Digital Commons Network^™

Volume 02, Joseph A. Mann, Kathryn J. Greenly, Scott E. Jenkins, Andrew E. Puckette, Daniel M. Honey, Jeffery P. Ravenhorst, Jamie Elizabeth Mesrobian, Thomas Scott, Jay Crowell, Sarah Spangenberg, Amy S. Eason, Kenny Wolfe, Liz Hale, Rachel Bouchard, Will Semonco, Carley York, Ryan Higgenbothom, Adrienne Heinbaugh, Melissa Dorton, Madeline Hunter, June Ashmore, Clark Barkley, Jay Haley

Incite: The Journal of Undergraduate Scholarship

Introduction from Dean Dr. Charles Ross

Mike's Nite: New Jazz for an Old Instrument by Joseph A. Mann

Investigation of the use of Cucumis Sativus for Remediation Of Chromium from Contaminated Environmental Matrices: An Interdisciplinary Instrumental Analysis Project by Kathryn J. Greenly, Scott E. Jenkins, and Andrew E. Puckette

Development of GC-MS and Chemometric Methods for the Analysis of Accelerants in Arson Cases by Scott Jenkins

Building and Measuring Scalable Computing Systems by Daniel M. Honey and Jeffery P. Ravenhorst

Nomini Hall: A Case Study in the Use of Archival Resources as Guides for Excavation at An Archaeological Site by …

Differential Response Of Amp Activated Protein Kinase (Ampk) And Hsp70 To Temperature Stress In The Gastropod, Nucella Lapillus, Emily Zimmermann

All Theses And Dissertations

Populations of the gastropod Nucella lapillus are polymorphic for shell color, with light-colored shells predominating on warmer, wave-protected shores and dark-colored shells limited primarily to cooler, wave-exposed shores. During thermal stress, darker shells attain higher body temperatures than lighter shells. These results suggest that heat stress may determine field distribution patterns. However, there is currently little evidence of physiological consequences of thermal stress in these organisms. Following the guiding hypothesis that heat stress leads to cellular energy depletion, we explored whether the central energy regulator AMP-activated Protein Kinase (AMPK) is activated by heat stress. We compared this response in both …

Investigation Of Protozoan Epibionts On Deep-Sea Nematodes, Alicia Leigh Gabriele

Honors Capstones

No abstract provided.

Fisheries Occasional Publication No. 66 - Scientific Review Of The West Coast Demersal Scalefish Fishery, Western Australia, Michael O'Neill, Department Of Fisheries Western Australia

Fisheries Occasional Publications

In December 2008 the Hon Norman Moore MLC, Minister for Fisheries Western Australia appointed two independent experts to assess separately 1) the validity of scientific advice to management and 2) options to manage recreational fishing of west coast demersal scalefish. The following review (1) assesses the validity of research outlining the status of baldchin groper (Choerodon rubescens), West Australian dhufish (Glaucosoma hebraicum) and snapper (Pagrus auratus) as described in the terms of reference. In addition to the terms of reference, an opinion was requested regarding the current appropriateness of the research advice (Wise et al 2007) and the resulting management …

Proteomic Comparison Of Entamoeba Histolytica And Entamoeba Dispar And The Role Of E. Histolytica Alcohol Dehydrogenase 3 In Virulence, Paul H. Davis, Minghe Chen, Xiaochun Zhang, C. Graham Clark, R. Reid Townsend, Samuel L. Stanley

Biology Faculty Publications

The protozoan intestinal parasite Entamoeba histolytica infects millions of people worldwide and is capable of causing amebic dysentery and amebic liver abscess. The closely related species Entamoeba dispar colonizes many more individuals, but this organism does not induce disease. To identify molecular differences between these two organisms that may account for their differential ability to cause disease in humans, we used two-dimensional gel-based (DIGE) proteomic analysis to compare whole cell lysates of E. histolytica and E. dispar. We observed 141 spots expressed at a substantially (.5- fold) higher level in E. histolytica HM-1:IMSS than E. dispar and 189 spots showing …

Seasonal Variation In Diet Of A Marginal Population Of The Hispid Cotton Rat, Sigmodon Hispidus, Lynn A. Walker, Robert K. Rose

Virginia Journal of Science

Cotton rats live in oldfields, habitats with a variety of mostly herbaceous plants. Based on other studies, the hispid cotton rat, Sigmodon hispidus, eats many kinds of herbaceous plants but grasses predominate. In contrast, our population of cotton rats ate many monocots but mostly they were not grasses. Our study sought to determine the diet of the cotton rat in eastern Virginia, near the northern limit of distribution on the Atlantic Coast. Fecal samples, collected each month during an on-going capture-mark-release demographic study of the rodent community, were analyzed using a standard method. A greater variety of foods (including …

Altered Regulation Of Aquaporin Gene Expression In Allergen And Il-13-Induced Mouse Models Of Asthma, Carissa M. Krane, Bijia Deng, Venkateshwar Mutyam, Casey A. Mcdonald, Stephen Pazdziorko, Lawrence Mason, Samuel Goldman, Marion Kasaian, Divya Chaudhary, Cara Williams, Melisa W.Y. Ho

Biology Faculty Publications

IL-13 is known to affect many processes that contribute to an asthmatic phenotype, including inflammation, fibrosis, and mucus production. Members of the aquaporin (AQP) family of transmembrane water channels are targets of regulation in models of lung injury and inflammation. Therefore, we examined AQP mRNA and protein expression in allergen and IL-13-induced mouse models of asthma. Lungs from ovalbumin sensitized and ovalbumin challenged (OVA/OVA) and IL-13 treated mice showed airway thickening, increased mucus production, and pulmonary eosinophilia. Pulmonary function tests showed a significant increase in methacholine-induced airway hyperreactivity in OVA/OVA and IL-13-treated mice as compared with controls. Quantitative PCR analysis …

N-Acetylcysteine Amide Decreases Oxidative Stress But Not Cell Death Induced By Doxorubicin In H9c2 Cardiomyocytes, Rong Shi, Chuan-Chin Huang, Robert Aronstam, Nuran Ercal, Adam Martin, Yue-Wern Huang

Biological Sciences Faculty Research & Creative Works

Background: While doxorubicin (DOX) is widely used in cancer chemotherapy, long-term severe cardiotoxicity limits its use. This is the first report of the chemoprotective efficacy of a relatively new thiol antioxidant, N-acetylcysteine amide (NACA), on DOX-induced cell death in cardiomyocytes. We hypothesized that NACA would protect H9c2 cardiomyocytes from DOX-induced toxicity by reducing oxidative stress. Accordingly, we determined the ability of NACA to mitigate the cytotoxicity of DOX in H9c2 cells and correlated these effects with the production of indicators of oxidative stress.

Results: DOX at 5 μM induced cardiotoxicity while 1) increasing the generation of reactive oxygen species (ROS), …

Sponges On Chumbe Island, Emily Marshall

Independent Study Project (ISP) Collection

The sponge population of Chumbe Island, off the western coast of Unguja Island was studied. Opportunistic observation, underwater photography, and sponge collection on the eastern side of the island was conducted. The sponge samples collected where then taxonomically analyzed in the lab. This is study will contribute to the limited amount of information known about sponge taxonomy and prevalence in the Western Indian Ocean region. It will increase the knowledge about the diversity of sponges in this region. The information collected from this experiment was compiled into a booklet that will be available to the tourists as well as the …

The Relative Ages Of Ectomycorrhizal Mushrooms And Their Plant Hosts Estimated Using Bayesian Relaxed Molecular Clock Analyses, David S. Hibbett, P. Brandon Matheny

Biology

Background: Ectomycorrhizae (ECM) are symbioses formed by polyphyletic assemblages of fungi (mostly Agaricomycetes) and plants (mostly Pinaceae and angiosperms in the rosid clade). Efforts to reconstruct the evolution of the ECM habit in Agaricomycetes have yielded vastly different results, ranging from scenarios with many relatively recent origins of the symbiosis and no reversals to the free-living condition; a single ancient origin of ECM and many subsequent transitions to the free-living condition; or multiple gains and losses of the association. To test the plausibility of these scenarios, we performed Bayesian relaxed molecular clock analyses including fungi, plants, and other eukaryotes, based …

Fisheries Occasional Publication No. 63 - Western Rock Lobster Ecological Risk Assessment, Department Of Fisheries, Western Australia, International Risk Consultants Group Of Companies

Fisheries Occasional Publications

This Ecological Risk Assessment, conducted by IRC Environment (part of International Risk Consultants) and Department of Fisheries WA (FWA) was the result of an initiative by the WA Fishing Industry Council (WAFIC) and (FWA). This report is based on a risk assessment workshop undertaken in February 2001 at the FWA Marine Research Laboratories in Waterman but includes additional background material to justify some of the rankings of the workshop.

The broad intent of the workshop was to provide a register of the potential main ecological risks that arise from the various activities carried out by the western rock lobster (WRL) …

Biogeography Of The Livebearing Fish Poecilia Gillii In Costa Rica: Are Phylogeographic Breaks Congruent With Fish Community Boundaries?, Jared Benjamin Lee

Theses and Dissertations

One of the original goals of phylogeography was to use genetic data to identify historical events that might contribute to breaks among biotic communities. In this study, we examine the phylogeography of a common livebearing fish (Poecilia gillii) from Costa Rica. Our goal was to see if phylogeographic breaks in this species were congruent with previously-defined boundaries among four fish community provinces. We hypothesized that if abiotic factors influence both community boundaries and genetic structuring in P. gillii then we would find four monophyletic clades within our focal species that were geographically separated along community boundary lines. Similarly, we expected …

Fisheries Occasional Publication No.057 - Introduced Marine Species In Western Australia, Department Of Fisheries Western Australia

Fisheries Occasional Publications

As the largest State in Australia, Western Australia (WA) has a long and relatively pristine coastline that stretches over 12,500 km, or over 20,700 km if the State’s 3,747 islands are included. The coast ranges over 20 degrees of latitude from the temperate south coast to the northern tip of the tropical Kimberley. There are a wide variety of coastal marine habitats in this vast area. The south coast has extensive white sandy beaches interspersed with granite headlands. A diverse range of nearly 800 species of temperate marine algae, or seaweeds, occurs in the area. With 26 species, the seagrasses …

Functional Differences Within A Guild Of Tropical Mammalian Frugivores, Jedidiah F. Brodie, Olga E. Helmy, Warren Y. Brockelman, John L. Maron

Biological Sciences Faculty Publications

Many plants interact with groups of mutualist pollinators and seed dispersers. A key issue for both basic ecology and conservation is whether the different species within these guilds of mutualist animals are functionally equivalent. Comparing the relative effects of sympatric mutualists is important for understanding the evolution of multispecies mutualisms and for predicting mutualism stability in the face of anthropogenic change. However, empirical comparisons of the population-level impacts of mutualist animals on their host plant are rare, particularly for seed dispersal mutualisms in species-rich ecosystems. We compared the influence of three seed-dispersing tropical mammals, lar gibbons (Hylobates lar), …

Phylogeography And Conservation Of The Arroyo Toad (Bufo Californicus), Robert Edward Lovich

Loma Linda University Electronic Theses, Dissertations & Projects

The Arroyo Toad (Bufo cakfomicus) is an endangered species found in rivers of southern California, USA and northern Baja California, Mexico. It has experienced population declines throughout its range, as a result of urbanization, hydrologic alterations, and overall habitat loss. As part of the Recovery Plan for this species, it was determined that more research was needed to assist in management decisions. One of those research needs was to better understand the intraspecific genetic variation within the Arroyo Toad. I conducted a range wide genetic study of the Arroyo Toad to uncover lineages and genetic variation among and between all …

Exercise-And Hypoxia-Induced Anaerobic Metabolism And Recovery: A Student Laboratory Exercise Using Teleost Fish, Bernard Rees

Biological Sciences Faculty Publications

Anaerobic metabolism is recruitedin vertebrates under conditions of intense exercise or lowered environmental oxygen availability (hypoxia), typically resulting in the accumulation of lactate in blood and tissues. Lactate will be cleared over time after the reoxygenation of tissues, eventually returning to control levels. Here, we present a laboratory exercise developed as part of an upper-level vertebrate physiology class that demonstrates the effects of exercise and hypoxia exposure on blood lactate in fish and the subsequent decrease in lactate during recovery. Typically, the results obtained by students demonstrate that both treatments cause significant increases in blood lactate concentrations (two to three …

Preliminary Characterization Of Mitochondrial Atp-Sensitive Potassium Channel (Mitokatp) Activity In Mouse Heart Mitochondria, Venkat Raghav Aachi

Dissertations and Theses

Myocardial ischemia, infarction, heart failure and arrhythmias are the manifestations of coronary artery disease. Reduction of ischemic damage is a major concern of cardiovascular biology research. As per recent studies, the mitochondrial ATP-sensitive potassium channel (mitoK_ATP) opening is believed to play key role in the physiology of cardioprotection, protection against ischemia-reperfusion injury or apoptosis. However, the structural information of mitoK_ATP is not precisely known. Elucidating the structural integrity and functioning of the mitoK_ATP is therefore a major goal of cardiovascular biology research. The known structure and function of the cell ATP-sensitive potassium channel (cellK_ATP) …

Wnt And Egf Pathways Act Together To Induce C. Elegans Male Hook Development, Hui Yu, Adeline Seah, Michael A. Herman, Edwin L. Ferguson, H. Robert Horvitz, Paul W. Sternberg

School of Biological Sciences: Faculty Publications

Comparative studies of vulva development between Caenorhabditis elegans and other nematode species have provided some insight into the evolution of patterning networks. However, molecular genetic details are available only in C. elegans and Pristionchus pacificus. To extend our knowledge on the evolution of patterning networks, we studied the C. elegans male hook competence group (HCG), an equivalence group that has similar developmental origins to the vulval precursor cells (VPCs), which generate the vulva in the hermaphrodite. Similar to VPC fate specification, each HCG cell adopts one of three fates (1°, 2°, 3°), and 2° HCG fate specification …

From Cells To Coastlines: How Can We Use Physiology To Forecast The Impacts Of Climate Change?, Brian Helmuth

Faculty Publications

The interdisciplinary fields of conservation physiology, macrophysiology, and mechanistic ecological forecasting have recently emerged as means of integrating detailed physiological responses to the broader questions of ecological and evolutionary responses to global climate change. Bridging the gap between large-scale records of weather and climate (as measured by remote sensing platforms, buoys and ground-based weather stations) and the physical world as experienced by organisms (niche-level measurements) requires a mechanistic understanding of how ‘environmental signals’ (parameters such as air, surface and water temperature, food availability, water flow) are translated into signals at the scale of the organism or cell (e.g. body temperature, …

Small Mammals In Portions Of Great Basin National Park Susceptible To Groundwater Withdrawal: Diversity And Stable Isotope Perspectives, Bryan T. Hamilton

Theses and Dissertations

To support population growth in Las Vegas, Nevada, large scale increases in groundwater pumping are planned across the state. This pumping could affect riparian areas in Great Basin National Park by lowering groundwater levels, reducing stream flows, and xerifying riparian vegetation. Great Basin National Park (GBNP) is mandated to manage its resources unimpaired for future generations. Loss of biodiversity is unacceptable under this mandate. If groundwater levels are reduced beyond a threshold, aquatic and riparian diversity would be lost, but the effects on small mammal communities are less clear. To provide baseline information and to consider the effects of groundwater …

Landscape Genomics And Biased Fst Approaches Reveal Single Nucleotide Polymorphisms Under Selection In Goat Breeds Of North-East Mediterranean, Lorraine Pariset, Stephane Joost, Paolo Ajmone Marsan, Alessio Valentini, Econogene Consortium

Biological Sciences Faculty Publications

Background: In this study we compare outlier loci detected using a F_st based method with those identified by a recently described method based on spatial analysis (SAM). We tested a panel of single nucleotide polymorphisms (SNPs) previously genotyped in individuals of goat breeds of southern areas of the Mediterranean basin (Italy, Greece and Albania). We evaluate how the SAM method performs with SNPs, which are increasingly employed due to their high number, low cost and easy of scoring.

Results: The combined use of the two outlier detection approaches, never tested before using SNP polymorphisms, resulted in the …

Avian Incubation Inhibits Growth And Diversification Of Bacterial Assemblages On Eggs, Matthew D. Shawkey, Mary K. Firestone, Eoin L. Brodie, Steven R. Beissinger

Biology Faculty Research

Microbial infection is a critical source of mortality for early life stages of oviparous vertebrates, but parental defenses against infection are less well known. Avian incubation has been hypothesized to reduce the risk of trans-shell infection by limiting microbial growth of pathogenic bacteria on eggshells, while enhancing growth of commensal or beneficial bacteria that inhibit or competitively exclude pathogens. We tested this hypothesis by comparing bacterial assemblages on naturally incubated and experimentally unincubated eggs at laying and late incubation using a universal 16S rRNA microarray containing probes for over 8000 bacterial taxa. Before treatment, bacterial assemblages on individual eggs from …

Accumulation Of Rhodopsin In Late Endosomes Triggers Photoreceptor Cell Degeneration, Yashodhan Chinchore, Amitavo Mitra, Patrick J. Dolph, Norbert Perrimon

Dartmouth Scholarship

Progressive retinal degeneration is the underlying feature of many human retinal dystrophies. Previous work using Drosophila as a model system and analysis of specific mutations in human rhodopsin have uncovered a connection between rhodopsin endocytosis and retinal degeneration. In these mutants, rhodopsin and its regulatory protein arrestin form stable complexes, and endocytosis of these complexes causes photoreceptor cell death. In this study we show that the internalized rhodopsin is not degraded in the lysosome but instead accumulates in the late endosomes. Using mutants that are defective in late endosome to lysosome trafficking, we were able to show that rhodopsin accumulates …

Correlation Between Animal And Mathematical Models For Prostate Cancer Progression, Zdzislaw Jackiewiczy, Cheryl L. Jorcyk, Mikhail K. Kolev, Barbara Zubik-Kowal

Biology Faculty Publications and Presentations

This work demonstrates that prostate tumour progression in vivo can be analysed by using solutions of a mathematical model supplemented by initial conditions chosen according to growth rates of cell lines in vitro. The mathematical model is investigated and solved numerically. Its numerical solutions are compared with experimental data from animal models. The numerical results confirm the experimental results with the growth rates in vivo.

Desiccation Survival In An Antarctic Nematode: Molecular Analysis Using Expressed Sequenced Tags, Byron J. Adams, Bishwo N. Adhikari, Diana H. Wall

Faculty Publications

Background: Nematodes are the dominant soil animals in Antarctic Dry Valleys and are capable of surviving desiccation and freezing in an anhydrobiotic state. Genes induced by desiccation stress have been successfully enumerated in nematodes; however we have little knowledge of gene regulation by Antarctic nematodes which can survive multiple environmental stresses. To address this problem we investigated the genetic responses of a nematode species, Plectus murrayi, that is capable of tolerating Antarctic environmental extremes, in particular desiccation and freezing. In this study, we provide the first insight into the desiccation induced transcriptome of an Antarctic nematode through cDNA library construction …

Induction Of Microrna-221 By Platelet-Derived Growth Factor Signaling Is Critical For Modulation Of Vascular Smooth Muscle Phenotype, Brandi N. Davis, Aaron C. Hilyard, Peter H. Nguyen, Giorgio Lagna, Akiko Hata

Biology

The platelet-derived growth factor (PDGF) signaling pathway is a critical regulator of animal development and homeostasis. Activation of the PDGF pathway leads to neointimal proliferative responses to artery injury; it promotes a switch of vascular smooth muscle cells (vSMC) to a less contractile phenotype by inhibiting the SMC-specific gene expression and increasing the rate of proliferation and migration. The molecular mechanism for these pleiotropic effects of PDGFs has not been fully described. Here, we identify the microRNA-221 (miR-221), a small noncoding RNA, as a modulator of the phenotypic change of vSMCs in response to PDGF signaling. We demonstrate that miR-221 …

Species Delimitation In Lemurs: Multiple Genetic Loci Reveal Low Levels Of Species Diversity In The Genus Cheirogaleus, Linn F. Groeneveld, David W. Weisrock, Rodin M. Rasoloarison, Anne D. Yoder, Peter M. Kappeler

Biology Faculty Publications

BACKGROUND: Species are viewed as the fundamental unit in most subdisciplines of biology. To conservationists this unit represents the currency for global biodiversity assessments. Even though Madagascar belongs to one of the top eight biodiversity hotspots of the world, the taxonomy of its charismatic lemuriform primates is not stable. Within the last 25 years, the number of described lemur species has more than doubled, with many newly described species identified among the nocturnal and small-bodied cheirogaleids. Here, we characterize the diversity of the dwarf lemurs (genus Cheirogaleus) and assess the status of the seven described species, based on phylogenetic and …

Observations Of Flotsam Entrapment In The Northern Diamond-Backed Watersnake (Nerodia R. Rhombifer), Jason Ortega, Frederic Zaidan

School of Integrative Biological & Chemical Sciences (Formerly Dept. of Biology)

—Small areas of protected land may act as islands of suitable habitat surrounded by human development. Although these areas receive protection, we have observed one way that the surrounding human population can still endanger the welfare of its inhabitants. During our observations of the Northern Diamond-backed Watersnake (Nerodia r. rhombifer) in a semi-protected nature park surrounded by human development, we encountered 13 individuals entangled with flotsam. Of the 220 juvenile through adult snakes that we captured, 12 were encircled by various types of objects (e.g., finger cots; latex sheaths that cover a single digit, dental elastics, and plastic bottle neck …

Synthesis: Evolutionary Ecology Of Microbial Wars: Within-Host Competition And (Incidental) Virulence, Sam Brown, Fredrik Inglis, François Taddei

Biology Department Faculty Works

Invading an occupied niche is a formidable ecological challenge, and one of particular human importance in the context of food-borne microbial pathogens. We discuss distinct categories of invader-triggered environmental change that facilitate invasion by emptying their niche of competitors. Evidence is reviewed that gut bacteria use such strategies to manipulate their environment (via bacteriocins, temperate phage viruses or immuno-manipulation) at the expense of their competitors are reviewed. The possible virulence implications of microbial warfare among multiple co-infecting strains are diverse. Killing competitors can reduce virulence by reducing overall microbial densities, or increase virulence if for example the allelopathic mechanism involves …

Evolutionary Ecology Of Microbial Wars: Within-Host Competition And (Incidental) Virulence, Sam Brown, R Inglis, François Taddei

Biology Department Faculty Works

Invading an occupied niche is a formidable ecological challenge, and one of particular human importance in the context of food-borne microbial pathogens. We discuss distinct categories of invader-triggered environmental change that facilitate invasion by emptying their niche of competitors. Evidence is reviewed that gut bacteria use such strategies to manipulate their environment (via bacteriocins, temperate phage viruses or immuno-manipulation) at the expense of their competitors are reviewed. The possible virulence implications of microbial warfare among multiple co-infecting strains are diverse. Killing competitors can reduce virulence by reducing overall microbial densities, or increase virulence if for example the allelopathic mechanism involves …