Biology Commons^™

An Interdisciplinary Research Course In Theoretical Ecology For Young Undergraduates, Glenn Ledder, Brigitte Tenhumberg, G. Travis Adams

School of Biological Sciences: Faculty Publications

As part of an interdepartmental effort to attract promising young students to research at the interface between mathematics and biology, we created a course in which groups of recent high school graduates and first-year college students conducted a research project in insect population dynamics. The students set up experiments, collected data, used the data to develop mathematical models, tested their models against further experiments, and prepared their results for dissemination. The course was self-contained in that the lecture portion developed the mathematical, statistical, and biological background needed for the research. A special writing component helped students learn the principles of …

White Bass Assessment In Regards To Changes In Water Level On Lake Traverse, Aaron Wilson

Journal of Earth and Life Science

Until recently the white bass Morone chrysops has been somewhat ignored by anglers, more so in Minnesota than other states; most likely due to their limited distribution throughout the state. However, with more anglers becoming aware of the sporting and culinary potentials of white bass, interests have risen. With this rise in angler interest, there should be a rise in white bass assessments. Knowing what factors may be influencing white bass population dynamics will allow fisheries professionals to better manage and protect white bass fisheries. White bass are often found in rivers and impoundments were dams are present and water …

2013 Ii Cu Suri (Common Poster), Vanessa Selimovic, Loriann Reese, Ruthie Nelson, Emma Sleeman, Hibery Ho, Maria Polozova

CUP Undergraduate Research

A common poster providing information for several research projects: aerosol particles, deoxycytidine kinase, squaraine rotaxanes, glycol nucleic acied, and Kombucha.

Refining Molecular Approaches For Bacterial Source Tracking (Bst) In Texas, Joy Truesdale

Open Access Theses & Dissertations

Bacterial source tracking (BST) is a new science that aids in identifying sources of human and animal fecal contamination of environmental water. There are currently two approaches used in BST, library-dependent and library-independent methods. The fecal bacterium E. coli is often used in library dependent methods because it indicates fecal contamination, has been used in human health risk assessments, and has water quality regulatory significance. A disadvantage of E. coli library dependent BST methods is that identification libraries of E. coli isolated from known fecal sources are needed to identify the sources of E. coli isolated from water samples. Further, …

Brown Trout Spawning Location And Relationship To Suitable Winter Habitat, Matthew L. Skoog

Journal of Earth and Life Science

Brown trout are a popular game fish throughout much of the world. Understanding habitat requirements is necessary for the successful management of brown trout. This study looks at the spawning habitat preferences and relationship of redd location to wintering habitat of brown trout in the Straight River, Minnesota. Brown trout in the Straight River were found to spawn in similar habitat to brown trout looked at in previous literature. All redds were located on gravel substrate. Seventy eight percent of redds were associated with some sort of cover. Water velocities at the redd sites. (mean=0.456 ms/cm), dissolved oxygen (mean=9.78 mg/L), …

Comparison Of A Length Size Limit Of Northern Pike Population On Two Lakes In North Central Minnesota, Ethan A. Puttonen

Journal of Earth and Life Science

Fisheries managers use length size limits on northern pike (Esox lucis) to improve the size structure in select lakes. The objective of this study was to compare two similar lakes, one with a length size limit and one without, to determine if a length size limit is improving the northern pike size structure. Blueberry Lake showed a higher abundance of larger fish than Stocking Lake. Of the fish caught, 25% in Blueberry Lake were over 600 mm (24 in), and were in the protected slot. Stocking Lake had a smaller portion of fish of this size with only …

A Multi-Method Study Of The Socioeconomic Status Of People Living On The Kumbon Landfill In Khon Kaen, Thailand, Candace Leflame

Whittier Scholars Program

This project is multidimensional including data from questionnaires, inventories, maps, life stories, focus groups and interviews to create a data analysis on the socioeconomic status of people living on the Kumbon landfill. This students shares history of the landfill and explains how the pile of waste has become both home and work to a population of people. They write, Socioeconomic studies in this community are very limited due to the overwhelming environmental health hazards that are affecting surrounding communities. Governments and individual research faculties have been more interested to the effect to the surrounding villages than to the actual people …

Innovative Applications Of Genetic Algorithms To Problems In Accelerator Physics, Alicia Hofler, Balša Terzić, Matthew Kramer, Anton Zvezdin, Vasiliy Morozov, Yves Roblin, Fanglei Lin, Colin Jarvis

Physics Faculty Publications

The genetic algorithm (GA) is a powerful technique that implements the principles nature uses in biological evolution to optimize a multidimensional nonlinear problem. The GA works especially well for problems with a large number of local extrema, where traditional methods (such as conjugate gradient, steepest descent, and others) fail or, at best, underperform. The field of accelerator physics, among others, abounds with problems which lend themselves to optimization via GAs. In this paper, we report on the successful application of GAs in several problems related to the existing Continuous Electron Beam Accelerator Facility nuclear physics machine, the proposed Medium-energy Electron-Ion …

Image-Level And Group-Level Models For Drosophila Gene Expression Pattern Annotation, Quian Sun, Sherin Muckatira, Lei Yuan, Shuiwang Ji, Stuart Newfeld, Sudhir Kumar, Jieping Ye

Computer Science Faculty Publications

Background: Drosophila melanogaster has been established as a model organism for investigating the developmental gene interactions. The spatio-temporal gene expression patterns of Drosophila melanogaster can be visualized by in situ hybridization and documented as digital images. Automated and efficient tools for analyzing these expression images will provide biological insights into the gene functions, interactions, and networks. To facilitate pattern recognition and comparison, many web-based resources have been created to conduct comparative analysis based on the body part keywords and the associated images. With the fast accumulation of images from high-throughput techniques, manual inspection of images will impose a serious impediment …

Computational Genetic Neuroanatomy Of The Developing Mouse Brain: Dimensionality Reduction, Visualization, And Clustering, Shuiwang Ji

Computer Science Faculty Publications

Background: The structured organization of cells in the brain plays a key role in its functional efficiency. This delicate organization is the consequence of unique molecular identity of each cell gradually established by precise spatiotemporal gene expression control during development. Currently, studies on the molecular-structural association are beginning to reveal how the spatiotemporal gene expression patterns are related to cellular differentiation and structural development.

Results: In this article, we aim at a global, data-driven study of the relationship between gene expressions and neuroanatomy in the developing mouse brain. To enable visual explorations of the high-dimensional data, we map the in …

A Mesh Generation And Machine Learning Framework For Drosophila Gene Expression Pattern Image Analysis, Wenlu Zhang, Daming Feng, Rongjian Li, Andrey Chernikov, Nikos Chrisochoides, Christopher Osgood, Charlotte Konikoff, Stuart Newfeld, Sudhir Kumar, Shuiwang Ji

Computer Science Faculty Publications

Background: Multicellular organisms consist of cells of many different types that are established during development. Each type of cell is characterized by the unique combination of expressed gene products as a result of spatiotemporal gene regulation. Currently, a fundamental challenge in regulatory biology is to elucidate the gene expression controls that generate the complex body plans during development. Recent advances in high-throughput biotechnologies have generated spatiotemporal expression patterns for thousands of genes in the model organism fruit fly Drosophila melanogaster. Existing qualitative methods enhanced by a quantitative analysis based on computational tools we present in this paper would provide …

Range Maps For Nebraska's Threatened And Endangered Species, Nebraska Natural Heritage Program

Nebraska Game and Parks Commission: White Papers, Conference Presentations, and Manuscripts

This document includes maps and associated information on the ranges of Nebraska’s federal and state-listed species. The information is current as of January 2013. The information is updated as needed. Contact the Nebraska Game and Parks Commission to determine if a more current version is available. The species treated are as follows: American Burying Beetle (Nicrophorus americanus), Salt Creek Tiger Beetle (Cicindela nevadica lincolniana), Swift Fox (Vulpes velox), River Otter (Lutra canadensis), Southern Flying Squirrel (Glaucomys volans), Pallid Sturgeon (Scaphirhyncus albus), Topeka Shiner (Notropis topeka), Sturgeon Chub (Macrhybopsis gelida), Blacknose Shiner (Notropis heterolepis), Lake Sturgeon (Acipenser fulvescens), Northern Redbelly Dace …

Wetting And Drying Cycles And The Fungal Communities On Leaf Litter In Streams, Kele Qwinn Thrailkill

Masters Theses

"Leaf litter is a major source of energy for streams in deciduous forests. Fungi play a critical role by converting the leaves into nutritional material for the rest of the food web. The breakdown of leaf litter and associated biota, including invertebrates and fungi, have been proposed as measures of stream health in systems affected by anthropogenic activity. Rates of leaf breakdown can be depressed in streams affected by acidity, metals, organic contaminants, and other stressors. Climate change may lead to alterations in stream hydrology such that streams experience more frequent floods as well as drying episodes. Fungal communities can …

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 …

Net Effects Of Batrachochytrium Dendrobatidis (Bd) And Fungicides On Anurans Across Life Stages, Jenise Brown

USF Tampa Graduate Theses and Dissertations

Amphibians are declining at alarming rates globally. Multiple factors contribute to these declines, including chemical contaminants and emergent diseases. In recent years, agrochemical use, especially fungicide applications, has increased considerably. Previous studies have demonstrated that these agrochemicals leave application sites and enter wetlands via runoff and have detrimental effects on non-target organisms. For example, exposure to contaminants can have multifarious effects on amphibians, such as reducing their ability to deal with a secondary stressor, such as disease.

A pathogen that is found concomitant with chemical contaminants in aquatic systems is Batrachochytrium dendrobatidis (Bd). Bd has decimated amphibian populations worldwide. Susceptibility …

Population Models, Jessica Hauer

EWU Masters Thesis Collection

This thesis will examine mathematical interpretations of biological situations through the study of differential equations. It will first explore the interactions of the lynx and hare populations in Canada based on data retrieved by the Hudson Bay Company. The purpose of this study is to find a suitable mathematical model, namely that of a three-variable Lotka-Volterra system. Also, the paper will explore short-term infectious disease models as they relate to particular epidemics throughout history, including the Iowa Mumps outbreak of 1966 and the Bubonic Plaque. The thesis will then work to make sense of the rise and fall patterns in …

Factors Influencing The Establishment And Survival Of Native Hardwood Tree Seedlings Of The Kentucky Inner Bluegrass Blue Ash-Oak Savanna-Woodland, James D. Shaffer

Theses and Dissertations--Biology

Historically, the Kentucky Inner Bluegrass blue ash-oak savanna-woodland was the primary ecosystem of the Inner Bluegrass Region (IBR) of Kentucky. After European settlement, the majority (>99%) of Bluegrass savanna was converted to agricultural and urban land uses. Currently remnant savanna tree species are failing to recruit. Therefore, a long-term restoration ecology project researching competition and disturbance on seedling establishment, survival, and growth has been established at Griffith Woods (the largest remaining savanna in Kentucky) in Harrison Co., KY. Fourteen native hardwood tree species (a total of 6,168 seedlings) have been experimentally planted. Light, soil, surrounding vegetation, and herbivory, factors …

Pronounced Genetic Structure In A Highly Mobile Coral Reef Fish, Caesio Cuning, In The Coral Triangle, Amanda S. Ackiss, Shinta Pardede, Eric D. Crandall, Ma Carmen A. Ablan-Lagman, Ambariyanto, November Romena, Paul H. Barber, Kent E. Carpenter

Biological Sciences Faculty Publications

The redbelly yellowtail fusilier Caesio cuning has a tropical Indo-West Pacific range that straddles the Coral Triangle, a region of dynamic geological history and the highest marine biodiversity on the planet. Previous genetic studies in the Coral Triangle indicate the presence of multiple limits to connectivity. However, these studies have focused almost exclusively on benthic, reef-dwelling species. Schooling, reef-associated fusiliers (Perciformes: Caesionidae) account for a sizable portion of the annual reef catch in the Coral Triangle, yet to date, there have been no indepth studies on the population structure of fusiliers or other mid-water, reef-associated planktivores across this region. We …

Identifying Requirements For The Invasion Of A Tick Species And Tick-Borne Pathogen Through Ticksim, Holly Gaff, Robyn Nadolny

Biological Sciences Faculty Publications

Ticks and tick-borne diseases have been on the move throughout the United State over the past twenty years. We use an agent-based model, TICKSIM, to identify the key parameters that determine the success of invasion of the tick and if that is successful, the success of the tick-borne pathogen. We find that if an area has competent hosts, an initial population of ten ticks is predicted to always establish a new population. The establishment of the tick-borne pathogen depends on three parameters: the initial prevalence in the ten founding ticks, the probability that a tick infects the longer-lived hosts and …

Computational Prediction Of The Sporulation Network In Clostridium Thermocellum, Changyi Jiang

Dissertations, Master's Theses and Master's Reports - Open

Sporulation is a process in which some bacteria divide asymmetrically to form tough protective endospores, which help them to survive in a hazardous environment for a quite long time. The factors which can trigger this process are diverse. Heat, radiation, chemicals and lacking of nutrition can all lead to the formation of endospores. This phenomenon will lead to low productivity during industrial production. However, the sporulation mechanism in a spore-forming bacterium, Clostridium theromcellum, is still unclear. Therefore, if a regulation network of sporulation can be built, we may figure out ways to inhibit this process. In this study, a …

Production Of 1,3-Propanediol From Glycerol Under Haloalkaline Conditions By Halanaerobium Hydrogeniformans, Daniel William Roush

Masters Theses

"With increased demands around the world to make modern lifestyles more environmentally friendly, the chemical commodity market has rapidly shifted. Through new technologies in chemical production, certain high value products have oversaturated the market and have become high-volume, low value waste products. The expansion of biodiesel production offers a prime example; high volumes of glycerol byproduct from this process have shifted glycerol from a high priced commodity to a common waste product. A number of microorganisms are known to synthesize the polymeric precursor 1,3-propanediol from glycerol; however, crude glycerol from biodiesel production creates a harsh environment for most microbes, and …

Assessment Of Water Quality And Benthic Macroinvertebrate Community In A Wastewater Receiving Constructed Wetland, Jennifer Lynn Martinez

Open Access Theses & Dissertations

In the El Paso region around the 1930s there was a loss of riparian areas and wetlands due to canalization of the Rio Grande. In an attempt to bring back native flora and fauna that once flourished in the floodplain of the Rio Grande region, the creation of Rio Bosque Wetlands Park (RBWP; El Paso Co., TX) was initiated in 1995. As part of the construction agreement, El Paso Water Utilities agreed to provide water to fill the wetland upon its completion. Beginning in 1998, RBWP was filled with treated effluent from the adjacent Roberto Bustamante Wastewater Treatment Plant (WWTP) …

Daily Temperature Fluctuations Unpredictably Influence Developmental Rate And Morphology At A Critical Early Larval Stage In A Frog, Juliana M. Arrighi, Ezra S. Lencer, Advait Jukar, Daesik Park, Patrick C. Phillips, Robert H. Kaplan

Complex Systems Faculty Publications and Presentations

Background: Environmental temperature has profound consequences for early amphibian development and many field and laboratory studies have examined this. Most laboratory studies that have characterized the influence of temperature on development in amphibians have failed to incorporate the realities of diel temperature fluctuations (DTF), which can be considerable for pond-breeding amphibians.

Results: We evaluated the effects of different ecologically relevant ranges of DTF compared with effects of constant temperatures on development of embryos and larvae of the Korean fire-bellied toad (Bombina orientalis). We constructed thermal reaction norms for developmental stage, snout- vent length, and tail length by fitting …

Birds And Butterflies Respond To Soil-Induced Habitat Heterogeneity In Experimental Plantings Of Native Tallgrass Prairie Species In Iowa, Usa, Benjamin J. Hoksch, Mark C. Myers, James T. Mason, Jarrett D. Pfrimmer, Andrew J. Ridgway

Undergraduate Student Work

We studied interrelationships between prairie plant establishment, habitat heterogeneity, and bird and butterfly biodiversity in an experimental prairie reconstruction in Iowa, USA. We seeded 48 research plots on three soil types with one of four treatments containing one, five, 16, or 32 species. During early establishment, neither bird nor butterfly abundance, species richness, or community diversity varied among the three soil types; however, there were significant treatment × soil type interactions when comparing bird and butterfly community composition among plots. Our results demonstrate that plots established with identical seed mixes and management practices developed variable habitat characteristics due to variation …

Phytoplankton In Virginia Lakes And Reservoirs, Harold G. Marshall

Biological Sciences Faculty Publications

This study involves a phytoplankton summer/autumn survey in 46 Virginia lakes and reservoirs during 2010-2012. A total of 307 taxa were identified which included several filamentous and colonial cyanabacteria in bloom concentrations. With the exception of one natural lake, the other sites sampled represent impoundments created decades ago, with the majority presently classified as meso- or eutrophic. Among the cyanobacteria were 6 known toxin producers (Anabaena circinalis, Anabaena spiroides, Aphanizomenon flos-aquae, Cylindrospermopsis raciborskii, Limnothrix redekei, and Microcystis aeruginosa). The study characterizes phytoplankton populations in these aging freshwater habitats taken from a large number …

Broad-Spectrum Antibacterial Properties Of Metal-Ion Doped Borate Bioactive Glasses For Clinical Applications, Megan Ottomeyer

Masters Theses

"Bioactive glasses with antimicrobial properties can be implemented as coatings on medical devices and implants, as well as a treatment for tissue repair and prevention of common hospital-acquired infections such as MRSA A borate-containing glass, B3, is also undergoing clinical trials to assess wound-healing properties. The sensitivities of various bacteria to B3, B3-Ag, B3-Ga, and B3-I bioactive glasses were tested. In addition, the mechanism of action for the glasses was studied by spectroscopic enzyme kinetics experiments, Live-Dead staining fluorescence microscopy, and luminescence assays using two gene fusion strains of Escherichia coli.

It was found that gram-positive bacteria were more …

Method Development For A Chemical And Biological Analysis Of Glucocorticoids In Wastewater, Maria Carmen Lozano

Open Access Theses & Dissertations

Glucocorticoids are a class of steroid hormones that can either be produced synthetically or naturally by the adrenal glands. The synthetic glucocorticoids are highly prescribed in the United States for their anti-inflammatory and immunosuppressive properties to treat a variety of ailments and diseases; however, these have been implicated in a number of adverse human conditions such as obesity, metabolic syndrome, immune-suppression, delayed puberty, adrenal insufficiency and Cushing Syndrome, among others. Ongoing research has shown that synthetic and natural hormones are transported to aquatic environments via mammalian excretion or wastewater effluent, and as a result, the release of glucocorticoids into the …

Endocrine Disrupting Compound 4-Nonylphenol And Neurodegeneration, Jessica Martinez Jurado

Open Access Theses & Dissertations

Neurodegeneration, a progressive loss of nerve cells (neurons), occurs in many neurological disorders including Alzheimer's disease, Parkinson's disease, Schizophrenia, and drug addiction. Cytoskeletal disruption in neurons and aggregation of proteins associated with these disorders is the hallmark of neurodegeneration. However, the cause of neurodegenerative disorders is unknown and currently there are no effective drug treatments. Aging is the most consistent risk factor for developing a neurodegenerative disorder, and recent evidence suggests that environmental factors, which act as endocrine disruptors, pose a risk in the disease process. 4- nonylphenol (4-NP), an endocrine-disrupting compound (EDC), has been shown to affect brain development …

Molecularly Imprinted Polymer Technology: A Powerful, Generic, Facile And Cost Effective Alternative For Enantio-Recognition And Separation: A Glance At Advances And Applications, Jyn Philip, Dms Mosha

Tanzania Journal of Science

The emerging Molecularly Imprinted Polymer (MIP) technology has yielded proof of concept, harnessing nature’s fundamentals to yield recognition receptor mimics from the miniaturized basics, borrowing on the ground rules, but conveniently avoiding the complexity, fragility, instability, costs and ethics of animal based bio-affinity matrices. Thus, the impact of bio-sciences on the future of technology is not via direct use of the molecules, but rather the lessons learned. Molecular imprinting is a powerful specialty representing the generic, cost effective and facile alternative for preparation of synthetic custom-tailored receptors. It achieves this via creation of specific selective recognition sites for a pre-determined …

The Lyme Disease Spirochete In Tick Species Collected From Warren County, Kentucky, Cheryl C. Onwu

Mahurin Honors College Capstone Experience/Thesis Projects

The overall goal of this present study was to determine the prevalence of the Lyme disease spirochete, Borrelia burgdorferi, in south central Kentucky. A survey of ticks collected from a single location in Warren County, Kentucky was conducted between the months of April and June, 2010. A total of 293 ticks were collected. Three species were identified: 264 (91.7 %) of the ticks were Amblyoma americanum, 18 (6.6%) were Dermacentor variabilis, and 1 (0.35%) was Ixodes scapularis. The ten remaining ticks were immature nymphs and could not be identified. After identifying the species and sex of …