Biology Commons^™

Diversification And Adaptation In The Andes: Insights From Phylogeography, Malaria, And Hemoglobin Of The House Wren (Troglodytes Aedon), Spencer C. Galen

Biology ETDs

The tropical Andes of South America represent a highly complex landscape characterized by physical barriers to dispersal and stark ecological gradients. The study of intraspecific genetic diversity in widespread Andean species has the potential to elucidate the historical biogeographic events that have driven diversification as well as the processes by which organisms have adapted to their environments in this region. The house wren (Troglodytes aedon) provides a convenient system for the study diversification and adaptation in the Andes, as it is distributed widely across both biogeographic barriers and heterogeneous environments. In chapter one, I utilize house wren and malaria parasite …

Improving Structural Features Prediction In Protein Structure Modeling, Ashraf Yaseen

Computer Science Theses & Dissertations

Proteins play a vital role in the biological activities of all living species. In nature, a protein folds into a specific and energetically favorable three-dimensional structure which is critical to its biological function. Hence, there has been a great effort by researchers in both experimentally determining and computationally predicting the structures of proteins.

The current experimental methods of protein structure determination are complicated, time-consuming, and expensive. On the other hand, the sequencing of proteins is fast, simple, and relatively less expensive. Thus, the gap between the number of known sequences and the determined structures is growing, and is expected to …

Evaluating The Utility Of Natural History Collections In Research And For The Public, Bethany L. Abrahamson

Biology ETDs

Natural history collections (NHCs) are useful in many fields of study, but knowledge about how they are used in the modern day is poor. The first part of this study, focused on the collections data held by the Museum of Southwestern Biology (MSB), analyzes specimen-based publications, specimen loan records, and guestbook information to determine how NHCs have been used in scientific study over time. Using a novel methodology, I objectively sorted the publications into ten research subjects via particular phrases found in publication titles, places of publication, and keywords. I observed from this dataset the proportions of particular subjects for …

Population And Metapopulation Ecology Of Childhood Diseases, Christian E. Gunning

Biology ETDs

Researchers have long used mathematical models and empirical data to explore the population ecology of childhood diseases such as measles and whooping cough. These diseases have proven ideal model systems for studying population dynamics over space and time. Here we present a novel dataset of weekly measles and whooping cough case reports in pre-vaccine era U.S. cities and states, along with a previously- studied dataset of measles in England & Wales. We first estimate per-population disease reporting probabilities. We find that disease reporting is highly variable over space and between diseases, and correlated with socioeconomic covariates including ethnic composition and …

The Microbiome Of Rainbow Trout (Oncorhynchus Mykiss), Liam T. Lowrey

Biology ETDs

Commensal organisms are an integral part of all vertebrates, contributing heavily to development, pathogen defense, and metabolism. Commensals reside at different body sites within vertebrate animals creating unique and distinct communities that vary between locations. The human microbiome project has revealed distinct bacterial community compositions at the diverse range of body sites that have been sampled, providing evidence for different functional purposes of each microbiome. Rainbow trout, Oncorhynchus mykiss, serves as a model organism for the study of mucosal physiology and immunology. Teleost fish are evolutionarily important as one of the first jawed vertebrates with a dedicated adaptive mucosal immune …

Defining The Complexities Of Mef2 Function And Regulation In Drosophila, Tyanna L. Lovato

Biology ETDs

The development of cardiac and somatic muscle is coordinated by many factors that are highly conserved across species. Mutations in the coding or regulatory sequences of a gene can alter the structure, function or levels of expression of the protein it encodes. We have identified the genetic mechanism underlying the temperature sensitive mutation in MEF2 (myocyte enhancer factor 2), which is required for the differentiation of all muscle lineages. In addition, we have identified a regulatory element upstream of the Mef2 gene that directs its expression from stage fourteen through the end of embryogenesis which is activated by the NK-homeobox …

The Effects Of Intestinal Sulfate-Reducing Bacteria On Cognitive Behavior And Intestinal Transit In Mice, Nathaniel Ritz

Biology ETDs

This research reports the effects of two metabolic groups of bacteria on physiological activity and cognitive function in C57BL/6 mice. In one experiment, the mice on a diet supplemented with red kidney bean for 24 hr were able to complete an eight-arm radial learning maze in a shorter time than mice on a diet without red kidney beans. The median time required for mice to complete the maze when fed red kidney beans was 118 sec while the median time for mice on standard diet to finish the maze was 270 sec. Based on the cycle threshold values when using …

Living On The Edge: A Comparative Phylogeographic Study Of Refugial And Insular Fragmentation, Yadéeh Escobedo Sawyer

Biology ETDs

Pleistocene glacial-interglacial cycles resulted in population isolation that led to inter- and intra- specific genetic divergence in many North American species. The magnitude of isolation also influenced species response to these climatic changes and set the stage for contemporary gene flow. We can refine our understanding of species response to historical climate change by identifying regions of ice-free persistence and refugia during glacial maxima, and geographic locations and genetic dynamics of post-glacial secondary contact. This dissertation examines the role of glacial cover, geographic barriers, habitat fragmentation as a result of changes in sea level, and insularity on the contemporary genetic …

Establishment Of Larrea Tridentata At The Northern Edge Of The Modern Mojave Desert: Insights From Neotoma Paleomiddens, Clare E. Steinberg

Biology ETDs

Shifting climates affect the composition of biological communities. If environmental conditions change sufficiently, new species can invade, leading to large-scale community turnover. Understanding how and why such shifts occur is crucial in this era of anthropogenic global change. Paleontological studies provide a valuable long-term perspective of the dynamics of community turnover. Here, we examine changes in the plant community over the past 34 thousand years in what is now the northern Mojave Desert. This time period includes the last glacial maximum as well as numerous smaller climatic fluctuations in the Holocene and the end of the Pleistocene. We quantified plant …

Human Influences On Anuran Distribution Changes In The Southeastern U.S.A., Michelle Diane Luce

Theses and Dissertations

As human populations continue to expand and grow, ecosystems and the species that inhabit them face ever-increasing stress. To conserve these ecosystems, scientists use indicator species to try to measure the impact of human-induced pressures on the environment. Anurans are exceptional indicator species because they are often the first vertebrates to respond to the direct and indirect effects of land use by humans. Sparse historical data have made it difficult to map the ‘natural’ distribution of many species and, therefore, to map any changes in distribution range as a result of human expansion. This study sought to address the lack …

Surface Water Inundation In The Boreal-Artic: Potential Impacts On Regional Methane Emissions, J. D. Watts, John S. Kimball, Annett Bartsch, Kyle C. Mcdonald

Biological Sciences Faculty Publications

Northern wetlands may be vulnerable to increased carbon losses from methane (CH₄), a potent greenhouse gas, under current warming trends. However, the dynamic nature of open water inundation and wetting/drying patterns may constrain regional emissions, offsetting the potential magnitude of methane release. Here we conduct a satellite data driven model investigation of the combined effects of surface warming and moisture variability on high northern latitude (45° N) wetland CH₄ emissions, by considering (1) sub-grid scale changes in fractional water inundation (Fw) at 15 day, monthly and annual intervals using 25 km resolution satellite microwave retrievals, and (2) …

The Foraging Behaviors And Decision-Making Strategies Of Overwintering Red-Tailed Hawks (Buteo Jamaicensis) And American Kestrels (Falco Sparverius) In Relation To Prey Density And Patch-Site Characteristics In Northeastern Arkansas, Melissa Marie Bobowski

Student Theses and Dissertations

I observed the wintering foraging behaviors of Red-tailed Hawks (Buteo jamaicensis) and American Kestrels (Falco sparverius) to determine the efficiency of their foraging strategies in relation to prey density and patch-site characteristics. The three cover-types (i.e., short rice stubble, soybean stubble, and fallow areas and roadsides) differed in densities of small mammals and vegetation cover. Cover-type was the most important predictor for the probability of making an attempt at prey for both species with the greatest probability at attempting was in fallow roadsides. Perch-type only influenced the probability of being successful at capturing a prey item for Red-tailed hawks with …

Ex Uno Plures: Clonal Reinforcement Drives Evolution Of A Simple Microbial Community, Margie A. Kinnersley, Jared Wenger, Evgueny Kroll, Julian Adams, Gavin Sherlock, Frank Rosenzweig

Biological Sciences Faculty Publications

A major goal of genetics is to define the relationship between phenotype and genotype, while a major goal of ecology is to identify the rules that govern community assembly. Achieving these goals by analyzing natural systems can be difficult, as selective pressures create dynamic fitness landscapes that vary in both space and time. Laboratory experimental evolution offers the benefit of controlling variables that shape fitness landscapes, helping to achieve both goals. We previously showed that a clonal population of E. coli experimentally evolved under continuous glucose limitation gives rise to a genetically diverse community consisting of one clone, CV103, that …

Manipulating The Tumor Microenvironment For Therapeutic Benefit, Kate M. Bailey

USF Tampa Graduate Theses and Dissertations

The physical tumor microenvironment contributes significantly to carcinogenesis, cancer progression and metastatic dissemination. Two main components of the tumor microenvironment, hypoxia and acidosis, are present in nearly every solid tumor and act as powerful selection forces against the tumor. Hypoxia and acidosis promote tumor heterogeneity and contribute to chemotherapy and radiotherapy resistance. This dissertation interrogates methods to target the tumor microenvironment including two novel studies describing mechanisms of buffer therapy resistance and targeting tumor hypoxia with vasodilators to enhance the efficacy of a hypoxia activated prodrug, TH-302.

In the first study, mechanisms of buffer therapy resistance were identified and detailed. …

Fty720 (Fingolimod) Provides Insight Into The Molecular Mechanisms Of Multiple Sclerosis, Madelyn Elizabeth Crawford

Pursuit - The Journal of Undergraduate Research at The University of Tennessee

Multiple sclerosis (MS) is a neurodegenerative disorder caused by a prolonged immune- mediated inflammatory response that targets myelin. Nearly all of the drugs approved for the treatment of MS are general immunosuppressants or only function in symptom management. The oral medication fingolimod, however, is reported to have direct therapeutic effects on cells of the central nervous system in addition to immunomodulatory functions. Fingolimod is known to interact with sphingosine-1-phosphate (S1P) receptors, and the most widely- accepted theory for its mechanism of action is functional antagonism of the receptor. This review examines significant neuromodulatory effects achieved by functional antagonism of the …

Rna Detection Technology For Applications In Marine Science: Microbes To Fish, Robert Michael Ulrich

USF Tampa Graduate Theses and Dissertations

The accurate identification of taxa from mixed assemblages using genetic analysis remains an important field of molecular biology research. The common principle behind the development of numerous documented genetic detection technologies is to exploit specific nucleotide sequences inherent to each taxon. This body of work focuses on practical applications of real-time nucleic acid sequence-based amplification (RT-NASBA) in marine science, and is presented in four case studies. Each study represents novel work in the genetic identification of respective taxa of interest using RT-NASBA. Two case studies documented the development of an assay targeting mitochondrial 16S rRNA to discern legally salable grouper …

From Co2 To Cell: Energetic Expense Of Creating Biomass Using The Calvin-Benson-Bassham And Reductive Citric Acid Cycles Based On Genomic Data, Mary Ann Mangiapia

USF Tampa Graduate Theses and Dissertations

Abstract

The ubiquity of the Calvin-Benson-Bassham cycle (CBB) amongst autotrophic organisms suggests that it provides an advantage over a wide range of environmental conditions. However, in some habitats, such as hydrothermal vents, the reductive citric acid cycle (rCAC) is an equally predominant carbon fixation pathway. It has been suggested that the CBB cycle poses a disadvantage under certain circumstances due to being more energetically demanding compared to other carbon fixation pathways. The purpose of this study was to compare the relative metabolic cost of cell biosynthesis by an autotrophic cell using either the CBB cycle or the rCAC. For both …

Early Developmental Impacts On Male Traits And Female Preference In Zebra Finches (Taeniopygia Guttata), Martyna Boruta

USF Tampa Graduate Theses and Dissertations

Some male sexually selected traits are sensitive to stressors early in life and provide females with information to discriminate among males with different developmental experiences. Moreover, female early life experiences could also impact which males they choose. Females might either choose honest traits indicative of male quality, no matter their own experiences, or they might choose mates to match or compensate for their own experiences. To determine how developmental stressors alter male sexually-selected traits and female preference thereof, I exposed zebra finches (Taeniopygia guttata, ZEFI) to i) lipopolysaccharide (LPS), an immunogenic, Gram-negative bacterial component, ii) corticosterone (CORT), an avian stress …

Nitrogen Inputs And Losses In Response To Chronic Co2 Exposure In A Subtropical Oak Woodland, B. A. Hungate, B. D. Duval, P. Dijkstra, D. W. Johnson, M. E. Ketterer, Peter Stiling, W. Cheng, J. Millman, A. Hartley, D. B. Stover

Integrative Biology Faculty and Staff Publications

Rising atmospheric CO₂ concentrations may alter the nitrogen (N) content of ecosystems by changing N inputs and N losses, but responses vary in field experiments, possibly because multiple mechanisms are at play. We measured N fixation and N losses in a subtropical oak woodland exposed to 11 years of elevated atmospheric CO₂ concentrations. We also explored the role of herbivory, carbon limitation, and competition for light or nutrients in shaping the response of N fixation to elevated CO₂. Elevated CO₂ did not significantly alter gaseous N losses, but lower recovery and deeper distribution in the …

Testing Predictions Of The Janzen–Connell Hypothesis: A Meta-Analysis Of Experimental Evidence For Distance- And Density- Dependent Seed And Seedling Survival, Liza S. Comita, Simon A. Queenborough, Stephen J. Murphy, Janelle L. Eck, Kaiyang Xu, Meghna Krishnadas, Noelle G. Beckman, Yan Zhu

Biology Faculty Publications

1. The Janzen–Connell hypothesis proposes that specialist natural enemies, such as herbivores and pathogens, maintain diversity in plant communities by reducing survival rates of conspecific seeds and seedlings located close to reproductive adults or in areas of high conspecific density. Variation in the strength of distance- and density-dependent effects is hypothesized to explain variation in plant species richness along climatic gradients, with effects predicted to be stronger in the tropics than the temperate zone and in wetter habitats compared to drier habitats.
2. We conducted a comprehensive literature search to identify peer-reviewed experimental studies published in the 40+ years since the hypothesis …

Anthropogenic Litter In Urban Freshwater Ecosystems: Distribution And Microbial Interactions, Timothy Hoellein, Miguel Rojas, Adam Pink, Joseph Gasior, John J. Kelly

Biology: Faculty Publications and Other Works

Accumulation of anthropogenic litter (i.e. garbage; AL) and its ecosystem effects in marine environments are well documented. Rivers receive AL from terrestrial habitats and represent a major source of AL to marine environments, but AL is rarely studied within freshwater ecosystems. Our objectives were to 1) quantify AL density in urban freshwaters, 2) compare AL abundance among freshwater, terrestrial, and marine ecosystems, and 3) characterize the activity and composition of AL biofilms in freshwater habitats. We quantified AL from the Chicago River and Chicago's Lake Michigan shoreline, and found that AL abundance in Chicago freshwater ecosystems was comparable to previously …

Mixed Species Flock, Nest Height, And Elevation Partially Explain Avian Haemoparasite Prevalence In Colombia, Angie González, Nubia Matta, Vincenzo Ellis, Eliot Miller, Robert Ricklefs, H. Gutiérrez

Biology Department Faculty Works

No abstract provided.

Identification Of Novel Small Rnas And Characterization Of The 6s Rna Of Coxiella Burnetii, Indu Warrier, Linda D. Hicks, James M. Battisti, Rahul Raghavan, Michael F. Minnick

Biological Sciences Faculty Publications

Coxiella burnetii, an obligate intracellular bacterial pathogen that causes Q fever, undergoes a biphasic developmental cycle that alternates between a metabolically-active large cell variant (LCV) and a dormant small cell variant (SCV). As such, the bacterium undoubtedly employs complex modes of regulating its lifecycle, metabolism and pathogenesis. Small RNAs (sRNAs) have been shown to play important regulatory roles in controlling metabolism and virulence in several pathogenic bacteria. We hypothesize that sRNAs are involved in regulating growth and development of C. burnetii and its infection of host cells. To address the hypothesis and identify potential sRNAs, we subjected total RNA …

Expression Patterns Of Aba And Ga Metabolism Genes And Hormone Levels During Rice Seed Development And Imbibition: A Comparison Of Dormant And Non-Dormant Rice Cultivars, Yang Liu, Jun Fang, Fan Xu, Jinfang Chu, Cunyu Yan, Michael Schläppi, Youping Wang, Chengcai Chu

Biological Sciences Faculty Research and Publications

Seed dormancy is an important agronomic trait in cereals. Using deep dormant (N22), medium dormant (ZH11), and non-dormant (G46B) rice cultivars, we correlated seed dormancy phenotypes with abscisic acid (ABA) and gibberellin (GA) metabolism gene expression profiles and phytohormone levels during seed development and imbibition. A time course analysis of ABA and GA content during seed development showed that N22 had a high ABA level at early and middle seed developmental stages, while at late developmental stage it declined to the level of ZH11; however, its ABA/GA ratio maintained at a high level …

Traversing Swanton Road, 16th Ed., James A. West

Academic, Government & Associated Organizational Research Resources

Situated at the northwest end of Santa Cruz County and occupying circa 30 square miles of sharply contrasted terrain, the Scott Creek Watershed concentrates within its geomorphological boundaries, at least 10-12% of California's flora, both native and introduced. Paradoxically, the use/abuse that the watershed has sustained over the past 140+ years, has not necessarily diminished the biodiversity and perhaps parallels the naturally disruptive but biologically energizing processes (fire, flooding, landslides and erosion), which have also been historically documented for the area for +60 years. This is an early edition of an extensive document by James A. West. Please visit the …

Metabolic Suppression In Mammalian Hibernation: The Role Of Mitochondria., James F Staples

Biology Publications

Hibernation evolved in some small mammals that live in cold environments, presumably to conserve energy when food supplies are low. Throughout the winter, hibernators cycle spontaneously between torpor, with low metabolism and near-freezing body temperatures, and euthermia, with high metabolism and body temperatures near 37°C. Understanding the mechanisms underlying this natural model of extreme metabolic plasticity is important for fundamental and applied science. During entrance into torpor, reductions in metabolic rate begin before body temperatures fall, even when thermogenesis is not active, suggesting active mechanisms of metabolic suppression, rather than passive thermal effects. Mitochondrial respiration is suppressed during torpor, especially …

Cytoplasmic Carboxypeptidase 5 Regulates Tubulin Glutamylation And Zebrafish Cilia Formation And Function, Narendra Pathak, Christina A. Austin-Tse, Yan Liu, Aleksandr Vasilyev, Iain A. Drummond

Neuroscience: Faculty Publications

Glutamylation is a functionally important tubulin posttranslational modification enriched on stable microtubules of neuronal axons, mitotic spindles, centrioles, and cilia. In vertebrates, balanced activities of tubulin glutamyl ligase and cytoplasmic carboxypeptidase deglutamylase enzymes maintain organelle- and cell type-specific tubulin glutamylation pat terns. Tubulin glutamylation in cilia is regulated via restricted subcellular localization or ex pression of tubulin glutamyl ligases (ttlls) and nonenzymatic proteins, including the zebrafish TPR repeat protein Fleer/Ift70. Here we analyze the expression patterns of ccp deglutamy lase genes during zebrafish development and the effects of ccp gene knockdown on cilia formation, morphology, and tubulin glutamylation. The deglutamylases …

Identification And Characterization Of An Operon, Msaabcr, That Controls Virulence And Biofilm Development In Staphlococcus Aureus, Gyan S. Sahukhal, Mohamed O. Elasri

Faculty Publications

Background

Community-acquired, methicillin-resistant Staphylococcus aureus strains often cause localized infections in immunocompromised hosts, but some strains show enhanced virulence leading to severe infections even among healthy individuals with no predisposing risk factors. The genetic basis for this enhanced virulence has yet to be determined. S. aureus possesses a wide variety of virulence factors, the expression of which is carefully coordinated by a variety of regulators. Several virulence regulators have been well characterized, but others have yet to be thoroughly investigated. Previously, we identified the msa gene as a regulator of several virulence genes, biofilm development, and antibiotic resistance. We also …

Body Shape Divergence In Invasive Round Goby, Cat Collins

DePaul Discoveries

The round goby, Neogobius melanostomus, originally native to the Black and Caspian seas, was introduced into the Great Lakes via ballast water in the 1990’s. Since then, the species has spread to all of the Great Lakes, thriving in the Lake Michigan region and spreading to surrounding bays and rivers. Invasive species are considered to have a high evolutionary potential. Differences in environmental conditions between native and introduced ranges stimulate adaptive evolution. Multiple introductions of an exotic species can result in separate instances of founder effects, further increasing the chance of evolutionary change. A total of 267 round goby specimens …

Arthropod Communities And Red-Headed Woodpecker (Melanerpes Erythrocephalus) Habitat Selection, Michael C. Lordon

DePaul Discoveries

Red-headed woodpecker populations are near-threatened. Their habitat selection and reproductive success may be related to the availability of arthropods. We sampled the arthropod community within 0.04 ha plots surrounding known nests and compared these findings to plots without nests in the same fragments of forest or park in Cook County, IL. After 14 days, the traps were recovered, yielding close to 45,000 arthropods across 10 orders. Nest and control site differences were not statistically significant. Differences between park and forest diversity were not statistically significant either, but the greater diversity values in forests were consistent with expectations. We conclude that …