs during dispersal, closely related individuals or siblings may settle in close proximity, generating the possibility of kin aggregation and consequent inbreeding. …

The Terrestrial Biogeochemical Cycle Of Barium: A Proposed Study To Examine Barium Flux In Mojave Desert Dust, Mehar Kaur

Scripps Senior Theses

Barium is a relatively abundant element in the crustal environments, Ba quantities can range from anywhere between 200ppm to 900ppm. Most common forms of Ba-minerals found in the environment are barite (BaSO₄), witherite (BaCO₃) and hollandite (Ba₂Mn₈O₁₆). Ba is a useful element; it is used in various industries as a component in drilling fluids, in medical research and in manufacturing of various substances such as glass, ceramics, printing paper etc. However high quantity of Ba can be potentially toxic for the human body and can impair plant growth. It is …

Utilisation Of Spent Dairy Yeast Kluyveromyces Marxianus For The Production Of Flavoured Yeast Extracts., Brendan Mccarra

Theses

Spent dairy yeast Kluyveromyces marxianus (SDYK), a by-product of whey to ethanol fermentations, was investigated as a natural biomass source for the production of alternative flavoured yeast extracts. SDYK which was characterised by a high protein content (55.3% (w/w) ± 0.8) and comparable levels of flavor enhancing amino acids to that of S. cerevisiae was prepared for induced autolysis at different pH values in the presence of inductors sodium chloride and the proteolytic enzyme papain. An induced autolysis process was developed for the production of flavoured yeast extracts in which pH and autolytic treatment applied were found to have a …

Phylogeography Of The Malagasy Ant Species Otontomachus Coquereli, Jason Jackson

Electronic Theses and Dissertations

Madagascar is an extremely diverse and geographically complex area boasting levels of endemism that blatantly raise questions about their origins. There is evidence that these endemics arose via insitu diversification during Madagascar's ~88 million year isolation, even though it was essentially in the middle of Gondwana with ample opportunity to acquire inhabitants. Madagascar's high levels of diversity and endemism make it an ideal location to study speciation, especially considering the evidence that such high levels speciation occurred in Madagascar itself. Several hypotheses have been formulated to relate the complex geography to genetic divergence, and thereby speciation. I explore three hypotheses …

Silver Nanoparticles Induce Developmental Stage-Specific Embryonic Phenotypes In Zebrafish, Kerry J. Lee, Lauren M. Browning, Prakash D. Nallathamby, Christopher J. Osgood, Xiao-Hong Nancy Xu

Chemistry & Biochemistry Faculty Publications

Much is anticipated from the development and deployment of nanomaterials in biological organisms, but concerns remain regarding their biocompatibility and target specificity. Here we report our study of the transport, biocompatibility and toxicity of purified and stable silver nanoparticles (Ag NPs, 13.1 ± 2.5 nm in diameter) upon the specific developmental stages of zebrafish embryos using single NP plasmonic spectroscopy. We find that single Ag NPs passively diffuse into five different developmental stages of embryos (cleavage, early-gastrula, early-segmentation, late-segmentation, and hatching stages), showing stage-independent diffusion modes and diffusion coefficients. Notably, the Ag NPs induce distinctive stage and dose-dependent phenotypes and …

Suitability Of Real-Time Quantitative Pcr To Estimate The Relative Telomere Length In European Hake (Merluccius Merluccius Linnaeus, 1758), Estabaliz López De Abechuco, Manuel Soto, Miguel Angel Pardo, Mark F. Haussmann, Guzmán Díez

Faculty Journal Articles

Telomere length measurement has been proposed as a promising tool to estimate the age of individuals in natural populations. We used real-time quantitative PCR (qPCR) to measure relative telomere length in four tissues (brain, kidney, liver and muscle) of European hake (Merluccius merluccius) in different groups based upon body length an otolith age estimate. We observed a high level of inter-individual differences in the measurements of relative telomere length in hakes of similar age and body length groups. The results of qPCR analysis showed a great variability in all measures and a lack of repeatability and reproducibility with significant statistical …

Habitat Use And Feeding Ecology Of Delphinids Inferred From Stable Isotopes And Fatty Acid Signatures, Nicole Browning

Electronic Theses and Dissertations

Prey availability, directly or indirectly, affects all aspects of a predator’s life history and is a primary factor influencing habitat selection and movements. This is especially true for delphinid species where it has been documented that the behaviors and movements of dolphins are strongly influenced by food availability. Unfortunately, the feeding ecology and habitat use patterns of many of these species are poorly understood. Many methodologies that have been employed to explore these facets of dolphin ecology have limitations and constraints or are logistically infeasible. Stable isotope and fatty acid signature analyses have been used extensively on a wide variety …

Assessing The Effectiveness Of Living Shoreline Restoration And Quantifying Wave Attenuation In Mosquito Lagoon, Florida, Jennifer Manis

Electronic Theses and Dissertations

Coastal counties make up only 17% of the land area in the continental United States, yet 53% of the nation’s population resides in these locations. With sea level rise, erosion, and human disturbances all effecting coastal areas, researchers are working to find strategies to protect and stabilize current and future shorelines. In order to maintain shoreline stability while maintaining intertidal habitat, multipurpose living shorelines have been developed to mimic natural shoreline assemblages while preventing erosion. This project determined the effectiveness of a living shoreline stabilization containing Crassostrea virginica (eastern oyster) and Spartina alterniflora (smooth cordgrass) in the field and through …

No Control Genes Required: Bayesian Analysis Of Qrt-Pcr Data., Mikhail V. Matz, Rachel M. Wright, James G. Scott

Biological Sciences: Faculty Publications

Model-based analysis of data from quantitative reverse-transcription PCR (qRT-PCR) is potentially more powerful and versatile than traditional methods. Yet existing model-based approaches cannot properly deal with the higher sampling variances associated with low-abundant targets, nor do they provide a natural way to incorporate assumptions about the stability of control genes directly into the model-fitting process. In our method, raw qPCR data are represented as molecule counts, and described using generalized linear mixed models under Poisson-lognormal error. A Markov Chain Monte Carlo (MCMC) algorithm is used to sample from the joint posterior distribution over all model parameters, thereby estimating the effects …

A New Method For Identifying Stem-Like Cells In Esophageal Cancer Cell Lines, Michael Eric Geusz, Taghreed N. Almanaa, Roudabeh J. Jamasbi

Biological Sciences Faculty Publications

Cancer stem cells (CSCs) appear to resist chemo-radiotherapy and initiate tumor recurrence in patients. Isolation and further characterization of this subpopulation is important for targeting CSCs. Flow cytometry using Aldefluor, a fluorescent substrate of aldehyde dehydrogenase, has been used to isolate CSCs from various cancer cell lines. However, newtechniques are needed to locate and identify CSCs in culture for live-cell analyses such as fluorescence microscopy without introducing artifacts during cell sorting and to observe CSC and non-CSC interactions. Previously, we characterized a distinct CSC subpopulation within human esophageal cancer cell lines (ESCC). In this study we introduce the attached-cell Aldefluor …

Characterization Of The Asian Citrus Psyllid Transcriptome, Justin Reese, Matthew K. Christenson, Nan Leng, Surya Saha, Brandi Cantarel, Magdalen Lindeberg, Cecilia Tamborindeguy, Justin Maccarthy, Andrew J. Trease, Steven V. Ready, Vincent M. David, Courtney Mccormick, Christian Haudenschild, Shunsheng Han, Shannon L. Johnson, Kent S. Shelby, Hong Huang, Blake R. Bextine, Robert G. Shatters, David G. Hall, Paul H. Davis, Wayne B. Hunter

Biology Faculty Publications

The Asian citrus psyllid, Diaphorina citri Kuwayama (Hemiptera: Psyllidae) is a vector for the causative agents of Huanglongbing, which threatens citrus production worldwide. This study reports and discusses the first D. citri transcriptomes, encompassing the three main life stages of D. citri, egg, nymph and adult. The transcriptomes were annotated using Gene Ontology (GO) and insecticide-related genes within each life stage were identified to aid the development of future D. citri insecticides. Transcriptome assemblies and other sequence data are available for download at the International Asian Citrus Psyllid Genome Consortium website [http://psyllid.org/download] and at NCBI [http://www.ncbi.nlm.nih.gov/bioproject/29447].

In Vivo Analysis Of Highly Conserved Nef Activities In Hiv-1 Replication And Pathogenesis, Richard L. Watkins, Wei Zou, Paul W. Denton, John F. Krisko, John L. Foster, J. Victor Garcia

Biology Faculty Publications

Background: The HIV-1 accessory protein, Nef, is decisive for progression to AIDS. In vitro characterization of the protein has described many Nef activities of unknown in vivo significance including CD4 downregulation and a number of activities that depend on Nef interacting with host SH3 domain proteins. Here, we use the BLT humanized mouse model of HIV-1 infection to assess their impact on viral replication and pathogenesis and the selection pressure to restore these activities using enforced in vivo evolution.

Results: We followed the evolution of HIV-1LAI (LAI) with a frame-shifted nef (LAINeffs) during infection of BLT mice. LAINeffs …

A Study Of The Sensitivity Of Plethodon Cinereus (Caudata: Plethodontidae) To Damage-Released Cues From Conspecifics, Aaron M. Sullivan, Gregory Jensen

Faculty Publications - Department of Biological & Molecular Science

Some prey species vary the intensity of antipredator responses according to the perceived level of threat associated with different concentrations of chemical cues related to predation. Here, we examine whether Red-Backed Salamanders (Plethodon cinereus) respond to different concentrations of damage-released cues from the tails of conspecifics in a threat-sensitive manner. We exposed salamanders either to a control or to damage-released cues from conspecifîcs at one of three different concentrations. We found that salamanders exposed to damage released cues significantly decreased their activity compared to salamanders exposed to a control. However, the intensity of the responses was not related to the …

Axolotl Paedomorphosis: A Comparison Of Juvenile, Metamorphic, And Paedomorphic Ambystoma Mexicanum Brain Gene Transcription, Carlena Johnson

Theses and Dissertations--Biology

Unlike many amphibians, the paedomorphic axolotl (Ambystoma mexicanum) rarely undergoes external morphological changes indicative of metamorphosis. However, internally, some axolotl tissues undergo cryptic metamorphic changes. A previous study examined interspecific patterns of larval brain gene expression and found that these species exhibited unique temporal expression patterns that were hypothesized to be morph specific. This thesis tested this hypothesis by examining differences in brain gene expression between juvenile (JUV), paedomorphic (PAED), and metamorphic (MET) axolotls. I identified 828 genes that were expressed differently between JUV, PAED, and MET. Expression estimates from JUV were compared to estimates from PAED and …

The Contribution Of Two Related Bbp-Binding Gyf Proteins, Smy2 And Syh1, To Cellular Rna Abundance And Genome Stability, Min Chen

Theses and Dissertations--Biology

Nuclear precursor of mature messenger RNA (pre-mRNA) splicing is one of the most highly regulated processes in eukaryotic organisms. In addition to its role in the removal of constitutive or alternative introns present in the pre-mRNA, splicing is also highly integrated into other layers of gene expression. This study investigates the potential role of the nuclear branchpoint binding protein (BBP) outside of the pre-mRNA splicing cycle. More specifically, we were interested in the biological relevance of its association with two cytoplasmic proteins Smy2 and Syh1. Smy2 and Syh1 belong to the GYF family of poly-proline binding proteins, and their roles …

Investigation Of Media Ingredients And Water Sources For Algae Co2 Capture At Different Scales To Demonstrate The Correlations Between Lab-Scale And Large-Scale Growth, Tabitha Graham

Theses and Dissertations--Biosystems and Agricultural Engineering

As energy use increases globally the environmental burdens increase alike. Many accusations have been made that carbon dioxide is a culprit of climate change. The University of Kentucky and Duke Energy Power have partnered to test carbon capture technology in a large scale project. To this end, the objective of this thesis is to investigate potential water media sources and nutrient sources at different volume scales for algae cultivation to help create a more environmentally viable and economically feasible solution. This work will conduct a life cycle assessment of water media sources and the effects of the inputs and outputs …